01/05/2020 7:03:56.85 C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty dist /MIR /COPYALL 1>nul ) & rmdir /S /Q dist\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty tests /MIR /COPYALL 1>nul ) & rmdir /S /Q tests\ & ) The system cannot find the file specified. C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current>((ROBOCOPY empty tmp /MIR /COPYALL 1>nul ) & rmdir /S /Q tmp\ & ) The system cannot find the file specified. libtbx libtbx.auto_build libtbx.bundle libtbx.command_line libtbx.development libtbx.phil libtbx.program_utils libtbx.queuing_system_utils libtbx.queuing_system_utils.processing libtbx.scheduling libtbx.server libtbx.sphinx libtbx.test_utils omptbx fable fable.command_line scitbx scitbx.array_family scitbx.boost_python scitbx.dtmin scitbx.examples scitbx.examples.bevington scitbx.glmtbx scitbx.graph scitbx.graphics_utils scitbx.iso_surface scitbx.lbfgs scitbx.linalg scitbx.lstbx scitbx.lstbx.tests scitbx.math scitbx.math.boost_python scitbx.math.tests scitbx.matrix scitbx.python_utils scitbx.random scitbx.rigid_body scitbx.rigid_body.essence scitbx.rigid_body.proto scitbx.source_generators scitbx.source_generators.array_family scitbx.sparse scitbx.stdlib scitbx.stl scitbx.suffixtree scitbx.wigner cctbx cctbx.adp_restraints cctbx.array_family cctbx.command_line cctbx.covariance cctbx.crystal cctbx.development cctbx.eltbx cctbx.eltbx.development cctbx.eltbx.xray_scattering cctbx.examples cctbx.examples.merging cctbx.examples.merging.samosa cctbx.examples.structure_factor_calculus cctbx.geometry cctbx.geometry_restraints cctbx.macro_mol cctbx.maptbx cctbx.masks cctbx.merging cctbx.miller cctbx.neutron cctbx.omz cctbx.regression cctbx.sgtbx cctbx.sgtbx.direct_space_asu cctbx.sgtbx.direct_space_asu.proto cctbx.source_generators cctbx.source_generators.eltbx cctbx.uctbx cctbx.uctbx.determine_unit_cell cctbx.web cctbx.web.asu_gallery cctbx.xray cctbx.xray.observations cctbx.xray.structure_factors cctbx.xray.targets smtbx smtbx.absolute_structure smtbx.ab_initio smtbx.ab_initio.tests smtbx.array_family smtbx.command_line smtbx.masks smtbx.refinement smtbx.refinement.constraints smtbx.refinement.constraints.geometrical smtbx.refinement.constraints.tests smtbx.refinement.restraints smtbx.regression smtbx.regression.test_data smtbx.source_generators smtbx.stl smtbx.structure_factors smtbx.structure_factors.direct iotbx iotbx.bioinformatics iotbx.ccp4_map iotbx.cif iotbx.cns iotbx.command_line iotbx.data_manager iotbx.detectors iotbx.detectors.context iotbx.detectors.util iotbx.dsn6 iotbx.dtrek iotbx.examples iotbx.fullprof iotbx.gui_tools iotbx.kriber iotbx.mrcfile iotbx.mtz iotbx.ncs iotbx.pdb iotbx.pdb.remediation iotbx.PrettyPrint iotbx.programs iotbx.regression iotbx.regression.ncs iotbx.scalepack iotbx.shelx iotbx.solve iotbx.xds iotbx.xplor dxtbx dxtbx.command_line dxtbx.data dxtbx.data.beamline_defs dxtbx.format dxtbx.masking dxtbx.model dxtbx.serialize dxtbx.tests dxtbx.tests.model dxtbx.util reduce reduce.command_line mmtbx mmtbx.alignment mmtbx.building mmtbx.building.alternate_conformations mmtbx.building.ligands mmtbx.building.loop_closure mmtbx.bulk_solvent mmtbx.cablam mmtbx.cablam.fingerprints mmtbx.chemical_components mmtbx.command_line mmtbx.conformation_dependent_library mmtbx.den mmtbx.density_modification mmtbx.disorder mmtbx.dynamics mmtbx.f_model mmtbx.geometry mmtbx.geometry_restraints mmtbx.geometry_restraints.torsion_restraints mmtbx.hydrogens mmtbx.ias mmtbx.idealized_aa_residues mmtbx.ions mmtbx.ions.svm mmtbx.kinemage mmtbx.ligands mmtbx.maps mmtbx.masks mmtbx.max_lik mmtbx.model mmtbx.monomer_library mmtbx.nci mmtbx.ncs mmtbx.pair_interaction mmtbx.polygon mmtbx.programs mmtbx.real_space mmtbx.refinement mmtbx.refinement.ensemble_refinement mmtbx.refinement.real_space mmtbx.regression mmtbx.regression.model mmtbx.regression.ncs mmtbx.regression.tls mmtbx.ringer mmtbx.rotamer mmtbx.rsr mmtbx.scaling mmtbx.secondary_structure mmtbx.secondary_structure.build mmtbx.sisa mmtbx.sisa.optimize mmtbx.solvent mmtbx.tls mmtbx.twinning mmtbx.utils mmtbx.validation mmtbx.validation.molprobity mmtbx.validation.ramachandran mmtbx.validation.regression mmtbx.wwpdb gltbx gltbx.command_line wxtbx wxtbx.command_line wxtbx.phil_controls wxtbx.plots wxtbx.reports chem_data chem_data.curated_datasets Plex elbow elbow.carbo_load elbow.cctbx_api elbow.chemistry elbow.command_line elbow.elbow_plugin elbow.formats elbow.molfiles elbow.pdb elbow.programs elbow.quantum elbow.regression elbow.saccharide elbow.scripts elbow.smiles elbow.test elbow.utilities phenix_regression phenix_regression.command_line phenix_regression.gui phenix_regression.ligand_pipeline phenix_regression.phenix_masks phenix_regression.real_space_refinement phenix_regression.real_space_refinement.test_00 phenix_regression.refinement phenix_regression.refinement.autobuild phenix_regression.refinement.autobuild.run_phenix_refine phenix_regression.refinement.ncs phenix_regression.rerefinement phenix_regression.tardy_action phenix_regression.windows phenix_regression.wizards phenix_regression.wizards.help_tests phenix_regression.wizards.help_tests.test_help solve_resolve solve_resolve.dev solve_resolve.dev.aep_ncs solve_resolve.dev.fit_loops solve_resolve.dev.p9_build solve_resolve.dev.trace solve_resolve.dev.trace_fusion solve_resolve.masks solve_resolve.resolve solve_resolve.resolve_python phaser_regression phaser_regression.command_line phaser_regression.unit phaser_regression.unit.pipeline phaser phaser.chisellib phaser.command_line phaser.logoutput phaser.logoutput_new phaser.phenix_adaptors phaser.phenix_interface phaser.pipeline phaser.pipeline.proxy phaser.utils phenix phenix.automation phenix.automation.polishing phenix.automation.protocols phenix.automation.structure_comparison phenix.autosol phenix.autosol.regression phenix.command_line phenix.erraser phenix.foundation phenix.heavy_search phenix.hidden phenix.hidden.tasks phenix.hidden.tasks.development phenix.hidden.tasks.examples phenix.hidden.tasks.export_xray_structure phenix.hidden.tasks.import_reflection_data phenix.hidden.tasks.phaser phenix.hidden.tasks.phaser.primitives phenix.hidden.tasks.substructure phenix.ligands phenix.loop_lib phenix.molrep phenix.mptbx phenix.pdb_tools phenix.pdb_tools.rama_z_score phenix.pds phenix.pds_server phenix.programs phenix.queue phenix.refinement phenix.refinement.customizations phenix.refinement.fsr phenix.rosetta phenix.server phenix.solve_driver phenix.substructure phenix.substructure.hyss phenix.tasks phenix.tasks.examples phenix.tasks.maps_and_models phenix.tasks.programming phenix.tasks.programming.compound phenix.tasks.programming.examples phenix.tasks.programming.fundamental phenix.tasks.solve phenix.tasks.solve.development phenix.tasks.solve.logic_tasks phenix.tasks.textal phenix.tracking phenix.utilities phenix.wizards spotfinder spotfinder.applications spotfinder.applications.heuristic_tbx spotfinder.applications.xfel spotfinder.array_family spotfinder.command_line spotfinder.core_toolbox spotfinder.diffraction spotfinder.dxtbx_toolbox spotfinder.math_support spotfinder.servers rstbx rstbx.apps rstbx.apps.stills rstbx.array_family rstbx.bandpass rstbx.bpcx rstbx.bpcx.detector_model rstbx.cftbx rstbx.command_line rstbx.detectors rstbx.dials_core rstbx.diffraction rstbx.diffraction.fastbragg rstbx.dps_core rstbx.indexing rstbx.indexing_api rstbx.new_horizons rstbx.outlier_spots rstbx.phil rstbx.simage rstbx.simulation rstbx.slip_viewer rstbx.sublattice_support rstbx.symmetry rstbx.symmetry.constraints rstbx.viewer labelit labelit.application labelit.application.best_support labelit.application.PIL labelit.array_family labelit.beamline labelit.command_line labelit.detectors labelit.diffraction labelit.diffraction.bragg labelit.diffraction.prior_cell labelit.distltbx labelit.dptbx labelit.graphics labelit.hidden_symmetry labelit.hidden_symmetry.matching labelit.mathsupport labelit.outlier_spots labelit.publications labelit.publications.ccn_visualization labelit.publications.direct_parallel labelit.publications.largecell1 labelit.publications.rsymop labelit.publications.sublattice labelit.strategy labelit.sublattice_support labelit.symmetry labelit.symmetry.metricsym labelit.webice_support cma_es simtbx simtbx.nanoBragg prime prime.command_line prime.index_ambiguity prime.isoform_cluster prime.postrefine xfel xfel.amo xfel.amo.pnccd_ana xfel.cftbx xfel.cftbx.detector xfel.clustering xfel.clustering.command_line xfel.command_line xfel.cxi xfel.cxi.clustering xfel.cxi.command_line xfel.cxi.cspad_ana xfel.cxi.gfx xfel.euxfel xfel.graph_proc xfel.merging xfel.merging.algorithms xfel.merging.algorithms.error_model xfel.merging.algorithms.postrefine xfel.merging.algorithms.statistics xfel.merging.application xfel.merging.application.balance xfel.merging.application.errors xfel.merging.application.filter xfel.merging.application.group xfel.merging.application.input xfel.merging.application.merge xfel.merging.application.model xfel.merging.application.modify xfel.merging.application.output xfel.merging.application.phil xfel.merging.application.postrefine xfel.merging.application.scale xfel.merging.application.statistics xfel.merging.application.tdata xfel.merging.application.utils xfel.merging.application.validation xfel.merging.command_line xfel.merging.database xfel.merging.model xfel.merging.report xfel.merging.report.graphs xfel.merging.report.tables xfel.metrology xfel.metrology.legacy_scale xfel.mono_simulation xfel.small_cell xfel.small_cell.command_line xfel.swissfel xfel.ui xfel.ui.command_line xfel.ui.components xfel.ui.db xfel.util xfel.vonHamos xfel.xpp dials dials.algorithms dials.algorithms.background dials.algorithms.background.glm dials.algorithms.background.gmodel dials.algorithms.background.median dials.algorithms.background.simple dials.algorithms.centroid dials.algorithms.centroid.simple dials.algorithms.clustering dials.algorithms.filtering dials.algorithms.image dials.algorithms.image.centroid dials.algorithms.image.connected_components dials.algorithms.image.fill_holes dials.algorithms.image.filter dials.algorithms.image.threshold dials.algorithms.indexing dials.algorithms.indexing.basis_vector_search dials.algorithms.indexing.lattice_search dials.algorithms.integration dials.algorithms.integration.bayes dials.algorithms.integration.fit dials.algorithms.integration.sum dials.algorithms.merging dials.algorithms.polygon dials.algorithms.polygon.clip dials.algorithms.profile_model dials.algorithms.profile_model.gaussian_rs dials.algorithms.profile_model.gaussian_rs.transform dials.algorithms.profile_model.modeller dials.algorithms.refinement dials.algorithms.refinement.analysis dials.algorithms.refinement.outlier_detection dials.algorithms.refinement.parameterisation dials.algorithms.refinement.prediction dials.algorithms.refinement.restraints dials.algorithms.rs_mapper dials.algorithms.scaling dials.algorithms.scaling.cross_validation dials.algorithms.scaling.error_model dials.algorithms.scaling.model dials.algorithms.scaling.model.components dials.algorithms.shadowing dials.algorithms.shoebox dials.algorithms.simulation dials.algorithms.spatial_indexing dials.algorithms.spot_finding dials.algorithms.spot_prediction dials.algorithms.statistics dials.algorithms.symmetry dials.algorithms.symmetry.absences dials.algorithms.symmetry.cosym dials.array_family dials.command_line dials.data dials.extensions dials.model dials.model.data dials.model.experiment dials.model.serialize dials.precommitbx dials.precommitbx._precommitbx dials.pychef dials.report dials.test dials.test.algorithms dials.test.algorithms.generate_test_reflections dials.test.algorithms.integration dials.test.algorithms.integration.profile dials.test.algorithms.refinement dials.test.algorithms.spot_prediction dials.test.command_line dials.test.model dials.test.model.data dials.test.util dials.util dials.util.image_viewer dials.util.image_viewer.slip_viewer dials.util.nexus dials.util.reciprocal_lattice dials.viewer xia2 xia2.Applications xia2.command_line xia2.Decorators xia2.Driver xia2.DriverExceptions xia2.Experts xia2.Handlers xia2.Interfaces xia2.Interfaces.ISPyB xia2.lib xia2.Modules xia2.Modules.Analysis xia2.Modules.Indexer xia2.Modules.Integrater xia2.Modules.MultiCrystal xia2.Modules.Refiner xia2.Modules.Report xia2.Modules.Scaler xia2.Schema xia2.Schema.Exceptions xia2.Schema.Interfaces xia2.Test xia2.Test.regression xia2.Test.Report xia2.Toolkit xia2.Wrappers xia2.Wrappers.CCP4 xia2.Wrappers.Cctbx xia2.Wrappers.Dials xia2.Wrappers.EMBL xia2.Wrappers.Mosflm xia2.Wrappers.Phenix xia2.Wrappers.XDS xia2.Wrappers.XIA iota.src.iota Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\cctbx_project\libtbx\command_line\import_all_ext.py", line 39, in import_modules exec("import %s" % full_module) File "", line 1, in ImportError: No module named src.iota Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\cctbx_project\libtbx\command_line\import_all_ext.py", line 94, in run(args=sys.argv[1:]) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\cctbx_project\libtbx\command_line\import_all_ext.py", line 47, in run import_modules() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\cctbx_project\libtbx\command_line\import_all_ext.py", line 43, in import_modules raise e ImportError: No module named src.iota Discovering pytest tests for smtbx: modules/cctbx_project/smtbx/refinement/constraints/tests/test_direction.py: 1 modules/cctbx_project/smtbx/refinement/constraints/tests/test_disorder.py: 1 modules/cctbx_project/smtbx/refinement/constraints/tests/test_occupancies.py: 1 modules/cctbx_project/smtbx/refinement/constraints/tests/test_rigid.py: 9 modules/cctbx_project/smtbx/refinement/constraints/tests/test_same_group.py: 2 modules/cctbx_project/smtbx/refinement/restraints/tests/test_adp_restraints.py: 4 modules/cctbx_project/smtbx/refinement/restraints/tests/test_manager.py: 1 modules/cctbx_project/smtbx/tests/test_utils.py: 1 Running 850 tests on 24 processors: libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\metric_prefixes.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\test_utils\__init__.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\queuing_system_utils\pbs_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\queuing_system_utils\sge_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\introspection.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_thread_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_easy_mp.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_easy_mp_state.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_easy_pickle.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_fully_buffered_timeout.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_scheduling.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\easy_run.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_containers.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_path.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_math_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\assert_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_str_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\table_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_dlite.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\phil\tst_tokenizer.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\phil\tst.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\phil\tst_experimental.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\phil\tst_interface.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_object_oriented_patterns.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\find_reference_cycles.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_binary_search.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_topological_sort.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\clusterTests.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_citations.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_python_code_parsing.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_representation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_find_unused_imports.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_program_template.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_python3_regression.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_xmlrpc_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_runtime_utils.py" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\boost_adaptbx\tests\tst_optional_copy" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_libc_backtrace.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_rational.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_optional.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_std_pair.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_tuple.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_stdout.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_stderr_stdout.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_python_streambuf.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\tst_smoothing.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\tst_basic.py" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_1" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_2" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_3" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_4" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_5" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_vec3" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_unsigned_float_arithmetic" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_mat3" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_sym_mat3" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_ref_matrix_facet" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_accessors" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_optional_copy" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_rectangular_full_packed" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_flex_argument_passing.py" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\serialization\tst_base_256" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_minimum_covering_ellipsoid.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_gaussian_fit_1d_analytical.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_cubic_equation.py" 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"c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lbfgs\tst_func_free_line_search.py" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\lbfgs\tst_lbfgs" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lbfgsb\boost_python\tst_lbfgsb.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\fftpack\boost_python\tst_fftpack.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\flex_grid.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\flex_array_loops.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\principal_axes_of_inertia.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\lbfgs_recipe.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\lbfgs_linear_least_squares_fit.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\chebyshev_lsq_example.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\immoptibox_ports.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\rigid_body_refinement_core.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\integrating_a_weighted_sinc_function.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\minimizer_comparisons.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\tst_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\rigidity.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\tst_rigidity.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\rigidity_matrix_symbolic.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\tst_tardy_tree_find_paths.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\tst_tardy_tree.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\test_cases_tardy_pdb.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\essence\tst_basic.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\essence\tst_tardy.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\essence\tst_energy_plots.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\tst.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\free_motion_reference_impl.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_featherstone.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_free_motion.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_free_motion_hard.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_joint_lib.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_singular.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_spherical_refinement.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_molecules.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\sparse\tests\tst_sparse.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\sparse\tests\tst_lu_factorization.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\iso_surface\tst_iso_surface.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\simplex.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\differential_evolution.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\golden_section_search.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\direct_search_simulated_annealing.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\random\tests\tst_random.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lstbx\tests\tst_normal_equations.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lstbx\tests\test_problems.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\glmtbx\tests\tst.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\dtmin\regression\tst_dtmin_basic.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\dtmin\regression\tst_dtmin_booth.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\dtmin\regression\tst_dtmin_twisted.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\suffixtree\test\tst_single.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_double_step_filtration.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\miller\tst_reindexing.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\miller\tst_map_to_asu_isym.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_data_manipulation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\omz\tst_bfgs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\omz\tst_dev.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry\tests\tst_geometry.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\covariance\tests\tst_covariance.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\symmetry_search\tests\tst_goodness_of_symmetry.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\symmetry_search\tests\tst_from_map.py" P312 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_adp_aniso_restraints.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\math\boost_python\tst_math.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\boost_python\tst_targets_fd.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\targets\tst_r1.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\targets\tst_shelxl_wght_ls.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\boost_python\tst_f_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\array_family\boost_python\tst_flex.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\uctbx\boost_python\tst_uctbx.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\uctbx\boost_python\tst_crystal_orientation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\boost_python\tst_sgtbx.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\boost_python\tst_N_fold_rot.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\crystal\tst_ext.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\crystal\tst_distance_based_connectivity.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\adptbx\boost_python\tst_adptbx.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\miller\boost_python\tst_miller.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_chemical_elements.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_xray_scattering.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_henke.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_icsd_radii.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_covalent_radii.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_neutron.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_sasaki.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_tiny_pse.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_wavelengths.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_formula.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_attenuation_coefficient.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\boost_python\tst_maptbx.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\dmtbx\boost_python\tst_dmtbx.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\translation_search\boost_python\tst_translation_search.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_ext.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_proxy_registry.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_nonbonded_overlaps.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_process_nonbonded_proxies.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_angle_derivs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_motif.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\adp_restraints\tst_ext.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_math_module.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_krivy_gruber.py" --Quick libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_itvb_2001_table_a1427_hall_symbols.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_space_group_type_tidy_cb_op_t.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_denominators.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_subgroups.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_lattice_symmetry.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_adp_constraints.py" P3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_adp_constraints_cartesian.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_site_constraints.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_reflection_statistics.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_harker.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_special_op_simplifier.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_twin_target.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\symbol_confidence.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\bravais_types.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_lookup_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_crystal.py" I41/acd libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_direct_space_asu.py" I41/acd libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_pair_asu_table.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_crystal_asu_clusters.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_coordination_sequences.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_crystal_close_packing.py" R-3mr libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_fourier_transform_real_part_at_x.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_mem.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_mem_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_reciprocal_space_asu.py" P312 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_triplet_generator.py" P41 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_emma.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_expand_to_p1.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_change_basis.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_wilson_plot.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray_derivatives.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray_fast_gradients.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray_minimization.py" --F P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray_minimization.py" --F_sq P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_maptbx_structure_factors.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_map_weights_for_symmetry_summation.py" Pmmm libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_real_space_refinement_simple.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_interpolation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_interpolation_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_loc_res.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_target_and_gradients.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_merge_equivalents.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_grouped_data.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_fft_map.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sampled_model_density.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_fast_nv1995.py" F222 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_geometry_restraints.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_geometry_restraints_lbfgs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_geometry_restraints_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_grm_pickling.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_french_wilson.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\development\make_cns_input.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\development\tst_cns_epsilon.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\development\tst_cns_hl.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\development\run_shelx76.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_pointgroup_tools.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\sub_lattice_tools.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\rational_matrices_point_groups.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\cosets.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\reticular_pg_tools.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\reticular_twin_laws.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_find_best_cell.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_amplitude_normalisation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_statistics_graphs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_web_change_basis.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\direct_space_asu\proto\tst_asu.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_tidy_pickling.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\masks\tests\tst_flood_fill.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_r_free_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\observations\tst_observations.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_ccp.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_mask.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_map_peak_3d_as_2d.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_asymmetric_map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_peak_volume_estimate.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_resolution_from_map_and_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_atom_curves.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_atom_radius_as_central_peak_width.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_get_percentile_cutoffs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sphericity.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_statistics.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\merging\brehm_diederichs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\multipolar\regression\tst_multipolar.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_connectivity.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_diffuse.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_grm_modifications.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\boost_python\tst_xray.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray.py" I41/acd libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_wildcard.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_simple_parser.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_phil.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_pdb_cif_inputs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_data_manager.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\ranges.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_crystal_symmetry_from_any.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_poscar.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\kriber\tst_strudat.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_geometry.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_lex_parse_build.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_restraints.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_validation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_ucif_examples_compilation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_parser.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_citations.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\shelx\tst_lex_parse_build.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\shelx\tst_hklf.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\shelx\tst_writer.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\shelx\tst_fvar_encoding.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_mmcif.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_mmcif_hierarchy.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_mmcif_hierarchy_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_tls.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\hybrid_36.py" exercise "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\iotbx\pdb\hybrid_36_fem" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_hierarchy.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_hierarchy_atom_sort.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_ext.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_atom_selection.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_rna_dna_atom_names.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_atom_name_interpretation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_extract_rfactors_resolutions_sigma.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\modified_aa_names.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\modified_rna_dna_names.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\secondary_structure\tst_sheet.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\secondary_structure\tst_annotation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\secondary_structure.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_atom_selection_string.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_secondary_structure.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_secondary_structure_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\examples\pdb_to_map_simple.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\examples\pdb_truncate_to_ala\tst.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\examples\pdb_tardy_conf_sampling_simple.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cns\space_group_symbols.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cns\tst_cns.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\scalepack\tst_merge.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\scalepack\no_merge_original_index.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\ccp4_map\tst.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_ext.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_extract_from_symmetry_lib.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_dano.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_miller_dict.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_unmerged.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\examples\tst_mtz_free_flipper.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reflection_file_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\detectors\tst_adsc.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\detectors\tst_detectors.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xplor\tst_xplormap.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_phases.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_pdbx_mmcif_tutorial.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_lattice_symmetry.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reflection_statistics.py" Fdd2 P31m libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_data_plots.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_csv_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_file_reader.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_bioinformatics.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_box_around_molecule.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_mmcif_segids.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_add_conformations.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_symmetry.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reindex.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reflection_file_editor.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_split_models.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_pdb_as_fasta.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_merging_statistics.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_simple_map_coefficients.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_sort_atoms.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xds\tests\tst_xparm.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xds\tests\tst_xds_inp.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xds\tests\tst_integrate_hkl.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xds\tests\tst_spots_xds.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_pdb_as_cif.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\scalepack\tst_no_merge_original_index.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_export_scalepack_unmerged.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\dsn6\tst.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_mtrix_biomt_cmdl.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_search_ligs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_search_broken_chain.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_groups_preprocessing.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_input.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_user_selections.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_read_mtrix_records_from_cif.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_show_systematic_absences.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_miller_sort_asu.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reflection_file_reader.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_xray_scale.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\bioinformatics\test\tst_alignment_as_hsearch.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\bioinformatics\test\tst_ebi_wu_blast_xml.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\bioinformatics\test\tst_ncbi_blast_xml.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_cif_as_pdb_1atom.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_split_data_cif.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_pdb.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_mtz_as_cif.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\detectors\tst_debug_write.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\absolute_structure\tests\tst_absolute_structure.py" --fix_random_seeds libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\ab_initio\tests\tst_ab_initio_ext.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\ab_initio\tests\tst_charge_flipping.py" --fix_seed --on=E "hall: P 1" "hall: P 3" "hall: -P 2ybc" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\masks\tests\tst_masks.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\structure_factors\direct\tests\tst_standard_xray.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\tests\tst_weighting_schemes.py" --fix_random_seeds libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\tst_lbfgs.py" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\smtbx\refinement\constraints\tests\tst_reparametrisation" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\smtbx\refinement\constraints\tests\tst_geometrical_hydrogens" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\smtbx\refinement\constraints\tests\tst_special_position" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\tst_reparametrisation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\tst_constrained_structure.py" --normal_eqns_solving_method=naive libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\regression\tst_commandline_refine.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\regression\tst_commandline_anomrefine.py" libtbx.python -m pytest -rsxX --basetemp=pytest\t001 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_direction.py::test_direction" libtbx.python -m pytest -rsxX --basetemp=pytest\t002 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_disorder.py::test_with_disorder" libtbx.python -m pytest -rsxX --basetemp=pytest\t003 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_occupancies.py::test_simple_disorder" libtbx.python -m pytest -rsxX --basetemp=pytest\t004 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_rigid_site_proxy" libtbx.python -m pytest -rsxX --basetemp=pytest\t005 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_rigid_pivoted_rotatable" libtbx.python -m pytest -rsxX --basetemp=pytest\t006 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_rotatable_expansion" libtbx.python -m pytest -rsxX --basetemp=pytest\t007 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_rotatable_rotation" libtbx.python -m pytest -rsxX --basetemp=pytest\t008 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_idealised_generation[Cp]" libtbx.python -m pytest -rsxX --basetemp=pytest\t009 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_idealised_generation[Ph]" libtbx.python -m pytest -rsxX --basetemp=pytest\t010 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_idealised_generation[CpStar]" libtbx.python -m pytest -rsxX --basetemp=pytest\t011 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_idealised_generation[Naphthalene]" libtbx.python -m pytest -rsxX --basetemp=pytest\t012 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_idealised_fitting" libtbx.python -m pytest -rsxX --basetemp=pytest\t013 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_same_group.py::test_basics" libtbx.python -m pytest -rsxX --basetemp=pytest\t014 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_same_group.py::test_real_life_structure" libtbx.python -m pytest -rsxX --basetemp=pytest\t015 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\restraints\tests\test_adp_restraints.py::test_adp_similarity" libtbx.python -m pytest -rsxX --basetemp=pytest\t016 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\restraints\tests\test_adp_restraints.py::test_rigid_bond" libtbx.python -m pytest -rsxX --basetemp=pytest\t017 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\restraints\tests\test_adp_restraints.py::test_isotropic_adp" libtbx.python -m pytest -rsxX --basetemp=pytest\t018 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\restraints\tests\test_adp_restraints.py::test_rigu" libtbx.python -m pytest -rsxX --basetemp=pytest\t019 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\restraints\tests\test_manager.py::test_manager" libtbx.python -m pytest -rsxX --basetemp=pytest\t020 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\tests\test_utils.py::test_connectivity_table" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\restraints\tests\tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\tests\tst_least_squares.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\svm\tst_classifier.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_ca_svm.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pickle.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_parameters.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_ca.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_mg.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_approx_zn.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_validate_ca.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_validate_mg.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_symmetry_axis.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_analysis.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_optimise_amplitudes.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_get_t_scheme.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_refinement_fft.py" --comprehensive --random_seed=2679941 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_00.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_01.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_02.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_03.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_04.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_as_xyz.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_formula_t_S_10_vs_11_2igd.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_formula_t_S_10_vs_11_4muy.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_angle.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\rotamer\tst_rotamer_eval.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\rotamer\tst_geostd_vs_sidechain_angles_props.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_idealized_aa.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_ml_estimate.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\density_modification\tst_density_modification.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_ramachandran.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_manager.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_map_type_parser.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\rsr\tst.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\polygon\tst.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\polygon\tst_gui.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\chemical_components\tst.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_add_h_to_water.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\rotamer\rotamer_eval.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\wwpdb\tst_standard_geometry_cif.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_pdbtools.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\real_space\tst.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ias\tst_ias.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_fit_rotamers.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_anomalous_scatterer_groups.py" P3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_rigid_body.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_rigid_body_groups_from_pdb_chains.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_refinement_flags.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model_ligands.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_mtrix.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_biomt_mtrix.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_neutralize_scatterers.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_set_hydrogen_bond_length.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_cart_ref_restraints.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_tors_ref_restraints.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_remove_alternative_conformations.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_get_vdw_radii.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_alignment.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel_fd.py" P31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\maps\tst_composite_omit_map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\maps\tst_composite_omit_map_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\maps\tst_composite_omit_map_3.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\maps\tst_correlation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_ncs_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_ncs_restraints_group_list.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_ncs_search.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_ncs_search_flips.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_restraints.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_geometry_minimization.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ncs\ncs.py" exercise libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_adp_restraints.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_metal_link_1.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_scaling.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_outlier.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_absences.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_xtriage.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_xtriage_twin_analyses.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\matthews.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\absence_likelihood.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\thorough_outlier_test.py" P21 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\twinning\probabalistic_detwinning.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_rna_sugar_pucker_analysis.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_cif_types.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_motif.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_cif_triage.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_rotamer_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_selection.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_tyr_from_gly_and_bnz.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_pdb_interpretation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_rna_dna_interpretation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_protein_interpretation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_pdb_interpretation_ncs_processing.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_geo_reduce_for_tardy.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_chg.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_neutron_distance.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_carbo_linking.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_paral_geo.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_altloc_remediate.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\build_hydrogens.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen.py" libtbx.python 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"c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_fit_kexpb_to_ktotal.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_scaler.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_flat_nonuniform.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_aniso_scaler.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_kb_sol_u_star_fd.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\invariant_domain.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_psi_phi_extraction.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\tst.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\tst_insertion_codes.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\tst_segid.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_reference_coordinate.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_reference_coordinate2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_c_beta_restraints.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_torsion_ncs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_cdl.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_cdl_esd.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_rdl.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_hpdl.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_cis_c_n_ca.py" libtbx.python 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"c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_chain_comparison.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_regularize_from_pdb.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_find_ncs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_minimize_chain.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_sequence_validation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_prune_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_real_space_correlation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_examples.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_sort_hetatms.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_aa_residue_axes_and_clusters.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_0.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_0H.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_1.py" libtbx.python 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"c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_6.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_selection.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_water.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_flipbase.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_individual_sites_1.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_individual_sites_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_individual_sites_3.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_monitor.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_rigid_body.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_weight.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\idealized_aa_residues\tst.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_dssp.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validation_summary.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_maps_misc.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cablam.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_anomalous_substructure.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_map_coeffs_simple.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel_no_cryst1.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel_misc.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_isomorphous_difference_misc.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_dynamics_cli.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ligands\tst_xtal_screens.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ligands\tst_ready_set_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_mtz2map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_ringer.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ringer\tst_emringer.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ringer\tst_em_rscc.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_arguments.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_waters.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_keep_hydrogens.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_mp_geo.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_rotalyze.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_ramalyze.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_ramalyze2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_clashscore.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_restraints.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_omegalyze.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_rna_validate.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_model_properties.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_3.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_hydrogen_addition_clashscore.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_symmetry_SS.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_do_flips_clashscore.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_find_region_max_value.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_select_best_starting_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_refine_anomalous_substructure.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_helix_sheet_recs_as_pdb_files.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_command_line_input.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cif_as_mtz_wavelengths.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\tst_extend_sidechains.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\tst_extend_sidechains_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\alternate_conformations\tst_backrub_conformers.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\alternate_conformations\tst_shear_conformers.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\alternate_conformations\tst_partial_omit_map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\disorder\tst.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\disorder\tst_backbone.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\disorder\tst_analyze_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_group.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_group_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_1.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_3.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_io.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_ss_id_ncs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_loop_closure.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_01.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_02.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_03.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_04.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_01.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_02.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_03.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_04.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_05.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_06.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_ligands.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_with_mtz.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_ext_map_01.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\utils\tst_switch_rotamers.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_occupancy_selections.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints3.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints_real_space.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_correct_hydrogens.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_superpose_ideal.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_iron_sulfur_clusters.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_plan_sad_experiment.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_models_to_from_chains.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tncs\tst_pair.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tncs\tst_epsfac_and_radius.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tncs\tst_fd.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tncs\tst_moments.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_rank_scale_map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_1.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_3.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_box.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_ccs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_map_model_cc.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_model_map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cis_trans_peptide_link.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_apply_cif_restraints.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_multi_residue_class.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_flip_symmetric.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_superpose.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_server.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_altloc.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_asa.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_clash.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_indexing.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_shared_types.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_sphere_surface_sampling.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_topology.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\nci\tst_hbond.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\wwpdb\tst_rcsb_web_services.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\wwpdb\tst_utils.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_all_cif_files.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_misc.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_real_space_simple.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_bayesian_estimator.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_mean_f_rms_f.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_sigmaa.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_massage_data.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_geometries.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_k.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_environment.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_table_one.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_msa.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_build_alt_confs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cc_star.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_rigid_bond_test.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cablam.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\tst_make_library.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\real_space_refine_chain\tst_00.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\real_space_refine_chain\tst_01.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_omega_cdl.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\fix_cablam\tst_basic_cl_operations.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\fix_cablam\tst_single_outliers_surroundings.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\fix_cablam\tst_one_resid_rotation.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\fix_cablam\tst_insertion_codes.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_scattering_type_registry.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_rama_z_01.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits_actions.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_add_arrows_on_plot.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_reduce_timeout.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_altloc_chain_break.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_geometry_minimization_ncs_constraints.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_clashes.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cbetadev.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_statistics_output.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_geo_min_restraints_phil.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_model_vs_map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_nqh_minimize.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_1.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_4.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_experimental.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cablam_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_metal_coordination.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_metal_coordination.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 6 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 7 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 8 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 9 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 10 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 11 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 12 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 13 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 14 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 15 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 16 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 17 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 18 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 19 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 20 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 21 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 22 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 23 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 24 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 25 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 26 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 27 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 28 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 29 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 30 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 31 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 32 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\metric_prefixes.py" [OK] 15.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\test_utils\__init__.py" [OK] 15.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\phil\tst_experimental.py" [OK] 16.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_path.py" [OK] 16.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_math_utils.py" [OK] 16.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\phil\tst_tokenizer.py" [OK] 16.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\phil\tst.py" [OK] 16.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\table_utils.py" [OK] 17.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_containers.py" [OK] 17.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_dlite.py" [OK] 18.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_fully_buffered_timeout.py" [OK] 21.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\queuing_system_utils\sge_utils.py" [OK] 21.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\assert_utils.py" [OK] 21.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_str_utils.py" [OK] 21.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\introspection.py" [OK] 21.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_easy_mp.py" [OK] 21.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_easy_pickle.py" [OK] 22.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\queuing_system_utils\pbs_utils.py" [OK] 22.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_easy_mp_state.py" [OK] 22.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\find_reference_cycles.py" [OK] 15.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_topological_sort.py" [OK] 15.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_xmlrpc_utils.py" [EXPECTED FAIL] 12.5s Time: 12.53 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_xmlrpc_utils.py", line 42, in exercise() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_xmlrpc_utils.py", line 19, in exercise log=log) TypeError: __init__() got an unexpected keyword argument 'command' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_rational.py" [OK] 12.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_libc_backtrace.py" [OK] 12.7s Standard error: show_stack(1): c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_libc_backtrace.py(9) run show_stack(2): c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_libc_backtrace.py(15) libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_object_oriented_patterns.py" [OK] 20.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_binary_search.py" [OK] 20.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\phil\tst_interface.py" [OK] 36.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\clusterTests.py" [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_python_code_parsing.py" [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_citations.py" [OK] 20.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_representation.py" [OK] 20.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_python3_regression.py" [FAIL] 16.9s Time: 16.89 Return code: 1 OKs: 0 Standard error: FAIL: Python3 compilation exited with unexpected STDERR output "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\boost_adaptbx\tests\tst_optional_copy" [OK] 16.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_program_template.py" [OK] 24.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_find_unused_imports.py" [OK] 25.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_optional.py" [OK] 21.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_tuple.py" [OK] 21.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_std_pair.py" [OK] 22.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_stderr_stdout.py" [OK] 19.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_thread_utils.py" [OK] 50.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\tst_smoothing.py" [OK] 20.8s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_2" [OK] 19.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_python_streambuf.py" [OK] 21.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_scheduling.py" [OK] 56.0s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_1" [OK] 20.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_utils.py" [OK] 59.8s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_3" [OK] 23.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_runtime_utils.py" [EXPECTED FAIL] 39.0s Time: 38.97 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_runtime_utils.py", line 81, in exercise() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_runtime_utils.py", line 37, in exercise """) AssertionError "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_4" [OK] 24.5s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_5" [OK] 25.5s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_vec3" [OK] 26.6s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_unsigned_float_arithmetic" [OK] 29.2s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_mat3" [OK] 28.4s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_sym_mat3" [OK] 29.2s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_ref_matrix_facet" [OK] 25.9s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_accessors" [OK] 25.8s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_optional_copy" [OK] 25.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_flex_argument_passing.py" [OK] 26.5s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_rectangular_full_packed" [OK] 27.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_stdout.py" [OK] 44.9s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\serialization\tst_base_256" [OK] 25.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_minimum_covering_ellipsoid.py" [OK] 25.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_gaussian_fit_1d_analytical.py" [OK] 24.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_cubic_equation.py" [OK] 24.3s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\math\tests\tst" [OK] 26.0s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\matrix\tests\tst_givens" [OK] 26.5s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\matrix\tests\tst_householder" [OK] 27.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\matrix\tests\tst_row_echelon.py" [OK] 24.2s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\matrix\tests\tst_svd" [OK] 25.5s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\matrix\tests\tst_cholesky" [OK] 25.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\linalg\tests\tst_matrix.py" [OK] 22.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\matrix\tests\tst_householder.py" [OK] 24.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\linalg\tests\tst_lapack_svd.py" [OK] 20.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\stl\tst_map.py" [OK] 18.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\linalg\tests\tst_eigensystem.py" [OK] 23.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\linalg\tests\tst_lapack_dsyev.py" [OK] 21.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\stl\tst_set.py" [OK] 19.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\stl\tst_vector.py" [OK] 20.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\linalg\tests\tst_cholesky.py" [OK] 28.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\linalg\tests\tst_svd.py" [OK] 25.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_numpy_bridge.py" [OK] 20.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\regression_test.py" [OK] 21.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_flex.py" [OK] 22.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_shared.py" [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_smart_selection.py" [OK] 20.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\tst_cubicle_neighbors.py" [OK] 17.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\matrix\__init__.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\python_utils\tst_graph.py" [OK] 15.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\tst_regular_grid_on_unit_sphere.py" [OK] 16.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_cost_of_m_handle_in_af_shared.py" [OK] 19.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\python_utils\tst_robust.py" [OK] 15.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\tst_r3_utils.py" [OK] 18.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\python_utils\tst_random_transform.py" [OK] 17.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\error\tst_error.py" [OK] 37.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\superpose.py" [OK] 19.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\incremental_SO3_sampling.py" [OK] 18.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_similarity_indices.py" [OK] 16.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_exp_functions.py" [OK] 16.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_weighted_correlation.py" [OK] 17.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_integer_offsets_vs_pointers.py" [OK] 27.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\spe.py" [OK] 21.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_gcd.py" [OK] 18.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_fit_quadratic_function.py" [OK] 18.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_line_search.py" [OK] 15.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_resample.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_quadrature.py" [OK] 15.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_bessel.py" [OK] 15.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_halton.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_math.py" [OK] 19.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_uniform_rotation_matrix.py" [OK] 16.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_superpose.py" [OK] 16.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_euler_angles.py" [OK] 17.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\sieve_of_eratosthenes.py" [OK] 13.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\besselk.py" [OK] 13.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tst_zernike_mom.py" [OK] 14.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_curve_fitting.py" [OK] 31.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_r3_rotation.py" [OK] 22.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_fit_peak.py" [OK] 14.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_clustering.py" [OK] 14.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_orthonormal_basis.py" [OK] 15.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tst_zernike.py" [OK] 20.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_g_function.py" [OK] 15.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_angle_derivative.py" [OK] 15.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_periodogram.py" [OK] 14.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_tetrahedron.py" [OK] 13.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tst_undirected_graph.py" [OK] 13.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tst_so3_lie_algebra.py" [OK] 13.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\minpack\tst.py" [OK] 13.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lbfgs\tst_ext.py" [OK] 12.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lbfgs\tst_curvatures.py" [OK] 14.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_error_propagation_matrix_inverse.py" [OK] 19.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lbfgs\tst_func_free_line_search.py" [OK] 16.0s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\lbfgs\tst_lbfgs" [OK] 15.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\scale_curves.py" [OK] 29.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\fftpack\boost_python\tst_fftpack.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lbfgsb\boost_python\tst_lbfgsb.py" [OK] 15.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\flex_grid.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_gaussian.py" [OK] 37.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\flex_array_loops.py" [OK] 16.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\principal_axes_of_inertia.py" [OK] 15.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\lbfgs_recipe.py" [OK] 17.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\lbfgs_linear_least_squares_fit.py" [OK] 17.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\tst_basic.py" [OK] 112.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\rigidity.py" [OK] 16.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\chebyshev_lsq_example.py" [OK] 17.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\tst_utils.py" [OK] 17.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\rigid_body_refinement_core.py" [OK] 17.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\tst_rigidity.py" [OK] 16.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\integrating_a_weighted_sinc_function.py" [OK] 18.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\rigidity_matrix_symbolic.py" [OK] 17.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\tst_tardy_tree.py" [OK] 13.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\test_cases_tardy_pdb.py" [OK] 13.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\essence\tst_basic.py" [OK] 14.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\essence\tst_energy_plots.py" [OK] 15.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\free_motion_reference_impl.py" [OK] 14.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\tst_tardy_tree_find_paths.py" [OK] 18.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_free_motion.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_featherstone.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\minimizer_comparisons.py" [OK] 23.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\tst.py" [OK] 17.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\immoptibox_ports.py" [OK] 25.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_joint_lib.py" [OK] 17.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_free_motion_hard.py" [OK] 17.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\essence\tst_tardy.py" [OK] 26.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\sparse\tests\tst_sparse.py" [OK] 16.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\sparse\tests\tst_lu_factorization.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\golden_section_search.py" [OK] 13.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_spherical_refinement.py" [OK] 16.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\differential_evolution.py" [OK] 14.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\simplex.py" [OK] 16.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_singular.py" [OK] 18.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lstbx\tests\test_problems.py" [OK] 12.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lstbx\tests\tst_normal_equations.py" [OK] 12.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\glmtbx\tests\tst.py" [OK] 12.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\dtmin\regression\tst_dtmin_basic.py" [OK] 11.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_molecules.py" [OK] 18.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\random\tests\tst_random.py" [OK] 15.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\dtmin\regression\tst_dtmin_booth.py" [OK] 12.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\dtmin\regression\tst_dtmin_twisted.py" [OK] 13.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\iso_surface\tst_iso_surface.py" [OK] 21.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\direct_search_simulated_annealing.py" [OK] 18.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_double_step_filtration.py" [OK] 14.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\suffixtree\test\tst_single.py" [WARNING] 16.5s Time: 16.48 Return code: 0 OKs: 0 Standard error: test_single_word (__main__.TestWord) ... ok test_branch (__main__.TestEdge) ... ok test_const_branch (__main__.TestEdge) ... ok test_const_leaf (__main__.TestEdge) ... ok test_const_root (__main__.TestEdge) ... ok test_leaf (__main__.TestEdge) ... ok test_root (__main__.TestEdge) ... ok test_const_root (__main__.TestPreOrder) ... ok test_r_b1 (__main__.TestPreOrder) ... ok test_r_b1_b1 (__main__.TestPreOrder) ... ok test_r_b2 (__main__.TestPreOrder) ... ok test_root (__main__.TestPreOrder) ... ok test_single_branch (__main__.TestPreOrder) ... ok test_single_leaf (__main__.TestPreOrder) ... ok test_single_root (__main__.TestPreOrder) ... ok test_const_root (__main__.TestPostOrder) ... ok test_r_b1 (__main__.TestPostOrder) ... ok test_r_b1_b1 (__main__.TestPostOrder) ... ok test_r_b2 (__main__.TestPostOrder) ... ok test_root (__main__.TestPostOrder) ... ok test_single_branch (__main__.TestPostOrder) ... ok test_single_leaf (__main__.TestPostOrder) ... ok test_single_root (__main__.TestPostOrder) ... ok test_tree (__main__.TestTree) ... ok test_ukkonen1 (__main__.TestTree) ... ok test_ukkonen2 (__main__.TestTree) ... ok test (__main__.TestMatchingStatistics) ... FAIL test (__main__.TestLeafIndices) ... FAIL ====================================================================== FAIL: test (__main__.TestMatchingStatistics) ---------------------------------------------------------------------- Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\suffixtree\test\tst_single.py", line 783, in test self.assertEqual( result, [ ( 0, ( tree.root, 0 ) ) ] * 3 ) AssertionError: Lists differ: [(0, (, 18446744073709551614L)) (0, (, 0)) Diff is 1062 characters long. Set self.maxDiff to None to see it. ====================================================================== FAIL: test (__main__.TestLeafIndices) ---------------------------------------------------------------------- Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\suffixtree\test\tst_single.py", line 840, in test self.assertEqual( result, [ ( 0, ( tree.root, 0 ) ) ] * 3 ) AssertionError: Lists differ: [(0, (, 18446744073709551614L)) (0, (, 0)) Diff is 1062 characters long. Set self.maxDiff to None to see it. ---------------------------------------------------------------------- Ran 28 tests in 0.016s FAILED (failures=2) libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\miller\tst_reindexing.py" [OK] 15.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\miller\tst_map_to_asu_isym.py" [OK] 15.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\omz\tst_bfgs.py" [OK] 15.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\omz\tst_dev.py" P31 [OK] 15.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry\tests\tst_geometry.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\covariance\tests\tst_covariance.py" [OK] 15.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\math\boost_python\tst_math.py" [OK] 14.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\targets\tst_r1.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\boost_python\tst_targets_fd.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\targets\tst_shelxl_wght_ls.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_adp_aniso_restraints.py" [OK] 19.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\boost_python\tst_f_model.py" [OK] 18.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\array_family\boost_python\tst_flex.py" [OK] 18.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\uctbx\boost_python\tst_uctbx.py" [OK] 19.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\uctbx\boost_python\tst_crystal_orientation.py" [OK] 17.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\boost_python\tst_N_fold_rot.py" [OK] 17.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\crystal\tst_ext.py" [OK] 16.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\crystal\tst_distance_based_connectivity.py" [OK] 16.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\boost_python\tst_sgtbx.py" [OK] 18.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\symmetry_search\tests\tst_from_map.py" P312 [OK] 24.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_data_manipulation.py" [OK] 27.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\adptbx\boost_python\tst_adptbx.py" [OK] 15.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\miller\boost_python\tst_miller.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_chemical_elements.py" [OK] 15.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_henke.py" [OK] 15.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_xray_scattering.py" [OK] 15.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_neutron.py" [OK] 14.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_icsd_radii.py" [OK] 16.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\symmetry_search\tests\tst_goodness_of_symmetry.py" [OK] 32.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_sasaki.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_covalent_radii.py" [OK] 17.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_tiny_pse.py" [OK] 16.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_wavelengths.py" [OK] 15.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_formula.py" [OK] 15.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_attenuation_coefficient.py" [OK] 15.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\dmtbx\boost_python\tst_dmtbx.py" [OK] 15.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\translation_search\boost_python\tst_translation_search.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_proxy_registry.py" [OK] 15.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_ext.py" [OK] 18.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_angle_derivs.py" [OK] 15.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\boost_python\tst_maptbx.py" [OK] 20.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_motif.py" [OK] 15.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\adp_restraints\tst_ext.py" [OK] 15.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_math_module.py" [OK] 15.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_itvb_2001_table_a1427_hall_symbols.py" [OK] 15.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_denominators.py" P31 [OK] 15.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_adp_constraints.py" P3 [OK] 14.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_subgroups.py" [OK] 15.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_adp_constraints_cartesian.py" [OK] 13.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_krivy_gruber.py" --Quick [OK] 17.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_space_group_type_tidy_cb_op_t.py" [OK] 16.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx.py" [OK] 17.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_site_constraints.py" [OK] 15.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_harker.py" [OK] 14.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_special_op_simplifier.py" [OK] 15.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_reflection_statistics.py" [OK] 16.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_lattice_symmetry.py" [OK] 20.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\symbol_confidence.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\bravais_types.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_lookup_utils.py" [OK] 16.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_crystal.py" I41/acd [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_pair_asu_table.py" [OK] 17.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_crystal_asu_clusters.py" [OK] 16.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_fourier_transform_real_part_at_x.py" P31 [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_reciprocal_space_asu.py" P312 [OK] 15.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_triplet_generator.py" P41 [OK] 13.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_crystal_close_packing.py" R-3mr [OK] 16.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_coordination_sequences.py" [OK] 17.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_expand_to_p1.py" P31 [OK] 12.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_emma.py" P31 [OK] 15.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_change_basis.py" P31 [OK] 13.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_wilson_plot.py" P31 [OK] 14.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_direct_space_asu.py" I41/acd [OK] 27.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray_fast_gradients.py" P31 [OK] 13.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray_derivatives.py" P31 [OK] 15.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray_minimization.py" --F_sq P31 [OK] 15.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_twin_target.py" [OK] 37.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray_minimization.py" --F P31 [OK] 19.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_maptbx_structure_factors.py" P31 [OK] 16.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_map_weights_for_symmetry_summation.py" Pmmm [OK] 16.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_real_space_refinement_simple.py" [OK] 16.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_merge_equivalents.py" P31 [OK] 17.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_mem_2.py" [OK] 35.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_grouped_data.py" P31 [OK] 17.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_loc_res.py" [OK] 20.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_fft_map.py" P31 [OK] 18.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sampled_model_density.py" P31 [OK] 18.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_target_and_gradients.py" [OK] 22.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_fast_nv1995.py" F222 [OK] 19.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller.py" P31 [OK] 42.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_geometry_restraints.py" [OK] 19.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_geometry_restraints_lbfgs.py" [OK] 19.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_geometry_restraints_2.py" [OK] 21.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\development\make_cns_input.py" P31 [OK] 18.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_mem.py" [OK] 51.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\development\tst_cns_epsilon.py" P31 [OK] 19.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\development\run_shelx76.py" P31 [OK] 17.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\development\tst_cns_hl.py" P31 [OK] 18.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_pointgroup_tools.py" [OK] 17.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\sub_lattice_tools.py" [OK] 17.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_grm_pickling.py" [OK] 24.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_french_wilson.py" [OK] 24.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_interpolation_2.py" [OK] 38.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\cosets.py" [OK] 17.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\reticular_pg_tools.py" [OK] 20.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\rational_matrices_point_groups.py" [OK] 22.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_find_best_cell.py" [OK] 17.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_amplitude_normalisation.py" [OK] 18.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_web_change_basis.py" [OK] 17.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_statistics_graphs.py" [OK] 19.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\masks\tests\tst_flood_fill.py" [OK] 15.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_tidy_pickling.py" [OK] 16.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\observations\tst_observations.py" [OK] 15.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_mask.py" [OK] 15.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_ccp.py" [OK] 18.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_map_peak_3d_as_2d.py" [OK] 17.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_r_free_utils.py" [OK] 20.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\reticular_twin_laws.py" [OK] 32.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_peak_volume_estimate.py" [OK] 19.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_get_percentile_cutoffs.py" [OK] 17.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sphericity.py" [OK] 17.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\merging\brehm_diederichs.py" [OK] 16.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_statistics.py" [OK] 17.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\direct_space_asu\proto\tst_asu.py" [OK] 33.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_atom_radius_as_central_peak_width.py" [OK] 25.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\multipolar\regression\tst_multipolar.py" [OK] 22.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_process_nonbonded_proxies.py" [OK] 108.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_connectivity.py" [OK] 21.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_resolution_from_map_and_model.py" [OK] 33.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_wildcard.py" [OK] 18.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\boost_python\tst_xray.py" [OK] 20.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_simple_parser.py" [OK] 17.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_grm_modifications.py" [OK] 23.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_phil.py" [OK] 19.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray.py" I41/acd [OK] 23.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_pdb_cif_inputs.py" [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\ranges.py" [OK] 17.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_poscar.py" [OK] 17.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_crystal_symmetry_from_any.py" [OK] 18.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\kriber\tst_strudat.py" [OK] 19.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_geometry.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_asymmetric_map.py" [OK] 46.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_lex_parse_build.py" [OK] 15.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_model.py" [OK] 16.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_parser.py" [OK] 14.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_restraints.py" [OK] 15.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_diffuse.py" [OK] 36.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_citations.py" [OK] 14.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_data_manager.py" [OK] 27.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_validation.py" [OK] 16.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\shelx\tst_lex_parse_build.py" [OK] 15.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_atom_curves.py" [OK] 51.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\shelx\tst_hklf.py" [OK] 17.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\shelx\tst_writer.py" [OK] 17.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\shelx\tst_fvar_encoding.py" [OK] 17.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_mmcif.py" [OK] 17.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\hybrid_36.py" exercise [OK] 14.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_mmcif_hierarchy_2.py" [OK] 20.3s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\iotbx\pdb\hybrid_36_fem" [OK] 16.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_hierarchy.py" [OK] 17.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_hierarchy_atom_sort.py" [OK] 17.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_rna_dna_atom_names.py" [OK] 16.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_atom_selection.py" [OK] 16.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_extract_rfactors_resolutions_sigma.py" [OK] 16.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_atom_name_interpretation.py" [OK] 16.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_ext.py" [OK] 17.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\modified_aa_names.py" [OK] 16.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\modified_rna_dna_names.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_mmcif_hierarchy.py" [OK] 25.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_tls.py" [OK] 23.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\secondary_structure\tst_sheet.py" [OK] 17.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\secondary_structure.py" [OK] 19.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\secondary_structure\tst_annotation.py" [OK] 21.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_atom_selection_string.py" [OK] 19.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_interpolation.py" [OK] 115.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_utils.py" [OK] 18.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\examples\pdb_to_map_simple.py" [OK] 16.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\examples\pdb_truncate_to_ala\tst.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_secondary_structure.py" [OK] 20.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cns\space_group_symbols.py" [OK] 14.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\examples\pdb_tardy_conf_sampling_simple.py" [OK] 14.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\scalepack\tst_merge.py" P31 [OK] 14.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cns\tst_cns.py" [OK] 15.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\scalepack\no_merge_original_index.py" [OK] 15.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_secondary_structure_2.py" [OK] 20.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\ccp4_map\tst.py" [OK] 16.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_ext.py" [OK] 17.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_dano.py" [OK] 18.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_extract_from_symmetry_lib.py" [OK] 19.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_miller_dict.py" [OK] 19.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_ucif_examples_compilation.py" [OK] 52.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_unmerged.py" [OK] 17.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst.py" P31 [OK] 19.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\detectors\tst_detectors.py" [OK] 16.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\examples\tst_mtz_free_flipper.py" [OK] 20.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reflection_file_utils.py" [OK] 20.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\detectors\tst_adsc.py" [OK] 18.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xplor\tst_xplormap.py" [OK] 16.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_phases.py" P31 [OK] 17.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_data_plots.py" [OK] 16.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_csv_utils.py" [OK] 17.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reflection_statistics.py" Fdd2 P31m [OK] 20.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_bioinformatics.py" [OK] 17.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_symmetry.py" [OK] 15.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_add_conformations.py" [OK] 16.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reindex.py" [OK] 15.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_mmcif_segids.py" [OK] 18.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xds\tests\tst_xparm.py" [OK] 14.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_pdb_as_fasta.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_pdbx_mmcif_tutorial.py" [OK] 31.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xds\tests\tst_xds_inp.py" [OK] 15.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reflection_file_editor.py" [OK] 24.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xds\tests\tst_integrate_hkl.py" [OK] 15.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xds\tests\tst_spots_xds.py" [OK] 15.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\scalepack\tst_no_merge_original_index.py" [OK] 15.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_export_scalepack_unmerged.py" [OK] 16.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\dsn6\tst.py" P31 [OK] 15.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_search_ligs.py" [OK] 15.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_search_broken_chain.py" [OK] 16.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_file_reader.py" [OK] 37.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_box_around_molecule.py" [OK] 36.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_pdb_as_cif.py" [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_split_models.py" [OK] 32.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_input.py" [OK] 17.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_user_selections.py" [OK] 17.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_merging_statistics.py" [OK] 34.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_groups_preprocessing.py" [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_read_mtrix_records_from_cif.py" [OK] 18.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_sort_atoms.py" [OK] 35.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_show_systematic_absences.py" [OK] 18.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_miller_sort_asu.py" [OK] 18.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs.py" [OK] 20.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reflection_file_reader.py" [OK] 17.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\bioinformatics\test\tst_alignment_as_hsearch.py" [OK] 17.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\bioinformatics\test\tst_ebi_wu_blast_xml.py" [OK] 17.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\bioinformatics\test\tst_ncbi_blast_xml.py" [OK] 17.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_xray_scale.py" [OK] 20.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_cif_as_pdb_1atom.py" [OK] 18.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_pdb.py" [OK] 19.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_mtz_as_cif.py" [OK] 24.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\detectors\tst_debug_write.py" [EXPECTED FAIL] 17.9s Time: 17.92 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\detectors\tst_debug_write.py", line 65, in run() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\detectors\tst_debug_write.py", line 61, in run exercise_debug_write() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\detectors\tst_debug_write.py", line 46, in exercise_debug_write a.read() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\detectors\detectorbase.py", line 64, in read self.fileLength() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\detectors\detectorbase.py", line 45, in fileLength self.readHeader() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\detectors\adsc.py", line 20, in readHeader assert stream.read(len(MAGIC_NUMBER)) == MAGIC_NUMBER AssertionError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\ab_initio\tests\tst_ab_initio_ext.py" [OK] 17.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\tests\tst_weighting_schemes.py" --fix_random_seeds [OK] 19.9s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\smtbx\refinement\constraints\tests\tst_reparametrisation" [OK] 19.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\absolute_structure\tests\tst_absolute_structure.py" --fix_random_seeds [OK] 23.3s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\smtbx\refinement\constraints\tests\tst_geometrical_hydrogens" [OK] 19.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\tst_reparametrisation.py" [OK] 16.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\ab_initio\tests\tst_charge_flipping.py" --fix_seed --on=E "hall: P 1" "hall: P 3" "hall: -P 2ybc" [OK] 22.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\masks\tests\tst_masks.py" [OK] 22.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\tst_lbfgs.py" [OK] 22.2s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\smtbx\refinement\constraints\tests\tst_special_position" [OK] 18.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\tst_constrained_structure.py" --normal_eqns_solving_method=naive [OK] 19.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_split_data_cif.py" [OK] 36.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\tst_constrained_structure.py" --normal_eqns_solving_method=levenberg-marquardt [OK] 20.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\structure_factors\direct\tests\tst_standard_xray.py" [OK] 27.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\regression\tst_commandline_refine.py" [OK] 20.4s libtbx.python -m pytest -rsxX --basetemp=pytest\t001 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_direction.py::test_direction" [OK] 23.5s libtbx.python -m pytest -rsxX --basetemp=pytest\t004 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_rigid_site_proxy" [OK] 18.1s libtbx.python -m pytest -rsxX --basetemp=pytest\t005 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_rigid_pivoted_rotatable" [OK] 17.7s libtbx.python -m pytest -rsxX --basetemp=pytest\t002 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_disorder.py::test_with_disorder" [OK] 23.0s libtbx.python -m pytest -rsxX --basetemp=pytest\t003 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_occupancies.py::test_simple_disorder" [OK] 22.4s libtbx.python -m pytest -rsxX --basetemp=pytest\t006 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_rotatable_expansion" [OK] 17.6s libtbx.python -m pytest -rsxX --basetemp=pytest\t007 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_rotatable_rotation" [OK] 17.3s libtbx.python -m pytest -rsxX --basetemp=pytest\t008 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_idealised_generation[Cp]" [OK] 17.5s libtbx.python -m pytest -rsxX --basetemp=pytest\t009 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_idealised_generation[Ph]" [OK] 17.4s libtbx.python -m pytest -rsxX --basetemp=pytest\t010 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_idealised_generation[CpStar]" [OK] 17.6s libtbx.python -m pytest -rsxX --basetemp=pytest\t011 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_idealised_generation[Naphthalene]" [OK] 18.9s libtbx.python -m pytest -rsxX --basetemp=pytest\t013 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_same_group.py::test_basics" [OK] 18.5s libtbx.python -m pytest -rsxX --basetemp=pytest\t012 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_rigid.py::test_idealised_fitting" [OK] 21.9s libtbx.python -m pytest -rsxX --basetemp=pytest\t014 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\test_same_group.py::test_real_life_structure" [OK] 21.4s libtbx.python -m pytest -rsxX --basetemp=pytest\t015 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\restraints\tests\test_adp_restraints.py::test_adp_similarity" [OK] 19.5s libtbx.python -m pytest -rsxX --basetemp=pytest\t016 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\restraints\tests\test_adp_restraints.py::test_rigid_bond" [OK] 19.8s libtbx.python -m pytest -rsxX --basetemp=pytest\t017 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\restraints\tests\test_adp_restraints.py::test_isotropic_adp" [OK] 19.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_simple_map_coefficients.py" [OK] 90.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\svm\tst_classifier.py" [OK] 17.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_ca_svm.py" [OK] 17.7s libtbx.python -m pytest -rsxX --basetemp=pytest\t018 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\restraints\tests\test_adp_restraints.py::test_rigu" [OK] 20.0s libtbx.python -m pytest -rsxX --basetemp=pytest\t019 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\restraints\tests\test_manager.py::test_manager" [OK] 19.2s libtbx.python -m pytest -rsxX --basetemp=pytest\t020 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\tests\test_utils.py::test_connectivity_table" [OK] 19.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_validate_ca.py" [OK] 18.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_utils.py" [OK] 18.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\regression\tst_commandline_anomrefine.py" [OK] 58.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\tests\tst_least_squares.py" [OK] 28.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\restraints\tests\tst_restraints.py" --verbose --scatterers=5 --resolution=0.2 [OK] 34.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_parameters.py" [OK] 33.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_lattice_symmetry.py" [OK] 124.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls.py" [OK] 28.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_utils.py" [OK] 21.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_optimise_amplitudes.py" [FAIL] 22.1s Time: 22.11 Return code: 1 OKs: 1 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_optimise_amplitudes.py", line 1218, in tst_optimise_amplitudes_single_group() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_optimise_amplitudes.py", line 375, in tst_optimise_amplitudes_single_group convergence_tolerance=1e-08, File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\tls\optimise_amplitudes.py", line 123, in run f_g_calculator = self.get_f_g_calculator() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\tls\optimise_amplitudes.py", line 98, in get_f_g_calculator weight_sum_of_amplitudes_squared = self.optimisation_weights.sum_of_amplitudes_squared, ValueError: invalid selection in base_atom_indices (10376306736294088890): attempting to select atom outside of array (size 10) libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_analysis.py" [OK] 26.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_03.py" [OK] 22.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_02.py" [OK] 24.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_get_t_scheme.py" [OK] 44.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_01.py" [OK] 39.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\rotamer\tst_geostd_vs_sidechain_angles_props.py" [OK] 24.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\rotamer\tst_rotamer_eval.py" [OK] 26.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_00.py" [OK] 48.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_idealized_aa.py" [OK] 25.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_04.py" [OK] 40.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_mg.py" [OK] 74.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_ml_estimate.py" [OK] 28.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_formula_t_S_10_vs_11_4muy.py" [OK] 44.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_symmetry_axis.py" [OK] 73.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_map_type_parser.py" [OK] 25.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\chemical_components\tst.py" [OK] 23.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_validate_mg.py" [OK] 85.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\rsr\tst.py" [OK] 31.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\polygon\tst_gui.py" [OK] 29.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_as_xyz.py" [OK] 64.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\polygon\tst.py" [OK] 30.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\wwpdb\tst_standard_geometry_cif.py" [OK] 20.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\rotamer\rotamer_eval.py" [OK] 23.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_formula_t_S_10_vs_11_2igd.py" [OK] 68.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_nonbonded_overlaps.py" [OK] 351.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pickle.py" [OK] 104.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_add_h_to_water.py" [OK] 30.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_mtrix_biomt_cmdl.py" [OK] 178.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_fit_rotamers.py" [OK] 20.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_refinement_flags.py" [OK] 18.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_anomalous_scatterer_groups.py" P3 [OK] 20.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ias\tst_ias.py" [OK] 27.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_rigid_body_groups_from_pdb_chains.py" [OK] 21.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_biomt_mtrix.py" [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_refinement_fft.py" --comprehensive --random_seed=2679941 [OK] 107.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_mtrix.py" [OK] 23.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_manager.py" [OK] 64.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_approx_zn.py" [OK] 125.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\density_modification\tst_density_modification.py" [OK] 78.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_2.py" [OK] 28.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_neutralize_scatterers.py" [OK] 24.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_set_hydrogen_bond_length.py" [OK] 24.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_remove_alternative_conformations.py" [OK] 19.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_ca.py" [OK] 137.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_cart_ref_restraints.py" [OK] 26.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_tors_ref_restraints.py" [OK] 24.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_ramachandran.py" [OK] 79.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_get_vdw_radii.py" [OK] 23.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\real_space\tst.py" [OK] 54.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_alignment.py" [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel_fd.py" P31 [OK] 24.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_ncs_utils.py" [OK] 20.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_rigid_body.py" [OK] 55.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_utils.py" [OK] 28.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\maps\tst_composite_omit_map_2.py" [OK] 26.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_ncs_search.py" [OK] 19.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_ncs_restraints_group_list.py" [OK] 20.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_restraints.py" [OK] 19.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ncs\ncs.py" exercise [OK] 18.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_ncs_search_flips.py" [OK] 21.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_adp_restraints.py" [OK] 19.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\maps\tst_correlation.py" [OK] 33.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_metal_link_1.py" [OK] 21.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_geometry_minimization.py" [OK] 26.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_outlier.py" [OK] 18.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_absences.py" [OK] 18.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\matthews.py" [OK] 17.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\absence_likelihood.py" [OK] 17.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_xtriage_twin_analyses.py" [OK] 18.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\thorough_outlier_test.py" P21 [OK] 18.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\twinning\probabalistic_detwinning.py" [OK] 15.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_rna_sugar_pucker_analysis.py" [OK] 15.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_cif_types.py" [OK] 15.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_motif.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_scaling.py" [OK] 31.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_cif_triage.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\easy_run.py" [OK] 617.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model.py" [OK] 80.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_rotamer_utils.py" [OK] 18.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_selection.py" [OK] 17.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_pdb_interpretation_ncs_processing.py" [OK] 17.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_rna_dna_interpretation.py" [OK] 18.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_tyr_from_gly_and_bnz.py" [OK] 20.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\maps\tst_composite_omit_map.py" [OK] 63.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\maps\tst_composite_omit_map_3.py" [OK] 62.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_geo_reduce_for_tardy.py" [OK] 20.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_protein_interpretation.py" [OK] 21.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_neutron_distance.py" [OK] 26.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen_2.py" [OK] 23.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_coefficients.py" [OK] 16.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst.py" [OK] 28.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_connectivity.py" [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_1.py" [OK] 20.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_manager.py" [OK] 21.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen.py" [FAIL] 32.3s Time: 32.31 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen.py", line 278, in run() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen.py", line 16, in run no_H_on_coordinating_CYS() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen.py", line 105, in no_H_on_coordinating_CYS not_contains = ' HG ') File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen.py", line 49, in compare_models assert ph_initial.is_similar_hierarchy(other=ph_h_added) AssertionError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\build_hydrogens.py" [OK] 32.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_carbo_linking.py" [OK] 37.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_2.py" [OK] 22.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model_ligands.py" [FAIL] 115.2s Time: 115.25 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model_ligands.py", line 134, in run() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model_ligands.py", line 131, in run tst_1() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model_ligands.py", line 128, in tst_1 Total # of reference model restraints: 1""") File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\test_utils\__init__.py", line 555, in assert_lines_in_file remove_white_spaces=remove_white_spaces, remove_newline=remove_newline) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\test_utils\__init__.py", line 544, in assert_lines_in_text "Lines:\n %s\n are not found" % (lines) AssertionError: Lines: Model: Reference: LIG A 1 <=====> LIG A 1 Total # of matched residue pairs: 1 Total # of reference model restraints: 1 are not found libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_3.py" [OK] 23.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_xtriage.py" [OK] 66.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_5.py" [OK] 20.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_validate_H.py" [OK] 37.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_4.py" [OK] 28.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_pdb_interpretation.py" [OK] 56.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_7.py" [OK] 21.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_8.py" [OK] 21.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_6.py" [OK] 22.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_minimize.py" [OK] 17.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_3.py" [OK] 19.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_4.py" [OK] 21.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\masks\tst_masks.py" [OK] 17.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\max_lik\tst_maxlik.py" [OK] 21.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_5.py" [OK] 26.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\dynamics\tst_cartesian_dynamics.py" [OK] 18.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_2.py" [OK] 34.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\examples\f_model_manager.py" [OK] 19.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_fit_kexpb_to_ktotal.py" [OK] 18.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_1.py" [OK] 39.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_flat_nonuniform.py" [OK] 21.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\max_lik\tst_max_lik.py" [OK] 30.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\invariant_domain.py" [OK] 19.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fix_xyz.py" [FAIL] 40.6s Time: 40.59 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fix_xyz.py", line 158, in exercise_00() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fix_xyz.py", line 69, in exercise_00 pdb_inp_refined = iotbx.pdb.input(file_name='tst_riding_fix_xyz_shaken_refine_001.pdb', source_info=None) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\pdb\__init__.py", line 785, in input raise_sorry_if_format_error=raise_sorry_if_format_error).file_content() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\pdb\__init__.py", line 715, in __init__ six.reraise(exc_info[0], exc_info[1], exc_info[2]) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\pdb\__init__.py", line 684, in __init__ raise_sorry_if_format_error=raise_sorry_if_format_error) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\pdb\__init__.py", line 736, in pdb_input lines=flex.split_lines(smart_open.for_reading(file_name).read())) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\smart_open.py", line 27, in for_reading + " "+str(e)) IOError: Cannot open file for reading: "tst_riding_fix_xyz_shaken_refine_001.pdb" [Errno 2] No such file or directory: 'tst_riding_fix_xyz_shaken_refine_001.pdb' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_kb_sol_u_star_fd.py" [OK] 23.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_scaler.py" [OK] 28.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_psi_phi_extraction.py" [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\tst_insertion_codes.py" [OK] 19.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_aniso_scaler.py" [OK] 28.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\masks\tst_asu_mask.py" [OK] 43.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_c_beta_restraints.py" [OK] 21.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\cdl_svl_database.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_reference_coordinate.py" [OK] 30.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_torsion_ncs.py" [OK] 26.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_cdl.py" [OK] 27.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_reference_coordinate2.py" [OK] 33.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_cdl_esd.py" [OK] 32.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel.py" [OK] 169.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_find_ss_structure.py" [OK] 18.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_mcl_02.py" [OK] 29.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_chain_comparison.py" [OK] 15.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\tst.py" [OK] 61.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_sequence_validation.py" [OK] 14.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_find_ncs.py" [OK] 22.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_regularize_from_pdb.py" [OK] 26.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\dynamics\tst_sa.py" [OK] 84.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fix_rotamer_outliers.py" [OK] 34.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_cis_c_n_ca.py" [OK] 51.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_mcl_01.py" [OK] 50.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_sort_hetatms.py" [OK] 18.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_real_space_correlation.py" [OK] 24.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_rdl.py" [OK] 59.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_prune_model.py" [OK] 35.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_aa_residue_axes_and_clusters.py" [OK] 22.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_0.py" [OK] 24.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_0H.py" [OK] 24.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_minimize_chain.py" [OK] 45.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_hpdl.py" [OK] 73.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_examples.py" [OK] 39.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\tst_segid.py" [OK] 87.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_3.py" [OK] 25.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_4.py" [OK] 25.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_5.py" [FAIL] 24.6s Time: 24.58 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_5.py", line 108, in exercise(pdb_poor_str = pdb_poor, resolution_factor=0.2) File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_5.py", line 105, in exercise tol = 0.30) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\refinement\real_space\__init__.py", line 92, in check_sites_match assert dist < tol, [dist, tol] AssertionError: [8.119241135977157, 0.3] libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_6.py" [OK] 26.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_2.py" [OK] 36.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_1.py" [OK] 41.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_2.py" [OK] 24.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_4.py" [OK] 24.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_3.py" [OK] 28.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_1H.py" [OK] 47.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_5.py" [OK] 31.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_6.py" [OK] 30.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_pH_mechanism.py" [OK] 108.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_flipbase.py" [OK] 32.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_rigid_body.py" [OK] 24.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_1.py" [OK] 56.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_water.py" [OK] 38.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_monitor.py" [OK] 25.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_individual_sites_3.py" [OK] 32.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_individual_sites_2.py" [OK] 39.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cablam.py" [OK] 16.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_selection.py" [OK] 50.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\idealized_aa_residues\tst.py" [OK] 31.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ligands\tst_xtal_screens.py" [OK] 14.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_weight.py" [OK] 39.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_bulk_solvent_and_scaling.py" [OK] 161.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_individual_sites_1.py" [OK] 60.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ringer\tst_emringer.py" [OK] 18.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ringer\tst_em_rscc.py" [OK] 13.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_dynamics_cli.py" [OK] 28.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_map_coeffs_simple.py" [OK] 39.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_anomalous_substructure.py" [OK] 40.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_ramalyze.py" [OK] 15.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel_misc.py" [OK] 46.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel_no_cryst1.py" [OK] 47.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_mp_geo.py" [OK] 17.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_mtz2map.py" [OK] 42.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_rotalyze.py" [OK] 20.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_waters.py" [OK] 34.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_ramalyze2.py" [OK] 17.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_angle.py" [OK] 391.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_dssp.py" [OK] 77.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_omegalyze.py" [OK] 17.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_restraints.py" [OK] 23.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_model_properties.py" [OK] 20.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_1H.py" [OK] 118.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_find_region_max_value.py" [OK] 16.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_maps_misc.py" [OK] 99.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_symmetry_SS.py" [OK] 35.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_helix_sheet_recs_as_pdb_files.py" [OK] 32.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_select_best_starting_model.py" [OK] 38.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_hydrogen_addition_clashscore.py" [OK] 49.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\tst_extend_sidechains_2.py" [OK] 21.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cif_as_mtz_wavelengths.py" [OK] 37.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_ringer.py" [OK] 105.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\tst_extend_sidechains.py" [OK] 30.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\disorder\tst.py" [OK] 16.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\alternate_conformations\tst_partial_omit_map.py" [OK] 24.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\alternate_conformations\tst_shear_conformers.py" [OK] 26.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\disorder\tst_backbone.py" [OK] 15.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_chg.py" [OK] 326.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_rna_validate.py" [OK] 88.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\alternate_conformations\tst_backrub_conformers.py" [OK] 35.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_group.py" [OK] 20.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_group_2.py" [OK] 20.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_refine_anomalous_substructure.py" [OK] 79.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_io.py" [OK] 22.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_1.py" [OK] 29.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_3.py" [OK] 36.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_loop_closure.py" [OK] 31.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_altloc_remediate.py" [OK] 361.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_isomorphous_difference_misc.py" [OK] 187.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_command_line_input.py" [OK] 118.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_do_flips_clashscore.py" [OK] 175.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\disorder\tst_analyze_model.py" [OK] 117.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_ss_id_ncs.py" [OK] 100.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ligands\tst_ready_set_utils.py" [OK] 259.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\utils\tst_switch_rotamers.py" [OK] 20.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_2.py" [OK] 190.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_3.py" [OK] 273.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_occupancy_selections.py" [OK] 49.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints.py" [FAIL] 28.7s Time: 28.73 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints.py", line 287, in exercise_without_geometry_restaints() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints.py", line 255, in exercise_without_geometry_restaints t.run_test() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints.py", line 180, in run_test refine_u_iso = self.u_iso) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\refinement\minimization_ncs_constraints.py", line 433, in __init__ ignore_line_search_failed_maxfev=True)) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\scitbx\lbfgs\__init__.py", line 278, in run line_search) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\scitbx\lbfgs\__init__.py", line 149, in run_c_plus_plus if (minimizer.run(x, f, g, gradient_only,line_search)): continue RuntimeError: lbfgs error: Line search failed: The step is at the upper bound stpmax(). libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints3.py" [OK] 20.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints2.py" [OK] 34.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lbfgs\tst_lbfgs_fem.py" [OK] 1059.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints_real_space.py" [OK] 25.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_plan_sad_experiment.py" [OK] 22.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_keep_hydrogens.py" [OK] 405.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tncs\tst_pair.py" [OK] 23.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_models_to_from_chains.py" [OK] 67.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_iron_sulfur_clusters.py" [OK] 95.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tncs\tst_moments.py" [OK] 26.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tncs\tst_fd.py" [OK] 31.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tncs\tst_epsfac_and_radius.py" [OK] 40.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_paral_geo.py" [OK] 717.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_rank_scale_map.py" [OK] 44.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder.py" [FAIL] 58.5s Time: 58.50 Return code: 1 OKs: 0 Standard error: The syntax of the command is incorrect. The syntax of the command is incorrect. Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder.py", line 241, in exercise_00() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder.py", line 198, in exercise_00 assert not easy_run.call(cmd) AssertionError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_2.py" [FAIL] 38.0s Time: 37.97 Return code: 1 OKs: 0 Standard error: The syntax of the command is incorrect. Sorry: [Errno 2] No such file or directory: 'tst_polder_2_1_polder_map_coeffs.mtz' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_3.py" [OK] 65.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_correct_hydrogens.py" [OK] 254.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_1.py" [OK] 112.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_ccs.py" [OK] 56.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_box.py" [OK] 75.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_clashscore.py" [OK] 603.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_model_map.py" [OK] 49.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_multi_residue_class.py" [OK] 27.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_map_model_cc.py" [OK] 72.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_02.py" [OK] 583.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_2.py" [OK] 682.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validation_summary.py" [OK] 760.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_server.py" [OK] 84.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py" [FAIL] 157.5s Time: 157.50 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py", line 192, in run() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py", line 186, in run run_test1() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py", line 90, in run_test1 vl_manager.run() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\validation\validate_ligands.py", line 151, in run results = self.parallel_populate(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\validation\validate_ligands.py", line 112, in parallel_populate self.nproc, File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\easy_mp.py", line 721, in multi_core_run for i, ( calc, res ) in enumerate(pfi): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\forward_compatibility.py", line 23, in next return type(self).__next__(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\scheduling\parallel_for.py", line 249, in __next__ self.state.fillup( pfi = self ) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\scheduling\parallel_for.py", line 174, in fillup cls.iterate( pfi = pfi ) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\scheduling\parallel_for.py", line 163, in iterate manager = pfi.manager, File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\scheduling\parallel_for.py", line 17, in submit_one_job manager.submit( target = target, args = args, kwargs = kwargs ), File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\scheduling\job_scheduler.py", line 143, in submit self.poll() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\scheduling\job_scheduler.py", line 221, in poll process.start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\process.py", line 130, in start self._popen = Popen(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 277, in __init__ dump(process_obj, to_child, HIGHEST_PROTOCOL) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 199, in dump ForkingPickler(file, protocol).dump(obj) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 224, in dump self.save(obj) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 331, in save self.save_reduce(obj=obj, *rv) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 425, in save_reduce save(state) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 655, in save_dict self._batch_setitems(obj.iteritems()) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 687, in _batch_setitems save(v) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 568, in save_tuple save(element) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 754, in save_global (obj, module, name)) pickle.PicklingError: Can't pickle : it's not found as mmtbx.validation.validate_ligands._run Traceback (most recent call last): File "", line 1, in File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 381, in main self = load(from_parent) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 1384, in load return Unpickler(file).load() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 864, in load dispatch[key](self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 886, in load_eof raise EOFError EOFError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_altloc.py" [OK] 38.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_clash.py" [OK] 31.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_superpose_ideal.py" [OK] 419.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_asa.py" [OK] 46.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_indexing.py" [OK] 25.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_shared_types.py" [OK] 23.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_sphere_surface_sampling.py" [OK] 23.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_topology.py" [OK] 32.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\wwpdb\tst_rcsb_web_services.py" [OK] 34.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_misc.py" [OK] 21.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\nci\tst_hbond.py" [OK] 38.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\wwpdb\tst_utils.py" [OK] 33.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_all_cif_files.py" [OK] 30.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_mean_f_rms_f.py" [OK] 20.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_sigmaa.py" [OK] 22.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_real_space_simple.py" [OK] 30.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_massage_data.py" [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_k.py" [OK] 21.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_apply_cif_restraints.py" [OK] 226.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_geometries.py" [OK] 40.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_table_one.py" [OK] 21.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_environment.py" [OK] 32.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_06.py" [OK] 680.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_build_alt_confs.py" [OK] 24.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cc_star.py" [OK] 26.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cablam.py" [OK] 22.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\tst_make_library.py" [OK] 24.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_03.py" [OK] 750.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_rigid_bond_test.py" [OK] 43.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_05.py" [WARNING] 718.7s Time: 718.67 Return code: 0 OKs: 279 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_01.py" [OK] 769.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_04.py" [OK] 759.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel_2.py" [OK] 55.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_omega_cdl.py" [OK] 22.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\real_space_refine_chain\tst_00.py" [OK] 37.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\real_space_refine_chain\tst_01.py" [OK] 36.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_02.py" [OK] 752.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_03.py" [OK] 754.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_superpose.py" [OK] 255.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_scattering_type_registry.py" [OK] 21.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_04.py" [OK] 765.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_pdbtools.py" [OK] 1224.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_reduce_timeout.py" [OK] 19.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\fix_cablam\tst_insertion_codes.py" [OK] 42.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_add_arrows_on_plot.py" [OK] 37.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cbetadev.py" [OK] 22.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits.py" [FAIL] 42.7s Time: 42.73 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits.py", line 308, in exercise() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits.py", line 304, in exercise exercise_angle_edits_change(mon_lib_srv, ener_lib) File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits.py", line 238, in exercise_angle_edits_change 100.00''' in geo_file_str AssertionError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_rama_z_01.py" [OK] 46.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\fix_cablam\tst_single_outliers_surroundings.py" [OK] 61.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\fix_cablam\tst_one_resid_rotation.py" [OK] 62.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_bayesian_estimator.py" [OK] 162.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_msa.py" [OK] 137.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_altloc_chain_break.py" [OK] 129.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cablam_2.py" [FAIL] 100.2s Time: 100.16 Return code: 1 OKs: 0 Standard error: Starting phenix.cablam.bat on Fri May 1 07:39:32 2020 by phaserbuilder =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 5o61.cif Processing PHIL parameters: ------------------------------------------------------------------------------- No PHIL parameters found Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "5o61.cif" } default_model = "5o61.cif" } Starting job =============================================================================== Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\cctbx_project\mmtbx\command_line\cablam.py", line 46, in run(sys.argv[1:]) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\cctbx_project\mmtbx\command_line\cablam.py", line 36, in run task.run() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\programs\cablam.py", line 76, in run quiet=False) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\validation\cablam.py", line 950, in __init__ self.all_results[chain].confs[conf].results[result].set_cablam_feedback() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\validation\cablam.py", line 567, in set_cablam_feedback and (self.prevres.scores.alpha >= ALPHA_CUTOFF or self.prevres.scores.threeten >= THREETEN_CUTOFF) AttributeError: 'NoneType' object has no attribute 'alpha' Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cablam_2.py", line 15, in exercise_01() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cablam_2.py", line 8, in exercise_01 assert not easy_run.call("phenix.cablam 5o61.cif"), "For Chris to fix" AssertionError: For Chris to fix libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_statistics_output.py" [OK] 126.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_nqh_minimize.py" [OK] 111.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_geo_min_restraints_phil.py" [OK] 136.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_4.py" [OK] 148.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_model_vs_map.py" [OK] 162.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_experimental.py" [OK] 154.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_clashes.py" [OK] 193.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_01.py" [OK] 984.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_flip_symmetric.py" [OK] 504.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits_actions.py" [OK] 281.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\fix_cablam\tst_basic_cl_operations.py" [OK] 319.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_ligands.py" [OK] 990.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_ext_map_01.py" [OK] 1031.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_with_mtz.py" [OK] 1056.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 2 [OK] 241.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 3 [OK] 244.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 4 [OK] 248.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 5 [OK] 245.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 6 [OK] 244.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 7 [OK] 248.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 8 [OK] 245.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 9 [OK] 248.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 10 [OK] 245.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_geometry_minimization_ncs_constraints.py" [OK] 460.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 11 [OK] 249.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 12 [OK] 248.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 1 [OK] 461.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_metal_coordination.py" 1 [OK] 472.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 13 [OK] 250.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_metal_coordination.py" 2 [OK] 478.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 14 [OK] 244.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_arguments.py" [OK] 1445.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 15 [OK] 242.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model.py" [OK] 562.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 16 [OK] 235.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 17 [OK] 234.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 18 [OK] 234.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 19 [OK] 232.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 21 [OK] 227.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 20 [OK] 230.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 22 [OK] 231.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 23 [OK] 211.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 24 [OK] 209.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 25 [OK] 209.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 26 [OK] 208.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 27 [OK] 199.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 28 [OK] 195.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 29 [OK] 182.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 30 [OK] 162.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 31 [OK] 162.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 32 [OK] 155.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cis_trans_peptide_link.py" [OK] 1188.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_1.py" [OK] 855.5s ================================================================================ Tests finished. Elapsed time: 2683.45s Distribution of test runtimes: 11.5s - 154.8s: 767 154.8s - 298.2s: 47 298.2s - 441.5s: 7 441.5s - 584.9s: 7 584.9s - 728.3s: 6 728.3s - 871.6s: 8 871.6s - 1015.0s: 2 1015.0s - 1158.3s: 3 1158.3s - 1301.7s: 2 1301.7s - 1445.1s: 1 Warning: the following jobs took at least 180 seconds: libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 29: 182.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_isomorphous_difference_misc.py": 187.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_2.py": 190.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_clashes.py": 193.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 28: 195.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 27: 199.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 26: 208.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 25: 209.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 24: 209.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 23: 211.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_apply_cif_restraints.py": 226.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 21: 227.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 20: 230.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 22: 231.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 19: 232.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 18: 234.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 17: 234.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 16: 235.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 2: 241.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 15: 242.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 14: 244.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 6: 244.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 3: 244.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 5: 245.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 10: 245.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 8: 245.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 9: 248.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 4: 248.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 7: 248.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 12: 248.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 11: 249.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 13: 250.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_correct_hydrogens.py": 254.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_superpose.py": 255.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ligands\tst_ready_set_utils.py": 259.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_3.py": 273.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits_actions.py": 281.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\fix_cablam\tst_basic_cl_operations.py": 319.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_chg.py": 326.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_nonbonded_overlaps.py": 351.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_altloc_remediate.py": 361.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_angle.py": 391.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_keep_hydrogens.py": 405.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_superpose_ideal.py": 419.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_geometry_minimization_ncs_constraints.py": 460.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 1: 461.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_metal_coordination.py" 1: 472.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_metal_coordination.py" 2: 478.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_flip_symmetric.py": 504.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model.py": 562.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_02.py": 583.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_clashscore.py": 603.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\easy_run.py": 617.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_06.py": 680.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_2.py": 682.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_paral_geo.py": 717.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_05.py": 718.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_03.py": 750.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_02.py": 752.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_03.py": 754.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_04.py": 759.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validation_summary.py": 760.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_04.py": 765.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_01.py": 769.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_1.py": 855.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_01.py": 984.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_ligands.py": 990.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_ext_map_01.py": 1031.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_with_mtz.py": 1056.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lbfgs\tst_lbfgs_fem.py": 1059.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cis_trans_peptide_link.py": 1188.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_pdbtools.py": 1224.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_arguments.py": 1445.1s Please try to reduce overall runtime - consider splitting up these tests. Error: the following jobs returned non-zero exit codes or suspicious stderr output: libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\suffixtree\test\tst_single.py" [WARNING] 16.5s Time: 16.48 Return code: 0 OKs: 0 Standard error: test_single_word (__main__.TestWord) ... ok test_branch (__main__.TestEdge) ... ok test_const_branch (__main__.TestEdge) ... ok test_const_leaf (__main__.TestEdge) ... ok test_const_root (__main__.TestEdge) ... ok test_leaf (__main__.TestEdge) ... ok test_root (__main__.TestEdge) ... ok test_const_root (__main__.TestPreOrder) ... ok test_r_b1 (__main__.TestPreOrder) ... ok test_r_b1_b1 (__main__.TestPreOrder) ... ok test_r_b2 (__main__.TestPreOrder) ... ok test_root (__main__.TestPreOrder) ... ok test_single_branch (__main__.TestPreOrder) ... ok test_single_leaf (__main__.TestPreOrder) ... ok test_single_root (__main__.TestPreOrder) ... ok test_const_root (__main__.TestPostOrder) ... ok test_r_b1 (__main__.TestPostOrder) ... ok test_r_b1_b1 (__main__.TestPostOrder) ... ok test_r_b2 (__main__.TestPostOrder) ... ok test_root (__main__.TestPostOrder) ... ok test_single_branch (__main__.TestPostOrder) ... ok test_single_leaf (__main__.TestPostOrder) ... ok test_single_root (__main__.TestPostOrder) ... ok test_tree (__main__.TestTree) ... ok test_ukkonen1 (__main__.TestTree) ... ok test_ukkonen2 (__main__.TestTree) ... ok test (__main__.TestMatchingStatistics) ... FAIL test (__main__.TestLeafIndices) ... FAIL ====================================================================== FAIL: test (__main__.TestMatchingStatistics) ---------------------------------------------------------------------- Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\suffixtree\test\tst_single.py", line 783, in test self.assertEqual( result, [ ( 0, ( tree.root, 0 ) ) ] * 3 ) AssertionError: Lists differ: [(0, (, 18446744073709551614L)) (0, (, 0)) Diff is 1062 characters long. Set self.maxDiff to None to see it. ====================================================================== FAIL: test (__main__.TestLeafIndices) ---------------------------------------------------------------------- Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\suffixtree\test\tst_single.py", line 840, in test self.assertEqual( result, [ ( 0, ( tree.root, 0 ) ) ] * 3 ) AssertionError: Lists differ: [(0, (, 18446744073709551614L)) (0, (, 0)) Diff is 1062 characters long. Set self.maxDiff to None to see it. ---------------------------------------------------------------------- Ran 28 tests in 0.016s FAILED (failures=2) libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_05.py" [WARNING] 718.7s Time: 718.67 Return code: 0 OKs: 279 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_python3_regression.py" [FAIL] 16.9s Time: 16.89 Return code: 1 OKs: 0 Standard error: FAIL: Python3 compilation exited with unexpected STDERR output libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_optimise_amplitudes.py" [FAIL] 22.1s Time: 22.11 Return code: 1 OKs: 1 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_optimise_amplitudes.py", line 1218, in tst_optimise_amplitudes_single_group() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_optimise_amplitudes.py", line 375, in tst_optimise_amplitudes_single_group convergence_tolerance=1e-08, File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\tls\optimise_amplitudes.py", line 123, in run f_g_calculator = self.get_f_g_calculator() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\tls\optimise_amplitudes.py", line 98, in get_f_g_calculator weight_sum_of_amplitudes_squared = self.optimisation_weights.sum_of_amplitudes_squared, ValueError: invalid selection in base_atom_indices (10376306736294088890): attempting to select atom outside of array (size 10) libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen.py" [FAIL] 32.3s Time: 32.31 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen.py", line 278, in run() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen.py", line 16, in run no_H_on_coordinating_CYS() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen.py", line 105, in no_H_on_coordinating_CYS not_contains = ' HG ') File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen.py", line 49, in compare_models assert ph_initial.is_similar_hierarchy(other=ph_h_added) AssertionError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model_ligands.py" [FAIL] 115.2s Time: 115.25 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model_ligands.py", line 134, in run() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model_ligands.py", line 131, in run tst_1() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model_ligands.py", line 128, in tst_1 Total # of reference model restraints: 1""") File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\test_utils\__init__.py", line 555, in assert_lines_in_file remove_white_spaces=remove_white_spaces, remove_newline=remove_newline) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\test_utils\__init__.py", line 544, in assert_lines_in_text "Lines:\n %s\n are not found" % (lines) AssertionError: Lines: Model: Reference: LIG A 1 <=====> LIG A 1 Total # of matched residue pairs: 1 Total # of reference model restraints: 1 are not found libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fix_xyz.py" [FAIL] 40.6s Time: 40.59 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fix_xyz.py", line 158, in exercise_00() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fix_xyz.py", line 69, in exercise_00 pdb_inp_refined = iotbx.pdb.input(file_name='tst_riding_fix_xyz_shaken_refine_001.pdb', source_info=None) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\pdb\__init__.py", line 785, in input raise_sorry_if_format_error=raise_sorry_if_format_error).file_content() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\pdb\__init__.py", line 715, in __init__ six.reraise(exc_info[0], exc_info[1], exc_info[2]) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\pdb\__init__.py", line 684, in __init__ raise_sorry_if_format_error=raise_sorry_if_format_error) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\pdb\__init__.py", line 736, in pdb_input lines=flex.split_lines(smart_open.for_reading(file_name).read())) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\smart_open.py", line 27, in for_reading + " "+str(e)) IOError: Cannot open file for reading: "tst_riding_fix_xyz_shaken_refine_001.pdb" [Errno 2] No such file or directory: 'tst_riding_fix_xyz_shaken_refine_001.pdb' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_5.py" [FAIL] 24.6s Time: 24.58 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_5.py", line 108, in exercise(pdb_poor_str = pdb_poor, resolution_factor=0.2) File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_5.py", line 105, in exercise tol = 0.30) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\refinement\real_space\__init__.py", line 92, in check_sites_match assert dist < tol, [dist, tol] AssertionError: [8.119241135977157, 0.3] libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints.py" [FAIL] 28.7s Time: 28.73 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints.py", line 287, in exercise_without_geometry_restaints() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints.py", line 255, in exercise_without_geometry_restaints t.run_test() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints.py", line 180, in run_test refine_u_iso = self.u_iso) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\refinement\minimization_ncs_constraints.py", line 433, in __init__ ignore_line_search_failed_maxfev=True)) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\scitbx\lbfgs\__init__.py", line 278, in run line_search) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\scitbx\lbfgs\__init__.py", line 149, in run_c_plus_plus if (minimizer.run(x, f, g, gradient_only,line_search)): continue RuntimeError: lbfgs error: Line search failed: The step is at the upper bound stpmax(). libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder.py" [FAIL] 58.5s Time: 58.50 Return code: 1 OKs: 0 Standard error: The syntax of the command is incorrect. The syntax of the command is incorrect. Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder.py", line 241, in exercise_00() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder.py", line 198, in exercise_00 assert not easy_run.call(cmd) AssertionError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_2.py" [FAIL] 38.0s Time: 37.97 Return code: 1 OKs: 0 Standard error: The syntax of the command is incorrect. Sorry: [Errno 2] No such file or directory: 'tst_polder_2_1_polder_map_coeffs.mtz' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py" [FAIL] 157.5s Time: 157.50 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py", line 192, in run() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py", line 186, in run run_test1() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py", line 90, in run_test1 vl_manager.run() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\validation\validate_ligands.py", line 151, in run results = self.parallel_populate(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\validation\validate_ligands.py", line 112, in parallel_populate self.nproc, File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\easy_mp.py", line 721, in multi_core_run for i, ( calc, res ) in enumerate(pfi): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\forward_compatibility.py", line 23, in next return type(self).__next__(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\scheduling\parallel_for.py", line 249, in __next__ self.state.fillup( pfi = self ) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\scheduling\parallel_for.py", line 174, in fillup cls.iterate( pfi = pfi ) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\scheduling\parallel_for.py", line 163, in iterate manager = pfi.manager, File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\scheduling\parallel_for.py", line 17, in submit_one_job manager.submit( target = target, args = args, kwargs = kwargs ), File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\scheduling\job_scheduler.py", line 143, in submit self.poll() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\scheduling\job_scheduler.py", line 221, in poll process.start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\process.py", line 130, in start self._popen = Popen(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 277, in __init__ dump(process_obj, to_child, HIGHEST_PROTOCOL) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 199, in dump ForkingPickler(file, protocol).dump(obj) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 224, in dump self.save(obj) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 331, in save self.save_reduce(obj=obj, *rv) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 425, in save_reduce save(state) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 655, in save_dict self._batch_setitems(obj.iteritems()) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 687, in _batch_setitems save(v) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 568, in save_tuple save(element) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 754, in save_global (obj, module, name)) pickle.PicklingError: Can't pickle : it's not found as mmtbx.validation.validate_ligands._run Traceback (most recent call last): File "", line 1, in File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 381, in main self = load(from_parent) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 1384, in load return Unpickler(file).load() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 864, in load dispatch[key](self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 886, in load_eof raise EOFError EOFError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits.py" [FAIL] 42.7s Time: 42.73 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits.py", line 308, in exercise() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits.py", line 304, in exercise exercise_angle_edits_change(mon_lib_srv, ener_lib) File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits.py", line 238, in exercise_angle_edits_change 100.00''' in geo_file_str AssertionError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cablam_2.py" [FAIL] 100.2s Time: 100.16 Return code: 1 OKs: 0 Standard error: Starting phenix.cablam.bat on Fri May 1 07:39:32 2020 by phaserbuilder =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 5o61.cif Processing PHIL parameters: ------------------------------------------------------------------------------- No PHIL parameters found Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "5o61.cif" } default_model = "5o61.cif" } Starting job =============================================================================== Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\cctbx_project\mmtbx\command_line\cablam.py", line 46, in run(sys.argv[1:]) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\cctbx_project\mmtbx\command_line\cablam.py", line 36, in run task.run() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\programs\cablam.py", line 76, in run quiet=False) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\validation\cablam.py", line 950, in __init__ self.all_results[chain].confs[conf].results[result].set_cablam_feedback() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\validation\cablam.py", line 567, in set_cablam_feedback and (self.prevres.scores.alpha >= ALPHA_CUTOFF or self.prevres.scores.threeten >= THREETEN_CUTOFF) AttributeError: 'NoneType' object has no attribute 'alpha' Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cablam_2.py", line 15, in exercise_01() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cablam_2.py", line 8, in exercise_01 assert not easy_run.call("phenix.cablam 5o61.cif"), "For Chris to fix" AssertionError: For Chris to fix Please verify these tests manually. Summary: Tests run : 850 Failures : 12 Warnings (possible failures) : 2 Known Failures ( 3) : 3 Known Unstable ( 1) : 0 Stderr output (discouraged) : 17 See run_tests_parallel_zlog for full output. ******************************************************************************** ERROR: 12 TEST FAILURES. PLEASE FIX BEFORE COMMITTING CODE. ******************************************************************************** libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\windows\tst_autosol_sad.py" Files not found, skipping libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\windows\tst_autosol_mad.py" Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\windows\tst_autosol_mad.py", line 23, in exercise() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\windows\tst_autosol_mad.py", line 8, in exercise assert (full_path is not None) AssertionError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\windows\tst_autobuild.py" Files not found, skipping libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\windows\tst_autobuild_omit.py" Files not found, skipping libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\windows\tst_ligandfit.py" Files not found, skipping libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\refinement\tst_refinement_nqh_flips.py" C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\conda_base\python.exe: can't open file 'c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\refinement\tst_refinement_nqh_flips.py': [Errno 2] No such file or directory libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\validation\tst_comprehensive.py" C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\conda_base\python.exe: can't open file 'c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\validation\tst_comprehensive.py': [Errno 2] No such file or directory libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\validation\tst_suitename.py" OK libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\gui\tst_hyss_gui.py" OK ################################################################################ # Number of test : 190 ################################################################################ Running 190 tests on 24 processors: libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cis_trans_enumerate.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zmatrix_construction.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sulfur_chiral.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sulfur_chiral.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 10 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 9 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 8 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 7 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 6 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_benzene_sdf.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_enumerate.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_enumerate.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 9 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 8 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 7 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 6 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_amino_acid_switch.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_elbow_general.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zinc_smiles.py" 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\tst_am1_ext.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\tst_am1_forces.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_generic_ringise.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_atom_ordering.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_linear_angle.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cif_writer.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_tripos_writer.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_lots_main.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zmatrix_order.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_aromatic_sulphur.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_libtbx_memory.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_bad_pdb_files.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_peptide_class.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_planar.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_initial_final.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_assign.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_atom_naming_polish.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_alternative_location.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_link_edits.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_bond_valence.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_hydrogenise.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_zmatrix.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_library.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_heavy_hydrogen.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_boron_geometry.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_am1_extended.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_all_am1_elements.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_unusual_pdb.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_2d_writer.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sugar.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_conformations_ext.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_synonyms.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_molfile_chiral.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_3_ring_mol.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_aromatic_nitrogens.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_r_s_chiral.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_chiral.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_multi_cif.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_peptide_planar_conform.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_xml.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ligand_linking.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chirals_more.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pass_throughs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_planar_radial_hydrogens.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_not_planar.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_geo_parser.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_elbow_generate_all.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\tst_lzw.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zinc_smiles.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zinc_smiles.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zinc_smiles.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 6 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 7 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 8 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 9 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 10 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 11 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 12 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 13 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 14 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 6 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 7 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 8 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 9 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 10 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 6 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 7 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 8 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 9 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 10 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 11 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 12 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 13 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 14 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 15 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 16 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_elbow_general.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 6 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 7 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 8 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 9 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 10 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 11 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_amino_acid_switch.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_amino_acid_switch.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_amino_acid_switch.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_amino_acid_switch.py" 5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 10 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 11 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 12 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 13 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 14 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 15 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 6 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 7 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 8 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 9 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 10 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 11 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 12 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 13 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 14 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 6 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 7 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 8 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 9 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zmatrix_construction.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 6 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 7 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 8 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 9 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 10 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 11 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 12 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 13 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 14 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 15 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 16 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cis_trans_enumerate.py" 2 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cis_trans_enumerate.py" 3 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cis_trans_enumerate.py" 4 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zmatrix_construction.py" 1 [OK] 23.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 5 [OK] 23.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 10 [OK] 24.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cis_trans_enumerate.py" 1 [OK] 27.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 1 [OK] 27.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 9 [OK] 32.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 6 [OK] 35.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_benzene_sdf.py" 1 [OK] 36.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 1 [OK] 45.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sulfur_chiral.py" 2 [OK] 60.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 1 [OK] 61.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 1 [OK] 65.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 4 [OK] 70.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 5 [OK] 70.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 3 [OK] 74.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 2 [OK] 77.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 8 [OK] 79.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 7 [OK] 54.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_enumerate.py" 2 [OK] 81.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 7 [OK] 84.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sulfur_chiral.py" 1 [OK] 85.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 2 [OK] 88.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 3 [OK] 52.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\tst_am1_forces.py" [OK] 18.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\tst_am1_ext.py" [OK] 20.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 3 [OK] 101.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 4 [OK] 105.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 1 [OK] 31.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_generic_ringise.py" [OK] 30.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 1 [OK] 122.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_enumerate.py" 1 [OK] 103.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_amino_acid_switch.py" 1 [OK] 75.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zinc_smiles.py" 1 [OK] 59.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 1 [OK] 74.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 1 [OK] 94.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_libtbx_memory.py" [OK] 52.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cif_writer.py" [OK] 78.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 1 [OK] 94.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_planar.py" [OK] 48.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_linear_angle.py" [OK] 90.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zmatrix_order.py" [OK] 83.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_assign.py" [OK] 48.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_bad_pdb_files.py" [OK] 73.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_link_edits.py" [OK] 36.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_peptide_class.py" [OK] 89.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_alternative_location.py" [OK] 53.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_atom_ordering.py" [OK] 129.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_hydrogenise.py" [OK] 47.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_aromatic_sulphur.py" [OK] 117.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_bond_valence.py" [OK] 64.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_atom_naming_polish.py" [OK] 87.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_boron_geometry.py" [OK] 48.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 9 [OK] 212.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_all_am1_elements.py" [OK] 40.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_elbow_general.py" 1 [OK] 173.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_am1_extended.py" [OK] 57.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 6 [OK] 221.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 4 [OK] 215.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_heavy_hydrogen.py" [OK] 67.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_synonyms.py" [OK] 30.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_unusual_pdb.py" [OK] 44.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sugar.py" [OK] 45.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_3_ring_mol.py" [OK] 32.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_zmatrix.py" [OK] 93.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_initial_final.py" [OK] 131.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 2 [OK] 226.0s libtbx.python 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"c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_conformations_ext.py" [OK] 79.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pass_throughs.py" [OK] 44.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_library.py" [OK] 124.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 5 [OK] 272.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\tst_lzw.py" [OK] 37.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_molfile_chiral.py" [OK] 76.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_tripos_writer.py" [OK] 209.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zinc_smiles.py" 2 [OK] 50.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 8 [OK] 299.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 2 [OK] 47.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_not_planar.py" [OK] 80.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 3 [OK] 51.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 6 [OK] 47.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 9 [OK] 42.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zinc_smiles.py" 3 [OK] 66.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 4 [OK] 54.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 7 [OK] 51.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zinc_smiles.py" 4 [OK] 67.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_r_s_chiral.py" [OK] 112.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 11 [OK] 47.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 12 [OK] 45.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 13 [OK] 44.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 10 [OK] 52.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 5 [OK] 70.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 8 [OK] 65.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_peptide_planar_conform.py" [OK] 119.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 14 [OK] 42.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chirals_more.py" [OK] 112.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 3 [OK] 54.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 2 [OK] 56.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 5 [OK] 65.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 7 [OK] 61.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 6 [OK] 67.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 9 [OK] 64.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 8 [OK] 65.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 10 [OK] 65.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 7 [OK] 56.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 11 [OK] 51.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_elbow_generate_all.py" [OK] 155.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 6 [OK] 68.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 9 [OK] 60.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 8 [OK] 63.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 12 [OK] 62.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 2 [OK] 105.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 10 [OK] 68.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_elbow_general.py" 2 [OK] 26.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 3 [OK] 26.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 5 [OK] 29.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 4 [OK] 32.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 7 [OK] 22.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 9 [OK] 24.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 4 [OK] 97.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 16 [OK] 45.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 11 [OK] 25.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 13 [OK] 53.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 2 [OK] 46.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 6 [OK] 41.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 10 [OK] 33.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 14 [OK] 57.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 15 [OK] 55.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 12 [OK] 25.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 13 [OK] 23.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 15 [OK] 21.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 2 [OK] 33.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 8 [OK] 65.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 4 [OK] 31.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_lots_main.py" [OK] 390.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_amino_acid_switch.py" 2 [OK] 63.2s libtbx.python 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50.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_amino_acid_switch.py" 4 [OK] 70.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 9 [OK] 39.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 11 [OK] 36.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 10 [OK] 41.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_2d_writer.py" [OK] 302.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 14 [OK] 28.6s libtbx.python 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libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 3 [OK] 228.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 7 [OK] 42.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 8 [OK] 42.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 3 [OK] 51.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 9 [OK] 39.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_geo_parser.py" [OK] 298.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 10 [OK] 38.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 6 [OK] 51.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 11 [OK] 38.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 5 [OK] 56.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 4 [OK] 79.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 12 [OK] 39.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 13 [OK] 31.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 4 [OK] 67.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 2 [OK] 74.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 4 [OK] 241.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 14 [OK] 35.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zmatrix_construction.py" 2 [OK] 80.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 10 [OK] 147.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 11 [OK] 146.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 14 [OK] 139.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 9 [OK] 94.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 15 [OK] 44.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 16 [OK] 42.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cis_trans_enumerate.py" 3 [OK] 45.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cis_trans_enumerate.py" 4 [OK] 45.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cis_trans_enumerate.py" 2 [OK] 50.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 5 [OK] 263.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 6 [OK] 145.2s ================================================================================ Tests finished. Elapsed time: 668.07s Distribution of test runtimes: 18.4s - 55.6s: 97 55.6s - 92.7s: 56 92.7s - 129.9s: 16 129.9s - 167.0s: 6 167.0s - 204.2s: 1 204.2s - 241.4s: 7 241.4s - 278.5s: 3 278.5s - 315.7s: 3 315.7s - 352.9s: 0 352.9s - 390.0s: 1 Warning: the following jobs took at least 180 seconds: libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_tripos_writer.py": 209.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 9: 212.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 4: 215.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 1: 218.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 6: 221.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 2: 226.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 3: 228.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 4: 241.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 5: 263.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 5: 272.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_geo_parser.py": 298.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 8: 299.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_2d_writer.py": 302.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_lots_main.py": 390.0s Please try to reduce overall runtime - consider splitting up these tests. Summary: Tests run : 190 Failures : 0 Warnings (possible failures) : 0 Known Failures ( 0) : 0 Known Unstable ( 0) : 0 Stderr output (discouraged) : 0 See run_tests_parallel_zlog for full output. Building PHENIX documentation in c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules The complete documentation will be in: c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc creating restructured text files reciprocal_space_arrays.txt map_value_at_point.txt fmodel.txt building HTML files from restructured text files converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\construction.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\construction.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\coot.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\coot.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\creating_windows_installer.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\creating_windows_installer.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\developer.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\developer.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\dictionary.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\dictionary.html Couldn't index: not well-formed (invalid token): line 916, column 85 converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\doc_procedures.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\doc_procedures.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\examples.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\examples.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\file_formats.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\file_formats.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\install-setup-run.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\install-setup-run.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\making_geometry_restraints.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\making_geometry_restraints.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\ManualPhenixBuild.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\ManualPhenixBuild.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\phenix-modules.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\phenix-modules.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\phenix_gui.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\phenix_gui.html Couldn't index: not well-formed (invalid token): line 497, column 135 converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\phenix_programs.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\phenix_programs.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\pymol.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\pymol.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\tutorials.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\what-is-phenix.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\what-is-phenix.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\WindowsBuild.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\.\WindowsBuild.html Couldn't index: not well-formed (invalid token): line 262, column 115 converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\faqs\cryo_fit2_FAQ.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\faqs\cryo_fit2_FAQ.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\faqs\cryo_fit_FAQ.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\faqs\cryo_fit_FAQ.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\faqs\experimental_phasing.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\faqs\experimental_phasing.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\faqs\index.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\faqs\index.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\faqs\ligands.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\faqs\ligands.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\faqs\model_building.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\faqs\model_building.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\faqs\mr.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\faqs\mr.html Couldn't index: not well-formed (invalid token): line 316, column 262 converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\faqs\refine.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\faqs\refine.html Couldn't index: not well-formed (invalid token): line 872, column 174 converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\overviews\cryo-em-structure-deposition.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\overviews\cryo-em-structure-deposition.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\overviews\density-modification.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\overviews\density-modification.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\overviews\ligands.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\overviews\ligands.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\overviews\validation.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\overviews\validation.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\overviews\validation_cryo_em.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\overviews\validation_cryo_em.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\overviews\xray-data-quality.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\overviews\xray-data-quality.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\overviews\xray-experimental-phasing.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\overviews\xray-experimental-phasing.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\overviews\xray-model-building.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\overviews\xray-model-building.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\overviews\xray-molecular-replacement.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\overviews\xray-molecular-replacement.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\overviews\xray-refinement.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\overviews\xray-refinement.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\overviews\xray-structure-deposition.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\overviews\xray-structure-deposition.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\afitt.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\afitt.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\amber.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\amber.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\anomalous_signal.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\anomalous_signal.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\apply_ncs.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\apply_ncs.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\assign_sequence.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\assign_sequence.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\atom_selections.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\atom_selections.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\autobuild.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\autobuild.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\autobuild_gui.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\autobuild_gui.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\automr.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\automr.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\autosol.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\autosol.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\autosol_gui.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\autosol_gui.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\auto_sharpen.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\auto_sharpen.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\build_one_model.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\build_one_model.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\cablam_training.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\cablam_training.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\cablam_validation.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\cablam_validation.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\carbo_builder.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\carbo_builder.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\carbo_load.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\carbo_load.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\carbo_primer.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\carbo_primer.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\chain_comparison.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\chain_comparison.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\cif_as_mtz.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\cif_as_mtz.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\citations.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\citations.html Couldn't index: not well-formed (invalid token): line 34, column 174 converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\combine_focused_maps.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\combine_focused_maps.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\combine_models.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\combine_models.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\composite_omit_map.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\composite_omit_map.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\create_maps.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\create_maps.html Couldn't index: not well-formed (invalid token): line 93, column 95 converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\cryo_fit.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\cryo_fit.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\cryo_fit2.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\cryo_fit2.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\cut_out_density.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\cut_out_density.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\data_viewer.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\data_viewer.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\density_modification.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\density_modification.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\density_outside_model.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\density_outside_model.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\den_refine.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\den_refine.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\dock_in_map.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\dock_in_map.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\dynamics.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\dynamics.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\elbow.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\elbow.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\elbow_gui.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\elbow_gui.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\emma.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\emma.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\ensembler.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\ensembler.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\ensembler_new.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\ensembler_new.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\ensemble_refinement.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\ensemble_refinement.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\erraser.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\erraser.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\explore_metric_symmetry.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\explore_metric_symmetry.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\f000.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\f000.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\fab_elbow_angle.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\fab_elbow_angle.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\fem.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\fem.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\find_all_ligands.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\find_all_ligands.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\find_alt_orig_sym_mate.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\find_alt_orig_sym_mate.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\find_helices_strands.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\find_helices_strands.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\find_ncs.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\find_ncs.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\find_ncs_from_density.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\find_ncs_from_density.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\find_peaks_holes.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\find_peaks_holes.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\find_program.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\find_program.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\fit_loops.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\fit_loops.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\fix_insertions_deletions.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\fix_insertions_deletions.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\fmodel.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\fmodel.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\geometry_minimization.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\geometry_minimization.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\get_cc_mtz_mtz.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\get_cc_mtz_mtz.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\get_cc_mtz_pdb.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\get_cc_mtz_pdb.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\get_pdb_validation_report.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\get_pdb_validation_report.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\guess_molecular_centers.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\guess_molecular_centers.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\guided_ligand_replacement.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\guided_ligand_replacement.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\hydrogens.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\hydrogens.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\hyss.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\hyss.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\index.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\index.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\ligandfit.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\ligandfit.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\ligandfit_gui.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\ligandfit_gui.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\ligand_identification.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\ligand_identification.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\ligand_pipeline.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\ligand_pipeline.html Couldn't index: not well-formed (invalid token): line 451, column 167 converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\maps.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\maps.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\map_box.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\map_box.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\map_symmetry.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\map_symmetry.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\map_to_model.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\map_to_model.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\map_to_object.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\map_to_object.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\map_to_structure_factors.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\map_to_structure_factors.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\map_value_at_point.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\map_value_at_point.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\model_idealization.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\model_idealization.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\model_vs_data.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\model_vs_data.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\molprobity_tool.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\molprobity_tool.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\morph_model.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\morph_model.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\MRage.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\MRage.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\mr_overview.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\mr_overview.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\mr_rosetta.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\mr_rosetta.html Couldn't index: not well-formed (invalid token): line 1001, column 262 converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\mtriage.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\mtriage.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\mtz2map.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\mtz2map.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\multimer_reconstruction.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\multimer_reconstruction.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\multi_crystal_average.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\multi_crystal_average.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\ncs_average.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\ncs_average.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\parallel_autobuild.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\parallel_autobuild.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\pdbtools.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\pdbtools.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\phaser.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\phaser.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\phaser_ep.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\phaser_ep.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\phaser_mr.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\phaser_mr.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\phase_and_build.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\phase_and_build.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\phenix_maps.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\phenix_maps.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\plan_sad_experiment.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\plan_sad_experiment.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\polder.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\polder.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\polder_box.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\polder_box.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\prepare_pdb_deposition.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\prepare_pdb_deposition.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\ready_set.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\ready_set.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\real_space_refine.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\real_space_refine.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\reciprocal_space_arrays.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\reciprocal_space_arrays.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\reel.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\reel.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\refinement.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\refinement.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\refine_ca_model.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\refine_ca_model.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\refine_gui.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\refine_gui.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\reflection_file_editor.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\reflection_file_editor.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\reflection_file_tools.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\reflection_file_tools.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\reflection_statistics.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\reflection_statistics.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\remove_free_from_map.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\remove_free_from_map.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\remove_poor_fragments.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\remove_poor_fragments.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\replace_side_chains.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\replace_side_chains.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\resolve_cryo_em.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\resolve_cryo_em.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\rosetta_install.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\rosetta_install.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\rosetta_refine.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\rosetta_refine.html Couldn't index: not well-formed (invalid token): line 177, column 262 converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\running-solve-resolve.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\running-solve-resolve.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\running-wizards.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\running-wizards.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\sad_data_from_pdb.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\sad_data_from_pdb.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\scales.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\scales.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\scale_and_merge.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\scale_and_merge.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\sceds.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\sceds.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\sculptor.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\sculptor.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\sculptor_new.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\sculptor_new.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\sculpt_ensemble.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\sculpt_ensemble.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\secondary_structure.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\secondary_structure.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\secondary_structure_restraints.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\secondary_structure_restraints.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\segment_and_split_map.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\segment_and_split_map.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\selection_editor.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\selection_editor.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\sequence_from_map.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\sequence_from_map.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\simple_homology_model.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\simple_homology_model.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\simple_ncs_from_pdb.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\simple_ncs_from_pdb.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\sort_hetatms.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\sort_hetatms.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\structural_domain_search.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\structural_domain_search.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\structure_comparison.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\structure_comparison.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\structure_search.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\structure_search.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\superpose_maps.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\superpose_maps.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\superpose_pdbs.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\superpose_pdbs.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\table_one.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\table_one.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\trace_and_build.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\trace_and_build.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\tutorial_channel.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\tutorial_channel.html Couldn't index: mismatched tag: line 37, column 176 converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\unmerged_data.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\unmerged_data.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\validation.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\validation.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\validation_cryo_em.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\validation_cryo_em.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\xmanip.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\xmanip.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\xtriage.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\xtriage.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\reference\xtriage_gui.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\reference\xtriage_gui.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\autobuild.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\autobuild.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\cryo_em_structure_solution_docking.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\cryo_em_structure_solution_docking.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\cryo_em_structure_solution_model_building.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\cryo_em_structure_solution_model_building.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\cryo_fit2_cmdline.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\cryo_fit2_cmdline.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\cryo_fit2_install.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\cryo_fit2_install.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\cryo_fit2_movie.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\cryo_fit2_movie.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\cryo_fit_cmdline.txt to c:\users\phaserbuilder\night:3: (WARNING/2) Duplicate explicit target name: "here". lybuilds\phenixvc2008\x64\current\doc\tutorials\cryo_fit_cmdline.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\cryo_fit_gui.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\cryo_fit_gui.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\cryo_fit_install.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\cryo_fit_install.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\cryo_fit_movie.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\cryo_fit_movie.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\elbow.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\elbow.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\ligandfit.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\ligandfit.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\ligandfit_cmdline.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\ligandfit_cmdline.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\mad_phasing.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\mad_phasing.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\mir_phasing.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\mir_phasing.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\molprobity.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\molprobity.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\mr.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\mr.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\mr_refine.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\mr_refine.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\rebuild.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\rebuild.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\refine.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\refine.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\refinement_examples.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\refinement_examples.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\sad_phasing.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\sad_phasing.html converting c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_html\rst_files\tutorials\twinning.txt to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\doc\tutorials\twinning.html copying images copying extras Splitting output to AutoSol_run_1_\AutoSol_run_1_1.log PHENIX autosol Fri May 1 08:07:27 2020 Phenix developers include: Paul Adams, Pavel Afonine, Vincent Chen, Ian Davis, Nathaniel Echols, Kreshna Gopal, Ralf Grosse-Kunstleve, Jeff Headd, Li-Wei Hung, Robert Immormino, Tom Ioerger, Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read, Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini, Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger, Peter Zwart Phenix home page: http://www.phenix-online.org/ ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Phenix components are copyrighted by: - Lawrence Berkeley National Laboratory - Los Alamos National Laboratory - University of Cambridge - Duke University - Texas Agricultural Experiment Station & Texas Engineering Experiment Station ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Major third-party components of Phenix include: Python, wxwidgets, wxPython, Boost, SCons, Clipper, PULCHRA, CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS Enter phenix.acknowledgments for details. If you use PHENIX please cite: Adams, P.D., Afonine, P.V., Chen, V., Echols, N., Headd, J. J., Hung, L.-W., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C. and Zwart, P. H. (2010) PHENIX - A Comprehensive Python-based System for Macromolecular Structure Solution. Acta Cryst. D66, 213-221. For help type: phenix.doc For access to full documentation please type: phenix.doc ------------------------------------------------------------ Starting AutoSol with the command: phenix.autosol \ data=c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca \ seq_file=c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\seq.dat \ atom_type=Se lambda=0.9792 crystal_info.resolution=2.5 Guessing c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca is a datafile at peak wavelength. autosol { atom_type = "Se" lambda = 0.9792 f_prime = None f_double_prime = None wavelength_name = peak inf high low remote sites = None sites_file = None seq_file = "c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\seq.dat" quick = None data = "c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\p9.sca" labels = None derscale = None crystal_info { unit_cell = None space_group = None solvent_fraction = None chain_type = *Auto PROTEIN DNA RNA resolution = 2.5 change_sg = False residues = None sequence = None } input_files { cif_def_file_list = None group_labels_list = None input_file_list = None input_phase_file = None input_phase_labels = None input_refinement_file = None input_refinement_labels = None input_seq_file = Auto refine_eff_file_list = None } wavelength { wavelength_name = peak inf high low remote data = None labels = None atom_type = None lambda = None res_hyss = None res_eval = None f_prime = None f_double_prime = None sites = None sites_file = None derscale = None group = 1 added_wavelength = True ignore = False } native { data = None labels = None lambda = None group = 1 added_native = True ignore = False } deriv { data = None labels = None atom_type = None sites = None sites_file = None res_hyss = None res_eval = None inano = noinano *inano anoonly f_prime = None f_double_prime = None lambda = None derscale = None group = 1 added_deriv = True ignore = False } decision_making { hyss_scoring { model_ha_iteration = None acceptable_r = 0.35 max_model_ha_iterations = None max_models_in_ha_iteration = None ha_iteration = None max_ha_iterations = None minimum_improvement = 0 } always_include_peak = True add_extra_if_fa = True create_scoring_table = None desired_coverage = None skip_hyss_other_derivs_if_quick = True self_diff_fourier = True combine_siblings = True max_cc_extra_unique_solutions = 0.5 max_choices = None max_composite_choices = 8 max_extra_unique_solutions = None max_range_to_keep = 4 min_fom = 0.05 low_fom = 0.2 minimum_merge_cc = 0.25 min_fom_for_dm = 0 extreme_dm = False fom_for_extreme_dm = 0.35 minimum_ncs_cc = 0.3 min_phased_each_deriv = 1 n_random = 6 res_eval = 0 score_individual_offset_list = None score_individual_scale_list = None score_individual_sd_list = None score_overall_offset = None score_overall_scale = None score_overall_sd = None score_type_list = SKEW CORR_RMS score_weight_list = None skip_score_list = None ncs_copies_min_for_overlap = 2 rho_overlap_min = 0.3 rho_overlap_min_scoring = 0.5 build_scoring { overall_score_method = *BAYES-CC Z-SCORE r_switch = 0.4 acceptable_quality = 40 acceptable_secondary_structure_cc = 0.35 trace_chain = False trace_chain_score = False include_dm_score = None use_map_model_cc = None quality_cc_min = 0.5 max_useful_dm_r = 0.4 } dev_scoring { random_scoring = False use_perfect = False hklperfect = None perfect_labels = None } } scaling { remove_aniso = Auto *True False b_iso = None max_b_iso = 40 target_b_ratio = 10 try_orig_sad_data_in_hyss = Auto localscale_before_phaser = True delta_b_for_auto_remove_aniso = 20 ratio_b_for_auto_remove_aniso = 1 test_remove_aniso = True use_sca_as_is = True derscale_list = None scale_only = False phase_only = False } heavy_atom_search { min_hyss_cc = 0.05 acceptable_cc_hyss = 0.2 good_cc_hyss = 0.3 n_add_res_max = 2 add_res_max = 2 try_recommended_resolution_for_hyss = True hyss_runs_min = 2 best_of_n_hyss = 1 best_of_n_hyss_always = 10 min_fraction_of_sites_found = 0.667 max_single_sites = 5 hyss_enable_early_termination = True hyss_general_positions_only = True hyss_min_distance = 3.5 hyss_n_fragments = 3 hyss_n_patterson_vectors = 33 hyss_random_seed = 792341 res_hyss = None try_low_res_for_cys = True direct_methods_only = False use_measurability = True use_phaser_rescoring = False use_automatic_hyss = True mad_ha_n = None mad_ha_type = "Se" } phasing { keep_atom_types = False do_madbst = True overallscale = False res_phase = 0 phase_full_resolution = True fixscattfactors = None fixscattfactors_in_phasing = False fix_xyz_in_phasing = None have_hand = False id_scale_ref = None ratio_out = 10 ratmin = 0 require_nat = True ikeepflag = 1 phasing_method = SOLVE *PHASER cluster_pdb_file = None input_partpdb_file = None input_part_map_ha_fraction = 0.75 phaser_sites_then_phase = False partpdb_rms = None input_part_map_coeffs_file = None input_part_map_coeffs_labels = "FC,PHIC" llgc_sigma = None phaser_completion = True use_phaser_hklstart = True combine_same_parent_only = False skip_extra_phasing = *Auto True False read_sites = False f_double_prime_list = None f_prime_list = None mad_ha_add_f_double_prime_list = None mad_ha_add_f_prime_list = None mad_ha_add_list = None n_ha_list = None nat_der_list = None } density_modification { add_classic_denmod = Auto skip_classic_if_worse_fom = True skip_ncs_in_add_classic = True tolerance_add_classic = 0.02 fix_xyz = False fix_xyz_after_denmod = None hl_in_resolve = False mask_type = *histograms probability wang classic test_mask_type = None mask_cycles = 5 minor_cycles = 10 thorough_denmod = None truncate_ha_sites_in_resolve = Auto *True False rad_mask = None use_ncs_in_denmod = True mask_as_mtz = False protein_output_mask_file = None ncs_output_mask_file = None omit_output_mask_file = None use_hl_anom_in_denmod = None use_hl_anom_in_denmod_with_model = None precondition = False } model_building { build = True phase_improve_and_build = True sort_hetatms = False map_to_object = None helices_strands_only = False resolution_helices_strands = 3.1 helices_strands_start = False cc_helix_min = None cc_strand_min = None build_type = *RESOLVE RESOLVE_AND_BUCCANEER resolve { n_cycle_build = None refine = True ncycle_refine = 3 number_of_builds = None number_of_models = None resolution_build = 0 fit_loops = True loop_cc_min = 0.4 group_ca_length = 4 group_length = 2 input_compare_file = None n_random_frag = 0 n_random_loop = 3 offsets_list = 53 7 23 remove_outlier_segments_z_cut = 3 resolve_command_list = None solve_command_list = None rms_random_frag = None rms_random_loop = None semet = None use_met_in_align = Auto *True False start_chains_list = None thorough_loop_fit = None trace_as_lig = False use_any_side = False loop_lib = False standard_loops = True trace_loops = False refine_trace_loops = True density_of_points = None a_cut_min = None max_density_of_points = None cutout_model_radius = None max_cutout_model_radius = 20 padding = 1 cut_out_density = True max_span = 30 max_c_ca_dist = 2.5 max_overlap_rmsd = 2 max_overlap = None min_overlap = None } } ncs { find_ncs = *Auto True False ncs_copies = None ncs_refine_coord_sigma_from_rmsd = False ncs_refine_coord_sigma_from_rmsd_ratio = 1 optimize_ncs = True refine_with_ncs = True ncs_in_refinement = *torsion cartesian None } refinement { refine_b = True refine_se_occ = True skip_clash_guard = True correct_special_position_tolerance = None use_mlhl = True generate_hl_if_missing = False place_waters = True refinement_resolution = 0 ordered_solvent_low_resolution = None link_distance_cutoff = 3 r_free_flags_fraction = 0.1 r_free_flags_max_free = 2000 r_free_flags_use_lattice_symmetry = True r_free_flags_lattice_symmetry_max_delta = 5 allow_overlapping = None fix_ligand_occupancy = None remove_outlier_segments = True twin_law = None use_hl_anom_in_refinement = None include_ha_in_refinement = None } display { number_of_solutions_to_display = 1 solution_to_display = 0 } general { data_quality = *moderate strong weak thoroughness = *quick medium thorough nproc = 1 nbatch = 1 keep_files = "overall_best*" "phaser_*.mtz" "resolve_*.mtz" "solve_*.mtz" \ "ha_*.pdb" "dataset*.log" coot_name = "coot" i_ran_seed = 72432 raise_sorry = False background = True check_wait_time = 1 max_wait_time = 1 wait_between_submit_time = 1 cache_resolve_libs = True resolve_size = "12" check_run_command = False run_command = "sh " queue_commands = None condor_universe = "vanilla" add_double_quotes_in_condor = True condor = None last_process_is_local = True skip_r_factor = False test_flag_value = Auto skip_xtriage = False base_path = None temp_dir = None local_temp_directory = None clean_up = None print_citations = True solution_output_pickle_file = None job_title = None top_output_dir = None wizard_directory_number = None verbose = False extra_verbose = False debug = False require_nonzero = True remove_path_word_list = None fill = False res_fill = None check_only = False } run_control { coot = None ignore_blanks = None stop = None display_facts = None display_summary = None carry_on = None run = None copy_run = None display_runs = None delete_runs = None display_labels = None dry_run = False params_only = False display_all = False } special_keywords { write_run_directory_to_file = None } non_user_parameters { gui_output_dir = None allow_negative_f_double_prime = False inano_list = None ha_sites_file = None expt_type = *Auto mad sir sad wavelength_list = None wavelength_name_list = None sg = None } } Groups of input data: [1] Datafiles for group 1 : ['c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\p9.sca'] Experiment type: Auto Sending output to Working directory: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_ COMPUTERNAME = AZIMUTH PROCESSOR_ARCHITECTURE = AMD64 USERNAME = phaserbuilder PID = 15180 ************************************************************ PHENIX AutoSol Fri May 1 08:07:27 2020 ************************************************************ Working directory: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark AutoSol_start AutoSol Run 1 Fri May 1 08:07:28 2020 INPUT FILE LIST: ['c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\p9.sca'] Setting chain_type to PROTEIN Copied c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\seq.dat to AutoSol_run_1_\sequence_autosol.dat Setting defaults for data_quality moderate NOTE: fixscattfactors is not applicable for sad dataset Setting thorough_denmod to 'True' Setting max_model_ha_iterations to '1' Setting fix_xyz_after_denmod to 'False' Setting max_ha_iterations to '2' Setting fixscattfactors to 'True' Setting defaults for thoroughness quick Setting max_extra_unique_solutions to '0' Setting number_of_builds to '1' Setting ha_iteration to 'None' Setting max_models_in_ha_iteration to '1' Setting create_scoring_table to 'False' Setting max_choices to '1' Setting n_cycle_build to '0' Setting number_of_models to '1' Setting desired_coverage to '0.8' Setting test_mask_type to 'False' Setting thorough_loop_fit to '' Set try_orig_sad_data_in_hyss=False as thoroughness=quick and extreme_dm=False Set use_hl_anom_in_denmod to False as input_part_map_coeffs_file is 'None' and phaser_sites_then_phase is False Set use_hl_anom_in_denmod_with_model to False as input_part_map_coeffs_file is 'None' and phaser_sites_then_phase is False Set use_hl_anom_in_refinement to False as input_part_map_coeffs_file is 'None' and phaser_sites_then_phase is False Trying to guess refinement file for later use from ['c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\p9.sca'] Choosing guess of refinement file for later use from all files: ['c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\p9.sca'] FILE TYPE scalepack_merge GUESS FILE TYPE MERGE TYPE sca premerged TARGET LABELS ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU'] Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) CONTENTS: ['c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\p9.sca', 'sca', 'premerged', 'I 4', [113.949, 113.949, 32.474, 90.0, 90.0, 90.0], 1.7443432606877811, ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU']] File c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca RES: 1.7 Guess of datafile for refinement: c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca Using c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca for refinement Specify input_refinement_file=c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca to change this HKLIN ENTRY: c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca FILE TYPE scalepack_merge GUESS FILE TYPE MERGE TYPE sca premerged TARGET LABELS ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU'] Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) CONTENTS: ['c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\p9.sca', 'sca', 'premerged', 'I 4', [113.949, 113.949, 32.474, 90.0, 90.0, 90.0], 1.7443432606877811, ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU']] Not checking SG as cell or sg not yet defined SG from c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca is: I 4 Not checking SG as cell or sg not yet defined CELL from c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca is: [113.949, 113.949, 32.474, 90.0, 90.0, 90.0] Total of 1 input data files ['c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\p9.sca'] DATAFILE_LIST: ['c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\p9.sca'] AutoSol_verify_crystal_info AutoSol Run 1 Fri May 1 08:07:28 2020 Sequence file: AutoSol_run_1_\sequence_autosol.dat SG:I 4 CELL: 113.9 113.9 32.5 90.0 90.0 90.0 Getting column labels from c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca for refinement data file Converting the files ['c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\p9.sca'] to mtz amplitude format before proceeding SAVING Facts in LastFacts INITIALIZING FACTS FOR NEW WIZARD ImportRawData LOADING DEFAULTS INTO FACTS ImportRawData_start ImportRawData Run 1 Fri May 1 08:07:29 2020 FINISH START Getting column labels from c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) Number of intensity arrays in this file: 1 Number of amplitude arrays in this file: 0 NOTE: To specify a particular set of data from c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca... you can specify one of the following as its labels: ...: 'I(+) SIGI(+) I(-) SIGI(-)' ImportRawData_output_files ImportRawData Run 1 Fri May 1 08:07:29 2020 summary of input files: hklin : c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca input labels:["I(+)", "SIGI(+)", "I(-)", "SIGI(-)"] OUTPUT FILE NAME: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\p9_PHX.mtz SPACE GROUP NAME: I 4 CELL: [113.949, 113.949, 32.474, 90.0, 90.0, 90.0] INPUT LABELS ID LIST: [['["I(+)", "SIGI(+)", "I(-)", "SIGI(-)"]']] OUTPUT FILES ID LIST: [['C:\\Users\\phaserbuilder\\NightlyBuilds\\PhenixVC2008\\x64\\Current\\tests\\phenix_regression.run_p9_sad_benchmark\\tst_p9_sad_benchmark\\AutoSol_run_1_\\p9_PHX.mtz']] INPUT FILES ID LIST: ['c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\p9.sca'] Creating output files from c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca in mtz format Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) Writing ["I(+)", "SIGI(+)", "I(-)", "SIGI(-)"] to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\p9_PHX.mtz averaging Friedel pairs Miller array info: None Observation type: xray.intensity Type of data: double, size=21557 Type of sigmas: double, size=21557 Number of Miller indices: 21557 Anomalous flag: False Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) Systematic absences: 0 Centric reflections: 1668 Resolution range: 28.4872 1.74434 Completeness in resolution range: 0.996809 Completeness with d_max=infinity: 0.996533 Converting intensities to amplitudes: OUTPUT MTZ COLUMN LABEL: F_from_p9 Miller array info: None Observation type: xray.amplitude Type of data: double, size=21557 Type of sigmas: double, size=21557 Number of Miller indices: 21557 Anomalous flag: False Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) RETURNING TO PREVIOUS WIZARD Returning to CallingWizard = AutoSol Restored values of OutputDir and RunInstance AutoSol_run_1_ _run_1_ LOADING DEFAULTS INTO FACTS AutoSol_Load_from_ImportRawData_refinement AutoSol Run 1 Fri May 1 08:07:30 2020 Load from ImportRawData for refinement file Best guess of converted file input_refinement_file : C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\p9_PHX.mtz AutoSol_verify_crystal_info AutoSol Run 1 Fri May 1 08:07:30 2020 Sequence file: AutoSol_run_1_\sequence_autosol.dat SG:I 4 CELL: 113.9 113.9 32.5 90.0 90.0 90.0 Getting column labels from C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\p9_PHX.mtz for refinement data file SG: I 4 Cell: [113.9489974975586, 113.9489974975586, 32.4739990234375, 90.0, 90.0, 90.0] Refinement file program labels: ['FP', 'SIGFP', 'FreeR_flag'] Refinement file input labels: ['F_from_p9', 'SIGF_from_p9', 'None'] Refinement file all input labels: ['F_from_p9', 'SIGF_from_p9', 'None'] AutoSol_refinement_file_info_inputs AutoSol Run 1 Fri May 1 08:07:30 2020 LABIN PROGRAM LABELS: ['FP', 'SIGFP', 'FreeR_flag'] LABIN INPUT LABELS: ['F_from_p9', 'SIGF_from_p9', 'None'] LABIN: FP=F_from_p9 SIGFP=SIGF_from_p9 AutoSol_set_params AutoSol Run 1 Fri May 1 08:07:30 2020 Setting defaults for thorough density modification Input sequence file is AutoSol_run_1_\sequence_autosol.dat AutoSol_build_params AutoSol Run 1 Fri May 1 08:07:30 2020 Copying fact resolution of 2.5 to resolution_build Recovering fact resolution of 2.5 AutoSol_guess_setup_for_scaling AutoSol Run 1 Fri May 1 08:07:30 2020 This is the last dataset to scale Guessing setup for scaling dataset 1 Guess of heavy-atom type: SE # ncs_and_number_of_ha # # Guess NCS copies and number of sites # Type phenix.doc for help Values of all params: ncs_and_number_of_ha { input_files { seq_file = "AutoSol_run_1_\\sequence_autosol.dat" data = None ncs_file = None } crystal_info { space_group = "I 4" unit_cell = 113.949 113.949 32.474 90 90 90 atom_type = "se" chain_type = "PROTEIN" ncs_copies = None number_of_sites = None ncs_operators_known = None } output_files { log = None params_out = None } directories { output_dir = "" } control { verbose = False raise_sorry = False debug = False dry_run = False } } Estimation of ncs_copies and number of heavy-atom sites Cell and space group: Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) Number of residues in unique chains in seq file: 139 Cell volume: 421654.58 Equivalent positions:8 Maximum number of NCS copies based on cell contents: 2 Best guess of number of NCS copies: 1 Estimate of solvent fraction: 0.64 Best guess of number of SE sites: 4 Warning: NCS copies set to 1, however it could be from 1 to 2 Working NCS copies: 1 Working solvent fraction: 0.64 Number of residues set to 139 Setting number of heavy atoms to 4 Total residues:139 Total Met:4 FILE TYPE scalepack_merge GUESS FILE TYPE MERGE TYPE sca premerged TARGET LABELS ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU'] Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) CONTENTS: ['c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\p9.sca', 'sca', 'premerged', 'I 4', [113.949, 113.949, 32.474, 90.0, 90.0, 90.0], 1.7443432606877811, ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU']] resolution estimate: 2.5 Wavelength for sad is 0.9792 A Guessing peak for sad dataset Guesses of scattering factors for Se Name Lambda f' f" datafile peak 0.9792 -8.0 4.5 p9.sca Effective parameters: #phil __ON__ scaling { input { asu_contents { sequence_file = None n_residues = 139 n_bases = None n_sites = 5 n_copies_per_asu = 1 } xray_data { file_name = "c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\p9-sad\\p9.sca" obs_labels = None calc_labels = None unit_cell = 113.9489975 113.9489975 32.47399902 90 90 90 space_group = "I 4" high_resolution = 2.5 low_resolution = None completeness_as_non_anomalous = True reference { data { file_name = None labels = None unit_cell = None space_group = None } structure { file_name = None } } } parameters { reporting { verbose = 1 log = "AutoSol_run_1_\\p9.sca_xtriage.log" loggraphs = False } merging { n_bins = 10 skip_merging = False } misc_twin_parameters { missing_symmetry { sigma_inflation = 1.25 } twinning_with_ncs { perform_analyses = False n_bins = 7 } twin_test_cuts { low_resolution = 10 high_resolution = None isigi_cut = 3 completeness_cut = 0.85 } apply_basic_filters_prior_to_twin_analysis = True } } optional { hklout = None hklout_type = mtz sca *Auto label_extension = "massaged" aniso { action = *remove_aniso None final_b = *eigen_min eigen_mean user_b_iso b_iso = None } outlier { action = *extreme basic beamstop None parameters { basic_wilson { level = 1e-06 } extreme_wilson { level = 0.01 } beamstop { level = 0.001 d_min = 10 } } } symmetry { action = detwin twin *None twinning_parameters { twin_law = None fraction = None } } } } gui { result_file = None output_dir = None job_title = None } } #phil __END__ Symmetry, cell and reflection file content summary Miller array info: c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca:I(+),SIGI(+),I(-),SIGI(-) Observation type: xray.intensity Type of data: double, size=14106 Type of sigmas: double, size=14106 Number of Miller indices: 14106 Anomalous flag: True Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) Systematic absences: 0 Centric reflections: 810 Resolution range: 28.4872 2.50041 Completeness in resolution range: 0.999079 Completeness with d_max=infinity: 0.998584 Anomalous completeness in resolution range: 0.998497 Bijvoet pairs: 6645 Lone Bijvoet mates: 6 Mean anomalous difference: 0.0733 ################################################################################ # Basic statistics # ################################################################################ =================== Solvent content and Matthews coefficient ================== Crystallized molecule(s) defined as 139 protein residues ------------------------------------------------------------------- | Solvent content analysis | |-----------------------------------------------------------------| | Copies | Solvent content | Matthews coeff. | P(solvent content) | |-----------------------------------------------------------------| | 1 | 0.635 | 3.37 | 0.879 | | 2 | 0.271 | 1.69 | 0.121 | ------------------------------------------------------------------- Best guess : 1 copy in the ASU Caution: this estimate is based on the distribution of solvent content across structures in the PDB, but it does not take into account the resolution of the data (which is strongly correlated with solvent content) or the physical properties of the model (such as oligomerization state, et cetera). If you encounter problems with molecular replacement and/or refinement, you may need to consider the possibility that the ASU contents are different than expected. Number of copies per asymmetric unit provided Will use user specified value of 1.0 ======================== Data strength and completeness ======================= Overall for this dataset is 15.5 ----------Completeness at I/sigma cutoffs---------- The following table lists the completeness in various resolution ranges, after applying a I/sigI cut. Miller indices for which individual I/sigI values are larger than the value specified in the top row of the table, are retained, while other intensities are discarded. The resulting completeness profiles are an indication of the strength of the data. ---------------------------------------------------------------------------------------- | Completeness and data strength | |--------------------------------------------------------------------------------------| | Res. range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | |--------------------------------------------------------------------------------------| | 28.49 - 6.15 | 99.8 | 99.6 | 99.3 | 98.7 | 95.8 | 87.8 | | 6.15 - 4.89 | 99.8 | 99.8 | 99.6 | 98.8 | 95.9 | 90.2 | | 4.89 - 4.27 | 99.6 | 99.4 | 98.6 | 97.6 | 96.0 | 91.0 | | 4.27 - 3.88 | 99.8 | 99.6 | 99.4 | 98.6 | 93.9 | 88.0 | | 3.88 - 3.60 | 100.0 | 99.8 | 99.6 | 97.3 | 92.4 | 84.6 | | 3.60 - 3.39 | 99.6 | 99.0 | 98.4 | 96.4 | 92.7 | 83.6 | | 3.39 - 3.22 | 98.8 | 97.9 | 96.7 | 94.4 | 91.8 | 83.5 | | 3.22 - 3.08 | 99.8 | 99.6 | 98.6 | 97.4 | 90.7 | 82.2 | | 3.08 - 2.96 | 98.7 | 97.5 | 95.8 | 94.5 | 88.8 | 75.4 | | 2.96 - 2.86 | 99.6 | 99.0 | 98.0 | 94.6 | 88.4 | 76.4 | | 2.86 - 2.77 | 99.8 | 98.6 | 97.4 | 95.1 | 85.1 | 69.9 | | 2.77 - 2.69 | 99.0 | 98.1 | 97.3 | 93.3 | 84.9 | 71.3 | | 2.69 - 2.62 | 99.2 | 98.0 | 96.8 | 93.5 | 83.6 | 68.4 | | 2.62 - 2.56 | 99.0 | 98.0 | 96.2 | 92.3 | 81.2 | 61.9 | ---------------------------------------------------------------------------------------- The completeness of data for which I/sig(I)>3.00, exceeds 85 % for resolution ranges lower than 2.56A. The data are cut at this resolution for the potential twin tests and intensity statistics. ----------Low resolution completeness analyses---------- The following table shows the completeness of the data to 5.0 A. Poor low-resolution completeness often leads to map distortions and other difficulties, and is typically caused by problems with the crystal orientation during data collection, overexposure of frames, interference with the beamstop, or omission of reflections by data-processing software. --------------------------------------------------------- | Resolution range | N(obs)/N(possible) | Completeness | --------------------------------------------------------- | 28.4877 - 10.6230 | [105/106] | 0.991 | | 10.6230 - 8.5057 | [105/105] | 1.000 | | 8.5057 - 7.4525 | [ 99/99 ] | 1.000 | | 7.4525 - 6.7812 | [ 95/95 ] | 1.000 | | 6.7812 - 6.3007 | [ 94/94 ] | 1.000 | | 6.3007 - 5.9328 | [ 97/97 ] | 1.000 | | 5.9328 - 5.6381 | [ 93/93 ] | 1.000 | | 5.6381 - 5.3944 | [ 92/93 ] | 0.989 | | 5.3944 - 5.1880 | [ 94/94 ] | 1.000 | | 5.1880 - 5.0100 | [109/109] | 1.000 | --------------------------------------------------------- ----------Completeness (log-binning)---------- The table below presents an alternative overview of data completeness, using the entire resolution range but on a logarithmic scale. This is more sensitive to missing low-resolution data (and is complementary to the separate table showing low-resolution completeness only). -------------------------------------------------- | Resolution | Reflections | Completeness | -------------------------------------------------- | 28.4872 - 12.9594 | 97/103 | 95.3% | | 12.9594 - 10.2406 | 102/102 | 100.0% | | 10.1792 - 8.0174 | 225/225 | 100.0% | | 7.9585 - 6.2918 | 452/452 | 100.0% | | 6.2792 - 4.9342 | 958/960 | 99.8% | | 4.9264 - 3.8748 | 1958/1959 | 99.9% | | 3.8737 - 3.0440 | 4036/4038 | 100.0% | | 3.0432 - 2.5004 | 6278/6282 | 100.0% | -------------------------------------------------- ----------Analysis of resolution limits---------- Your data have been examined to determine the resolution limits of the data along the reciprocal space axes (a*, b*, and c*). These are expected to vary slightly depending on unit cell parameters and overall resolution, but should never be significantly different for complete data. (This is distinct from the amount of anisotropy present in the data, which changes the effective resolution but does not actually exclude reflections.) overall d_min = 2.500 d_min along a* = 2.532 d_min along b* = 2.532 d_min along c* = 2.706 max. difference between axes = 0.174 Resolution limits are within expected tolerances. ================================== Input data ================================= ----------Summary---------- File name: p9.sca Data labels: I(+),SIGI(+),I(-),SIGI(-) Space group: I 4 Unit cell: 113.949, 113.949, 32.474, 90, 90, 90 Data type: xray.intensity Resolution: 28.4872 - 2.50041 Anomalous: True Number of reflections (non-anomalous): 7461 Completeness (non-anomalous): 99.87% Number of reflections (all): 14106 Completeness (all): 99.86% Anomalous completeness: 99.85% Completeness (non-anomalous) is the completeness of the data after merging Friedel pairs. Completeness (all) is the completeness of the data before merging Friedel pairs. Completeness (anomalous) is the completeness of the anomalous data. The anomalous completeness is calcluated by dividing the number of measured acentric, Bijvoet mates by the total possible number of acentric indices. Completeness (non-anomalous) should be used to determine if there is sufficient data for non-anomalous purposes (refinement, model-building). A value greater than 90% is generally desired, while a value less than 75% is considered poor. Values in between will provide less than optimal results. Completeness (anomalous) should be used to determine if there is sufficient data for anomalous purposes (phasing, finding anomalous atoms, refinement of anomalous occupancies or scattering factors). A value greater than 80% is generally desired, while a value less than 50% is considered poor. Values in between will provide less than optimal results. =============================== Anomalous signal ============================== ----------Measurability of anomalous signal---------- The full resolution range seems to contain a useful amount of anomalous signal. Depending on your specific substructure, you could use all the data available for the location of the heavy atoms, or cut the resolution to speed up the search. Table of measurability as a function of resolution: ---------------------------------------------------------- | Resolution range | N(obs)/N(possible) | Measurability | ---------------------------------------------------------- | 28.4891 - 5.3761 | [1405/1409] | 0.2929 | | 5.3761 - 4.2718 | [1418/1419] | 0.1723 | | 4.2718 - 3.7332 | [1398/1399] | 0.1348 | | 3.7332 - 3.3924 | [1434/1435] | 0.1536 | | 3.3924 - 3.1496 | [1404/1406] | 0.1407 | | 3.1496 - 2.9641 | [1388/1389] | 0.1781 | | 2.9641 - 2.8158 | [1470/1470] | 0.1514 | | 2.8158 - 2.6933 | [1346/1348] | 0.1811 | | 2.6933 - 2.5897 | [1467/1467] | 0.1447 | | 2.5897 - 2.5004 | [1376/1377] | 0.1540 | ---------------------------------------------------------- The measurability is defined as the fraction of Bijvoet related intensity differences for which the following relationship holds: |delta_I|/sigma_delta_I > 3.0 min[I(+)/sigma_I(+), I(-)/sigma_I(-)] > 3.0 The measurability provides an intuitive feeling of the quality of the data, as it is related to the number of reliable Bijvoet differences. When the data are processed properly and the standard deviations have been estimated accurately, values larger than 0.05 are encouraging. Note that this analysis relies on the correctness of the estimated standard deviations of the intensities. ===================== Absolute scaling and Wilson analysis ==================== ----------Maximum likelihood isotropic Wilson scaling---------- ML estimate of overall B value: 23.61 A**2 Estimated -log of scale factor: 0.10 The overall B value ("Wilson B-factor", derived from the Wilson plot) gives an isotropic approximation for the falloff of intensity as a function of resolution. Note that this approximation may be misleading for anisotropic data (where the crystal is poorly ordered along an axis). The Wilson B is strongly correlated with refined atomic B-factors but these may differ by a significant amount, especially if anisotropy is present. ----------Maximum likelihood anisotropic Wilson scaling---------- ML estimate of overall B_cart value: 20.14, 0.00, 0.00 20.14, 0.00 32.13 Equivalent representation as U_cif: 0.26, -0.00, -0.00 0.26, 0.00 0.41 Eigen analyses of B-cart: ------------------------------------------------- | Eigenvector | Value | Vector | ------------------------------------------------- | 1 | 32.132 | ( 0.00, 0.00, 1.00) | | 2 | 20.144 | (-0.71, 0.71, -0.00) | | 3 | 20.144 | ( 0.71, 0.71, -0.00) | ------------------------------------------------- ML estimate of -log of scale factor: 0.11 ----------Anisotropy analyses---------- For the resolution shell spanning between 2.63 - 2.50 Angstrom, the mean I/sigI is equal to 12.89. 93.9 % of these intensities have an I/sigI > 3. When sorting these intensities by their anisotropic correction factor and analysing the I/sigI behavior for this ordered list, we can gauge the presence of 'anisotropy induced noise amplification' in reciprocal space. The quarter of Intensities *least* affected by the anisotropy correction show : 1.33e+01 Fraction of I/sigI > 3 : 9.43e-01 ( Z = 0.40 ) The quarter of Intensities *most* affected by the anisotropy correction show : 1.16e+01 Fraction of I/sigI > 3 : 9.26e-01 ( Z = 1.21 ) Z-scores are computed on the basis of a Bernoulli model assuming independence of weak reflections with respect to anisotropy. ----------Wilson plot---------- The Wilson plot shows the falloff in intensity as a function in resolution; this is used to calculate the overall B-factor ("Wilson B-factor") for the data shown above. The expected plot is calculated based on analysis of macromolecule structures in the PDB, and the distinctive appearance is due to the non-random arrangement of atoms in the crystal. Some variation is natural, but major deviations from the expected plot may indicate pathological data (including ice rings, detector problems, or processing errors). ----------Mean intensity analyses---------- Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59. The following resolution shells are worrisome: ----------------------------------------------------------------- | Mean intensity by shell (outliers) | |---------------------------------------------------------------| | d_spacing | z_score | completeness | / | |---------------------------------------------------------------| | 8.449 | 5.55 | 1.00 | 0.594 | ----------------------------------------------------------------- Possible reasons for the presence of the reported unexpected low or elevated mean intensity in a given resolution bin are : - missing overloaded or weak reflections - suboptimal data processing - satellite (ice) crystals - NCS - translational pseudo symmetry (detected elsewhere) - outliers (detected elsewhere) - ice rings (detected elsewhere) - other problems Note that the presence of abnormalities in a certain region of reciprocal space might confuse the data validation algorithm throughout a large region of reciprocal space, even though the data are acceptable in those areas. ----------Possible outliers---------- Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764 Acentric reflections: None Centric reflections: None ----------Ice ring related problems---------- The following statistics were obtained from ice-ring insensitive resolution ranges: mean bin z_score : 1.57 ( rms deviation : 1.24 ) mean bin completeness : 1.00 ( rms deviation : 0.00 ) The following table shows the Wilson plot Z-scores and completeness for observed data in ice-ring sensitive areas. The expected relative intensity is the theoretical intensity of crystalline ice at the given resolution. Large z-scores and high completeness in these resolution ranges might be a reason to re-assess your data processsing if ice rings were present. ------------------------------------------------------------- | d_spacing | Expected rel. I | Data Z-score | Completeness | ------------------------------------------------------------- | 3.897 | 1.000 | 2.00 | 0.99 | | 3.669 | 0.750 | 0.67 | 1.00 | | 3.441 | 0.530 | 0.83 | 1.00 | | 2.671 | 0.170 | 0.42 | 1.00 | ------------------------------------------------------------- Abnormalities in mean intensity or completeness at resolution ranges with a relative ice ring intensity lower than 0.10 will be ignored. No ice ring related problems detected. If ice rings were present, the data does not look worse at ice ring related d_spacings as compared to the rest of the data set. ################################################################################ # Twinning and symmetry analyses # ################################################################################ ============================= Systematic absences ============================= ----------Table of systematic absence rules---------- The following table gives information about systematic absences allowed for the specified intensity point group. For each operator, the reflections are split in three classes: Systematic absence: Reflections that are absent for this operator. Non absence : Reflections of the same type (i.e. (0,0,l)) as above, but they should be present. Other reflections : All other reflections. For each class, the is reported, as well as the number of violations. A violation is a reflection that is absent when it is expected to be present for a particular space group, or present when it is expected to be absent. The criteria are: Systematic absence violation: I/sigI > 3.0 Non absence violation : I/sigI < 3.0 Other relections violation : I/sigI < 3.0 Operators with low associated violations for *both* systematically absent and non absent reflections, are likely to be true screw axis or glide planes. Both the number of violations and their percentages are given. The number of violations within the 'other reflections' class, can be used as a comparison for the number of violations in the non-absent class. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | Operator | # expected systematic absences | (violations) | # expected non absences | (violations) | # other reflections | (violations) | Score | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | 4_0 (c) | 0 | 0.00 (0, 0.0%) | 3 | 10.48 (0, 0.0%) | 6845 | 15.70 (360, 5.3%) | 5.03e+00 | | 4_1 (c) | 0 | 0.00 (0, 0.0%) | 3 | 10.48 (0, 0.0%) | 6845 | 15.70 (360, 5.3%) | 5.03e+00 | | 4_2 (c) | 0 | 0.00 (0, 0.0%) | 3 | 10.48 (0, 0.0%) | 6845 | 15.70 (360, 5.3%) | 5.03e+00 | | 4_3 (c) | 0 | 0.00 (0, 0.0%) | 3 | 10.48 (0, 0.0%) | 6845 | 15.70 (360, 5.3%) | 5.03e+00 | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ----------Space group identification---------- Analyses of the absences table indicates a number of likely space group candidates, which are listed below. For each space group, the number of systematic absence violations are listed under the '+++' column. The number of non-absence violations (weak reflections) are listed under '---'. The last column is a likelihood based score for the particular space group. Note that enantiomorphic spacegroups will have equal scores. Also, if absences were removed while processing the data, they will be regarded as missing information, rather then as enforcing that absence in the space group choices. ------------------------------------------------------------------------------------ | space group | # absent | _absent | _absent | +++ | --- | score | ------------------------------------------------------------------------------------ | I 41 | 0 | 0.00 | 0.00 | 0 | 0 | 0.000e+00 | | I 4 | 0 | 0.00 | 0.00 | 0 | 0 | 5.029e+00 | ------------------------------------------------------------------------------------ ----------List of individual systematic absences---------- Note: this analysis uses the original input data rather than the filtered data used for twinning detection; therefore, the results shown here may include more reflections than shown above. I 4 (input space group): no absences found I 41: no absences found =============== Diagnostic tests for twinning and pseudosymmetry ============== Using data between 10.00 to 2.56 Angstrom. ----------Patterson analyses---------- Largest Patterson peak with length larger than 15 Angstrom: Frac. coord. : 0.054 -0.367 0.000 Distance to origin : 42.219 Height relative to origin : 6.512 % p_value(height) : 5.986e-01 Explanation The p-value, the probability that a peak of the specified height or larger is found in a Patterson function of a macromolecule that does not have any translational pseudo-symmetry, is equal to 5.986e-01. p_values smaller than 0.05 might indicate weak translational pseudo symmetry, or the self vector of a large anomalous scatterer such as Hg, whereas values smaller than 1e-3 are a very strong indication for the presence of translational pseudo symmetry. ----------Wilson ratio and moments---------- Acentric reflections: /^2 :2.004 (untwinned: 2.000; perfect twin 1.500) ^2/ :0.786 (untwinned: 0.785; perfect twin 0.885) <|E^2 - 1|> :0.736 (untwinned: 0.736; perfect twin 0.541) Centric reflections: /^2 :2.976 (untwinned: 3.000; perfect twin 2.000) ^2/ :0.646 (untwinned: 0.637; perfect twin 0.785) <|E^2 - 1|> :0.973 (untwinned: 0.968; perfect twin 0.736) ----------NZ test for twinning and TNCS---------- The NZ test is diagnostic for both twinning and translational NCS. Note however that if both are present, the effects may cancel each other out, therefore the results of the Patterson analysis and L-test also need to be considered. Maximum deviation acentric : 0.008 Maximum deviation centric : 0.029 _acentric : -0.002 _centric : -0.016 ---------------------------------------------------------------------------------------------------------- | NZ test | |--------------------------------------------------------------------------------------------------------| | z | Acentric observed | Acentric untwinned | Centric observed | Centric untwinned | |--------------------------------------------------------------------------------------------------------| | 0 | 0 | 0 | 0 | 0 | | 0.1 | 0.0943798 | 0.0952 | 0.246217 | 0.2481 | | 0.2 | 0.176716 | 0.1813 | 0.345254 | 0.3453 | | 0.3 | 0.253973 | 0.2592 | 0.405777 | 0.4187 | | 0.4 | 0.325414 | 0.3297 | 0.455296 | 0.4738 | | 0.5 | 0.38522 | 0.3935 | 0.507565 | 0.5205 | | 0.6 | 0.449369 | 0.4512 | 0.5337 | 0.5614 | | 0.7 | 0.50213 | 0.5034 | 0.572215 | 0.5972 | | 0.8 | 0.550139 | 0.5507 | 0.599725 | 0.6289 | | 0.9 | 0.595363 | 0.5934 | 0.629986 | 0.6572 | | 1 | 0.636654 | 0.6321 | 0.660248 | 0.6833 | ---------------------------------------------------------------------------------------------------------- ----------L test for acentric data---------- Using difference vectors (dh,dk,dl) of the form: (2hp, 2kp, 2lp) where hp, kp, and lp are random signed integers such that 2 <= |dh| + |dk| + |dl| <= 8 Mean |L| :0.494 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.328 (untwinned: 0.333; perfect twin: 0.200) The distribution of |L| values indicates a twin fraction of 0.00. Note that this estimate is not as reliable as obtained via a Britton plot or H-test if twin laws are available. --------------------------------------------------------------------------------------------------------------------------------- | L test, acentric data | |-------------------------------------------------------------------------------------------------------------------------------| | |l| | Observed | Acentric theory | Acentric theory, perfect twin | |-------------------------------------------------------------------------------------------------------------------------------| | 0 | 0 | 0 | 0 | | 0.02 | 0.0202151 | 0.02 | 0.029996 | | 0.04 | 0.0417248 | 0.04 | 0.059968 | | 0.06 | 0.0614419 | 0.06 | 0.089892 | | 0.08 | 0.082852 | 0.08 | 0.119744 | | 0.1 | 0.103266 | 0.1 | 0.1495 | | 0.12 | 0.126369 | 0.12 | 0.179136 | | 0.14 | 0.148576 | 0.14 | 0.208628 | | 0.16 | 0.170285 | 0.16 | 0.237952 | | 0.18 | 0.191794 | 0.18 | 0.267084 | | 0.2 | 0.212806 | 0.2 | 0.296 | | 0.22 | 0.232125 | 0.22 | 0.324676 | | 0.24 | 0.250747 | 0.24 | 0.353088 | | 0.26 | 0.270962 | 0.26 | 0.381212 | | 0.28 | 0.29297 | 0.28 | 0.409024 | | 0.3 | 0.312488 | 0.3 | 0.4365 | | 0.32 | 0.3334 | 0.32 | 0.463616 | | 0.34 | 0.350428 | 0.34 | 0.490348 | | 0.36 | 0.370444 | 0.36 | 0.516672 | | 0.38 | 0.390062 | 0.38 | 0.542564 | | 0.4 | 0.40958 | 0.4 | 0.568 | | 0.42 | 0.428401 | 0.42 | 0.592956 | | 0.44 | 0.450209 | 0.44 | 0.617408 | | 0.46 | 0.467238 | 0.46 | 0.641332 | | 0.48 | 0.488747 | 0.48 | 0.664704 | | 0.5 | 0.50956 | 0.5 | 0.6875 | | 0.52 | 0.530273 | 0.52 | 0.709696 | | 0.54 | 0.550488 | 0.54 | 0.731268 | | 0.56 | 0.568214 | 0.56 | 0.752192 | | 0.58 | 0.588528 | 0.58 | 0.772444 | | 0.6 | 0.606552 | 0.6 | 0.792 | | 0.62 | 0.62627 | 0.62 | 0.810836 | | 0.64 | 0.647082 | 0.64 | 0.828928 | | 0.66 | 0.664808 | 0.66 | 0.846252 | | 0.68 | 0.685421 | 0.68 | 0.862784 | | 0.7 | 0.703744 | 0.7 | 0.8785 | | 0.72 | 0.721071 | 0.72 | 0.893376 | | 0.74 | 0.746365 | 0.74 | 0.907388 | | 0.76 | 0.766282 | 0.76 | 0.920512 | | 0.78 | 0.784605 | 0.78 | 0.932724 | | 0.8 | 0.804919 | 0.8 | 0.944 | | 0.82 | 0.823143 | 0.82 | 0.954316 | | 0.84 | 0.843756 | 0.84 | 0.963648 | | 0.86 | 0.861482 | 0.86 | 0.971972 | | 0.88 | 0.880203 | 0.88 | 0.979264 | | 0.9 | 0.900418 | 0.9 | 0.9855 | | 0.92 | 0.920833 | 0.92 | 0.990656 | | 0.94 | 0.940052 | 0.94 | 0.994708 | | 0.96 | 0.960864 | 0.96 | 0.997632 | | 0.98 | 0.980382 | 0.98 | 0.999404 | --------------------------------------------------------------------------------------------------------------------------------- Reference: J. Padilla & T. O. Yeates. A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning. Acta Crystallogr. D59, 1124-30, 2003. ================================== Twin laws ================================== ----------Twin law identification---------- Possible twin laws: ------------------------------------------------------------------------------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ------------------------------------------------------------------------------- | M | 2-fold | 0.000 | 0.000 | 0.000 | -k,-h,-l | ------------------------------------------------------------------------------- 1 merohedral twin operators found 0 pseudo-merohedral twin operators found In total, 1 twin operators were found Please note that the possibility of twin laws only means that the lattice symmetry permits twinning; it does not mean that the data are actually twinned. You should only treat the data as twinned if the intensity statistics are abnormal. ----------Twin law-specific tests---------- The following tests analyze the input data with each of the possible twin laws applied. If twinning is present, the most appropriate twin law will usually have a low R_abs_twin value and a consistent estimate of the twin fraction (significantly above 0) from each test. The results are also compiled in the summary section. WARNING: please remember that the possibility of twin laws, and the results of the specific tests, does not guarantee that twinning is actually present in the data. Only the presence of abnormal intensity statistics (as judged by the Wilson moments, NZ-test, and L-test) is diagnostic for twinning. ----------Analysis of twin law -k,-h,-l---------- H-test on acentric data Only 50.0 % of the strongest twin pairs were used. mean |H| : 0.469 (0.50: untwinned; 0.0: 50% twinned) mean H^2 : 0.309 (0.33: untwinned; 0.0: 50% twinned) Estimation of twin fraction via mean |H|: 0.031 Estimation of twin fraction via cum. dist. of H: 0.024 Britton analyses Extrapolation performed on 0.00 < alpha < 0.495 Estimated twin fraction: 0.006 Correlation: 0.9994 R vs R statistics R_abs_twin = <|I1-I2|>/<|I1+I2|> (Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95) R_abs_twin observed data : 0.478 R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> R_sq_twin observed data : 0.318 No calculated data available. R_twin for calculated data not determined. ======================= Exploring higher metric symmetry ====================== The point group of data as dictated by the space group is I 4 The point group in the niggli setting is I 4 (-y+z,x+y,-x+y) The point group of the lattice is I 4 2 2 (-y+z,x+y,-x+y) A summary of R values for various possible point groups follow. ---------------------------------------------------------------------------------------------------------- | Point group | mean R_used | max R_used | mean R_unused | min R_unused | BIC | choice | ---------------------------------------------------------------------------------------------------------- | I 4 (-y+z,x+y,-x+y) | None | None | 0.478 | 0.478 | 6.122e+04 | | | I 4 2 2 (-y+z,x+y,-x+y) | 0.478 | 0.478 | None | None | 2.885e+05 | | ---------------------------------------------------------------------------------------------------------- R_used: mean and maximum R value for symmetry operators *used* in this point group R_unused: mean and minimum R value for symmetry operators *not used* in this point group An automated point group suggestion is made on the basis of the BIC (Bayesian information criterion). The likely point group of the data is: I 4 (-y+z,x+y,-x+y) Possible space groups in this point group are: Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 41 (No. 80) Note that this analysis does not take into account the effects of twinning. If the data are (almost) perfectly twinned, the symmetry will appear to be higher than it actually is. ================== Twinning and intensity statistics summary ================== ----------Final verdict---------- The largest off-origin peak in the Patterson function is 6.51% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. ----------Statistics independent of twin laws---------- /^2 : 2.004 (untwinned: 2.0, perfect twin: 1.5) ^2/ : 0.786 (untwinned: 0.785, perfect twin: 0.885) <|E^2-1|> : 0.736 (untwinned: 0.736, perfect twin: 0.541) <|L|> : 0.494 (untwinned: 0.500; perfect twin: 0.375) : 0.328 (untwinned: 0.333; perfect twin: 0.200) Multivariate Z score L-test: 1.520 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not necessarily exclude it. Note that the expected values for perfect twinning are for merohedrally twinned structures, and deviations from untwinned will be larger for perfect higher-order twinning. ----------Statistics depending on twin laws---------- ----------------------------------------------------------------- | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ----------------------------------------------------------------- | -k,-h,-l | M | 0.478 | 0.006 | 0.024 | 0.022 | ----------------------------------------------------------------- AutoSol_setup_for_scaling AutoSol Run 1 Fri May 1 08:07:34 2020 Shifting to Automatic mode.... Setting up for scaling dataset resolution: 2.5 solvent_fraction: 0.64 ncs_copies: 1 Scoring criteria will be: ['SKEW', 'CORR_RMS'] Scoring method will be: BAYES-CC AutoSol_scale_and_analyze_mad AutoSol Run 1 Fri May 1 08:07:34 2020 scale_and_analyze_mad for dataset 1 File type :sca readdenzo merge type :premerged Testing anisotropy in c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca ... Applying overall anisotropic B correction to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca to yield AutoSol_run_1_\TEMP0\ANISO_p9.sca Overall B set to minimum of the trace of B values Range of aniso B: 20.1441579272 32.1319450351 Max b_iso target allowed is 40.00 A**2 Min B aniso from datafiles is 20.14 A**2 Target aniso B set to 20.14 A**2 Setting anisotropic overall B to 20.1441579272 Removing anisotropy from c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca ..result in AutoSol_run_1_\TEMP0\ANISO_p9.sca Applying overall anisotropic B correction to c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca to yield AutoSol_run_1_\TEMP0\ANISO_p9.sca Overall B set to 20.1441579272 Range of aniso B: 20.1441579272 32.1319450351 Using aniso-corrected data files as 'remove_aniso' is set Using data with aniso correction ['ANISO_p9.sca'] current merge type: premerged new merge type after aniso correction: premerged FILE TYPE scalepack_merge GUESS FILE TYPE MERGE TYPE sca premerged TARGET LABELS ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU'] Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) CONTENTS: ['AutoSol_run_1_\\TEMP0\\ANISO_p9.sca', 'sca', 'premerged', 'I 4', [113.949, 113.949, 32.474, 90.0, 90.0, 90.0], 2.5004123485471093, ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU']] File ANISO_p9.sca RES: 2.5 Guess of most complete dataset: 1 with resolution of 2.5 for dataset 1 File with highest resolution to be used with anomalous refinement data: c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\p9-sad\p9.sca File: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\ANISO_p9.sca Recommended resolution: 2.500412 signal to noise: 1.616098 FILE TYPE scalepack_merge GUESS FILE TYPE MERGE TYPE sca premerged TARGET LABELS ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU'] Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) CONTENTS: ['C:\\Users\\phaserbuilder\\NightlyBuilds\\PhenixVC2008\\x64\\Current\\tests\\phenix_regression.run_p9_sad_benchmark\\tst_p9_sad_benchmark\\AutoSol_run_1_\\TEMP0\\ANISO_p9.sca', 'sca', 'premerged', 'I 4', [113.949, 113.949, 32.474, 90.0, 90.0, 90.0], 2.5004123485471093, ['IPLUS', 'SIGIPLUS', 'IMINU', 'SIGIMINU']] Saved C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\ANISO_p9.sca_ano_1.sca in PDS Saved Miller arrays in PDS as ANISO_p9.sca_ano_1.sca_as_miller_arrays Dataset = 1 Saved mad_fpfm.scl in PDS Saved mad_fbar.scl in PDS Saved mad_fbar.mtz in PDS FILE DATA:C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\ANISO_p9.sca sn: 1.616098 order of datasets for trying phasing:['C:\\Users\\phaserbuilder\\NightlyBuilds\\PhenixVC2008\\x64\\Current\\tests\\phenix_regression.run_p9_sad_benchmark\\tst_p9_sad_benchmark\\AutoSol_run_1_\\TEMP0\\ANISO_p9.sca'] SCALED DATASET 1 DONE WITH SCALING 1 DATASETS AutoSol_guess_files_for_ha_solution AutoSol Run 1 Fri May 1 08:08:24 2020 Guessing input_ha_files for dataset 1 RANGE to KEEP:1.28 SN_LIST: [1.616098] datafile_sn: ['C:\\Users\\phaserbuilder\\NightlyBuilds\\PhenixVC2008\\x64\\Current\\tests\\phenix_regression.run_p9_sad_benchmark\\tst_p9_sad_benchmark\\AutoSol_run_1_\\TEMP0\\ANISO_p9.sca'] Minimum S/N to include in list: -12798.383902 Considering file C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\ANISO_p9.sca for starting HA search: Guess of list of files for HYSS: ['C:\\Users\\phaserbuilder\\NightlyBuilds\\PhenixVC2008\\x64\\Current\\tests\\phenix_regression.run_p9_sad_benchmark\\tst_p9_sad_benchmark\\AutoSol_run_1_\\TEMP0\\ANISO_p9.sca'] AutoSol_files_for_ha_solution AutoSol Run 1 Fri May 1 08:08:24 2020 SN 1.62 SN+ 1.62 Data file choices for HYSS search for dataset #1: AutoSol_hyss AutoSol Run 1 Fri May 1 08:08:24 2020 DATA FILE INFO: file name: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\ANISO_p9.sca file type: sca merge_type: premerged sg as listed in original datafile: I 4 cell_params: 113.95 113.95 32.47 90.00 90.00 90.00 wavelength: 0.9792 wavelength_name: peak ano_signal_to_noise: None ha_type: None nat_der: None res_eval: 0.0 res_hyss: None f_prime: -8.0 f_double_prime: 4.5 resolution: 2.5 recommended_resolution: 2.5 datafile_for_hyss: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\ANISO_p9.sca_ano_1.sca aniso_corrected: True aniso_b_min: 20.1 aniso_range_of_b: 12.0 RUNNING HYSS on ANISO_p9.sca_ano_1.sca from PDS as miller arrays Using automatic Hyss run for SAD data Command line arguments: 4 Se wavelength=" 0.979" nproc=1 pdb_only=true write_output_model=false space_group="I 4" unit_cell="113.948997498 113.948997498 32.4739990234 90.0 90.0 90.0" default_high_resolution_to_try=3.0 random_seed=366532 data = None data_label = None n_sites = 4 scattering_type = "Se" wavelength = 0.979 space_group = "I 4" unit_cell = 113.9489975 113.9489975 32.47399902 90 90 90 symmetry = None resolution = None low_resolution = None search = *fast full root = None output_dir = None strategy = *Auto simple brute_force rescore = *Auto correlation phaser-refine phaser-complete llgc_sigma = 5 nproc = 1 phaser_resolution = None phaser_low_resolution = None rms_cutoff = 3.5 sigma_cutoff = 1 verbose = False pdb_only = True cluster_termination = False max_view = 10 minimum_reflections_for_phaser = 300 cluster_compound_structure = None auto_control { lowest_high_resolution_to_try = None highest_high_resolution_to_try = None default_high_resolution_to_try = 3 direct_methods = True complete_direct_methods = False phaser_completion = True try_multiple_resolutions = True try_full_resolution = False max_multiple = 5 max_groups = 5 seeds_to_use = None starting_seed = None default_seeds_to_use = 20 solutions_to_save = 20 max_tries = None write_output_model = False } brute_force_completion { n_top_patt = 99 n_top_patt_min = 10 n_top_llg = 20 min_sigma_in_brute_force = 1 n_top_iter = 5 n_llg_add_at_once = 2 n_iter_max = 3 include_base_scatterers = True score_additions_with_completion = True select_matching = None fraction_select_matching = 0.67 n_select_matching = 3 n_select_matching_patt = 1 comparison_tolerance = 0 n_print = 20 } termination { matches_must_not_share_patterson_vector = True n_top_models_to_compare = None } parameter_estimation { solvent_content = 0.55 molecular_weight = None } search_control { random_seed = 366532 site_min_distance = 3.5 site_min_distance_sym_equiv = None site_min_cross_distance = None skip_consensus = False } direct_methods { real_space_squaring = False extrapolation = *fast_nv1995 phaser-map } fragment_search { minimum_fragments_to_consider = 0 n_patterson_vectors = None input_emma_model_list = None input_add_model = None keep_seed_sites = False n_shake = 0 rms_shake = 1 score_initial_solutions = False dump_all_fragments = False dump_all_models = False score_only = False } comparison_files { comparison_emma_model = None comparison_emma_model_tolerance = 1.5 } job_title = None chunk { n = 1 i = 0 } ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: dev Release tag: svn+SVN User: phaserbuilder ------------------------------------------------------------------------------- HySS: Hybrid Substructure Search ------------------------------------------------------------------------------- Phenix developers include: Paul Adams, Pavel Afonine, Gabor Bunkoczi, Tom Burnley, Vincent Chen, Youval Dar, Ian Davis, Eli Draizen, Nathaniel Echols, Richard Gildea, Piet Gros, Ralf Grosse-Kunstleve, Jeffrey Headd, Bradley Hintze, Li-Wei Hung, Tom Ioerger, Dorothee Liebschner, Airlie McCoy, Erik McKee, Nigel Moriarty, Robert Oeffner, Billy Poon, Randy Read, Jane Richardson, David Richardson, Jim Sacchettini, Nicholas Sauter, Oleg Sobolev, Laurent Storoni, Tom Terwilliger, Christopher Williams, Peter Zwart Phenix home page: http://www.phenix-online.org/ ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Phenix components are copyrighted by: - Lawrence Berkeley National Laboratory - Los Alamos National Laboratory - University of Cambridge - Duke University - Texas Agricultural Experiment Station & Texas Engineering Experiment Station ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Major third-party components of Phenix include: Python, wxWidgets, wxPython, Boost, SCons, Clipper, CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS, MUSCLE, KSDSSP, PULCHRA, ANTLRv3 Enter phenix.acknowledgments for details. ------------------------------------------------------------------------------- SELECTING ANOMALOUS DATA Input Miller array: Miller array info: AutoSol_run_1_\TEMP0\solve_1.sca:I(+),SIGI(+),I(-),SIGI(-) Observation type: xray.intensity Type of data: double, size=14065 Type of sigmas: double, size=14065 Number of Miller indices: 14065 Anomalous flag: True Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) Systematic absences: 0 Centric reflections: 805 Resolution range: 28.4872 2.50041 Completeness in resolution range: 0.996175 Completeness with d_max=infinity: 0.995682 Anomalous completeness in resolution range: 0.993388 Bijvoet pairs: 6611 Lone Bijvoet mates: 38 Mean anomalous difference: 0.0728 Removing systematic absences: Number of reflections: 14065 Removing zero or negative observations: Number of reflections: 14065 Converting intensities to amplitudes. ************************ Mean anomalous difference: 0.0728 ************************ Applying resolution limits: 15 2.50041 Number of reflections: 14006 Applying sigma cutoff: 1 Number of reflections: 14004 Computing anomalous differences Number of reflections: 6590 Applying difference sigma cutoff: 0.5 Number of reflections: 5298 Applying rms outlier cutoff: 3.5 Number of reflections: 5290 Final anomalous difference array: Miller array info: None Observation type: None Type of data: double, size=5290 Type of sigmas: double, size=5290 Number of Miller indices: 5290 Anomalous flag: False Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) Systematic absences: 0 Centric reflections: 0 Resolution range: 14.8035 2.50041 Completeness in resolution range: 0.712554 Completeness with d_max=infinity: 0.708071 Fraction of original data: 1/1.33 = 75.2% Starting the search procedure (fast mode): --- RUNNING IN AUTOMATIC MODE --- Base number of seeds: 20 Multiples of seeds to try: [1, 5] Volume of asymmetric unit: 52706.8 A**3 Volume per site : 13176.7 A**3 Half distance between sites : 12.0 A High-resolution: 2.5 Using lowest_high_resolution of 6.0 First high_resolution set by user to 3.0 Highest high_resolution set to 3.0 High-resolution limits to be tried: 3.0 A 4.0 A 5.0 A Note: stopping early if top 4 solutions match --NEW SET OF SEARCH PARAMETERS -- Resolution: 3.00 A No previous search results at this resolution --- GETTING PATTERSON SEEDS --- High-resolution limit: 3.00 A Total of 495 Patterson seeds identified --- RUNNING DIRECT METHODS WITH PATTERSON SEEDS --- Number of seeds: 20 Evaluations per processor per group: 7 nproc: 1 Total tries in each group: 7 Total groups 3 High-resolution limit: 3.00 --- GROUP 1 OF DIRECT METHODS WITH PATTERSON SEEDING --- Starting with working fragment list Entering search loop: p = peaklist index in Patterson map or model number f = peaklist index in two-site translation function ess = score after extrapolation scan r = number of dual-space recycling cycles score = final score p=000 f=000 ess=0.411 (cc) r=015 score=0.541 (cc) [ best score: 0.541 (cc) ] Sites: 6 model 0 p=000 f=001 ess=0.402 (cc) r=015 score=0.542 (cc) [ best score: 0.542 (cc) ] Sites: 6 model 1 p=000 f=002 ess=0.356 (cc) r=015 score=0.536 (cc) [ best score: 0.542 (cc) ] Sites: 6 model 2 p=001 f=000 ess=0.416 (cc) r=015 score=0.544 (cc) [ best score: 0.544 (cc) 0.542 (cc) ] Sites: 6 model 3 Number of matching sites of top 2 structures: 5 p=001 f=001 ess=0.389 (cc) r=015 score=0.537 (cc) [ best score: 0.544 (cc) 0.542 (cc) ] Sites: 6 model 4 p=001 f=002 ess=0.397 (cc) r=015 score=0.536 (cc) [ best score: 0.544 (cc) 0.542 (cc) ] Sites: 6 model 5 p=002 f=000 ess=0.374 (cc) r=015 score=0.536 (cc) [ best score: 0.544 (cc) 0.542 (cc) 0.536 (cc) ] Sites: 6 model 6 Number of matching sites of top 2 structures: 5 Number of matching sites of top 3 structures: 5 Top 3 scores: p=001 f=000 ess=0.416 (cc) r=015 score=0.544 (cc) Sites: 6 p=000 f=001 ess=0.402 (cc) r=015 score=0.542 (cc) Sites: 6 p=002 f=000 ess=0.374 (cc) r=015 score=0.536 (cc) Sites: 6 Match summary: Operator: rotation: {{-1, 0, 0}, {0, -1, 0}, {0, 0, -1}} translation: {-1.12847*^-36, 9.0278*^-36, 0.364092} rms coordinate differences: 0.04 Pairs: 5 site001 site001 0.039 site002 site002 0.014 site003 site003 0.025 site005 site004 0.049 site006 site005 0.047 Singles model 1: 0 Singles model 2: 1 site006 Score for consensus model (5 sites, before truncation): 0.549 (cc) Truncating consensus model to expected number of sites. Correlation coefficient for consensus model (4 sites, after truncation): 0.563 Search finished. Taking current result as new best (no existing best) Identifying current best solution... Scoring basis: correlation at 3.0 A Results from search: Score: 0.5498 Consensus model: REMARK phenix.hyss consensus model REMARK Number of scatterers: 4 REMARK At special positions: 0 REMARK Cartesian coordinates CRYST1 113.949 113.949 32.474 90.00 90.00 90.00 I 4 SCALE1 0.008776 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030794 0.00000 ATOM 1 SE SUB 1 -20.497 12.808 5.759 1.00 0.00 SE ATOM 2 SE SUB 2 -33.394 18.744 18.967 0.83 0.00 SE ATOM 3 SE SUB 3 -29.914 21.134 20.920 0.81 0.00 SE ATOM 4 SE SUB 4 -33.153 -11.414 20.511 0.08 0.00 SE END Current search result at resolution of 3.00 A kept with score of 0.5498 --- END OF GROUP 1 OF DIRECT METHODS WITH PATTERSON SEEDING --- --- GROUP 2 OF DIRECT METHODS WITH PATTERSON SEEDING --- Including 7 previous structures from direct methods at this resolution Starting with working fragment list Entering search loop: p = peaklist index in Patterson map or model number f = peaklist index in two-site translation function ess = score after extrapolation scan r = number of dual-space recycling cycles score = final score p=002 f=001 ess=0.343 (cc) r=015 score=0.535 (cc) [ best score: 0.544 (cc) 0.542 (cc) 0.536 (cc) ] Sites: 6 model 7 Number of matching sites of top 2 structures: 5 Number of matching sites of top 3 structures: 5 p=002 f=002 ess=0.427 (cc) r=015 score=0.537 (cc) [ best score: 0.544 (cc) 0.542 (cc) 0.537 (cc) ] Sites: 6 model 8 Number of matching sites of top 2 structures: 5 Number of matching sites of top 3 structures: 5 p=003 f=000 ess=0.410 (cc) r=015 score=0.536 (cc) [ best score: 0.544 (cc) 0.542 (cc) 0.537 (cc) 0.536 (cc) ] Sites: 6 model 9 Number of matching sites of top 2 structures: 5 Number of matching sites of top 3 structures: 5 Number of matching sites of top 4 structures: 5 Early termination based on 4 matching structures with 5 matches Top 4 scores: p=001 f=000 ess=0.416 (cc) r=015 score=0.544 (cc) Sites: 6 p=000 f=001 ess=0.402 (cc) r=015 score=0.542 (cc) Sites: 6 p=002 f=002 ess=0.427 (cc) r=015 score=0.537 (cc) Sites: 6 p=003 f=000 ess=0.410 (cc) r=015 score=0.536 (cc) Sites: 6 Match summary: Operator: rotation: {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}} translation: {7.52316*^-37, 4.5139*^-36, 0.452007} rms coordinate differences: 0.04 Pairs: 5 site001 site001 0.020 site002 site002 0.045 site003 site003 0.004 site005 site004 0.079 site006 site005 0.009 Singles model 1: 0 Singles model 2: 1 site006 Score for consensus model (5 sites, before truncation): 0.549 (cc) Truncating consensus model to expected number of sites. Correlation coefficient for consensus model (4 sites, after truncation): 0.563 Done...early termination based on matching solutions. Search finished. Identifying current best solution... Scoring basis: correlation at 3.0 A Results from search: Score: 0.5498 Consensus model: REMARK phenix.hyss consensus model REMARK Number of scatterers: 4 REMARK At special positions: 0 REMARK Cartesian coordinates CRYST1 113.949 113.949 32.474 90.00 90.00 90.00 I 4 SCALE1 0.008776 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030794 0.00000 ATOM 1 SE SUB 1 -20.497 12.808 5.759 1.00 0.00 SE ATOM 2 SE SUB 2 -33.394 18.744 18.967 0.83 0.00 SE ATOM 3 SE SUB 3 -29.914 21.134 20.920 0.81 0.00 SE ATOM 4 SE SUB 4 -33.153 -11.414 20.511 0.08 0.00 SE END Keeping search result as it terminated early and is similar in score to best result Previous best score: 0.5498 New best search result at resolution of 3.00 A with score of 0.5498 Scoring basis: correlation Finished with search... --- END OF GROUP 2 OF DIRECT METHODS WITH PATTERSON SEEDING --- --GETTING BEST OVERALL SEARCH RESULT SO FAR-- Taking current result as new best (no existing best) Identifying current best solution... Scoring basis: correlation at 3.0 A Results from search: Score: 0.5498 Consensus model: REMARK phenix.hyss consensus model REMARK Number of scatterers: 4 REMARK At special positions: 0 REMARK Cartesian coordinates CRYST1 113.949 113.949 32.474 90.00 90.00 90.00 I 4 SCALE1 0.008776 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030794 0.00000 ATOM 1 SE SUB 1 -20.497 12.808 5.759 1.00 0.00 SE ATOM 2 SE SUB 2 -33.394 18.744 18.967 0.83 0.00 SE ATOM 3 SE SUB 3 -29.914 21.134 20.920 0.81 0.00 SE ATOM 4 SE SUB 4 -33.153 -11.414 20.511 0.08 0.00 SE END Current search result at resolution of 3.00 A kept with score of 0.5498 --- TOP-SCORING MODEL OVERALL --- Score: 0.550 (cc) This search terminated early based on matching solutions REMARK phenix.hyss consensus model REMARK Number of scatterers: 4 REMARK At special positions: 0 REMARK Cartesian coordinates CRYST1 113.949 113.949 32.474 90.00 90.00 90.00 I 4 SCALE1 0.008776 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030794 0.00000 ATOM 1 SE SUB 1 -20.497 12.808 5.759 1.00 0.00 SE ATOM 2 SE SUB 2 -33.394 18.744 18.967 0.83 0.00 SE ATOM 3 SE SUB 3 -29.914 21.134 20.920 0.81 0.00 SE ATOM 4 SE SUB 4 -33.153 -11.414 20.511 0.08 0.00 SE END If HySS was helpful please cite: Acta Cryst. 2003, D59, 1966-1973 http://cci.lbl.gov/publications/download/ba5048_reprint.pdf See also: http://www.phenix-online.org/download/documentation/cci_apps/hyss/ For help enter: phenix.hyss --help Send bug reports to: bugs@phenix-online.org For help write to: help@phenix-online.org Total CPU time: 25.34 seconds HA MODEL: [[-0.17988005769816073, 0.11240283832442222, 0.17734948012235474], [-0.2930600844331806, 0.1644928083333424, 0.5840717730322992], [-0.2625215647420481, 0.18546548916678315, 0.644221584709051], [-0.2909441088926113, -0.10017042051532782, 0.6316171588735998]] New best HYSS CC: 0.563 This is a good HYSS solution with CC > 0.30 Creating Solution for Dataset #1 based on None New solution for dataset #1 FINAL SITES: [-0.17988005769816073, 0.11240283832442222, 0.17734948012235474] FINAL SITES: [-0.2930600844331806, 0.1644928083333424, 0.5840717730322992] FINAL SITES: [-0.2625215647420481, 0.18546548916678315, 0.644221584709051] FINAL SITES: [-0.2909441088926113, -0.10017042051532782, 0.6316171588735998] Writing out solution 1 : I 4 xyz -0.180 0.112 0.177 1.00 Se xyz -0.293 0.164 0.584 0.83 Se xyz -0.263 0.185 0.644 0.81 Se xyz -0.291 -0.100 0.632 0.08 Se Writing out solution 2 : I 4 xyz 0.180 -0.112 -0.177 1.00 Se xyz 0.293 -0.164 -0.584 0.83 Se xyz 0.263 -0.185 -0.644 0.81 Se xyz 0.291 0.100 -0.632 0.08 Se DONE WITH HYSS on 1 DATASETS AutoSol_score_ha_solutions AutoSol Run 1 Fri May 1 08:08:50 2020 Total number of solutions to score: 2 Skipping extra phasing steps as skip_extra_phasing=Auto and phasing_method=PHASER SCORING SOLUTION 1: Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4", with 4 sites Number of scoring criteria: 2 Using BAYES-CC (Bayesian estimate of CC of map to perfect) as scores Evaluating solution 1 Copied mad_fpfm.scl from PDS to AutoSol_run_1_\TEMP0 Copied mad_fbar.scl from PDS to AutoSol_run_1_\TEMP0 Copied mad_fbar.mtz from PDS to AutoSol_run_1_\TEMP0 Using ANISO_p9.sca_ano_1.sca (localscaled version of C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\ANISO_p9.sca ) as input to PHASER List of all scatterers to be considered: Se : fo= 34.00 f'= -8.00 f''= 4.50 f'-adjusted -8.00 Using default HA type of Se Phasing based on ANISO_p9.sca_ano_1.sca Converting intensities to amplitudes Averaging Bijvoet mates for saved data... Setting resolution limit for phasing to 2.5 F-prime value for this data: -8.0 F-double_prime value for this data: 4.5 Using protein sequence information from AutoSol_run_1_\sequence_autosol.dat for content estimation along with copy number of 1.0 Anisotropy Correction Data read from: AutoSol_run_1_\TEMP0\TEMP_sca.mtz Data output to : AutoSol_run_1_\F_ano.mtz Spacegroup Name (Hall symbol) = I 4 ( I 4) Unitcell = 113.95 113.95 32.47 90.00 90.00 90.00 Principal components = 0.48 0.48 -0.96 Range of principal components = 1.44 Wilson Scale = 2.06 Wilson B-factor = 17.76 Completing sites: True Starting with 4 input sites Scattering factors for Se will be f'= -8.00 f''= 4.50 Data output to : AutoSol_run_1_\TEMP0\phaser_mtz Running phaser with both hands of the heavy-atom substructure/SG logfile: AutoSol_run_1_\TEMP0\phaser_1.log SAD phasing Data read from: AutoSol_run_1_\TEMP0\TEMP_sca.mtz Data output to : AutoSol_run_1_\TEMP0\phaser_mtz.1.mtz Spacegroup Name (Hall symbol) = I 4 ( I 4) Unitcell = (113.9489974975586, 113.9489974975586, 32.4739990234375, 90.0, 90.0, 90.0) LogLikelihood = -1745.8348211 5 refined atoms atom x y z occupancy u-iso fp fpp SE -0.1798 0.1128 0.1768 1.6306 0.2404 -8.00 4.84 SE -0.2948 0.1655 0.5808 1.1354 0.2009 -8.00 4.84 SE -0.2623 0.1854 0.6479 1.4136 -1.0000 -8.00 4.84 SE 0.0280 0.7575 0.7634 0.2580 0.2368 -8.00 4.84 SE 0.1597 0.2864 0.6026 0.3158 0.1924 -8.00 4.84 Reading from ... AutoSol_run_1_\TEMP0\phaser_mtz.1.mtz Including HLA HLB HLC HLD from AutoSol_run_1_\TEMP0\phaser_mtz.1.mtz and writing to AutoSol_run_1_\TEMP0\phaser_1.mtz Including HLanomA HLanomB HLanomC HLanomD (anomalous information only, no real scattering information) from AutoSol_run_1_\TEMP0\phaser_mtz.1.mtz as HLanomA HLanomB HLanomC HLanomD ...and writing them to AutoSol_run_1_\TEMP0\phaser_1.mtz FP SIGFP PHIB FOM HLA HLB HLC HLD FWT PHIFWT written to AutoSol_run_1_\TEMP0\phaser_1.mtz Wrote FWT PHIFWT as FP PHIB FOM to phaser_1_fwt.mtz Final sites: Reading from ... AutoSol_run_1_\TEMP0\phaser_mtz.1.hand.mtz Including HLA HLB HLC HLD from AutoSol_run_1_\TEMP0\phaser_mtz.1.hand.mtz and writing to AutoSol_run_1_\TEMP0\phaser_1.1.hand.mtz Including HLanomA HLanomB HLanomC HLanomD (anomalous information only, no real scattering information) from AutoSol_run_1_\TEMP0\phaser_mtz.1.hand.mtz as HLanomA HLanomB HLanomC HLanomD ...and writing them to AutoSol_run_1_\TEMP0\phaser_1.1.hand.mtz FP SIGFP PHIB FOM HLA HLB HLC HLD FWT PHIFWT written to AutoSol_run_1_\TEMP0\phaser_1.1.hand.mtz Wrote FWT PHIFWT as FP PHIB FOM to phaser_1_fwt.1.hand.mtz Final sites: FOM found: 0.555 REFINED HA FRACTIONAL COORDS AND OCCUPANCIES: SE -0.180 0.113 0.177 1.63 SE -0.295 0.165 0.581 1.14 SE -0.262 0.185 0.648 1.41 SE 0.028 0.758 0.763 0.26 SE 0.160 0.286 0.603 0.32 Number of scoring criteria: 2 Using BAYES-CC (Bayesian estimate of CC of map to perfect) as scores Evaluate_solution Scoring for this solution now... AutoSol_run_1_\TEMP0\resolve.scores SKEW 0.2505443 AutoSol_run_1_\TEMP0\resolve.scores CORR_RMS 0.9190313 Reading NCS information from: AutoSol_run_1_\TEMP0\resolve.log based on [ha_1.pdb,phaser_1.mtz] CC-EST (BAYES-CC) SKEW : 55.3 +/- 18.7 CC-EST (BAYES-CC) CORR_RMS : 62.5 +/- 29.2 ESTIMATED MAP CC x 100: 59.1 +/- 13.7 (2SD) FOM for solution 1 : 0.555 phaser_1.log 1 Reformatting ha_1.pdb and putting it in ha_1.pdb_formatted.pdb SCORING SOLUTION 2: Solution 2 using HYSS on ANISO_p9.sca_ano_1.sca and taking inverse. Dataset #1 SG="I 4", with 4 sites Evaluating solution 2 Copied mad_fpfm.scl from PDS to AutoSol_run_1_\TEMP0 Copied mad_fbar.scl from PDS to AutoSol_run_1_\TEMP0 Copied mad_fbar.mtz from PDS to AutoSol_run_1_\TEMP0 Using existing inverse files phaser_1.1.hand.mtz FOM found: 0.555 REFINED HA FRACTIONAL COORDS AND OCCUPANCIES: SE 0.180 -0.113 -0.177 1.63 SE 0.295 -0.165 -0.581 1.14 SE 0.262 -0.185 -0.648 1.41 SE -0.028 -0.758 -0.763 0.26 SE -0.160 -0.286 -0.603 0.32 Number of scoring criteria: 2 Using BAYES-CC (Bayesian estimate of CC of map to perfect) as scores Evaluate_solution Scoring for this solution now... AutoSol_run_1_\TEMP0\resolve.scores SKEW -0.029591678 AutoSol_run_1_\TEMP0\resolve.scores CORR_RMS 0.8525503 Reading NCS information from: AutoSol_run_1_\TEMP0\resolve.log based on [ha_2.pdb,phaser_2.mtz] CC-EST (BAYES-CC) SKEW : 11.4 +/- 27.6 CC-EST (BAYES-CC) CORR_RMS : 50.5 +/- 39.1 ESTIMATED MAP CC x 100: 17.7 +/- 37.0 (2SD) FOM for solution 2 : 0.555 phaser_2.log 1 Reformatting ha_2.pdb and putting it in ha_2.pdb_formatted.pdb RANGE to KEEP:1.28 Confident of the hand (Quality diff from opp hand is 2.1 sigma) MARKING DUPLICATES FROM solutions AutoSol_guess_solution_descriptions_for_phasing AutoSol Run 1 Fri May 1 08:09:30 2020 RANGE to KEEP:1.28 No more solutions added as number of datasets is 1 GUESS SOLUTIONS FOR PHASING: ['Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4"'] ALL SOLUTIONS FOR PHASING: ['Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4"', 'Solution 2 using HYSS on ANISO_p9.sca_ano_1.sca and taking inverse. Dataset #1 SG="I 4"'] AutoSol_choose_solutions_for_phasing AutoSol Run 1 Fri May 1 08:09:30 2020 NEW SOLUTION FOR PHASING: Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4" AutoSol_phasing AutoSol Run 1 Fri May 1 08:09:30 2020 Phasing solution 1 Resolution for phasing >= scaling: skipping madbst and scale Setting res_phase based on overall resolution of: 2.5 Resolution for phasing: 2.5 Fixing xyz in this phasing run Copied mad_fpfm.scl from PDS to AutoSol_run_1_\TEMP0 Copied mad_fbar.scl from PDS to AutoSol_run_1_\TEMP0 Copied mad_fbar.mtz from PDS to AutoSol_run_1_\TEMP0 SKIPPING EXTRA PHASING FOM for solution 1 : 0.555 phaser_1.log 1 Reformatting ha_1.pdb and putting it in ha_1.pdb_formatted.pdb PHASED SOLUTION: Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4" MARKING DUPLICATES FROM solutions AutoSol_guess_phased_solution_descriptions_for_denmod AutoSol Run 1 Fri May 1 08:09:30 2020 RANGE to KEEP:1.28 Allowed local range... 1.28 Considering... Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4" with delta quality= 0.0 Considering... Solution 2 using HYSS on ANISO_p9.sca_ano_1.sca and taking inverse. Dataset #1 SG="I 4" with delta quality= 2.1 GUESS SOLUTIONS FOR DM: ['Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4"'] ALL SOLUTIONS FOR DM: ['Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4"', 'Solution 2 using HYSS on ANISO_p9.sca_ano_1.sca and taking inverse. Dataset #1 SG="I 4"'] AutoSol_choose_solutions_for_denmod AutoSol Run 1 Fri May 1 08:09:30 2020 AutoSol_denmod AutoSol Run 1 Fri May 1 08:09:30 2020 SOLUTION USED TO START DEN MOD: Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4" HKLIN: phaser_1.mtz Using FWT and PHIFWT from phaser_1_fwt.mtz to start density modification Using FOM of 0.56 as starting FOM for density modification Truncating ha sites at start of resolve Mask types to consider: ['histograms'] Testing density modification with mask_type = histograms RFACTOR: 0.2378 Best mask type so far is histograms Copying AutoSol_run_1_\TEMP0\resolve_histograms_1.mtz to AutoSol_run_1_\denmod_1.mtz DM SOLUTION: Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4" R=0.2378 AutoSol_choose_solutions_for_build AutoSol Run 1 Fri May 1 08:09:53 2020 Solution suitable for build:Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4" Quality: 59.0946759105 Maximum number of builds: 2 Solution for build: Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4" AutoSol_build AutoSol Run 1 Fri May 1 08:09:53 2020 SOLUTION FOR MODEL-BUILDING: Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4" DM SOLUTION USED FOR MODEL-BUILDING 1:Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4" SG: I 4 Cell: [113.9489974975586, 113.9489974975586, 32.4739990234375, 90.0, 90.0, 90.0] Using FWT and PHIFWT from phaser_1_fwt.mtz to start density modification Using FOM of 0.56 as starting FOM for density modification Merging C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\p9_PHX.mtz and AutoSol_run_1_\phaser_1.mtz and adding free R flags (if necessary) for refinement phased input and program labels: ['FP', 'SIGFP', 'PHIB', 'FOM', 'HLA', 'HLB', 'HLC', 'HLD'] ['FP', 'SIGFP', 'PHIB', 'FOM', 'HLA', 'HLB', 'HLC', 'HLD'] prog,inp refinement labels: ['FP', 'SIGFP', 'FreeR_flag'] ['F_from_p9', 'SIGF_from_p9', 'None'] Merged program label list: ['FP', 'SIGFP', 'PHIB', 'FOM', 'HLA', 'HLB', 'HLC', 'HLD'] Merged input label list: ['F_from_p9', 'SIGF_from_p9', 'PHIB', 'FOM', 'HLA', 'HLB', 'HLC', 'HLD'] Refinement labels to use: ['F_from_p9', 'SIGF_from_p9'] Phased labels to use: ['PHIB', 'FOM', 'HLA', 'HLB', 'HLC', 'HLD'] Selecting arrays from C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\p9_PHX.mtz : ['F_from_p9', 'SIGF_from_p9'] Selecting arrays from AutoSol_run_1_\phaser_1.mtz : ['PHIB'] ['FOM'] ['HLA', 'HLB', 'HLC', 'HLD'] Output space group: I 4 (No. 79) Columns of data in AutoSol_run_1_\TEMP0\TEMP_ref_file.mtz: H K L F_from_p9 SIGF_from_p9 PHIB FOM HLA HLB HLC HLD H H H F Q P W A A A A Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) input_data_file_use: AutoSol_run_1_\TEMP0\TEMP_ref_file.mtz labin_use: FP=F_from_p9 SIGFP=SIGF_from_p9 PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB labin HLC=HLC HLD=HLD FreeR_flag added to TEMP_ref_file.mtz New file: TEMP0.mtz New labin: FP=F_from_p9 SIGFP=SIGF_from_p9 PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB labin HLC=HLC HLD=HLD FreeR_flag=FreeR_flag Copying TEMP0.mtz to exptl_fobs_phases_freeR_flags_1.mtz Columns used: FP=F_from_p9 SIGFP=SIGF_from_p9 PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB labin HLC=HLC HLD=HLD FreeR_flag=FreeR_flag Checking for HL coeffs in exptl_fobs_phases_freeR_flags_1.mtz True Removing columns of data with all zeroes (if any) All columns of data have non-zero values Refinement file with freeR flags is in AutoSol_run_1_\TEMP0\exptl_fobs_phases_freeR_flags_1.mtz Using default test_flag_value of 1 from AutoSol_run_1_\TEMP0\exptl_fobs_phases_freeR_flags_1.mtz Removing anisotropy and sharpening refinement file (AutoSol_run_1_\TEMP0\exptl_fobs_phases_freeR_flags_1.mtz) to b_iso= 20.14... yielding AutoSol_run_1_\TEMP0\aniso_refinement_data_PHX.mtz Aniso-corrected data to be written to AutoSol_run_1_\TEMP0\aniso_refinement_data_PHX.mtz Aniso B offset for refinement file: 0.55 NOTE: using same file for hklin_exp and hklin_ref: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\aniso_refinement_data_PHX.mtz NOTE: Using phase information from input files in refinement and density modification Refinement file with free R flags (not aniso corrected): C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\exptl_fobs_phases_freeR_flags_1.mtz Copying AutoSol_run_1_\resolve_histograms_1.mtz to map_coeffs_1.mtz as input map coeffs Columns used: FP=FWT PHIB=PHWT Input map file is FWT PHWT or equiv Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) wrote anomalous data to: AutoSol_run_1_\TEMP0\p9_anom_data.mtz Adding anomalous data from AutoSol_run_1_\TEMP0\p9_anom_data.mtz to AutoSol_run_1_\TEMP0\exptl_fobs_phases_freeR_flags_1.mtz to yield AutoSol_run_1_\TEMP0\exptl_fobs_phases_freeR_flags_1_with_anom_data.mtz MERGING: AutoSol_run_1_\TEMP0\exptl_fobs_phases_freeR_flags_1.mtz AutoSol_run_1_\TEMP0\p9_anom_data.mtz with labels [['I(+)', 'SIGI(+)', 'I(-)', 'SIGI(-)']] Selecting arrays from AutoSol_run_1_\TEMP0\exptl_fobs_phases_freeR_flags_1.mtz : ['FP', 'SIGFP'] ['PHIM'] ['FOMM'] ['HLAM', 'HLBM', 'HLCM', 'HLDM'] ['FreeR_flag'] ['FWT', 'PHWT'] Selecting arrays from AutoSol_run_1_\TEMP0\p9_anom_data.mtz : ['I(+)', 'SIGI(+)', 'I(-)', 'SIGI(-)'] Output space group: I 4 (No. 79) Columns of data in AutoSol_run_1_\TEMP0\exptl_fobs_phases_freeR_flags_1_with_anom_data.mtz: H K L FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag FWT PHWT I(+) SIGI(+) I(-) SIGI(-) H H H F Q P W A A A A I F P K M K M Output labels: ['FP', 'SIGFP', 'PHIM', 'FOMM', 'HLAM', 'HLBM', 'HLCM', 'HLDM', 'FreeR_flag', 'FWT', 'PHWT', 'I(+)', 'SIGI(+)', 'I(-)', 'SIGI(-)'] Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) Set self.Facts['hl_anom_label']: HLanomA,HLanomB,HLanomC,HLanomD self.Facts['hl_label']: HLA,HLB,HLC,HLD Adding HLanom coeffs from AutoSol_run_1_\phaser_1.mtz to AutoSol_run_1_\TEMP0\aniso_refinement_data_PHX.mtz to yield AutoSol_run_1_\TEMP0\aniso_refinement_data_PHX_with_hl_anom.mtz MERGING: AutoSol_run_1_\TEMP0\aniso_refinement_data_PHX.mtz AutoSol_run_1_\phaser_1.mtz with labels ['HLanomA', 'HLanomB', 'HLanomC', 'HLanomD'] Selecting arrays from AutoSol_run_1_\TEMP0\aniso_refinement_data_PHX.mtz : ['FP', 'SIGFP'] ['PHIM'] ['FOMM'] ['HLAM', 'HLBM', 'HLCM', 'HLDM'] ['FreeR_flag'] ['FWT', 'PHWT'] Selecting arrays from AutoSol_run_1_\phaser_1.mtz : ['HLanomA', 'HLanomB', 'HLanomC', 'HLanomD'] Output space group: I 4 (No. 79) Columns of data in AutoSol_run_1_\TEMP0\aniso_refinement_data_PHX_with_hl_anom.mtz: H K L FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag FWT PHWT HLanomA HLanomB HLanomC HLanomD H H H F Q P W A A A A I F P A A A A Output labels: ['FP', 'SIGFP', 'PHIM', 'FOMM', 'HLAM', 'HLBM', 'HLCM', 'HLDM', 'FreeR_flag', 'FWT', 'PHWT', 'HLanomA', 'HLanomB', 'HLanomC', 'HLanomD'] Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) Set self.Facts['hl_anom_label']: HLanomA,HLanomB,HLanomC,HLanomD self.Facts['hl_label']: HLA,HLB,HLC,HLD Adding HLanom coeffs from AutoSol_run_1_\phaser_1.mtz to AutoSol_run_1_\TEMP0\exptl_fobs_phases_freeR_flags_1_with_anom_data.mtz to yield AutoSol_run_1_\TEMP0\exptl_fobs_phases_freeR_flags_1_with_anom_data_with_hl_anom.mtz MERGING: AutoSol_run_1_\TEMP0\exptl_fobs_phases_freeR_flags_1_with_anom_data.mtz AutoSol_run_1_\phaser_1.mtz with labels ['HLanomA', 'HLanomB', 'HLanomC', 'HLanomD'] Selecting arrays from AutoSol_run_1_\TEMP0\exptl_fobs_phases_freeR_flags_1_with_anom_data.mtz : ['FP', 'SIGFP'] ['PHIM'] ['FOMM'] ['HLAM', 'HLBM', 'HLCM', 'HLDM'] ['FreeR_flag'] ['FWT', 'PHWT'] ['I(+)', 'SIGI(+)', 'I(-)', 'SIGI(-)'] Selecting arrays from AutoSol_run_1_\phaser_1.mtz : ['HLanomA', 'HLanomB', 'HLanomC', 'HLanomD'] Output space group: I 4 (No. 79) Columns of data in AutoSol_run_1_\TEMP0\exptl_fobs_phases_freeR_flags_1_with_anom_data_with_hl_anom.mtz: H K L FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag FWT PHWT I(+) SIGI(+) I(-) SIGI(-) HLanomA HLanomB HLanomC HLanomD H H H F Q P W A A A A I F P K M K M A A A A Output labels: ['FP', 'SIGFP', 'PHIM', 'FOMM', 'HLAM', 'HLBM', 'HLCM', 'HLDM', 'FreeR_flag', 'FWT', 'PHWT', 'I(+)', 'SIGI(+)', 'I(-)', 'SIGI(-)', 'HLanomA', 'HLanomB', 'HLanomC', 'HLanomD'] Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) Set self.Facts['hl_anom_label']: HLanomA,HLanomB,HLanomC,HLanomD self.Facts['hl_label']: HLAM,HLBM,HLCM,HLDM Have HLanom in refinement file Not using HLanom in refinement. Phase labels=HLAM,HLBM,HLCM,HLDM Saving exptl_fobs_phases_freeR_flags_1_with_anom_data_with_hl_anom.mtz for refinement THE FILE AutoSol_run_1_\resolve_histograms_1.mtz will be used for model-building THE FILE aniso_refinement_data_PHX_with_hl_anom.mtz will be used for refinement Copying fact resolution_build of 2.5 to resolution Building model for solution 1 Carrying out phase improvement and model building using phenix.phase_and_build Unit cell: (113.949, 113.949, 32.474, 90, 90, 90) Space group: I 4 (No. 79) Setting include_ha_in_refinement=True as it is not set and this is a sad experiment Setting allow_overlapping=False as it is not set and this is a SeMet structure (we do not want both the Se and MSE present) Building model with selenomethionine Including anomalous substructure in refinement # phase_and_build # # Iterative model-building refinement and density modification # Type phenix.doc for help usage: phenix.phase_and_build mtzfile.mtz sequence.dat [pdbfile.pdb] [labin='FP=FP PHIB=PHIM ] Values of all params: phase_and_build { input_files { data = "AutoSol_run_1_\\TEMP0\\aniso_refinement_data_PHX_with_hl_anom.mtz" labin = None aniso_corrected_data = None labin_aniso_corrected_data = None map_file_fom = 0.82 map_file_is_density_modified = True ha_file = "AutoSol_run_1_\\TEMP0\\ha_1.pdb_formatted.pdb" seq_file = "AutoSol_run_1_\\sequence_autosol.dat" pdb_in = None map_coeffs = "AutoSol_run_1_\\TEMP0\\map_coeffs_1.mtz" map_coeffs_labels = None labin_map_coeffs = "FP=FWT PHIB=PHWT" ncs_info_file = "AutoSol_run_1_\\TEMP0\\AutoSol_1.ncs_spec" remove_free { free_in = None labin_free = None map_coeffs_no_free = None map_coeffs_labels_no_free = None labin_no_free = None test_flag_value = None } } output_files { mtz_out = "AutoSol_run_1_\\TEMP0\\phase_and_build_map_coeffs_1.mtz" refine_data = "AutoSol_run_1_\\TEMP0\\phase_and_build_map_coeffs_1.mtz" ncs_out = "AutoSol_run_1_\\TEMP0\\phase_and_build_ncs_1.ncs_spec" pdb_out = "AutoSol_run_1_\\TEMP0\\phase_and_build_1.pdb" log = "AutoSol_run_1_\\TEMP0\\phase_and_build_1.log" params_out = "AutoSol_run_1_\\TEMP0\\phase_and_build_params_1.eff" job_title = None } cycles { ncycle = 1 nmodels = 1 } ncs { find_ncs = False update_ncs = True use_ha_in_ncs = True optimize_ncs = True minimum_ncs_cc = 0.3 } density_modification { add_classic_denmod = True truncate_ha_sites_in_resolve = True use_hl_anom_in_denmod = False use_hl_anom_in_denmod_with_model = False extreme_dm = False fom_for_extreme_dm = 0.35 wang_radius_extreme_dm = None } refinement { rs_refine = True use_all_in_refine = False macro_cycles = 3 rs_refine_adp = False real_space_refine_before_merge = False macro_cycles_in_refine_before_merge = 3 refine = True refine_pdb_in = False use_hl_anom_in_refinement = False include_ha_in_refinement = True refine_se_occ = True ordered_solvent = True flood_with_waters = False add_free_r_if_needed = True allow_overlapping = False fix_ligand_occupancy = False skip_hexdigest = False ncs_in_refinement = *torsion cartesian None correct_special_position_tolerance = None } model_building { score_with_cc = False fit_loops = True trace_loops = False standard_loops = True loop_lib = False assign_sequence = True min_percent_assigned_for_assign_sequence = 50 quick = True extend_only = True extend = True helices_strands_only = None insert_helices = None include_strands = None build_rna_helices = None n_build_repeat = 0 n_random_frag = None delta_phi = None rna_rho_min_main_base = -1 rna_rho_min_main_low = -1 rna_rho_min_main_seg = -1 rna_rho_min_side_seg = -1 cc_min = 0.4 cc_min_rna = 0.25 merge_with_combine_models = True merge_by_segment_correlation = True merge_remainder = True standard_merge = True use_cc_in_combine_extend = False } directories { temp_dir = "AutoSol_run_1_\\TEMP0\\build_1" output_dir = "AutoSol_run_1_\\TEMP0" top_output_dir = "" base_gui_dir = None } crystal_info { ncs_copies = None resolution = 2.5 solvent_fraction = None chain_type = *PROTEIN DNA RNA scattering_table = *n_gaussian wk1995 it1992 electron neutron semet = True } control { verbose = False raise_sorry = False debug = False carry_on = False dry_run = False do_only_one_thing = False write_run_directory_to_file = None multiprocessing = *multiprocessing sge lsf pbs condor pbspro slurm queue_run_command = None parallel_step = *final_assembly assembly peak_search all nproc = 1 i_ran_seed = 712341 remove_pdb_block = None model_start = None model_end = None resolve_size = 12 resolve_command_list = None } } Running phase_and_build Working directory: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark Date: Fri May 1 08:10:00 2020 Setting starting solvent_fraction and NCS copies Number of residues in unique chains in seq file: 139 Cell volume: 421654.55 Equivalent positions:8 Maximum number of NCS copies based on cell contents: 2 Best guess of number of NCS copies: 1 Estimate of solvent fraction: 0.64 Final data file in AutoSol_run_1_\TEMP0\phase_and_build_map_coeffs_1.mtz Using AutoSol_run_1_\TEMP0\aniso_refinement_data_PHX_with_hl_anom.mtz (assumed not aniso-corrected) for refinement and density modification. NOTE: No NCS operators read from AutoSol_run_1_\TEMP0\AutoSol_1.ncs_spec Selecting arrays from AutoSol_run_1_\TEMP0\map_coeffs_1.mtz : ['FWT', 'PHWT'] Output space group: I 4 (No. 79) Columns of data in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\TEMP_map_coeffs.mtz: H K L FWT PHWT H H H F P Copied map coeffs to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\TEMP_map_coeffs.mtz Phase improvement cycle 1 Building one model based on map in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\TEMP_map_coeffs.mtz Map coeffs labels: FWT,PHWT Array assignments: map_coeffs : FWT PHWT Array assignments: map_coeffs : FWT PHWT Map coeffs labels: FWT,PHWT Array assignments: map_coeffs : FWT PHWT Using C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\TEMP_map_coeff_freer_removed.mtz for real-space refinement Array assignments: map_coeffs : FWT PHWT Running template search using 1 processors then merging... Wrote output model to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\model_1.pdb Peak search log file: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\peak_search.log Files for merging: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\model_1.pdb Merging and extending secondary structure ... Merging with combine_models... Merging/extending log file: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\merge_and_build.log Running real-space refinement with C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\init_build.pdb Editing C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\init_build.pdb to replace any MET with MSE and copying to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\init_build_SEMET.pdb Appending atoms in AutoSol_run_1_\TEMP0\ha_1.pdb_formatted.pdb to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\init_build_SEMET.pdb to create C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\refinement_input.pdb This model has selenomethionine as MSE Refinement results for: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\rs__real_space_refined.pdb CC (entire map): 0.16 CC (around atoms): 0.79 Refinement log file is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\rs__real_space_refined.log Checking map correlation for 5 segments... Sorting models...chain types: PROTEIN Scoring 5 models... Sorted list with 4 entries: Output model written to: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\initial_build_cycle_1.pdb Map-model CC: 0.49 (overall) and 0.78 (local) for 118 residues in 4 chains in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\initial_build_cycle_1.pdb Model is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\initial_build_cycle_1.pdb Running refinement with C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\initial_build_cycle_1.pdb Editing C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\initial_build_cycle_1.pdb to replace any MET with MSE and copying to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\initial_build_cycle_1_SEMET.pdb Appending atoms in AutoSol_run_1_\TEMP0\ha_1.pdb_formatted.pdb to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\initial_build_cycle_1_SEMET.pdb to create C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\refinement_input.pdb This model has selenomethionine as MSE Adding waters in refinement Setting macro_cycles to 3 Refining occupancies of SE atoms in MSE Refinement results for: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\initial_build_cycle_1_ref_001.pdb R: 0.26 Rfree: 0.30 Refinement log file is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\initial_build_cycle_1_ref_001.log Current best: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\initial_build_cycle_1_ref_001.pdb with R/Rfree= 0.26/ 0.30 and map-model CC = 0.82 Density modification using: Model in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\initial_build_cycle_1_ref_001.pdb Data in AutoSol_run_1_\TEMP0\aniso_refinement_data_PHX_with_hl_anom.mtz Starting map from C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\TEMP_map_coeffs.mtz Truncating density at heavy-atom sites in resolve Summary of output files for Solution 1 from rebuild cycle 2 --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- refine_data: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\AutoBuild_run_1_\overall_best_refine_data.mtz --- Density-modification log file --- log_denmod: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\AutoBuild_run_1_\overall_best.log_denmod --- Density-modified map coefficients FWT PHWT --- denmod_map_coeffs: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\AutoBuild_run_1_\overall_best_denmod_map_coeffs.mtz New map fom is 0.82 New map: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\denmod_cycle_1.mtz Density modification log: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\denmod_cycle_1.log Full model-building cycle Building 1 model(s) using C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\denmod_cycle_1.mtz Building model 1 using C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\denmod_cycle_1.mtz Map coeffs labels: FWT,PHWT Array assignments: map_coeffs : FWT PHWT Array assignments: map_coeffs : FWT PHWT Map coeffs labels: FWT,PHWT Array assignments: map_coeffs : FWT PHWT Using C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\TEMP_map_coeff_freer_removed.mtz for real-space refinement Array assignments: map_coeffs : FWT PHWT Running template search using 1 processors then merging... Wrote output model to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\model_1.pdb Peak search log file: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\peak_search.log Files for merging: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\model_1.pdb Merging and extending secondary structure ... Merging with combine_models... Merging/extending log file: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\merge_and_build.log Running real-space refinement with C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\init_build.pdb Editing C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\init_build.pdb to replace any MET with MSE and copying to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\init_build_SEMET.pdb Appending atoms in AutoSol_run_1_\TEMP0\ha_1.pdb_formatted.pdb to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\init_build_SEMET.pdb to create C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\refinement_input.pdb This model has selenomethionine as MSE Refinement results for: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\rs__real_space_refined.pdb CC (entire map): 0.10 CC (around atoms): 0.46 Refinement log file is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\rs__real_space_refined.log Checking map correlation for 7 segments... Sorting models...chain types: PROTEIN Scoring 7 models... Sorted list with 3 entries: Output model written to: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_1.pdb Map-model CC: 0.47 (overall) and 0.69 (local) for 111 residues in 3 chains in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_1.pdb Model is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_1.pdb Running refinement with C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_1.pdb Editing C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_1.pdb to replace any MET with MSE and copying to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_1_SEMET.pdb Appending atoms in AutoSol_run_1_\TEMP0\ha_1.pdb_formatted.pdb to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_1_SEMET.pdb to create C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\refinement_input.pdb This model has selenomethionine as MSE Setting macro_cycles to 3 Refining occupancies of SE atoms in MSE Refinement results for: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_1_ref_001.pdb R: 0.31 Rfree: 0.36 Refinement log file is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_1_ref_001.log Working model list: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\initial_build_cycle_1_ref_001.pdb (R = 0.26) C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_1_ref_001.pdb (R = 0.31) Combining/extending model(s) : ['C:\\Users\\phaserbuilder\\NightlyBuilds\\PhenixVC2008\\x64\\Current\\tests\\phenix_regression.run_p9_sad_benchmark\\tst_p9_sad_benchmark\\AutoSol_run_1_\\TEMP0\\build_1\\initial_build_cycle_1_ref_001.pdb', 'C:\\Users\\phaserbuilder\\NightlyBuilds\\PhenixVC2008\\x64\\Current\\tests\\phenix_regression.run_p9_sad_benchmark\\tst_p9_sad_benchmark\\AutoSol_run_1_\\TEMP0\\build_1\\full_model_1_ref_001.pdb'] using C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\denmod_cycle_1.mtz Map coeffs labels: FWT,PHWT Array assignments: map_coeffs : FWT PHWT Array assignments: map_coeffs : FWT PHWT Map coeffs labels: FWT,PHWT Array assignments: map_coeffs : FWT PHWT Using C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\TEMP_map_coeff_freer_removed.mtz for real-space refinement Array assignments: map_coeffs : FWT PHWT Running template search using 1 processors then merging... Wrote output model to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\model_1.pdb Peak search log file: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\peak_search.log Files for merging: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\model_1.pdb Merging and extending secondary structure ... Merging with combine_models... Merging/extending log file: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\merge_and_build.log Running real-space refinement with C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\init_build.pdb Editing C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\init_build.pdb to replace any MET with MSE and copying to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\init_build_SEMET.pdb Appending atoms in AutoSol_run_1_\TEMP0\ha_1.pdb_formatted.pdb to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\init_build_SEMET.pdb to create C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\refinement_input.pdb This model has selenomethionine as MSE Refinement results for: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\rs__real_space_refined.pdb CC (entire map): 0.12 CC (around atoms): 0.47 Refinement log file is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\rs__real_space_refined.log Checking map correlation for 5 segments... Sorting models...chain types: PROTEIN Scoring 5 models... Sorted list with 4 entries: Output model written to: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_combine.pdb Map-model CC: 0.50 (overall) and 0.69 (local) for 122 residues in 4 chains in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_combine.pdb Model is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_combine.pdb Running refinement with C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_combine.pdb Editing C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_combine.pdb to replace any MET with MSE and copying to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_combine_SEMET.pdb Appending atoms in AutoSol_run_1_\TEMP0\ha_1.pdb_formatted.pdb to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_combine_SEMET.pdb to create C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\refinement_input.pdb This model has selenomethionine as MSE Adding waters in refinement Setting macro_cycles to 3 Refining occupancies of SE atoms in MSE Refinement results for: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_combine_ref_001.pdb R: 0.25 Rfree: 0.27 Refinement log file is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_combine_ref_001.log Current best: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_combine_ref_001.pdb with R/Rfree= 0.25/ 0.27 and map-model CC = 0.83 Model is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\full_model_combine_ref_001.pdb Assigning sequence and joining segments Trimmed 4 residues from C-terminal end of segment PDB file after assign_sequence is C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\sequence_assigned.pdb Log file for assign_sequence is C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\sequence_assigned.log Sequence-assigned model is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\sequence_assigned.pdb Current residues built: 118 placed: 118 Fitting loops.... Unsuccessful loop fitting Log file for loop fitting: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\fit_loops.log Running refinement with C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\sequence_assigned.pdb Editing C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\sequence_assigned.pdb to replace any MET with MSE and copying to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\sequence_assigned_SEMET.pdb Appending atoms in AutoSol_run_1_\TEMP0\ha_1.pdb_formatted.pdb to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\sequence_assigned_SEMET.pdb to create C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\refinement_input.pdb This model has selenomethionine as MSE Adding waters in refinement Setting macro_cycles to 3 Refining occupancies of SE atoms in MSE Refinement results for: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\sequence_assigned_ref_001.pdb R: 0.25 Rfree: 0.28 Refinement log file is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\sequence_assigned_ref_001.log Current best: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\sequence_assigned_ref_001.pdb with R/Rfree= 0.25/ 0.28 and map-model CC = 0.83 Best overall model: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\sequence_assigned_ref_001.pdb (R/Rfree = 0.25/ 0.28) Copying final model from C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\sequence_assigned_ref_001.pdb to AutoSol_run_1_\TEMP0\phase_and_build_1.pdb Copying final map coeffs from C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\build_1\denmod_cycle_1.mtz to AutoSol_run_1_\TEMP0\phase_and_build_map_coeffs_1.mtz Final map is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\phase_and_build_map_coeffs_1.mtz Final model is in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\phase_and_build_1.pdb Summary of model C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\phase_and_build_1.pdb Map coeffs file C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\TEMP0\phase_and_build_map_coeffs_1.mtz Map coeffs labin FP=FWT PHIB=PHWT R : 0.25 Rfree : 0.28 Built: 118 Placed: 118 Chains: 3 Model-map CC (whole map): 0.83 Model-map CC (around atoms): 0.69 Copying AutoSol_run_1_\TEMP0\phase_and_build_map_coeffs_1.mtz to AutoSol_run_1_\denmod_1.mtz Recovering fact resolution of 2.5 DM/BUILD SOLUTION: Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4" Model built with RESOLVE PLACED: 118 CHAINS: 3 CC: 0.831 Acceptable build found Fully acceptable model with R= 0.25 available Acceptable model built... No iteration as acceptable model with R= 0.25 available finished AutoSol Run 1 Fri May 1 09:13:00 2020 Finishing AutoSol Run 1 Facts written to AutoSol_run_1_\AutoSol_Facts.dat Warnings: Warning: NCS copies set to 1, however it could be from 1 to 2 Writing out files for solution # 1 Creating overall_best files ... Refining AutoSol_run_1_\phase_and_build_1.pdb against original data in AutoSol_run_1_\exptl_fobs_phases_freeR_flags_1_with_anom_data_with_hl_anom.mtz Setting refinement resolution to 2.5 Using test_flag_value of 1 in refinement After refinement of AutoSol_run_1_\phase_and_build_1.pdb against original data, new file is C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_final_refine_001.pdb CIF version of model written to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_final_refine_001.cif New values of R/Rfree: 0.25/ 0.28 Saved PDB file refined against original data in PDS as overall_best_final_refine_001.pdb Saved PDB file refined against original data in PDS as CIF in overall_best_final_refine_001.cif Copying files to overall_best Copying C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\phaser_1.mtz to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_hklout_phased.mtz Copying C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\exptl_fobs_phases_freeR_flags_1_with_anom_data_with_hl_anom.mtz to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_refine_data.mtz Copying C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\phase_and_build_map_coeffs_1.mtz to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_denmod_map_coeffs.mtz Copying C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\ha_1.pdb_formatted.pdb to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_ha_pdb.pdb Copying C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\AutoSol_1.ncs_spec to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_ncs_file.ncs_spec Copying C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_final_refine_001.pdb to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best.pdb Copying C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_final_refine_001.cif to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best.cif Copying C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\dataset_1_scale.log to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_log_scale.log Copying C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\phaser_1.log to C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_log_phased.log Summary of output files for Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4" --- Phased data with HL coeffs --- hklout_phased: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_hklout_phased.mtz --- Phased data for refinement --- refine_data: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_refine_data.mtz --- Map coefficients FWT PHWT (density modified with model) --- denmod_map_coeffs: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_denmod_map_coeffs.mtz --- Heavy-atom PDB file --- ha_pdb: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_ha_pdb.pdb --- NCS information file --- ncs_file: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_ncs_file.ncs_spec --- Model --- pdb_file: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best.pdb --- Model as CIF --- cif_pdb_file: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best.cif --- Scaling log file --- log_scale: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_log_scale.log --- Phasing log file --- log_phased: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_p9_sad_benchmark\tst_p9_sad_benchmark\AutoSol_run_1_\overall_best_log_phased.log Copying out overall best files AutoSol Run 1 -----------CURRENT SOLUTIONS FOR RUN 1 : ------------------- *** FILES ARE IN THE DIRECTORY: AutoSol_run_1_ **** Solution # 1 BAYES-CC: 59.1 +/- 13.7 (2SD) Dataset #1 FOM: 0.56 Solution 1 using HYSS on ANISO_p9.sca_ano_1.sca. Dataset #1 SG="I 4" Dataset number: 1 Dataset type: sad Datafiles used: ['C:\\Users\\phaserbuilder\\NightlyBuilds\\PhenixVC2008\\x64\\Current\\tests\\phenix_regression.run_p9_sad_benchmark\\tst_p9_sad_benchmark\\AutoSol_run_1_\\TEMP0\\ANISO_p9.sca'] Anisotropy correction applied to all data except overall_best_refine_data.mtz Sites: 4 (Already used for Phasing at resol of 2.5) Refined Sites: 5 No NCS found Experimental phases in: overall_best_hklout_phased.mtz Experimental phases plus FreeR_flags for refinement in: overall_best_refine_data.mtz Map coefficients (Density-modified phases using model) in: overall_best_denmod_map_coeffs.mtz HA sites (PDB format) in: overall_best_ha_pdb.pdb Sequence file in: sequence_autosol.dat Model in: overall_best.pdb Model as CIF in: overall_best.cif Residues built: 118 Side-chains built: 118 Chains: 3 Overall model-map correlation: 0.831 R/R-free: 0.25/0.28 Scaling logfile in: overall_best_log_scale.log Phasing logfile in: overall_best_log_phased.log Score type: SKEW CORR_RMS Raw scores: 0.25 0.92 100x EST OF CC: 55.35 62.48 Refined heavy atom sites (fractional): ATOM X Y Z OCC SE -0.180 0.113 0.177 1.63 SE -0.295 0.165 0.581 1.14 SE -0.262 0.185 0.648 1.41 SE 0.028 0.758 0.763 0.26 SE 0.160 0.286 0.603 0.32 Solution # 2 BAYES-CC: 17.7 +/- 37.0 (2SD) Dataset #1 FOM: 0.56 NOTE: Output files for this solution not written out (in PDS only) Adjust 'number_of_solutions_to_display' (currently 1) to write them out. Solution 2 using HYSS on ANISO_p9.sca_ano_1.sca and taking inverse. Dataset #1 SG="I 4" Dataset number: 1 Dataset type: sad Datafiles used: ['C:\\Users\\phaserbuilder\\NightlyBuilds\\PhenixVC2008\\x64\\Current\\tests\\phenix_regression.run_p9_sad_benchmark\\tst_p9_sad_benchmark\\AutoSol_run_1_\\TEMP0\\ANISO_p9.sca'] Anisotropy correction applied to all data except overall_best_refine_data.mtz Sites: 4 Refined Sites: 5 No NCS found Experimental phases in: phaser_2.mtz HA sites (PDB format) in: ha_2.pdb_formatted.pdb Sequence file in: sequence_autosol.dat Scaling logfile in: dataset_1_scale.log Phasing logfile in: phaser_2.log Score type: SKEW CORR_RMS Raw scores: -0.03 0.85 100x EST OF CC: 11.40 50.47 Refined heavy atom sites (fractional): ATOM X Y Z OCC SE 0.180 -0.113 -0.177 1.63 SE 0.295 -0.165 -0.581 1.14 SE 0.262 -0.185 -0.648 1.41 SE -0.028 -0.758 -0.763 0.26 SE -0.160 -0.286 -0.603 0.32 Citations for AutoSol: Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD. (2012) Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 68:352-67. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD. (2019) Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Cryst. D75:861-877. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. (2007) Phaser crystallographic software. J Appl Crystallogr 40:658-674. Moriarty NW, Grosse-Kunstleve RW, Adams PD. (2009) electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Crystallogr D Biol Crystallogr 65:1074-80. Terwilliger T. (2003) SOLVE and RESOLVE: automated structure solution, density modification and model building. J Synchrotron Radiat 11:49-52. Terwilliger TC, Adams PD, Read RJ, McCoy AJ, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW. (2009) Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Crystallogr D Biol Crystallogr 65:582-601. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung L-W, Read RJ, Adams PD. (2008) Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Cryst. D64:61-69. Zwart PH, Grosse-Kunstleve RW, Adams PD. (2005) Xtriage and Fest: automatic assessment of X-ray data and substructure structure factor estimation. CCP4 Newsletter Winter:Contribution 7. RUNTIME: 4073.3s INPUT Reading model from c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\hipip-refine\hipip.pdb Writing effective parameters to hipip.eff Preparation for phenix.refine Add hydrogens - to protein model using phenix.reduce - to ligands using eLBOW, phenix.elbow No unknown residues OUTPUT Writing model to hipip.updated.pdb Optimize H/D positions using phenix.geometry_minimization phenix.geometry_minimization "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_hipip_refine_benchmark\hipip.updated.pdb" use_neutron_distances=False output_file_name_prefix=hipip.updated selection="element H or element D" write_geo_file=False fix_rotamer_outliers=False silent=True correct_hydrogens=True # Date 2020-05-01 Time 09:15:56 GMT Daylight Time +0100 (1588320956.00 s) #phil __OFF__ Command line arguments: "hipip.updated.pdb" "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\hipip-refine\hipip.mtz" COMPUTERNAME = AZIMUTH PROCESSOR_ARCHITECTURE = AMD64 USERNAME = phaserbuilder PID = 11584 ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: dev Release tag: svn+SVN User: phaserbuilder ------------------------------------------------------------------------------- phenix.refine: Macromolecular Structure Refinement ------------------------------------------------------------------------------- Phenix developers include: Paul Adams, Pavel Afonine, Gabor Bunkoczi, Tom Burnley, Vincent Chen, Youval Dar, Ian Davis, Eli Draizen, Nathaniel Echols, Richard Gildea, Piet Gros, Ralf Grosse-Kunstleve, Jeffrey Headd, Bradley Hintze, Li-Wei Hung, Tom Ioerger, Dorothee Liebschner, Airlie McCoy, Erik McKee, Nigel Moriarty, Robert Oeffner, Billy Poon, Randy Read, Jane Richardson, David Richardson, Jim Sacchettini, Nicholas Sauter, Oleg Sobolev, Laurent Storoni, Tom Terwilliger, Christopher Williams, Peter Zwart Phenix home page: http://www.phenix-online.org/ ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Phenix components are copyrighted by: - Lawrence Berkeley National Laboratory - Los Alamos National Laboratory - University of Cambridge - Duke University - Texas Agricultural Experiment Station & Texas Engineering Experiment Station ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Major third-party components of Phenix include: Python, wxWidgets, wxPython, Boost, SCons, Clipper, CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS, MUSCLE, KSDSSP, PULCHRA, ANTLRv3 Enter phenix.acknowledgments for details. ------------------------------------------------------------------------------- Processing inputs. This may take a minute or two. No user-defined map coefficients or files defined; will use default map outputs instead. Working crystal symmetry after inspecting all inputs: Unit cell: (44.697, 58.272, 23.454, 90, 90, 90) Space group: P 21 21 21 (No. 19) ================================== X-ray data ================================= F-obs: c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\hipip-refine\hipip.mtz:FP,SIGFP Miller array info: c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\hipip-refine\hipip.mtz:FP,SIGFP Observation type: xray.amplitude Type of data: double, size=63422 Type of sigmas: double, size=63422 Number of Miller indices: 63422 Anomalous flag: False Unit cell: (44.697, 58.272, 23.454, 90, 90, 90) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 5680 Resolution range: 14.9598 0.801074 Completeness in resolution range: 0.972134 Completeness with d_max=infinity: 0.971925 Wavelength: 0.0000 Number of F-obs in resolution range: 63422 Number of F-obs<0 (these reflections will be rejected): 0 Number of F-obs=0 (these reflections will be used in refinement): 1973 Refinement resolution range: d_max = 14.9598 d_min = 0.8011 R-free flags: c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\hipip-refine\hipip.mtz:FreeRflag Miller array info: c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_examples\hipip-refine\hipip.mtz:FreeRflag Observation type: None Type of data: int, size=63422 Type of sigmas: None Number of Miller indices: 63422 Anomalous flag: False Unit cell: (44.697, 58.272, 23.454, 90, 90, 90) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 5680 Resolution range: 14.9598 0.801074 Completeness in resolution range: 0.972134 Completeness with d_max=infinity: 0.971925 Wavelength: 0.0000 Test (R-free flags) flag value: 0 Number of work/free reflections by resolution: work free %free bin 1: 14.9624 - 1.7251 [6819/6861] 6482 337 4.9% bin 2: 1.7251 - 1.3695 [6590/6601] 6257 333 5.1% bin 3: 1.3695 - 1.1965 [6512/6565] 6200 312 4.8% bin 4: 1.1965 - 1.0871 [6436/6510] 6106 330 5.1% bin 5: 1.0871 - 1.0092 [6326/6469] 5988 338 5.3% bin 6: 1.0092 - 0.9497 [6289/6479] 5990 299 4.8% bin 7: 0.9497 - 0.9022 [6187/6427] 5881 306 4.9% bin 8: 0.9022 - 0.8629 [6149/6449] 5825 324 5.3% bin 9: 0.8629 - 0.8297 [6139/6465] 5849 290 4.7% bin 10: 0.8297 - 0.8011 [5975/6414] 5663 312 5.2% overall 60241 3181 5.0% No array of experimental phases found. Monomer Library directory: "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\chem_data\mon_lib" Total number of atoms: 1315 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1207 Unusual residues: {'FE ': 4} Inner-chain residues flagged as termini: ['pdbres="GLY A 83 " segid="A "'] Classifications: {'undetermined': 4, 'peptide': 83} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 76, None: 4} Not linked: pdbres="GLY A 83 " segid="A " pdbres="FE A 84 " segid="A " Not linked: pdbres="FE A 84 " segid="A " pdbres="FE A 85 " segid="A " Not linked: pdbres="FE A 85 " segid="A " pdbres="FE A 86 " segid="A " Not linked: pdbres="FE A 86 " segid="A " pdbres="FE A 87 " segid="A " Chain: " " Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 108 Unusual residues: {'SO4': 3} Classifications: {'undetermined': 3, 'water': 93} Link IDs: {None: 95} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 610 SG CYS A 43 24.030 35.736 16.637 1.00 3.32 A S ATOM 644 SG CYS A 46 29.085 39.245 18.555 1.00 3.39 A S ATOM 859 SG CYS A 61 25.540 36.639 22.952 1.00 3.86 A S ATOM 1081 SG CYS A 75 23.061 41.222 20.132 1.00 3.33 A S Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" O HOH 6080 " occ=0.55 residue: pdb=" O HOH 6081 " occ=0.48 residue: pdb=" O HOH 6082 " occ=0.60 residue: pdb=" O HOH 6083 " occ=0.68 residue: pdb=" O HOH 6084 " occ=0.36 residue: pdb=" O HOH 6085 " occ=0.46 residue: pdb=" O HOH 6086 " occ=0.45 Time building chain proxies: 0.64, per 1000 atoms: 0.49 Number of scatterers: 1315 At special positions: 0 Unit cell: (44.697, 58.272, 23.454, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 8 16.00 O 223 8.00 N 110 7.00 C 383 6.00 H 587 1.00 sf(0) = scattering factor at diffraction angle 0. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 25.93 3 S 8 15.96 3 O 223 7.98 3 N 110 6.98 3 C 383 5.99 3 H 587 1.00 3 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : False - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 63.0 milliseconds Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 587 1.04 - 1.24: 79 1.24 - 1.44: 201 1.44 - 1.64: 357 1.64 - 1.84: 6 Bond restraints: 1230 Sorted by residual: bond pdb=" CD GLN A 62 " segid="A " pdb=" NE2 GLN A 62 " segid="A " ideal model delta sigma weight residual 1.328 1.240 0.088 2.10e-02 2.27e+03 1.76e+01 bond pdb=" C GLY A 83 " segid="A " pdb=" OXT GLY A 83 " segid="A " ideal model delta sigma weight residual 1.231 1.292 -0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" CD GLN A 62 " segid="A " pdb=" OE1 GLN A 62 " segid="A " ideal model delta sigma weight residual 1.231 1.285 -0.054 1.90e-02 2.77e+03 8.19e+00 bond pdb=" C ASP A 11 " segid="A " pdb=" O ASP A 11 " segid="A " ideal model delta sigma weight residual 1.239 1.274 -0.035 1.29e-02 6.01e+03 7.52e+00 bond pdb=" O1 SO4 902 " pdb=" S SO4 902 " ideal model delta sigma weight residual 1.460 1.407 0.053 2.00e-02 2.50e+03 7.04e+00 ... (remaining 1225 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.15: 26 105.15 - 112.31: 1357 112.31 - 119.47: 346 119.47 - 126.64: 473 126.64 - 133.80: 21 Bond angle restraints: 2223 Sorted by residual: angle pdb=" CA ASP A 11 " segid="A " pdb=" CB ASP A 11 " segid="A " pdb=" CG ASP A 11 " segid="A " ideal model delta sigma weight residual 112.60 121.16 -8.56 1.00e+00 1.00e+00 7.33e+01 angle pdb=" O ALA A 9 " segid="A " pdb=" C ALA A 9 " segid="A " pdb=" N ASP A 10 " segid="A " ideal model delta sigma weight residual 122.22 128.60 -6.38 1.17e+00 7.31e-01 2.97e+01 angle pdb=" CA ALA A 9 " segid="A " pdb=" C ALA A 9 " segid="A " pdb=" O ALA A 9 " segid="A " ideal model delta sigma weight residual 120.10 114.01 6.09 1.13e+00 7.83e-01 2.91e+01 angle pdb=" CA ASP A 11 " segid="A " pdb=" C ASP A 11 " segid="A " pdb=" N PRO A 12 " segid="A " ideal model delta sigma weight residual 118.87 123.62 -4.75 9.00e-01 1.23e+00 2.79e+01 angle pdb=" CA ASN A 52 " segid="A " pdb=" CB ASN A 52 " segid="A " pdb=" CG ASN A 52 " segid="A " ideal model delta sigma weight residual 112.60 107.75 4.85 1.00e+00 1.00e+00 2.35e+01 ... (remaining 2218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.06: 292 13.06 - 26.11: 27 26.11 - 39.17: 5 39.17 - 52.22: 2 52.22 - 65.27: 2 Dihedral angle restraints: 328 sinusoidal: 210 harmonic: 118 Sorted by residual: dihedral pdb=" CA ASP A 10 " segid="A " pdb=" C ASP A 10 " segid="A " pdb=" N ASP A 11 " segid="A " pdb=" CA ASP A 11 " segid="A " ideal model delta harmonic sigma weight residual 180.00 162.98 17.02 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA TRP A 74 " segid="A " pdb=" C TRP A 74 " segid="A " pdb=" N CYS A 75 " segid="A " pdb=" CA CYS A 75 " segid="A " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA LEU A 36 " segid="A " pdb=" C LEU A 36 " segid="A " pdb=" N PRO A 37 " segid="A " pdb=" CA PRO A 37 " segid="A " ideal model delta harmonic sigma weight residual 180.00 165.43 14.57 0 5.00e+00 4.00e-02 8.49e+00 ... (remaining 325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 31 0.047 - 0.093: 27 0.093 - 0.140: 18 0.140 - 0.186: 11 0.186 - 0.233: 4 Chirality restraints: 91 Sorted by residual: chirality pdb=" CA ASN A 45 " segid="A " pdb=" N ASN A 45 " segid="A " pdb=" C ASN A 45 " segid="A " pdb=" CB ASN A 45 " segid="A " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASP A 10 " segid="A " pdb=" N ASP A 10 " segid="A " pdb=" C ASP A 10 " segid="A " pdb=" CB ASP A 10 " segid="A " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA PRO A 38 " segid="A " pdb=" N PRO A 38 " segid="A " pdb=" C PRO A 38 " segid="A " pdb=" CB PRO A 38 " segid="A " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.96e-01 ... (remaining 88 not shown) Planarity restraints: 193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 78 " segid="A " 0.045 2.00e-02 2.50e+03 1.69e-02 1.14e+01 pdb=" CG TRP A 78 " segid="A " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 78 " segid="A " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 78 " segid="A " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 78 " segid="A " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 78 " segid="A " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 78 " segid="A " -0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 78 " segid="A " 0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 78 " segid="A " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 78 " segid="A " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 78 " segid="A " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TRP A 78 " segid="A " 0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP A 78 " segid="A " -0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 78 " segid="A " 0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 78 " segid="A " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 78 " segid="A " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 35 " segid="A " -0.012 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C GLY A 35 " segid="A " 0.040 2.00e-02 2.50e+03 pdb=" O GLY A 35 " segid="A " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 36 " segid="A " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 10 " segid="A " 0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C ASP A 10 " segid="A " -0.037 2.00e-02 2.50e+03 pdb=" O ASP A 10 " segid="A " 0.014 2.00e-02 2.50e+03 pdb=" N ASP A 11 " segid="A " 0.013 2.00e-02 2.50e+03 ... (remaining 190 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 244 2.27 - 2.85: 3000 2.85 - 3.43: 4018 3.43 - 4.02: 6008 4.02 - 4.60: 8854 Nonbonded interactions: 22124 Sorted by model distance: nonbonded pdb="HE21 GLN A 21 " segid="A " pdb=" O HOH 6075 " model vdw 1.687 1.850 nonbonded pdb=" HZ2 LYS A 18 " segid="A " pdb=" O HOH 6011 " model vdw 1.834 1.850 nonbonded pdb=" HZ1 LYS A 18 " segid="A " pdb=" O HOH 6082 " model vdw 1.838 1.850 nonbonded pdb=" OD1 ASP A 22 " segid="A " pdb=" HG1 THR A 24 " segid="A " model vdw 1.839 1.850 nonbonded pdb=" HH TYR A 19 " segid="A " pdb=" O HOH 6081 " model vdw 1.875 1.850 ... (remaining 22119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=individual ******************************************************************************* n_use = 1315 n_use_u_iso = 1315 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 1315 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (1315 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1315 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (74 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { crystal_symmetry { unit_cell = 44.6969986 58.27199936 23.45400047 90 90 90 space_group = "P 21 21 21" } input { pdb { file_name = "hipip.updated.pdb" } xray_data { file_name = "c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\hipip-refine\\hipip.mtz" labels = "FP,SIGFP" r_free_flags { file_name = "c:\\users\\phaserbuilder\\nightlybuilds\\phenixvc2008\\x64\\current\\modules\\phenix_examples\\hipip-refine\\hipip.mtz" label = "FreeRflag" test_flag_value = 0 } } } output { prefix = "hipip.updated_refine" serial = 1 } electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } main { nproc = Auto } hydrogens { refine = *individual riding Auto } pdb_interpretation { c_beta_restraints = False } } #phil __OFF__ =================== Write initial parameters into .eff file =================== CPU time processing inputs: 11.06 =============================== refinement start ============================== ================================== Hydrogens ================================== Total: count: 587 occupancy sum: 567.49 (% of total atoms 44.33) Rotatable: count: 151 occupancy sum: 145.15 (% of total atoms 11.34) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.80 - 14.96 A, n_refl.=63422 (all), 5.02 % free)------------| | | | r_work= 0.2521 r_free= 0.2549 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 4.021590 | | target function (ml) not normalized (work): 242264.628882 | | target function (ml) not normalized (free): 12821.464656 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 14.96 - 2.28 0.99 2890 141 0.2371 0.2172 5.583 5.4457| | 2: 2.28 - 1.81 1.00 2773 142 0.1826 0.1694 4.9962 4.9161| | 3: 1.81 - 1.58 1.00 2741 143 0.2276 0.2356 4.7712 4.8186| | 4: 1.58 - 1.43 1.00 2711 162 0.2319 0.2522 4.5778 4.6078| | 5: 1.43 - 1.33 0.99 2701 143 0.2280 0.2281 4.3972 4.4089| | 6: 1.33 - 1.25 0.99 2700 137 0.2266 0.2432 4.2982 4.3442| | 7: 1.25 - 1.19 0.99 2678 125 0.2312 0.2640 4.3163 4.3728| | 8: 1.19 - 1.14 0.99 2676 143 0.2441 0.2388 4.329 4.2827| | 9: 1.14 - 1.10 0.99 2626 153 0.2535 0.2506 4.265 4.2464| | 10: 1.10 - 1.06 0.98 2621 135 0.2642 0.2835 4.1612 4.1865| | 11: 1.06 - 1.02 0.99 2621 152 0.2729 0.2877 4.0328 4.0793| | 12: 1.02 - 1.00 0.97 2615 137 0.2698 0.3048 3.9384 3.9791| | 13: 1.00 - 0.97 0.97 2563 138 0.2811 0.2765 3.8939 3.87| | 14: 0.97 - 0.95 0.97 2620 126 0.2865 0.3071 3.7808 3.825| | 15: 0.95 - 0.92 0.95 2551 124 0.2941 0.2965 3.714 3.7202| | 16: 0.92 - 0.90 0.97 2569 142 0.3133 0.3114 3.6419 3.6387| | 17: 0.90 - 0.89 0.95 2510 143 0.3182 0.3218 3.6112 3.6759| | 18: 0.89 - 0.87 0.97 2550 128 0.3329 0.3557 3.4871 3.5745| | 19: 0.87 - 0.85 0.94 2523 153 0.3447 0.3552 3.4152 3.4843| | 20: 0.85 - 0.84 0.96 2543 117 0.3665 0.3781 3.3115 2.9726| | 21: 0.84 - 0.83 0.94 2530 132 0.3822 0.3933 3.2524 3.2755| | 22: 0.83 - 0.81 0.95 2509 130 0.4023 0.3637 3.1094 3.3549| | 23: 0.81 - 0.80 0.91 2420 135 0.4168 0.3948 3.0769 3.1758| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 14.96 - 2.28 2890 141 0.85 20.13 0.93 1.02 7533.72| | 2: 2.28 - 1.81 2773 142 0.87 19.77 1.02 1.15 3932.74| | 3: 1.81 - 1.58 2741 143 0.88 19.21 1.09 1.19 1859.56| | 4: 1.58 - 1.43 2711 162 0.86 20.70 1.03 1.17 1382.24| | 5: 1.43 - 1.33 2701 143 0.85 22.01 0.99 1.12 1050.60| | 6: 1.33 - 1.25 2700 137 0.85 22.12 1.02 1.15 881.61| | 7: 1.25 - 1.19 2678 125 0.87 20.09 1.07 1.21 816.38| | 8: 1.19 - 1.14 2676 143 0.87 19.78 1.12 1.26 768.29| | 9: 1.14 - 1.10 2626 153 0.87 20.60 1.13 1.25 724.69| | 10: 1.10 - 1.06 2621 135 0.84 22.96 1.13 1.24 651.64| | 11: 1.06 - 1.02 2621 152 0.81 25.83 1.12 1.20 568.66| | 12: 1.02 - 1.00 2615 137 0.81 26.30 1.11 1.21 485.97| | 13: 1.00 - 0.97 2563 138 0.81 25.75 1.16 1.22 412.54| | 14: 0.97 - 0.95 2620 126 0.80 26.63 1.16 1.26 364.09| | 15: 0.95 - 0.92 2551 124 0.81 26.31 1.16 1.28 318.84| | 16: 0.92 - 0.90 2569 142 0.79 27.89 1.15 1.29 300.38| | 17: 0.90 - 0.89 2510 143 0.78 29.08 1.12 1.27 285.20| | 18: 0.89 - 0.87 2550 128 0.75 31.76 1.10 1.23 269.07| | 19: 0.87 - 0.85 2523 153 0.73 33.62 1.08 1.14 244.83| | 20: 0.85 - 0.84 2543 117 0.71 35.31 1.03 1.09 218.10| | 21: 0.84 - 0.83 2530 132 0.68 37.76 1.02 1.06 207.53| | 22: 0.83 - 0.81 2509 130 0.65 40.13 1.00 1.02 197.58| | 23: 0.81 - 0.80 2420 135 0.63 42.00 1.00 0.93 185.77| |alpha: min = 0.93 max = 1.29 mean = 1.17| |beta: min = 185.77 max = 7533.72 mean = 1078.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.80| |phase err.(work): min = 0.00 max = 90.00 mean = 26.55| |phase err.(test): min = 0.00 max = 90.00 mean = 26.55| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- min max mean iso aniso Overall: 3.03 70.96 9.05 2.12 728 0 Protein: 3.12 53.12 6.49 2.00 616 0 Water: 4.64 70.96 25.34 N/A 93 0 Other: 3.03 23.95 12.29 N/A 19 0 Chain A: 3.03 53.12 6.47 N/A 620 0 Chain : 4.64 70.96 23.87 N/A 108 0 Histogram: Values Number of atoms 3.03 - 9.82 569 9.82 - 16.62 72 16.62 - 23.41 35 23.41 - 30.20 18 30.20 - 36.99 13 36.99 - 43.79 10 43.79 - 50.58 4 50.58 - 57.37 3 57.37 - 64.17 3 64.17 - 70.96 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 0.80 - 14.96 A, n_refl.=63422 (all), 5.02 % free)------------| | | | r_work= 0.2521 r_free= 0.2549 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 4.021590 | | target function (ml) not normalized (work): 242264.628882 | | target function (ml) not normalized (free): 12821.464656 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2523 0.2521 0.2549 n_refl.: 63422 re-set all scales: r(all,work,free)=0.2523 0.2521 0.2549 n_refl.: 63422 remove outliers: r(all,work,free)=0.2523 0.2522 0.2549 n_refl.: 63421 overall B=-0.49 to atoms: r(all,work,free)=0.2471 0.2470 0.2492 n_refl.: 63421 bulk-solvent and scaling: r(all,work,free)=0.2290 0.2291 0.2272 n_refl.: 63421 remove outliers: r(all,work,free)=0.2234 0.2235 0.2218 n_refl.: 61781 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 14.960-7.253 99.02 95 6 0.3463 260.484 236.026 0.942 0.998 0.391 7.246-5.773 99.01 98 2 0.2712 263.466 241.864 1.000 0.999 0.311 5.768-4.607 98.95 180 9 0.2221 278.149 264.140 0.999 0.999 0.287 4.593-3.659 92.73 341 16 0.1756 311.805 301.046 1.008 1.002 0.262 3.656-2.912 98.75 675 36 0.1976 248.143 239.341 1.025 0.999 0.162 2.911-2.318 100.00 1343 59 0.2176 183.341 176.742 0.990 0.999 0.000 2.318-1.845 100.00 2587 143 0.1753 161.888 158.517 1.037 0.999 0.000 1.845-1.469 99.85 5060 262 0.2192 104.432 100.433 1.069 0.999 0.000 1.469-1.169 99.19 9852 508 0.2180 71.754 68.679 1.000 1.001 0.000 1.169-0.931 96.65 18810 1002 0.2250 49.856 47.844 1.063 1.001 0.000 0.931-0.801 88.70 19639 1058 0.2832 27.107 25.614 0.986 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0572 b_overall=0.1775 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.2235 r_free=0.2218 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2235 r_free=0.2218 ========================= Local real-space refinement ========================= Before: r_work=0.2235 r_free=0.2218 rotamer outliers: 0.00 % outliers start: 0 chain: A residue: ASN 5 start: score: 22.226 CA: 4.36 CB: 4.56 CG: 4.03 OD1: 5.72 ND2: 3.56 p0 fitting: score: 22.275 CA: 4.36 CB: 4.56 CG: 4.06 OD1: 5.72 ND2: 3.57 p0 tuneup: score: 22.271 CA: 4.36 CB: 4.56 CG: 4.08 OD1: 5.73 ND2: 3.54 p0 revert: score: 22.275 CA: 4.36 CB: 4.56 CG: 4.06 OD1: 5.72 ND2: 3.57 p0 chain: A residue: THR 8 start: score: 15.166 CA: 3.31 CB: 2.50 CG2: 1.65 OG1: 3.03 p fitting: score: 15.166 CA: 3.31 CB: 2.50 CG2: 1.65 OG1: 3.03 p tuneup: score: 15.166 CA: 3.31 CB: 2.50 CG2: 1.65 OG1: 3.03 p revert: score: 15.166 CA: 3.31 CB: 2.50 CG2: 1.65 OG1: 3.03 p chain: A residue: ASP 10 start: score: 5.317 CA: 2.22 CB: 0.90 CG: 0.69 OD1: 0.15 OD2: 1.35 p0 fitting: score: 5.798 CA: 2.22 CB: 0.90 CG: 0.80 OD1: 1.31 OD2: 0.57 p0 tuneup: score: 5.704 CA: 2.22 CB: 0.90 CG: 0.81 OD1: 1.29 OD2: 0.48 p0 revert: score: 5.798 CA: 2.22 CB: 0.90 CG: 0.80 OD1: 1.31 OD2: 0.57 p0 chain: A residue: ILE 15 start: score: 22.526 CA: 5.32 CB: 4.59 CG1: 3.58 CG2: 4.31 CD1: 2.37 mt fitting: score: 22.505 CA: 5.32 CB: 4.59 CG1: 3.74 CG2: 4.38 CD1: 2.24 mt tuneup: score: 22.505 CA: 5.32 CB: 4.59 CG1: 3.74 CG2: 4.38 CD1: 2.24 mt revert: score: 22.526 CA: 5.32 CB: 4.59 CG1: 3.58 CG2: 4.31 CD1: 2.37 mt chain: A residue: LEU 17 start: score: 41.809 CA: 6.84 CB: 7.38 CG: 7.14 CD1: 5.61 CD2: 4.62 mt fitting: score: 41.716 CA: 6.84 CB: 7.38 CG: 7.33 CD1: 5.45 CD2: 4.63 mt tuneup: score: 41.059 CA: 6.84 CB: 7.38 CG: 7.33 CD1: 5.67 CD2: 4.09 mt revert: score: 41.809 CA: 6.84 CB: 7.38 CG: 7.14 CD1: 5.61 CD2: 4.62 mt chain: A residue: LYS 18 start: score: 24.070 CA: 7.17 CB: 6.03 CG: 4.31 CD: 1.84 CE: 1.38 NZ: 1.67 mmtm fitting: score: 32.007 CA: 7.17 CB: 6.03 CG: 5.40 CD: 3.65 CE: 2.53 NZ: 3.61 mmtt tuneup: score: 32.570 CA: 7.17 CB: 6.03 CG: 5.44 CD: 3.84 CE: 2.86 NZ: 3.62 mmtt chain: A residue: TYR 19 start: score: 77.988 CA: 7.58 CB: 6.91 CG: 6.88 CZ: 6.39 OH: 9.48 CD1: 7.03 CD2: 5.75 CE1: 6.38 CE2: 5.71 t80 fitting: score: 77.988 CA: 7.58 CB: 6.91 CG: 6.88 CZ: 6.39 OH: 9.48 CD1: 7.03 CD2: 5.75 CE1: 6.38 CE2: 5.71 t80 tuneup: score: 71.272 CA: 7.58 CB: 6.91 CG: 7.11 CZ: 5.42 OH: 7.66 CD1: 6.95 CD2: 5.46 CE1: 6.01 CE2: 5.10 t80 revert: score: 77.988 CA: 7.58 CB: 6.91 CG: 6.88 CZ: 6.39 OH: 9.48 CD1: 7.03 CD2: 5.75 CE1: 6.38 CE2: 5.71 t80 chain: A residue: ASN 20 start: score: 34.088 CA: 7.18 CB: 6.31 CG: 6.33 OD1: 9.38 ND2: 4.88 t0 fitting: score: 34.197 CA: 7.18 CB: 6.31 CG: 6.30 OD1: 9.51 ND2: 4.90 t0 tuneup: score: 34.012 CA: 7.18 CB: 6.31 CG: 6.32 OD1: 9.45 ND2: 4.75 t0 revert: score: 34.197 CA: 7.18 CB: 6.31 CG: 6.30 OD1: 9.51 ND2: 4.90 t0 chain: A residue: THR 24 start: score: 35.794 CA: 6.35 CB: 5.00 CG2: 4.56 OG1: 7.66 p fitting: score: 35.821 CA: 6.35 CB: 5.00 CG2: 4.50 OG1: 7.74 p tuneup: score: 35.779 CA: 6.35 CB: 5.00 CG2: 4.43 OG1: 7.79 p revert: score: 35.821 CA: 6.35 CB: 5.00 CG2: 4.50 OG1: 7.74 p chain: A residue: LYS 25 start: score: 29.070 CA: 7.08 CB: 5.19 CG: 3.70 CD: 2.41 CE: 3.29 NZ: 3.70 mmtm fitting: score: 29.070 CA: 7.08 CB: 5.19 CG: 3.70 CD: 2.41 CE: 3.29 NZ: 3.70 mmtm tuneup: score: 28.176 CA: 7.08 CB: 5.19 CG: 3.75 CD: 2.20 CE: 3.06 NZ: 3.45 mmtm revert: score: 29.070 CA: 7.08 CB: 5.19 CG: 3.70 CD: 2.41 CE: 3.29 NZ: 3.70 mmtm chain: A residue: ARG 28 start: score: 60.517 CA: 7.28 CB: 7.87 CG: 7.09 CD: 7.57 NE: 8.39 CZ: 7.18 NH1: 7.82 NH2: 7.33 ptt180 fitting: score: 60.517 CA: 7.28 CB: 7.87 CG: 7.09 CD: 7.57 NE: 8.39 CZ: 7.18 NH1: 7.82 NH2: 7.33 ptt180 tuneup: score: 60.489 CA: 7.28 CB: 7.87 CG: 7.09 CD: 7.60 NE: 8.49 CZ: 7.15 NH1: 7.76 NH2: 7.24 ptt180 revert: score: 60.517 CA: 7.28 CB: 7.87 CG: 7.09 CD: 7.57 NE: 8.39 CZ: 7.18 NH1: 7.82 NH2: 7.33 ptt180 chain: A residue: VAL 29 start: score: 33.842 CA: 6.94 CB: 6.56 CG1: 5.41 CG2: 4.75 t fitting: score: 34.166 CA: 6.94 CB: 6.56 CG1: 5.40 CG2: 4.93 t tuneup: score: 33.501 CA: 6.94 CB: 6.56 CG1: 5.44 CG2: 4.56 t revert: score: 34.166 CA: 6.94 CB: 6.56 CG1: 5.40 CG2: 4.93 t chain: A residue: ARG 33 start: score: 44.405 CA: 6.27 CB: 5.82 CG: 5.48 CD: 5.43 NE: 6.30 CZ: 4.88 NH1: 5.59 NH2: 4.61 mmm160 fitting: score: 44.405 CA: 6.27 CB: 5.82 CG: 5.48 CD: 5.43 NE: 6.30 CZ: 4.88 NH1: 5.59 NH2: 4.61 mmm160 tuneup: score: 43.163 CA: 6.27 CB: 5.82 CG: 5.63 CD: 5.17 NE: 6.43 CZ: 4.57 NH1: 5.21 NH2: 4.05 mmm160 revert: score: 44.405 CA: 6.27 CB: 5.82 CG: 5.48 CD: 5.43 NE: 6.30 CZ: 4.88 NH1: 5.59 NH2: 4.61 mmm160 chain: A residue: LEU 36 start: score: 32.284 CA: 5.77 CB: 4.79 CG: 4.72 CD1: 4.60 CD2: 3.90 mt fitting: score: 32.284 CA: 5.77 CB: 4.79 CG: 4.72 CD1: 4.60 CD2: 3.90 mt tuneup: score: 32.553 CA: 5.77 CB: 4.79 CG: 4.78 CD1: 4.73 CD2: 3.88 mt chain: A residue: HIS 42 start: score: 37.806 CA: 7.96 CB: 6.25 CG: 6.22 ND1: 4.95 CD2: 4.67 CE1: 2.63 NE2: 5.13 p-80 fitting: score: 37.827 CA: 7.96 CB: 6.25 CG: 6.27 ND1: 5.00 CD2: 4.68 CE1: 2.66 NE2: 5.01 p-80 tuneup: score: 37.049 CA: 7.96 CB: 6.25 CG: 6.57 ND1: 4.68 CD2: 4.60 CE1: 2.72 NE2: 4.27 p-80 revert: score: 37.827 CA: 7.96 CB: 6.25 CG: 6.27 ND1: 5.00 CD2: 4.68 CE1: 2.66 NE2: 5.01 p-80 chain: A residue: CYS 43 start: score: 47.131 CA: 7.37 CB: 7.32 SG: 32.44 m fitting: score: 23.246 CA: 7.37 CB: 7.32 SG: 8.55 m tuneup: score: 47.142 CA: 7.37 CB: 7.32 SG: 32.45 m chain: A residue: ASN 45 start: score: 39.128 CA: 7.70 CB: 6.95 CG: 6.87 OD1: 11.18 ND2: 6.43 p0 fitting: score: 39.128 CA: 7.70 CB: 6.95 CG: 6.87 OD1: 11.18 ND2: 6.43 p0 tuneup: score: 38.838 CA: 7.70 CB: 6.95 CG: 6.92 OD1: 11.23 ND2: 6.04 p0 revert: score: 39.128 CA: 7.70 CB: 6.95 CG: 6.87 OD1: 11.18 ND2: 6.43 p0 chain: A residue: CYS 46 start: score: 45.966 CA: 7.93 CB: 6.86 SG: 31.17 t fitting: score: 45.966 CA: 7.93 CB: 6.86 SG: 31.17 t tuneup: score: 45.966 CA: 7.93 CB: 6.86 SG: 31.17 t revert: score: 45.966 CA: 7.93 CB: 6.86 SG: 31.17 t chain: A residue: MET 49 start: score: 30.247 CA: 6.57 CB: 6.68 CG: 4.62 SD: 9.43 CE: 1.47 ttp fitting: score: 30.394 CA: 6.57 CB: 6.68 CG: 4.53 SD: 9.65 CE: 1.48 ttp tuneup: score: 30.683 CA: 6.57 CB: 6.68 CG: 4.60 SD: 9.66 CE: 1.58 ttp chain: A residue: GLN 50 start: score: 25.117 CA: 5.35 CB: 4.87 CG: 4.49 CD: 4.07 OE1: 4.36 NE2: 1.97 mt0 fitting: score: 25.117 CA: 5.35 CB: 4.87 CG: 4.49 CD: 4.07 OE1: 4.36 NE2: 1.97 mt0 tuneup: score: 25.183 CA: 5.35 CB: 4.87 CG: 4.49 CD: 4.07 OE1: 4.38 NE2: 2.02 mt0 chain: A residue: ASN 52 start: score: 19.448 CA: 5.70 CB: 4.40 CG: 3.21 OD1: 2.93 ND2: 3.22 m-40 fitting: score: 19.549 CA: 5.70 CB: 4.40 CG: 3.16 OD1: 3.34 ND2: 2.95 m110 tuneup: score: 19.345 CA: 5.70 CB: 4.40 CG: 3.26 OD1: 3.27 ND2: 2.71 m110 revert: score: 19.549 CA: 5.70 CB: 4.40 CG: 3.16 OD1: 3.34 ND2: 2.95 m110 chain: A residue: VAL 53 start: score: 32.212 CA: 6.40 CB: 6.26 CG1: 5.38 CG2: 4.39 t fitting: score: 32.212 CA: 6.40 CB: 6.26 CG1: 5.38 CG2: 4.39 t tuneup: score: 31.875 CA: 6.40 CB: 6.26 CG1: 5.44 CG2: 4.17 t revert: score: 32.212 CA: 6.40 CB: 6.26 CG1: 5.38 CG2: 4.39 t chain: A residue: TRP 58 start: score: 56.541 CA: 6.79 CB: 6.11 CG: 5.61 CD1: 5.19 CD2: 5.67 NE1: 5.93 CE2: 4.47 CE3: 5.05 CZ2: 3.64 CZ3: 4.30 CH2: 3.78 m100 fitting: score: 56.541 CA: 6.79 CB: 6.11 CG: 5.61 CD1: 5.19 CD2: 5.67 NE1: 5.93 CE2: 4.47 CE3: 5.05 CZ2: 3.64 CZ3: 4.30 CH2: 3.78 m100 tuneup: score: 51.102 CA: 6.79 CB: 6.11 CG: 5.63 CD1: 4.92 CD2: 4.96 NE1: 5.31 CE2: 4.13 CE3: 4.50 CZ2: 2.30 CZ3: 3.81 CH2: 2.65 m100 revert: score: 56.541 CA: 6.79 CB: 6.11 CG: 5.61 CD1: 5.19 CD2: 5.67 NE1: 5.93 CE2: 4.47 CE3: 5.05 CZ2: 3.64 CZ3: 4.30 CH2: 3.78 m100 chain: A residue: LYS 59 start: score: 41.514 CA: 6.76 CB: 6.16 CG: 5.99 CD: 5.37 CE: 4.52 NZ: 6.36 mmmt fitting: score: 41.514 CA: 6.76 CB: 6.16 CG: 5.99 CD: 5.37 CE: 4.52 NZ: 6.36 mmmt tuneup: score: 42.007 CA: 6.76 CB: 6.16 CG: 5.99 CD: 5.40 CE: 4.53 NZ: 6.59 mmmt chain: A residue: LEU 63 start: score: 42.981 CA: 7.17 CB: 6.96 CG: 6.43 CD1: 5.41 CD2: 5.80 mt fitting: score: 43.187 CA: 7.17 CB: 6.96 CG: 6.43 CD1: 5.46 CD2: 5.85 mt tuneup: score: 42.646 CA: 7.17 CB: 6.96 CG: 6.44 CD1: 5.51 CD2: 5.53 mt revert: score: 43.187 CA: 7.17 CB: 6.96 CG: 6.43 CD1: 5.46 CD2: 5.85 mt chain: A residue: PHE 64 start: score: 51.468 CA: 6.63 CB: 6.60 CG: 6.92 CD1: 7.25 CD2: 6.44 CE1: 6.24 CE2: 5.75 CZ: 5.64 m-80 fitting: score: 51.700 CA: 6.63 CB: 6.60 CG: 6.95 CD1: 7.33 CD2: 6.37 CE1: 6.27 CE2: 5.88 CZ: 5.66 m-80 tuneup: score: 49.822 CA: 6.63 CB: 6.60 CG: 7.06 CD1: 6.96 CD2: 6.17 CE1: 5.93 CE2: 5.27 CZ: 5.21 m-80 revert: score: 51.700 CA: 6.63 CB: 6.60 CG: 6.95 CD1: 7.33 CD2: 6.37 CE1: 6.27 CE2: 5.88 CZ: 5.66 m-80 chain: A residue: LYS 67 start: score: 27.727 CA: 5.92 CB: 5.72 CG: 3.73 CD: 3.13 CE: 2.53 NZ: 3.35 mttm fitting: score: 28.189 CA: 5.92 CB: 5.72 CG: 3.81 CD: 3.10 CE: 2.57 NZ: 3.54 mttm tuneup: score: 28.286 CA: 5.92 CB: 5.72 CG: 3.91 CD: 3.24 CE: 2.52 NZ: 3.49 mttm chain: A residue: LEU 68 start: score: 40.588 CA: 6.14 CB: 6.66 CG: 6.44 CD1: 5.28 CD2: 5.40 mt fitting: score: 40.864 CA: 6.14 CB: 6.66 CG: 6.52 CD1: 5.27 CD2: 5.51 mt tuneup: score: 40.698 CA: 6.14 CB: 6.66 CG: 6.52 CD1: 5.27 CD2: 5.42 mt revert: score: 40.864 CA: 6.14 CB: 6.66 CG: 6.52 CD1: 5.27 CD2: 5.51 mt chain: A residue: ILE 69 start: score: 36.676 CA: 7.09 CB: 6.50 CG1: 6.49 CG2: 4.97 CD1: 5.81 pp fitting: score: 36.787 CA: 7.09 CB: 6.50 CG1: 6.45 CG2: 4.91 CD1: 5.92 pp tuneup: score: 35.902 CA: 7.09 CB: 6.50 CG1: 6.62 CG2: 5.12 CD1: 5.29 pp revert: score: 36.787 CA: 7.09 CB: 6.50 CG1: 6.45 CG2: 4.91 CD1: 5.92 pp chain: A residue: VAL 71 start: score: 32.063 CA: 6.24 CB: 6.06 CG1: 4.82 CG2: 5.06 m fitting: score: 32.101 CA: 6.24 CB: 6.06 CG1: 4.83 CG2: 5.07 m tuneup: score: 31.931 CA: 6.24 CB: 6.06 CG1: 4.84 CG2: 4.97 m revert: score: 32.101 CA: 6.24 CB: 6.06 CG1: 4.83 CG2: 5.07 m chain: A residue: TRP 74 start: score: 85.712 CA: 8.10 CB: 7.27 CG: 8.61 CD1: 8.26 CD2: 7.77 NE1: 9.50 CE2: 7.56 CE3: 8.37 CZ2: 6.50 CZ3: 7.08 CH2: 6.70 t60 fitting: score: 85.724 CA: 8.10 CB: 7.27 CG: 8.61 CD1: 8.28 CD2: 7.76 NE1: 9.51 CE2: 7.57 CE3: 8.29 CZ2: 6.52 CZ3: 7.16 CH2: 6.67 t60 tuneup: score: 85.724 CA: 8.10 CB: 7.27 CG: 8.61 CD1: 8.28 CD2: 7.76 NE1: 9.51 CE2: 7.57 CE3: 8.29 CZ2: 6.52 CZ3: 7.16 CH2: 6.67 t60 revert: score: 85.724 CA: 8.10 CB: 7.27 CG: 8.61 CD1: 8.28 CD2: 7.76 NE1: 9.51 CE2: 7.57 CE3: 8.29 CZ2: 6.52 CZ3: 7.16 CH2: 6.67 t60 chain: A residue: SER 77 start: score: 24.497 CA: 6.86 CB: 6.37 OG: 5.63 m fitting: score: 24.540 CA: 6.86 CB: 6.37 OG: 5.65 m tuneup: score: 24.540 CA: 6.86 CB: 6.37 OG: 5.65 m revert: score: 24.540 CA: 6.86 CB: 6.37 OG: 5.65 m chain: A residue: TRP 78 start: score: 83.881 CA: 7.96 CB: 8.04 CG: 7.83 CD1: 7.43 CD2: 6.99 NE1: 9.18 CE2: 8.19 CE3: 7.21 CZ2: 6.96 CZ3: 7.33 CH2: 6.77 t60 fitting: score: 83.881 CA: 7.96 CB: 8.04 CG: 7.83 CD1: 7.43 CD2: 6.99 NE1: 9.18 CE2: 8.19 CE3: 7.21 CZ2: 6.96 CZ3: 7.33 CH2: 6.77 t60 tuneup: score: 72.338 CA: 7.96 CB: 8.04 CG: 7.86 CD1: 6.87 CD2: 6.21 NE1: 7.46 CE2: 6.67 CE3: 6.56 CZ2: 5.16 CZ3: 5.45 CH2: 4.09 t60 revert: score: 83.881 CA: 7.96 CB: 8.04 CG: 7.83 CD1: 7.43 CD2: 6.99 NE1: 9.18 CE2: 8.19 CE3: 7.21 CZ2: 6.96 CZ3: 7.33 CH2: 6.77 t60 chain: A residue: THR 79 start: score: 31.176 CA: 6.31 CB: 5.83 CG2: 3.30 OG1: 6.22 m fitting: score: 31.216 CA: 6.31 CB: 5.83 CG2: 3.30 OG1: 6.24 m tuneup: score: 31.216 CA: 6.31 CB: 5.83 CG2: 3.30 OG1: 6.24 m revert: score: 31.216 CA: 6.31 CB: 5.83 CG2: 3.30 OG1: 6.24 m chain: A residue: LEU 80 start: score: 29.447 CA: 6.08 CB: 4.78 CG: 4.97 CD1: 3.69 CD2: 3.12 tp fitting: score: 29.756 CA: 6.08 CB: 4.78 CG: 5.12 CD1: 3.72 CD2: 3.17 tp tuneup: score: 29.390 CA: 6.08 CB: 4.78 CG: 5.18 CD1: 3.64 CD2: 3.04 tp revert: score: 29.756 CA: 6.08 CB: 4.78 CG: 5.12 CD1: 3.72 CD2: 3.17 tp chain: A residue: LYS 81 start: score: 35.486 CA: 6.49 CB: 6.83 CG: 5.48 CD: 4.98 CE: 4.35 NZ: 3.68 tttp fitting: score: 35.486 CA: 6.49 CB: 6.83 CG: 5.48 CD: 4.98 CE: 4.35 NZ: 3.68 tttp tuneup: score: 35.385 CA: 6.49 CB: 6.83 CG: 5.49 CD: 4.98 CE: 4.40 NZ: 3.60 tttp revert: score: 35.486 CA: 6.49 CB: 6.83 CG: 5.48 CD: 4.98 CE: 4.35 NZ: 3.68 tttp outliers after map fit: 0 tune up outliers final: 0 Did it for: 36 After: r_work=0.2232 r_free=0.2215 rotamer outliers: 0.00 % ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 20.182646 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.105376 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ============================= Fit rotatable H or D ============================ ====================== XYZ individual (reciprocal space) ====================== R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT TARGETS work free delta bonds angl data restr 22.32 22.15 -0.17 0.016 1.7 6.5 0.0 0.0 0 none 0.056 0.0839 22.18 22.78 0.59 0.007 0.9 3.3 0.0 0.0 0 10.091 0.053 0.0260 Legend: - first line corresponds to starting state (before refinement) - R-factors reported in percent - delta is Rfree-Rwork in percent - CLASH is all-atom Molprobity clashscore - ROTA is percent of side-chain rotamer outliers - RAMA is percent of Ramachandran plot outliers - CBET is number of Cbeta deviations - WEIGHT is relative weight between X-ray (or neutron) target and restraints - TARGETS: the values of X-ray (or neutron) and restraints target functions ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.18 22.78 0.59 1.536 7.578 0.105 0.053 22.86 23.74 0.89 1.306 7.978 0.105 0.055 min max mean iso aniso Overall: 2.41 65.47 8.48 1.52 728 0 Protein: 2.55 47.63 6.48 1.42 616 0 Water: 4.17 65.47 21.08 N/A 93 0 Other: 2.41 20.34 11.64 N/A 19 0 Chain A: 2.41 47.63 6.46 N/A 620 0 Chain : 4.17 65.47 20.11 N/A 108 0 Histogram: Values Number of atoms 2.41 - 8.71 557 8.71 - 15.02 95 15.02 - 21.33 32 21.33 - 27.63 14 27.63 - 33.94 16 33.94 - 40.24 5 40.24 - 46.55 3 46.55 - 52.86 2 52.86 - 59.16 3 59.16 - 65.47 1 =========================== ADP refinement (H only) =========================== |- start----------------------------------------------------------------------| | target_work(ls_wunit_k1) = 0.0550784 r_work = 0.2286 r_free = 0.2374 | |-----------------------------------------------------------------------------| |- final----------------------------------------------------------------------| | target_work(ls_wunit_k1) = 0.0538973 r_work = 0.2273 r_free = 0.2388 | |-----------------------------------------------------------------------------| ======================== Occupancy refinement (H only) ======================== |- start----------------------------------------------------------------------| | target_work(ls_wunit_k1) = 0.0538973 r_work = 0.2273 r_free = 0.2388 | |-----------------------------------------------------------------------------| |- final----------------------------------------------------------------------| | target_work(ls_wunit_k1) = 0.0515477 r_work = 0.2266 r_free = 0.2400 | |-----------------------------------------------------------------------------| ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2266 r_free = 0.2400 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2251 r_free = 0.2365 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 0.80 - 14.96 A, n_refl.=61781 (all), 5.02 % free)------------| | | | r_work= 0.2251 r_free= 0.2365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.051494 | | target function (ls_wunit_k1) not normalized (work): 3021.682446 | | target function (ls_wunit_k1) not normalized (free): 176.488073 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2257 0.2251 0.2365 n_refl.: 61781 re-set all scales: r(all,work,free)=0.2449 0.2442 0.2591 n_refl.: 61781 remove outliers: r(all,work,free)=0.2449 0.2442 0.2591 n_refl.: 61781 overall B=0.00 to atoms: r(all,work,free)=0.2449 0.2442 0.2591 n_refl.: 61781 bulk-solvent and scaling: r(all,work,free)=0.2247 0.2241 0.2359 n_refl.: 61781 remove outliers: r(all,work,free)=0.2247 0.2241 0.2359 n_refl.: 61781 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 14.960-7.253 99.02 95 6 0.2358 260.484 248.388 0.929 0.998 0.400 7.246-5.773 99.01 98 2 0.2094 263.466 250.690 0.949 0.999 0.324 5.768-4.607 98.95 180 9 0.1784 278.149 267.760 0.940 0.999 0.292 4.593-3.659 92.73 341 16 0.1440 311.805 304.826 0.939 1.003 0.280 3.656-2.912 98.75 675 36 0.1766 248.143 241.886 0.955 0.999 0.180 2.911-2.318 100.00 1343 59 0.2021 183.341 178.711 0.927 0.999 0.000 2.318-1.845 100.00 2587 143 0.1710 161.888 158.692 0.980 0.999 0.000 1.845-1.469 99.85 5060 262 0.2170 104.432 100.769 1.012 0.999 0.000 1.469-1.169 99.19 9852 508 0.2278 71.754 68.496 0.962 1.001 0.000 1.169-0.931 96.65 18810 1002 0.2335 49.856 47.780 1.057 1.001 0.000 0.931-0.801 88.70 19639 1058 0.2975 27.107 25.475 0.967 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0335 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2241 r_free=0.2359 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN Total number of N/Q/H flips: 1 r_work=0.2242 r_free=0.2362 ========================= Local real-space refinement ========================= Before: r_work=0.2242 r_free=0.2362 rotamer outliers: 0.00 % outliers start: 0 chain: A residue: ASN 5 start: score: 21.959 CA: 4.50 CB: 4.46 CG: 3.72 OD1: 5.41 ND2: 3.87 p0 fitting: score: 22.156 CA: 4.50 CB: 4.46 CG: 3.76 OD1: 5.51 ND2: 3.92 p0 tuneup: score: 22.143 CA: 4.50 CB: 4.46 CG: 3.78 OD1: 5.52 ND2: 3.88 p0 revert: score: 22.156 CA: 4.50 CB: 4.46 CG: 3.76 OD1: 5.51 ND2: 3.92 p0 chain: A residue: THR 8 start: score: 14.177 CA: 3.16 CB: 2.40 CG2: 1.64 OG1: 2.67 p fitting: score: 14.621 CA: 3.16 CB: 2.40 CG2: 1.63 OG1: 2.90 p tuneup: score: 14.583 CA: 3.16 CB: 2.40 CG2: 1.61 OG1: 2.90 p revert: score: 14.621 CA: 3.16 CB: 2.40 CG2: 1.63 OG1: 2.90 p chain: A residue: ASP 10 start: score: 5.355 CA: 2.20 CB: 0.74 CG: 0.68 OD1: 1.07 OD2: 0.66 p0 fitting: score: 5.476 CA: 2.20 CB: 0.74 CG: 0.67 OD1: 1.22 OD2: 0.64 p0 tuneup: score: 5.444 CA: 2.20 CB: 0.74 CG: 0.68 OD1: 1.15 OD2: 0.66 p0 revert: score: 5.476 CA: 2.20 CB: 0.74 CG: 0.67 OD1: 1.22 OD2: 0.64 p0 chain: A residue: ILE 15 start: score: 22.204 CA: 5.14 CB: 4.41 CG1: 3.72 CG2: 4.75 CD1: 2.10 mt fitting: score: 22.204 CA: 5.14 CB: 4.41 CG1: 3.72 CG2: 4.75 CD1: 2.10 mt tuneup: score: 22.153 CA: 5.14 CB: 4.41 CG1: 3.81 CG2: 4.83 CD1: 1.98 mt revert: score: 22.204 CA: 5.14 CB: 4.41 CG1: 3.72 CG2: 4.75 CD1: 2.10 mt chain: A residue: LEU 17 start: score: 40.588 CA: 6.85 CB: 7.12 CG: 7.14 CD1: 5.30 CD2: 4.44 mt fitting: score: 40.678 CA: 6.85 CB: 7.12 CG: 7.20 CD1: 5.20 CD2: 4.56 mt tuneup: score: 40.078 CA: 6.85 CB: 7.12 CG: 7.20 CD1: 5.40 CD2: 4.06 mt revert: score: 40.678 CA: 6.85 CB: 7.12 CG: 7.20 CD1: 5.20 CD2: 4.56 mt chain: A residue: LYS 18 start: score: 33.923 CA: 6.80 CB: 5.90 CG: 5.77 CD: 4.10 CE: 3.26 NZ: 4.05 mmtt fitting: score: 33.923 CA: 6.80 CB: 5.90 CG: 5.77 CD: 4.10 CE: 3.26 NZ: 4.05 mmtt tuneup: score: 33.803 CA: 6.80 CB: 5.90 CG: 5.79 CD: 4.03 CE: 3.16 NZ: 4.06 mmtt revert: score: 33.923 CA: 6.80 CB: 5.90 CG: 5.77 CD: 4.10 CE: 3.26 NZ: 4.05 mmtt chain: A residue: TYR 19 start: score: 77.341 CA: 7.32 CB: 6.97 CG: 7.04 CZ: 6.35 OH: 9.38 CD1: 6.73 CD2: 5.79 CE1: 6.26 CE2: 5.76 t80 fitting: score: 77.341 CA: 7.32 CB: 6.97 CG: 7.04 CZ: 6.35 OH: 9.38 CD1: 6.73 CD2: 5.79 CE1: 6.26 CE2: 5.76 t80 tuneup: score: 77.345 CA: 7.32 CB: 6.97 CG: 7.13 CZ: 6.29 OH: 9.33 CD1: 7.03 CD2: 5.79 CE1: 6.46 CE2: 5.43 t80 chain: A residue: GLN 21 start: score: 18.913 CA: 6.42 CB: 3.50 CG: 3.17 CD: 2.11 OE1: 2.01 NE2: 1.70 pt0 fitting: score: 19.118 CA: 6.42 CB: 3.50 CG: 3.16 CD: 2.10 OE1: 1.88 NE2: 2.05 pt0 tuneup: score: 18.671 CA: 6.42 CB: 3.50 CG: 3.17 CD: 2.12 OE1: 1.67 NE2: 1.79 pt0 revert: score: 19.118 CA: 6.42 CB: 3.50 CG: 3.16 CD: 2.10 OE1: 1.88 NE2: 2.05 pt0 chain: A residue: THR 24 start: score: 33.689 CA: 5.97 CB: 4.65 CG2: 4.42 OG1: 7.12 p fitting: score: 34.184 CA: 5.97 CB: 4.65 CG2: 4.31 OG1: 7.47 p tuneup: score: 34.090 CA: 5.97 CB: 4.65 CG2: 4.20 OG1: 7.54 p revert: score: 34.184 CA: 5.97 CB: 4.65 CG2: 4.31 OG1: 7.47 p chain: A residue: LYS 25 start: score: 28.579 CA: 6.74 CB: 4.83 CG: 3.88 CD: 2.53 CE: 3.32 NZ: 3.64 mmtm fitting: score: 28.423 CA: 6.74 CB: 4.83 CG: 3.92 CD: 2.57 CE: 3.48 NZ: 3.44 mmtm tuneup: score: 27.980 CA: 6.74 CB: 4.83 CG: 3.97 CD: 2.39 CE: 3.13 NZ: 3.46 mmtm revert: score: 28.579 CA: 6.74 CB: 4.83 CG: 3.88 CD: 2.53 CE: 3.32 NZ: 3.64 mmtm chain: A residue: ARG 28 start: score: 58.395 CA: 7.02 CB: 7.49 CG: 6.66 CD: 7.12 NE: 8.15 CZ: 7.20 NH1: 7.38 NH2: 7.37 ptt180 fitting: score: 58.395 CA: 7.02 CB: 7.49 CG: 6.66 CD: 7.12 NE: 8.15 CZ: 7.20 NH1: 7.38 NH2: 7.37 ptt180 tuneup: score: 58.342 CA: 7.02 CB: 7.49 CG: 6.75 CD: 7.03 NE: 8.40 CZ: 7.17 NH1: 7.28 NH2: 7.20 ptt180 revert: score: 58.395 CA: 7.02 CB: 7.49 CG: 6.66 CD: 7.12 NE: 8.15 CZ: 7.20 NH1: 7.38 NH2: 7.37 ptt180 chain: A residue: VAL 29 start: score: 33.607 CA: 6.49 CB: 6.21 CG1: 5.20 CG2: 5.26 t fitting: score: 33.607 CA: 6.49 CB: 6.21 CG1: 5.20 CG2: 5.26 t tuneup: score: 33.348 CA: 6.49 CB: 6.21 CG1: 5.36 CG2: 4.96 t revert: score: 33.607 CA: 6.49 CB: 6.21 CG1: 5.20 CG2: 5.26 t chain: A residue: ARG 33 start: score: 43.392 CA: 5.95 CB: 5.71 CG: 5.55 CD: 5.38 NE: 6.06 CZ: 4.90 NH1: 5.58 NH2: 4.25 mmm160 fitting: score: 43.392 CA: 5.95 CB: 5.71 CG: 5.55 CD: 5.38 NE: 6.06 CZ: 4.90 NH1: 5.58 NH2: 4.25 mmm160 tuneup: score: 40.771 CA: 5.95 CB: 5.71 CG: 5.73 CD: 4.76 NE: 5.93 CZ: 4.27 NH1: 4.73 NH2: 3.69 mmm160 revert: score: 43.392 CA: 5.95 CB: 5.71 CG: 5.55 CD: 5.38 NE: 6.06 CZ: 4.90 NH1: 5.58 NH2: 4.25 mmm160 chain: A residue: LEU 36 start: score: 31.931 CA: 5.30 CB: 4.42 CG: 4.71 CD1: 4.77 CD2: 3.98 mt fitting: score: 32.252 CA: 5.30 CB: 4.42 CG: 4.71 CD1: 4.79 CD2: 4.13 mt tuneup: score: 32.082 CA: 5.30 CB: 4.42 CG: 4.75 CD1: 4.78 CD2: 4.03 mt revert: score: 32.252 CA: 5.30 CB: 4.42 CG: 4.71 CD1: 4.79 CD2: 4.13 mt chain: A residue: HIS 42 start: score: 39.203 CA: 7.60 CB: 6.56 CG: 7.00 ND1: 5.09 CD2: 4.75 CE1: 2.94 NE2: 5.26 p-80 fitting: score: 39.391 CA: 7.60 CB: 6.56 CG: 6.85 ND1: 4.99 CD2: 4.94 CE1: 2.92 NE2: 5.52 p-80 tuneup: score: 39.382 CA: 7.60 CB: 6.56 CG: 7.00 ND1: 5.09 CD2: 4.93 CE1: 2.94 NE2: 5.25 p-80 revert: score: 39.391 CA: 7.60 CB: 6.56 CG: 6.85 ND1: 4.99 CD2: 4.94 CE1: 2.92 NE2: 5.52 p-80 chain: A residue: CYS 43 start: score: 47.010 CA: 7.43 CB: 7.28 SG: 32.31 m fitting: score: 23.473 CA: 7.43 CB: 7.28 SG: 8.77 m tuneup: score: 47.141 CA: 7.43 CB: 7.28 SG: 32.44 m chain: A residue: ASN 45 start: score: 39.057 CA: 7.56 CB: 6.70 CG: 7.00 OD1: 11.47 ND2: 6.33 p0 fitting: score: 39.057 CA: 7.56 CB: 6.70 CG: 7.00 OD1: 11.47 ND2: 6.33 p0 tuneup: score: 38.479 CA: 7.56 CB: 6.70 CG: 7.03 OD1: 11.14 ND2: 6.05 p0 revert: score: 39.057 CA: 7.56 CB: 6.70 CG: 7.00 OD1: 11.47 ND2: 6.33 p0 chain: A residue: CYS 46 start: score: 44.982 CA: 7.81 CB: 6.38 SG: 30.79 t fitting: score: 44.982 CA: 7.81 CB: 6.38 SG: 30.79 t tuneup: score: 45.117 CA: 7.81 CB: 6.38 SG: 30.93 t chain: A residue: GLN 47 start: score: 35.615 CA: 6.96 CB: 6.39 CG: 4.78 CD: 5.06 OE1: 7.41 NE2: 5.02 tp40 fitting: score: 35.710 CA: 6.96 CB: 6.39 CG: 4.78 CD: 4.95 OE1: 7.57 NE2: 5.06 tp40 tuneup: score: 32.734 CA: 6.96 CB: 6.39 CG: 4.80 CD: 4.34 OE1: 6.69 NE2: 3.56 tp40 revert: score: 35.710 CA: 6.96 CB: 6.39 CG: 4.78 CD: 4.95 OE1: 7.57 NE2: 5.06 tp40 chain: A residue: PHE 48 start: score: 49.052 CA: 6.53 CB: 6.66 CG: 7.33 CD1: 6.61 CD2: 6.20 CE1: 5.53 CE2: 5.15 CZ: 5.05 m-80 fitting: score: 49.304 CA: 6.53 CB: 6.66 CG: 7.30 CD1: 6.28 CD2: 6.76 CE1: 4.97 CE2: 5.67 CZ: 5.14 m-80 tuneup: score: 44.708 CA: 6.53 CB: 6.66 CG: 7.46 CD1: 5.82 CD2: 5.89 CE1: 4.28 CE2: 4.25 CZ: 3.81 m-80 revert: score: 49.304 CA: 6.53 CB: 6.66 CG: 7.30 CD1: 6.28 CD2: 6.76 CE1: 4.97 CE2: 5.67 CZ: 5.14 m-80 chain: A residue: MET 49 start: score: 29.933 CA: 6.45 CB: 6.41 CG: 4.65 SD: 9.19 CE: 1.62 ttp fitting: score: 29.853 CA: 6.45 CB: 6.41 CG: 4.62 SD: 9.36 CE: 1.50 ttp tuneup: score: 30.014 CA: 6.45 CB: 6.41 CG: 4.68 SD: 9.42 CE: 1.53 ttp chain: A residue: GLN 50 start: score: 24.839 CA: 5.02 CB: 4.74 CG: 4.22 CD: 4.00 OE1: 4.55 NE2: 2.32 mt0 fitting: score: 24.839 CA: 5.02 CB: 4.74 CG: 4.22 CD: 4.00 OE1: 4.55 NE2: 2.32 mt0 tuneup: score: 24.875 CA: 5.02 CB: 4.74 CG: 4.22 CD: 4.00 OE1: 4.62 NE2: 2.28 mt0 chain: A residue: ASN 52 start: score: 18.219 CA: 5.24 CB: 4.30 CG: 2.95 OD1: 2.95 ND2: 2.78 m-40 fitting: score: 18.774 CA: 5.24 CB: 4.30 CG: 2.99 OD1: 3.20 ND2: 3.05 m110 tuneup: score: 18.375 CA: 5.24 CB: 4.30 CG: 3.06 OD1: 3.04 ND2: 2.73 m110 revert: score: 18.774 CA: 5.24 CB: 4.30 CG: 2.99 OD1: 3.20 ND2: 3.05 m110 chain: A residue: VAL 53 start: score: 31.118 CA: 6.14 CB: 6.00 CG1: 5.06 CG2: 4.43 t fitting: score: 31.118 CA: 6.14 CB: 6.00 CG1: 5.06 CG2: 4.43 t tuneup: score: 30.891 CA: 6.14 CB: 6.00 CG1: 5.09 CG2: 4.29 t revert: score: 31.118 CA: 6.14 CB: 6.00 CG1: 5.06 CG2: 4.43 t chain: A residue: TRP 58 start: score: 56.980 CA: 6.54 CB: 5.97 CG: 5.76 CD1: 5.03 CD2: 5.62 NE1: 6.06 CE2: 4.68 CE3: 5.00 CZ2: 4.07 CZ3: 4.27 CH2: 3.99 m100 fitting: score: 56.980 CA: 6.54 CB: 5.97 CG: 5.76 CD1: 5.03 CD2: 5.62 NE1: 6.06 CE2: 4.68 CE3: 5.00 CZ2: 4.07 CZ3: 4.27 CH2: 3.99 m100 tuneup: score: 54.119 CA: 6.54 CB: 5.97 CG: 5.76 CD1: 4.87 CD2: 4.99 NE1: 5.92 CE2: 4.58 CE3: 4.78 CZ2: 3.33 CZ3: 4.05 CH2: 3.34 m100 revert: score: 56.980 CA: 6.54 CB: 5.97 CG: 5.76 CD1: 5.03 CD2: 5.62 NE1: 6.06 CE2: 4.68 CE3: 5.00 CZ2: 4.07 CZ3: 4.27 CH2: 3.99 m100 chain: A residue: CYS 61 start: score: 40.600 CA: 7.68 CB: 6.42 SG: 26.49 t fitting: score: 40.600 CA: 7.68 CB: 6.42 SG: 26.49 t tuneup: score: 41.006 CA: 7.68 CB: 6.42 SG: 26.90 t chain: A residue: GLN 62 start: score: 27.406 CA: 6.83 CB: 5.52 CG: 4.27 CD: 3.47 OE1: 3.43 NE2: 3.89 mt0 fitting: score: 27.712 CA: 6.83 CB: 5.52 CG: 4.33 CD: 3.46 OE1: 3.56 NE2: 4.02 mt0 tuneup: score: 27.741 CA: 6.83 CB: 5.52 CG: 4.33 CD: 3.46 OE1: 3.53 NE2: 4.06 mt0 chain: A residue: LEU 63 start: score: 42.488 CA: 6.87 CB: 6.92 CG: 6.48 CD1: 5.49 CD2: 5.62 mt fitting: score: 42.558 CA: 6.87 CB: 6.92 CG: 6.46 CD1: 5.45 CD2: 5.70 mt tuneup: score: 42.532 CA: 6.87 CB: 6.92 CG: 6.48 CD1: 5.54 CD2: 5.59 mt revert: score: 42.558 CA: 6.87 CB: 6.92 CG: 6.46 CD1: 5.45 CD2: 5.70 mt chain: A residue: PHE 64 start: score: 49.699 CA: 6.47 CB: 6.36 CG: 6.85 CD1: 7.16 CD2: 6.07 CE1: 5.78 CE2: 5.68 CZ: 5.33 m-80 fitting: score: 49.912 CA: 6.47 CB: 6.36 CG: 6.90 CD1: 7.14 CD2: 6.00 CE1: 5.80 CE2: 5.88 CZ: 5.37 m-80 tuneup: score: 48.320 CA: 6.47 CB: 6.36 CG: 6.99 CD1: 6.79 CD2: 5.82 CE1: 5.43 CE2: 5.43 CZ: 5.02 m-80 revert: score: 49.912 CA: 6.47 CB: 6.36 CG: 6.90 CD1: 7.14 CD2: 6.00 CE1: 5.80 CE2: 5.88 CZ: 5.37 m-80 chain: A residue: LYS 67 start: score: 28.595 CA: 5.45 CB: 5.54 CG: 4.12 CD: 2.98 CE: 2.77 NZ: 3.87 mttm fitting: score: 28.595 CA: 5.45 CB: 5.54 CG: 4.12 CD: 2.98 CE: 2.77 NZ: 3.87 mttm tuneup: score: 28.935 CA: 5.45 CB: 5.54 CG: 4.12 CD: 3.06 CE: 2.91 NZ: 3.93 mttm chain: A residue: LEU 68 start: score: 39.662 CA: 5.81 CB: 6.62 CG: 6.27 CD1: 5.35 CD2: 5.13 mt fitting: score: 39.768 CA: 5.81 CB: 6.62 CG: 6.24 CD1: 5.34 CD2: 5.21 mt tuneup: score: 39.732 CA: 5.81 CB: 6.62 CG: 6.28 CD1: 5.35 CD2: 5.17 mt revert: score: 39.768 CA: 5.81 CB: 6.62 CG: 6.24 CD1: 5.34 CD2: 5.21 mt chain: A residue: ILE 69 start: score: 37.192 CA: 6.80 CB: 6.57 CG1: 6.82 CG2: 5.28 CD1: 5.86 pp fitting: score: 37.549 CA: 6.80 CB: 6.57 CG1: 6.91 CG2: 5.40 CD1: 5.93 pp tuneup: score: 37.549 CA: 6.80 CB: 6.57 CG1: 6.91 CG2: 5.40 CD1: 5.93 pp revert: score: 37.549 CA: 6.80 CB: 6.57 CG1: 6.91 CG2: 5.40 CD1: 5.93 pp chain: A residue: ASN 70 start: score: 30.477 CA: 6.37 CB: 5.61 CG: 6.13 OD1: 7.69 ND2: 4.68 t0 fitting: score: 30.491 CA: 6.37 CB: 5.61 CG: 6.13 OD1: 7.69 ND2: 4.69 t0 tuneup: score: 30.491 CA: 6.37 CB: 5.61 CG: 6.13 OD1: 7.69 ND2: 4.69 t0 revert: score: 30.491 CA: 6.37 CB: 5.61 CG: 6.13 OD1: 7.69 ND2: 4.69 t0 chain: A residue: VAL 71 start: score: 30.659 CA: 6.09 CB: 5.94 CG1: 4.35 CG2: 4.97 m fitting: score: 30.667 CA: 6.09 CB: 5.94 CG1: 4.36 CG2: 4.96 m tuneup: score: 30.667 CA: 6.09 CB: 5.94 CG1: 4.36 CG2: 4.96 m revert: score: 30.667 CA: 6.09 CB: 5.94 CG1: 4.36 CG2: 4.96 m chain: A residue: TRP 74 start: score: 83.247 CA: 8.06 CB: 6.81 CG: 8.29 CD1: 7.93 CD2: 7.33 NE1: 9.13 CE2: 7.56 CE3: 8.10 CZ2: 6.36 CZ3: 6.88 CH2: 6.81 t60 fitting: score: 83.478 CA: 8.06 CB: 6.81 CG: 8.34 CD1: 8.02 CD2: 7.30 NE1: 9.14 CE2: 7.67 CE3: 8.16 CZ2: 6.40 CZ3: 7.00 CH2: 6.58 t60 tuneup: score: 83.478 CA: 8.06 CB: 6.81 CG: 8.34 CD1: 8.02 CD2: 7.30 NE1: 9.14 CE2: 7.67 CE3: 8.16 CZ2: 6.40 CZ3: 7.00 CH2: 6.58 t60 revert: score: 83.478 CA: 8.06 CB: 6.81 CG: 8.34 CD1: 8.02 CD2: 7.30 NE1: 9.14 CE2: 7.67 CE3: 8.16 CZ2: 6.40 CZ3: 7.00 CH2: 6.58 t60 chain: A residue: SER 77 start: score: 25.513 CA: 6.64 CB: 6.07 OG: 6.40 m fitting: score: 25.553 CA: 6.64 CB: 6.07 OG: 6.42 m tuneup: score: 25.553 CA: 6.64 CB: 6.07 OG: 6.42 m revert: score: 25.553 CA: 6.64 CB: 6.07 OG: 6.42 m chain: A residue: TRP 78 start: score: 81.508 CA: 7.53 CB: 7.89 CG: 8.05 CD1: 7.40 CD2: 6.69 NE1: 9.08 CE2: 8.03 CE3: 6.70 CZ2: 6.46 CZ3: 7.14 CH2: 6.56 t60 fitting: score: 81.508 CA: 7.53 CB: 7.89 CG: 8.05 CD1: 7.40 CD2: 6.69 NE1: 9.08 CE2: 8.03 CE3: 6.70 CZ2: 6.46 CZ3: 7.14 CH2: 6.56 t60 tuneup: score: 74.665 CA: 7.53 CB: 7.89 CG: 8.07 CD1: 7.00 CD2: 6.13 NE1: 8.05 CE2: 7.35 CE3: 6.36 CZ2: 5.50 CZ3: 5.82 CH2: 4.98 t60 revert: score: 81.508 CA: 7.53 CB: 7.89 CG: 8.05 CD1: 7.40 CD2: 6.69 NE1: 9.08 CE2: 8.03 CE3: 6.70 CZ2: 6.46 CZ3: 7.14 CH2: 6.56 t60 chain: A residue: THR 79 start: score: 30.896 CA: 6.18 CB: 5.70 CG2: 3.31 OG1: 6.20 m fitting: score: 30.906 CA: 6.18 CB: 5.70 CG2: 3.32 OG1: 6.19 m tuneup: score: 30.906 CA: 6.18 CB: 5.70 CG2: 3.32 OG1: 6.19 m revert: score: 30.906 CA: 6.18 CB: 5.70 CG2: 3.32 OG1: 6.19 m chain: A residue: LEU 80 start: score: 29.979 CA: 6.11 CB: 4.52 CG: 5.13 CD1: 3.94 CD2: 3.16 tp fitting: score: 30.123 CA: 6.11 CB: 4.52 CG: 5.12 CD1: 4.02 CD2: 3.16 tp tuneup: score: 30.123 CA: 6.11 CB: 4.52 CG: 5.12 CD1: 4.02 CD2: 3.16 tp revert: score: 30.123 CA: 6.11 CB: 4.52 CG: 5.12 CD1: 4.02 CD2: 3.16 tp chain: A residue: LYS 81 start: score: 34.326 CA: 6.41 CB: 6.51 CG: 5.20 CD: 4.66 CE: 4.13 NZ: 3.71 tttp fitting: score: 34.326 CA: 6.41 CB: 6.51 CG: 5.20 CD: 4.66 CE: 4.13 NZ: 3.71 tttp tuneup: score: 34.231 CA: 6.41 CB: 6.51 CG: 5.20 CD: 4.66 CE: 4.15 NZ: 3.65 tttp revert: score: 34.326 CA: 6.41 CB: 6.51 CG: 5.20 CD: 4.66 CE: 4.13 NZ: 3.71 tttp outliers after map fit: 0 tune up outliers final: 0 Did it for: 40 After: r_work=0.2259 r_free=0.2365 rotamer outliers: 0.00 % ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.646693 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.079633 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ============================= Fit rotatable H or D ============================ ====================== XYZ individual (reciprocal space) ====================== R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT TARGETS work free delta bonds angl data restr 22.59 23.65 1.06 0.007 0.9 2.5 0.0 0.0 0 none 4.087 0.0263 22.32 23.22 0.90 0.005 0.9 2.5 0.0 0.0 0 1.823 4.068 0.0234 Legend: - first line corresponds to starting state (before refinement) - R-factors reported in percent - delta is Rfree-Rwork in percent - CLASH is all-atom Molprobity clashscore - ROTA is percent of side-chain rotamer outliers - RAMA is percent of Ramachandran plot outliers - CBET is number of Cbeta deviations - WEIGHT is relative weight between X-ray (or neutron) target and restraints - TARGETS: the values of X-ray (or neutron) and restraints target functions ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.32 23.22 0.90 24.935 16.860 0.080 4.068 22.32 23.28 0.95 23.259 16.911 0.080 4.068 min max mean iso aniso Overall: 2.05 63.14 8.53 2.04 728 0 Protein: 2.05 46.85 6.52 1.97 616 0 Water: 4.47 63.14 21.29 N/A 93 0 Other: 2.57 19.85 10.96 N/A 19 0 Chain A: 2.05 46.85 6.50 N/A 620 0 Chain : 4.47 63.14 20.16 N/A 108 0 Histogram: Values Number of atoms 2.05 - 8.16 508 8.16 - 14.27 127 14.27 - 20.38 47 20.38 - 26.49 16 26.49 - 32.60 14 32.60 - 38.71 6 38.71 - 44.82 3 44.82 - 50.93 3 50.93 - 57.04 3 57.04 - 63.14 1 =========================== ADP refinement (H only) =========================== |- start----------------------------------------------------------------------| | target_work(ml) = 4.06771 r_work = 0.2232 r_free = 0.2328 | |-----------------------------------------------------------------------------| |- final----------------------------------------------------------------------| | target_work(ml) = 4.0664 r_work = 0.2227 r_free = 0.2333 | |-----------------------------------------------------------------------------| ======================== Occupancy refinement (H only) ======================== |- start----------------------------------------------------------------------| | target_work(ml) = 4.0664 r_work = 0.2227 r_free = 0.2333 | |-----------------------------------------------------------------------------| |- final----------------------------------------------------------------------| | target_work(ml) = 4.06444 r_work = 0.2216 r_free = 0.2331 | |-----------------------------------------------------------------------------| ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2216 r_free = 0.2331 target_work(ml) = 4.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2224 r_free = 0.2337 target_work(ml) = 4.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 0.80 - 14.96 A, n_refl.=61781 (all), 5.02 % free)------------| | | | r_work= 0.2224 r_free= 0.2337 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.065469 | | target function (ml) not normalized (work): 238561.720564 | | target function (ml) not normalized (free): 12728.957859 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2229 0.2224 0.2337 n_refl.: 61781 re-set all scales: r(all,work,free)=0.2436 0.2430 0.2558 n_refl.: 61781 remove outliers: r(all,work,free)=0.2436 0.2430 0.2558 n_refl.: 61781 overall B=-0.00 to atoms: r(all,work,free)=0.2436 0.2430 0.2558 n_refl.: 61781 bulk-solvent and scaling: r(all,work,free)=0.2228 0.2222 0.2334 n_refl.: 61781 remove outliers: r(all,work,free)=0.2228 0.2222 0.2334 n_refl.: 61781 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 14.960-7.253 99.02 95 6 0.2491 260.484 245.961 0.952 0.997 0.414 7.246-5.773 99.01 98 2 0.2174 263.466 247.514 0.942 0.998 0.302 5.768-4.607 98.95 180 9 0.1867 278.149 265.422 0.944 0.999 0.277 4.593-3.659 92.73 341 16 0.1498 311.805 303.365 0.944 1.003 0.273 3.656-2.912 98.75 675 36 0.1853 248.143 241.030 0.964 0.999 0.180 2.911-2.318 100.00 1343 59 0.2060 183.341 178.230 0.937 0.999 0.000 2.318-1.845 100.00 2587 143 0.1734 161.888 158.192 0.993 0.999 0.000 1.845-1.469 99.85 5060 262 0.2175 104.432 100.648 1.028 0.999 0.000 1.469-1.169 99.19 9852 508 0.2231 71.754 68.485 0.978 1.001 0.000 1.169-0.931 96.65 18810 1002 0.2276 49.856 47.827 1.078 1.001 0.000 0.931-0.801 88.70 19639 1058 0.2908 27.107 25.512 1.010 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=-0.0810 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2222 r_free=0.2334 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN Total number of N/Q/H flips: 1 r_work=0.2222 r_free=0.2335 ========================= Local real-space refinement ========================= Before: r_work=0.2222 r_free=0.2335 rotamer outliers: 0.00 % outliers start: 0 chain: A residue: ASN 5 start: score: 21.776 CA: 4.36 CB: 4.54 CG: 3.77 OD1: 5.55 ND2: 3.56 p0 fitting: score: 21.832 CA: 4.36 CB: 4.54 CG: 3.79 OD1: 5.59 ND2: 3.55 p0 tuneup: score: 21.832 CA: 4.36 CB: 4.54 CG: 3.79 OD1: 5.59 ND2: 3.55 p0 revert: score: 21.832 CA: 4.36 CB: 4.54 CG: 3.79 OD1: 5.59 ND2: 3.55 p0 chain: A residue: THR 8 start: score: 14.330 CA: 3.10 CB: 2.38 CG2: 1.75 OG1: 2.67 p fitting: score: 14.437 CA: 3.10 CB: 2.38 CG2: 1.73 OG1: 2.75 p tuneup: score: 14.349 CA: 3.10 CB: 2.38 CG2: 1.69 OG1: 2.75 p revert: score: 14.437 CA: 3.10 CB: 2.38 CG2: 1.73 OG1: 2.75 p chain: A residue: ASP 10 start: score: 5.115 CA: 2.16 CB: 0.66 CG: 0.64 OD1: 1.06 OD2: 0.59 p0 fitting: score: 5.118 CA: 2.16 CB: 0.66 CG: 0.64 OD1: 1.07 OD2: 0.59 p0 tuneup: score: 5.117 CA: 2.16 CB: 0.66 CG: 0.64 OD1: 1.06 OD2: 0.60 p0 revert: score: 5.118 CA: 2.16 CB: 0.66 CG: 0.64 OD1: 1.07 OD2: 0.59 p0 chain: A residue: ILE 15 start: score: 22.814 CA: 5.45 CB: 4.80 CG1: 3.75 CG2: 4.90 CD1: 1.96 mt fitting: score: 22.814 CA: 5.45 CB: 4.80 CG1: 3.75 CG2: 4.90 CD1: 1.96 mt tuneup: score: 22.539 CA: 5.45 CB: 4.80 CG1: 3.81 CG2: 4.79 CD1: 1.85 mt revert: score: 22.814 CA: 5.45 CB: 4.80 CG1: 3.75 CG2: 4.90 CD1: 1.96 mt chain: A residue: LEU 17 start: score: 40.259 CA: 6.89 CB: 7.27 CG: 7.36 CD1: 5.18 CD2: 4.19 mt fitting: score: 40.348 CA: 6.89 CB: 7.27 CG: 7.51 CD1: 5.11 CD2: 4.23 mt tuneup: score: 39.651 CA: 6.89 CB: 7.27 CG: 7.51 CD1: 5.26 CD2: 3.73 mt revert: score: 40.348 CA: 6.89 CB: 7.27 CG: 7.51 CD1: 5.11 CD2: 4.23 mt chain: A residue: LYS 18 start: score: 35.638 CA: 6.97 CB: 6.02 CG: 6.02 CD: 4.42 CE: 3.55 NZ: 4.33 mmtt fitting: score: 35.638 CA: 6.97 CB: 6.02 CG: 6.02 CD: 4.42 CE: 3.55 NZ: 4.33 mmtt tuneup: score: 34.919 CA: 6.97 CB: 6.02 CG: 6.10 CD: 4.20 CE: 3.35 NZ: 4.14 mmtt revert: score: 35.638 CA: 6.97 CB: 6.02 CG: 6.02 CD: 4.42 CE: 3.55 NZ: 4.33 mmtt chain: A residue: TYR 19 start: score: 77.691 CA: 7.38 CB: 6.97 CG: 6.71 CZ: 6.39 OH: 9.50 CD1: 6.94 CD2: 5.88 CE1: 6.31 CE2: 5.72 t80 fitting: score: 77.691 CA: 7.38 CB: 6.97 CG: 6.71 CZ: 6.39 OH: 9.50 CD1: 6.94 CD2: 5.88 CE1: 6.31 CE2: 5.72 t80 tuneup: score: 74.357 CA: 7.38 CB: 6.97 CG: 6.86 CZ: 5.94 OH: 8.36 CD1: 6.99 CD2: 5.81 CE1: 6.32 CE2: 5.42 t80 revert: score: 77.691 CA: 7.38 CB: 6.97 CG: 6.71 CZ: 6.39 OH: 9.50 CD1: 6.94 CD2: 5.88 CE1: 6.31 CE2: 5.72 t80 chain: A residue: THR 24 start: score: 34.112 CA: 5.95 CB: 4.64 CG2: 4.22 OG1: 7.54 p fitting: score: 34.174 CA: 5.95 CB: 4.64 CG2: 4.25 OG1: 7.54 p tuneup: score: 34.174 CA: 5.95 CB: 4.64 CG2: 4.25 OG1: 7.54 p revert: score: 34.174 CA: 5.95 CB: 4.64 CG2: 4.25 OG1: 7.54 p chain: A residue: LYS 25 start: score: 28.036 CA: 6.94 CB: 4.88 CG: 3.75 CD: 2.36 CE: 3.41 NZ: 3.35 mmtm fitting: score: 28.036 CA: 6.94 CB: 4.88 CG: 3.75 CD: 2.36 CE: 3.41 NZ: 3.35 mmtm tuneup: score: 26.920 CA: 6.94 CB: 4.88 CG: 3.89 CD: 2.22 CE: 2.79 NZ: 3.10 mmtm revert: score: 28.036 CA: 6.94 CB: 4.88 CG: 3.75 CD: 2.36 CE: 3.41 NZ: 3.35 mmtm chain: A residue: ARG 28 start: score: 58.523 CA: 6.95 CB: 7.62 CG: 6.79 CD: 6.94 NE: 8.26 CZ: 6.99 NH1: 7.65 NH2: 7.33 ptt180 fitting: score: 58.523 CA: 6.95 CB: 7.62 CG: 6.79 CD: 6.94 NE: 8.26 CZ: 6.99 NH1: 7.65 NH2: 7.33 ptt180 tuneup: score: 58.400 CA: 6.95 CB: 7.62 CG: 6.84 CD: 7.06 NE: 8.29 CZ: 7.00 NH1: 7.45 NH2: 7.19 ptt180 revert: score: 58.523 CA: 6.95 CB: 7.62 CG: 6.79 CD: 6.94 NE: 8.26 CZ: 6.99 NH1: 7.65 NH2: 7.33 ptt180 chain: A residue: VAL 29 start: score: 34.311 CA: 6.57 CB: 6.57 CG1: 5.54 CG2: 5.04 t fitting: score: 34.311 CA: 6.57 CB: 6.57 CG1: 5.54 CG2: 5.04 t tuneup: score: 34.237 CA: 6.57 CB: 6.57 CG1: 5.66 CG2: 4.88 t revert: score: 34.311 CA: 6.57 CB: 6.57 CG1: 5.54 CG2: 5.04 t chain: A residue: ARG 33 start: score: 43.014 CA: 5.98 CB: 5.55 CG: 5.38 CD: 5.40 NE: 6.16 CZ: 4.87 NH1: 5.48 NH2: 4.18 mmm160 fitting: score: 43.014 CA: 5.98 CB: 5.55 CG: 5.38 CD: 5.40 NE: 6.16 CZ: 4.87 NH1: 5.48 NH2: 4.18 mmm160 tuneup: score: 41.821 CA: 5.98 CB: 5.55 CG: 5.47 CD: 4.97 NE: 6.32 CZ: 4.59 NH1: 5.15 NH2: 3.79 mmm160 revert: score: 43.014 CA: 5.98 CB: 5.55 CG: 5.38 CD: 5.40 NE: 6.16 CZ: 4.87 NH1: 5.48 NH2: 4.18 mmm160 chain: A residue: LEU 36 start: score: 31.569 CA: 5.56 CB: 4.40 CG: 4.53 CD1: 4.68 CD2: 3.86 mt fitting: score: 31.581 CA: 5.56 CB: 4.40 CG: 4.53 CD1: 4.68 CD2: 3.87 mt tuneup: score: 31.428 CA: 5.56 CB: 4.40 CG: 4.56 CD1: 4.69 CD2: 3.76 mt revert: score: 31.581 CA: 5.56 CB: 4.40 CG: 4.53 CD1: 4.68 CD2: 3.87 mt chain: A residue: HIS 42 start: score: 37.529 CA: 7.53 CB: 6.36 CG: 6.29 ND1: 4.87 CD2: 4.81 CE1: 2.64 NE2: 5.03 p-80 fitting: score: 37.550 CA: 7.53 CB: 6.36 CG: 6.35 ND1: 4.93 CD2: 4.80 CE1: 2.66 NE2: 4.91 p-80 tuneup: score: 37.389 CA: 7.53 CB: 6.36 CG: 6.44 ND1: 4.88 CD2: 4.81 CE1: 2.72 NE2: 4.65 p-80 revert: score: 37.550 CA: 7.53 CB: 6.36 CG: 6.35 ND1: 4.93 CD2: 4.80 CE1: 2.66 NE2: 4.91 p-80 chain: A residue: CYS 43 start: score: 45.825 CA: 7.38 CB: 7.11 SG: 31.34 m fitting: score: 22.878 CA: 7.38 CB: 7.11 SG: 8.39 m tuneup: score: 45.803 CA: 7.38 CB: 7.11 SG: 31.32 m revert: score: 45.825 CA: 7.38 CB: 7.11 SG: 31.34 m chain: A residue: ASN 45 start: score: 38.948 CA: 7.45 CB: 6.95 CG: 7.00 OD1: 11.29 ND2: 6.26 p0 fitting: score: 38.948 CA: 7.45 CB: 6.95 CG: 7.00 OD1: 11.29 ND2: 6.26 p0 tuneup: score: 38.325 CA: 7.45 CB: 6.95 CG: 7.09 OD1: 11.00 ND2: 5.84 p0 revert: score: 38.948 CA: 7.45 CB: 6.95 CG: 7.00 OD1: 11.29 ND2: 6.26 p0 chain: A residue: CYS 46 start: score: 44.845 CA: 7.57 CB: 6.58 SG: 30.69 t fitting: score: 44.845 CA: 7.57 CB: 6.58 SG: 30.69 t tuneup: score: 44.845 CA: 7.57 CB: 6.58 SG: 30.69 t revert: score: 44.845 CA: 7.57 CB: 6.58 SG: 30.69 t chain: A residue: GLN 47 start: score: 35.845 CA: 6.96 CB: 6.36 CG: 4.92 CD: 5.34 OE1: 7.32 NE2: 4.94 tp40 fitting: score: 35.845 CA: 6.96 CB: 6.36 CG: 4.92 CD: 5.34 OE1: 7.32 NE2: 4.94 tp40 tuneup: score: 32.933 CA: 6.96 CB: 6.36 CG: 4.94 CD: 4.31 OE1: 6.20 NE2: 4.17 tp40 revert: score: 35.845 CA: 6.96 CB: 6.36 CG: 4.92 CD: 5.34 OE1: 7.32 NE2: 4.94 tp40 chain: A residue: MET 49 start: score: 29.988 CA: 6.30 CB: 6.79 CG: 4.41 SD: 9.52 CE: 1.49 ttp fitting: score: 29.817 CA: 6.30 CB: 6.79 CG: 4.35 SD: 9.68 CE: 1.35 ttp tuneup: score: 29.919 CA: 6.30 CB: 6.79 CG: 4.40 SD: 9.74 CE: 1.34 ttp revert: score: 29.988 CA: 6.30 CB: 6.79 CG: 4.41 SD: 9.52 CE: 1.49 ttp chain: A residue: GLN 50 start: score: 25.353 CA: 5.50 CB: 5.09 CG: 4.14 CD: 3.85 OE1: 4.49 NE2: 2.29 mt0 fitting: score: 25.353 CA: 5.50 CB: 5.09 CG: 4.14 CD: 3.85 OE1: 4.49 NE2: 2.29 mt0 tuneup: score: 25.369 CA: 5.50 CB: 5.09 CG: 4.14 CD: 3.85 OE1: 4.50 NE2: 2.29 mt0 chain: A residue: ASN 52 start: score: 18.566 CA: 5.53 CB: 4.08 CG: 3.06 OD1: 3.07 ND2: 2.83 m-40 fitting: score: 19.001 CA: 5.53 CB: 4.08 CG: 3.06 OD1: 3.21 ND2: 3.11 m110 tuneup: score: 18.631 CA: 5.53 CB: 4.08 CG: 3.14 OD1: 2.98 ND2: 2.91 m110 revert: score: 19.001 CA: 5.53 CB: 4.08 CG: 3.06 OD1: 3.21 ND2: 3.11 m110 chain: A residue: VAL 53 start: score: 31.406 CA: 6.39 CB: 6.33 CG1: 5.11 CG2: 4.24 t fitting: score: 31.406 CA: 6.39 CB: 6.33 CG1: 5.11 CG2: 4.24 t tuneup: score: 31.198 CA: 6.39 CB: 6.33 CG1: 5.15 CG2: 4.09 t revert: score: 31.406 CA: 6.39 CB: 6.33 CG1: 5.11 CG2: 4.24 t chain: A residue: TRP 58 start: score: 55.917 CA: 6.52 CB: 5.96 CG: 5.58 CD1: 5.05 CD2: 5.76 NE1: 6.04 CE2: 4.40 CE3: 5.01 CZ2: 3.96 CZ3: 3.93 CH2: 3.71 m100 fitting: score: 55.917 CA: 6.52 CB: 5.96 CG: 5.58 CD1: 5.05 CD2: 5.76 NE1: 6.04 CE2: 4.40 CE3: 5.01 CZ2: 3.96 CZ3: 3.93 CH2: 3.71 m100 tuneup: score: 53.076 CA: 6.52 CB: 5.96 CG: 5.60 CD1: 4.89 CD2: 5.11 NE1: 5.88 CE2: 4.28 CE3: 4.71 CZ2: 3.30 CZ3: 3.68 CH2: 3.14 m100 revert: score: 55.917 CA: 6.52 CB: 5.96 CG: 5.58 CD1: 5.05 CD2: 5.76 NE1: 6.04 CE2: 4.40 CE3: 5.01 CZ2: 3.96 CZ3: 3.93 CH2: 3.71 m100 chain: A residue: CYS 61 start: score: 40.990 CA: 7.73 CB: 6.51 SG: 26.75 t fitting: score: 40.990 CA: 7.73 CB: 6.51 SG: 26.75 t tuneup: score: 41.389 CA: 7.73 CB: 6.51 SG: 27.15 t chain: A residue: GLN 62 start: score: 28.789 CA: 7.26 CB: 6.08 CG: 4.57 CD: 3.50 OE1: 3.56 NE2: 3.81 mt0 fitting: score: 28.789 CA: 7.26 CB: 6.08 CG: 4.57 CD: 3.50 OE1: 3.56 NE2: 3.81 mt0 tuneup: score: 28.754 CA: 7.26 CB: 6.08 CG: 4.58 CD: 3.50 OE1: 3.50 NE2: 3.84 mt0 revert: score: 28.789 CA: 7.26 CB: 6.08 CG: 4.57 CD: 3.50 OE1: 3.56 NE2: 3.81 mt0 chain: A residue: LEU 63 start: score: 43.919 CA: 7.02 CB: 6.98 CG: 6.61 CD1: 5.43 CD2: 6.22 mt fitting: score: 43.962 CA: 7.02 CB: 6.98 CG: 6.62 CD1: 5.48 CD2: 6.19 mt tuneup: score: 43.706 CA: 7.02 CB: 6.98 CG: 6.64 CD1: 5.54 CD2: 5.99 mt revert: score: 43.962 CA: 7.02 CB: 6.98 CG: 6.62 CD1: 5.48 CD2: 6.19 mt chain: A residue: PHE 64 start: score: 50.022 CA: 6.67 CB: 6.42 CG: 6.75 CD1: 7.13 CD2: 6.24 CE1: 5.84 CE2: 5.71 CZ: 5.27 m-80 fitting: score: 50.064 CA: 6.67 CB: 6.42 CG: 6.79 CD1: 7.17 CD2: 6.18 CE1: 5.88 CE2: 5.64 CZ: 5.31 m-80 tuneup: score: 48.009 CA: 6.67 CB: 6.42 CG: 6.87 CD1: 6.67 CD2: 5.98 CE1: 5.44 CE2: 5.07 CZ: 4.89 m-80 revert: score: 50.064 CA: 6.67 CB: 6.42 CG: 6.79 CD1: 7.17 CD2: 6.18 CE1: 5.88 CE2: 5.64 CZ: 5.31 m-80 chain: A residue: LYS 67 start: score: 28.723 CA: 5.73 CB: 5.62 CG: 4.04 CD: 2.79 CE: 2.76 NZ: 3.89 mttm fitting: score: 28.723 CA: 5.73 CB: 5.62 CG: 4.04 CD: 2.79 CE: 2.76 NZ: 3.89 mttm tuneup: score: 28.678 CA: 5.73 CB: 5.62 CG: 4.04 CD: 2.79 CE: 2.77 NZ: 3.87 mttm revert: score: 28.723 CA: 5.73 CB: 5.62 CG: 4.04 CD: 2.79 CE: 2.76 NZ: 3.89 mttm chain: A residue: LEU 68 start: score: 39.718 CA: 5.84 CB: 6.65 CG: 6.58 CD1: 5.05 CD2: 5.28 mt fitting: score: 39.718 CA: 5.84 CB: 6.65 CG: 6.58 CD1: 5.05 CD2: 5.28 mt tuneup: score: 39.715 CA: 5.84 CB: 6.65 CG: 6.61 CD1: 5.04 CD2: 5.27 mt revert: score: 39.718 CA: 5.84 CB: 6.65 CG: 6.58 CD1: 5.05 CD2: 5.28 mt chain: A residue: ILE 69 start: score: 36.311 CA: 6.82 CB: 6.47 CG1: 6.72 CG2: 4.96 CD1: 5.67 pp fitting: score: 36.566 CA: 6.82 CB: 6.47 CG1: 6.78 CG2: 5.05 CD1: 5.72 pp tuneup: score: 35.961 CA: 6.82 CB: 6.47 CG1: 6.80 CG2: 4.96 CD1: 5.46 pp revert: score: 36.566 CA: 6.82 CB: 6.47 CG1: 6.78 CG2: 5.05 CD1: 5.72 pp chain: A residue: ASN 70 start: score: 30.857 CA: 6.32 CB: 5.75 CG: 6.53 OD1: 7.57 ND2: 4.68 t0 fitting: score: 30.853 CA: 6.32 CB: 5.75 CG: 6.56 OD1: 7.65 ND2: 4.57 t0 tuneup: score: 30.870 CA: 6.32 CB: 5.75 CG: 6.56 OD1: 7.50 ND2: 4.73 t0 chain: A residue: VAL 71 start: score: 30.737 CA: 6.15 CB: 6.03 CG1: 4.31 CG2: 4.97 m fitting: score: 30.740 CA: 6.15 CB: 6.03 CG1: 4.31 CG2: 4.97 m tuneup: score: 30.740 CA: 6.15 CB: 6.03 CG1: 4.31 CG2: 4.97 m revert: score: 30.740 CA: 6.15 CB: 6.03 CG1: 4.31 CG2: 4.97 m chain: A residue: TRP 74 start: score: 83.034 CA: 7.72 CB: 6.98 CG: 8.24 CD1: 8.17 CD2: 7.35 NE1: 9.30 CE2: 7.46 CE3: 8.11 CZ2: 6.12 CZ3: 6.72 CH2: 6.85 t60 fitting: score: 83.223 CA: 7.72 CB: 6.98 CG: 8.31 CD1: 8.29 CD2: 7.45 NE1: 9.27 CE2: 7.52 CE3: 8.19 CZ2: 6.10 CZ3: 6.63 CH2: 6.76 t60 tuneup: score: 83.223 CA: 7.72 CB: 6.98 CG: 8.31 CD1: 8.29 CD2: 7.45 NE1: 9.27 CE2: 7.52 CE3: 8.19 CZ2: 6.10 CZ3: 6.63 CH2: 6.76 t60 revert: score: 83.223 CA: 7.72 CB: 6.98 CG: 8.31 CD1: 8.29 CD2: 7.45 NE1: 9.27 CE2: 7.52 CE3: 8.19 CZ2: 6.10 CZ3: 6.63 CH2: 6.76 t60 chain: A residue: SER 77 start: score: 24.511 CA: 6.68 CB: 5.98 OG: 5.92 m fitting: score: 24.561 CA: 6.68 CB: 5.98 OG: 5.95 m tuneup: score: 24.561 CA: 6.68 CB: 5.98 OG: 5.95 m revert: score: 24.561 CA: 6.68 CB: 5.98 OG: 5.95 m chain: A residue: TRP 78 start: score: 81.839 CA: 7.46 CB: 7.86 CG: 8.00 CD1: 7.45 CD2: 6.74 NE1: 8.92 CE2: 8.12 CE3: 7.03 CZ2: 6.62 CZ3: 7.11 CH2: 6.52 t60 fitting: score: 81.839 CA: 7.46 CB: 7.86 CG: 8.00 CD1: 7.45 CD2: 6.74 NE1: 8.92 CE2: 8.12 CE3: 7.03 CZ2: 6.62 CZ3: 7.11 CH2: 6.52 t60 tuneup: score: 74.776 CA: 7.46 CB: 7.86 CG: 8.04 CD1: 7.02 CD2: 6.17 NE1: 7.92 CE2: 7.35 CE3: 6.80 CZ2: 5.44 CZ3: 5.85 CH2: 4.87 t60 revert: score: 81.839 CA: 7.46 CB: 7.86 CG: 8.00 CD1: 7.45 CD2: 6.74 NE1: 8.92 CE2: 8.12 CE3: 7.03 CZ2: 6.62 CZ3: 7.11 CH2: 6.52 t60 chain: A residue: THR 79 start: score: 30.564 CA: 6.16 CB: 5.70 CG2: 3.21 OG1: 6.15 m fitting: score: 30.719 CA: 6.16 CB: 5.70 CG2: 3.23 OG1: 6.19 m tuneup: score: 30.719 CA: 6.16 CB: 5.70 CG2: 3.23 OG1: 6.19 m revert: score: 30.719 CA: 6.16 CB: 5.70 CG2: 3.23 OG1: 6.19 m chain: A residue: LEU 80 start: score: 28.530 CA: 6.18 CB: 4.43 CG: 5.13 CD1: 3.72 CD2: 2.67 tp fitting: score: 28.530 CA: 6.18 CB: 4.43 CG: 5.13 CD1: 3.72 CD2: 2.67 tp tuneup: score: 28.268 CA: 6.18 CB: 4.43 CG: 5.14 CD1: 3.62 CD2: 2.64 tp revert: score: 28.530 CA: 6.18 CB: 4.43 CG: 5.13 CD1: 3.72 CD2: 2.67 tp chain: A residue: LYS 81 start: score: 34.821 CA: 6.56 CB: 6.85 CG: 5.56 CD: 4.73 CE: 4.22 NZ: 3.45 tttp fitting: score: 34.821 CA: 6.56 CB: 6.85 CG: 5.56 CD: 4.73 CE: 4.22 NZ: 3.45 tttp tuneup: score: 34.656 CA: 6.56 CB: 6.85 CG: 5.58 CD: 4.75 CE: 4.28 NZ: 3.32 tttp revert: score: 34.821 CA: 6.56 CB: 6.85 CG: 5.56 CD: 4.73 CE: 4.22 NZ: 3.45 tttp outliers after map fit: 0 tune up outliers final: 0 Did it for: 38 After: r_work=0.2236 r_free=0.2350 rotamer outliers: 0.00 % ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.925112 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.127758 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ============================= Fit rotatable H or D ============================ ====================== XYZ individual (reciprocal space) ====================== R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT TARGETS work free delta bonds angl data restr 22.36 23.50 1.14 0.005 0.9 2.5 0.0 0.0 0 none 4.072 0.0235 22.16 23.35 1.20 0.005 0.9 3.3 0.0 0.0 0 1.963 4.063 0.0228 Legend: - first line corresponds to starting state (before refinement) - R-factors reported in percent - delta is Rfree-Rwork in percent - CLASH is all-atom Molprobity clashscore - ROTA is percent of side-chain rotamer outliers - RAMA is percent of Ramachandran plot outliers - CBET is number of Cbeta deviations - WEIGHT is relative weight between X-ray (or neutron) target and restraints - TARGETS: the values of X-ray (or neutron) and restraints target functions ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.16 23.35 1.20 23.274 16.415 0.128 4.063 22.21 23.28 1.07 22.134 16.431 0.128 4.062 min max mean iso aniso Overall: 2.47 60.97 8.61 1.95 728 0 Protein: 2.47 46.15 6.64 1.91 616 0 Water: 4.64 60.97 21.15 N/A 93 0 Other: 2.66 19.69 11.10 N/A 19 0 Chain A: 2.47 46.15 6.61 N/A 620 0 Chain : 4.64 60.97 20.06 N/A 108 0 Histogram: Values Number of atoms 2.47 - 8.32 511 8.32 - 14.17 120 14.17 - 20.02 49 20.02 - 25.87 18 25.87 - 31.72 12 31.72 - 37.57 7 37.57 - 43.42 4 43.42 - 49.27 3 49.27 - 55.12 3 55.12 - 60.97 1 =========================== ADP refinement (H only) =========================== |- start----------------------------------------------------------------------| | target_work(ml) = 4.06225 r_work = 0.2221 r_free = 0.2328 | |-----------------------------------------------------------------------------| |- final----------------------------------------------------------------------| | target_work(ml) = 4.06076 r_work = 0.2216 r_free = 0.2331 | |-----------------------------------------------------------------------------| ======================== Occupancy refinement (H only) ======================== |- start----------------------------------------------------------------------| | target_work(ml) = 4.06076 r_work = 0.2216 r_free = 0.2331 | |-----------------------------------------------------------------------------| |- final----------------------------------------------------------------------| | target_work(ml) = 4.05948 r_work = 0.2205 r_free = 0.2327 | |-----------------------------------------------------------------------------| ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2205 r_free = 0.2327 target_work(ml) = 4.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 90 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2214 r_free = 0.2333 target_work(ml) = 4.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 90 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.80 - 14.96 A, n_refl.=61781 (all), 5.02 % free)------------| | | | r_work= 0.2214 r_free= 0.2333 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.060118 | | target function (ml) not normalized (work): 238247.742650 | | target function (ml) not normalized (free): 12704.197319 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 14.96 - 2.24 0.99 3013 146 0.1902 0.1905 5.3475 5.3158| | 2: 2.24 - 1.78 1.00 2894 154 0.1761 0.1730 4.9312 4.9127| | 3: 1.78 - 1.56 1.00 2872 149 0.2108 0.2327 4.7239 4.8411| | 4: 1.56 - 1.41 1.00 2838 163 0.2306 0.2611 4.544 4.5989| | 5: 1.41 - 1.31 0.99 2796 154 0.2238 0.2437 4.3573 4.4089| | 6: 1.31 - 1.24 0.99 2808 132 0.2195 0.2264 4.2795 4.2863| | 7: 1.24 - 1.17 0.99 2785 134 0.2184 0.2338 4.2824 4.395| | 8: 1.17 - 1.12 0.99 2782 162 0.2149 0.2020 4.2505 4.2386| | 9: 1.12 - 1.08 0.98 2765 142 0.2220 0.2422 4.1757 4.2606| | 10: 1.08 - 1.04 0.97 2717 145 0.2252 0.2601 4.0708 4.1459| | 11: 1.04 - 1.01 0.97 2687 162 0.2399 0.2410 3.9591 3.9441| | 12: 1.01 - 0.98 0.97 2697 136 0.2410 0.2882 3.8732 3.9989| | 13: 0.98 - 0.95 0.94 2653 138 0.2326 0.2267 3.794 3.8198| | 14: 0.95 - 0.93 0.95 2661 125 0.2360 0.2517 3.7223 3.7989| | 15: 0.93 - 0.91 0.93 2594 146 0.2544 0.2899 3.6744 3.722| | 16: 0.91 - 0.89 0.92 2562 132 0.2672 0.2803 3.6575 3.8113| | 17: 0.89 - 0.87 0.92 2537 135 0.2712 0.2839 3.6088 3.6539| | 18: 0.87 - 0.86 0.90 2482 149 0.2877 0.3108 3.5568 3.6253| | 19: 0.86 - 0.84 0.89 2491 115 0.3062 0.2987 3.5068 3.3875| | 20: 0.84 - 0.83 0.87 2422 121 0.3213 0.3374 3.4809 3.4967| | 21: 0.83 - 0.81 0.86 2379 130 0.3169 0.3089 3.4023 3.5126| | 22: 0.81 - 0.80 0.81 2245 131 0.3225 0.3609 3.4051 3.359| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 14.96 - 2.24 3013 146 0.89 16.44 1.00 1.15 5535.40| | 2: 2.24 - 1.78 2894 154 0.87 19.02 1.00 1.17 3383.79| | 3: 1.78 - 1.56 2872 149 0.86 20.37 1.02 1.14 1991.11| | 4: 1.56 - 1.41 2838 163 0.84 22.36 0.96 1.13 1478.69| | 5: 1.41 - 1.31 2796 154 0.84 23.25 0.97 1.09 1086.18| | 6: 1.31 - 1.24 2808 132 0.85 22.33 1.01 1.15 897.57| | 7: 1.24 - 1.17 2785 134 0.87 20.24 1.06 1.17 781.50| | 8: 1.17 - 1.12 2782 162 0.88 19.16 1.01 1.18 710.84| | 9: 1.12 - 1.08 2765 142 0.86 20.71 1.01 1.15 635.43| | 10: 1.08 - 1.04 2717 145 0.85 21.78 1.01 1.13 548.11| | 11: 1.04 - 1.01 2687 162 0.83 23.80 0.98 1.13 463.40| | 12: 1.01 - 0.98 2697 136 0.84 23.65 0.99 1.12 390.59| | 13: 0.98 - 0.95 2653 138 0.83 24.27 1.01 1.12 346.33| | 14: 0.95 - 0.93 2661 125 0.83 24.04 1.01 1.16 310.99| | 15: 0.93 - 0.91 2594 146 0.82 25.41 1.08 1.19 283.16| | 16: 0.91 - 0.89 2562 132 0.82 25.61 1.05 1.21 262.69| | 17: 0.89 - 0.87 2537 135 0.80 26.98 1.03 1.18 251.79| | 18: 0.87 - 0.86 2482 149 0.79 28.52 1.01 1.15 233.47| | 19: 0.86 - 0.84 2491 115 0.78 29.43 0.96 1.09 204.99| | 20: 0.84 - 0.83 2422 121 0.76 30.63 0.95 1.06 188.57| | 21: 0.83 - 0.81 2379 130 0.73 33.38 0.94 0.97 184.83| | 22: 0.81 - 0.80 2245 131 0.69 37.11 0.94 0.87 197.19| |alpha: min = 0.87 max = 1.21 mean = 1.13| |beta: min = 184.83 max = 5535.40 mean = 986.09| |figures of merit: min = 0.00 max = 1.00 mean = 0.83| |phase err.(work): min = 0.00 max = 90.00 mean = 24.16| |phase err.(test): min = 0.00 max = 90.00 mean = 24.13| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2220 0.2214 0.2333 n_refl.: 61781 re-set all scales: r(all,work,free)=0.2434 0.2428 0.2565 n_refl.: 61781 remove outliers: r(all,work,free)=0.2434 0.2428 0.2565 n_refl.: 61781 overall B=-0.00 to atoms: r(all,work,free)=0.2434 0.2428 0.2565 n_refl.: 61781 bulk-solvent and scaling: r(all,work,free)=0.2219 0.2213 0.2333 n_refl.: 61781 remove outliers: r(all,work,free)=0.2219 0.2213 0.2333 n_refl.: 61781 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 14.960-7.253 99.02 95 6 0.2535 260.484 246.106 0.978 0.997 0.409 7.246-5.773 99.01 98 2 0.2193 263.466 248.364 0.969 0.999 0.330 5.768-4.607 98.95 180 9 0.1850 278.149 265.757 0.971 0.999 0.296 4.593-3.659 92.73 341 16 0.1492 311.805 302.693 0.970 1.003 0.283 3.656-2.912 98.75 675 36 0.1840 248.143 240.905 0.988 0.999 0.200 2.911-2.318 100.00 1343 59 0.2065 183.341 178.052 0.963 0.999 0.000 2.318-1.845 100.00 2587 143 0.1718 161.888 158.256 1.020 0.999 0.000 1.845-1.469 99.85 5060 262 0.2156 104.432 100.685 1.059 0.999 0.000 1.469-1.169 99.19 9852 508 0.2212 71.754 68.584 1.010 1.001 0.000 1.169-0.931 96.65 18810 1002 0.2285 49.856 47.774 1.115 1.001 0.000 0.931-0.801 88.70 19639 1058 0.2885 27.107 25.569 1.053 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=-0.1260 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2521 0.2549 0.016 1.703 3.0 71.0 9.0 93 0.000 1_bss: 0.2235 0.2218 0.016 1.703 2.5 70.5 8.6 93 0.000 1_settarget: 0.2235 0.2218 0.016 1.703 2.5 70.5 8.6 93 0.000 1_nqh: 0.2235 0.2218 0.016 1.703 2.5 70.5 8.6 93 0.000 1_realsrl: 0.2232 0.2215 0.016 1.703 2.5 70.5 8.6 93 0.043 1_weight: 0.2232 0.2215 0.016 1.703 2.5 70.5 8.6 93 0.043 1_fitrh: 0.2232 0.2215 0.016 1.703 2.5 70.5 8.6 93 0.043 1_xyzrec: 0.2218 0.2278 0.007 0.913 2.5 70.5 8.6 93 0.089 1_adp: 0.2286 0.2374 0.007 0.913 2.4 65.5 8.5 93 0.089 1_adph: 0.2273 0.2388 0.007 0.913 2.4 65.5 8.5 93 0.089 1_occh: 0.2266 0.2400 0.007 0.913 2.4 65.5 8.5 93 0.089 1_occ: 0.2251 0.2365 0.007 0.913 2.4 65.5 8.5 93 0.089 2_bss: 0.2241 0.2359 0.007 0.913 2.4 65.5 8.5 93 0.089 2_settarget: 0.2241 0.2359 0.007 0.913 2.4 65.5 8.5 93 0.089 2_updatecdl: 0.2241 0.2359 0.007 0.917 2.4 65.5 8.5 93 0.089 2_nqh: 0.2242 0.2362 0.007 0.917 2.4 65.5 8.5 93 0.083 2_realsrl: 0.2259 0.2365 0.007 0.917 2.4 65.5 8.5 93 0.124 2_weight: 0.2259 0.2365 0.007 0.917 2.4 65.5 8.5 93 0.124 2_fitrh: 0.2259 0.2365 0.007 0.917 2.4 65.5 8.5 93 0.124 2_xyzrec: 0.2232 0.2322 0.005 0.868 2.4 65.5 8.5 93 0.113 2_adp: 0.2232 0.2328 0.005 0.868 2.1 63.1 8.5 93 0.113 2_adph: 0.2227 0.2333 0.005 0.868 2.1 63.1 8.5 93 0.113 2_occh: 0.2216 0.2331 0.005 0.868 2.1 63.1 8.5 93 0.113 2_occ: 0.2224 0.2337 0.005 0.868 2.1 63.1 8.5 93 0.113 3_bss: 0.2222 0.2334 0.005 0.868 2.1 63.1 8.5 93 0.113 3_settarget: 0.2222 0.2334 0.005 0.868 2.1 63.1 8.5 93 0.113 3_updatecdl: 0.2222 0.2334 0.005 0.868 2.1 63.1 8.5 93 0.113 3_nqh: 0.2222 0.2335 0.005 0.868 2.1 63.1 8.5 93 0.108 3_realsrl: 0.2236 0.2350 0.005 0.868 2.1 63.1 8.5 93 0.115 3_weight: 0.2236 0.2350 0.005 0.868 2.1 63.1 8.5 93 0.115 3_fitrh: 0.2236 0.2350 0.005 0.868 2.1 63.1 8.5 93 0.115 3_xyzrec: 0.2216 0.2335 0.005 0.874 2.1 63.1 8.5 93 0.114 3_adp: 0.2221 0.2328 0.005 0.874 2.5 61.0 8.6 93 0.114 3_adph: 0.2216 0.2331 0.005 0.874 2.5 61.0 8.6 93 0.114 3_occh: 0.2205 0.2327 0.005 0.874 2.5 61.0 8.6 93 0.114 3_occ: 0.2214 0.2333 0.005 0.874 2.5 61.0 8.6 93 0.114 end: 0.2213 0.2333 0.005 0.874 2.5 61.0 8.6 93 0.114 ------------------------------------------------------------------------ CPU time actual refinement: 470.34 ============================== Exporting results ============================== Writing refined structure to CIF file: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_hipip_refine_benchmark\hipip.updated_refine_001.cif Writing default parameters for subsequent refinement: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_hipip_refine_benchmark\hipip.updated_refine_002.def NUMBER OF MASK CALCS= 0 Total CPU time: 8.95 minutes from_scatterers_fft: 457 calls, 90.92 s gradients_fft: 384 calls, 94.19 s =========================== phenix.refine: finished =========================== # Date 2020-05-01 Time 09:28:43 GMT Daylight Time +0100 (1588321723.20 s) wall clock time: 768.62 s Start R-work = 0.2235, R-free = 0.2218 Final R-work = 0.2213, R-free = 0.2333 RUNTIME: 858.2s Running 333 tests on 8 processors: libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\ampl_int_autobuild_tests\test_ampl_int_autobuild\tst_ampl_int_autobuild.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_A001\tst_AutoBuild_A001.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_build\tst_AutoBuild_build.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_extend\tst_AutoBuild_extend.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_gap\tst_AutoBuild_gap.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_hires\tst_AutoBuild_hires.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_lig\tst_AutoBuild_lig.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_mult\tst_AutoBuild_mult.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_ncs\tst_AutoBuild_ncs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_omit\tst_AutoBuild_omit.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_outside\tst_AutoBuild_outside.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_std\tst_AutoBuild_std.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_truncate\tst_AutoBuild_truncate.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoMR_tests\test_AutoMR_std\tst_AutoMR_std.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mad\tst_AutoSol_mad.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mir\tst_AutoSol_mir.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_phaser\tst_AutoSol_phaser.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_phaser_mr\tst_AutoSol_phaser_mr.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_rna\tst_AutoSol_rna.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_sir_sad\tst_AutoSol_sir_sad.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_std\tst_AutoSol_std.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\autosol_unmerged_tests\test_autosol_unmerged\tst_autosol_unmerged.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\commands_in_doc_tests\test_commands_in_doc\tst_commands_in_doc.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_autobuild_quick\tst_autobuild_quick.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_automr_remark\tst_automr_remark.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_build_one_model\tst_build_one_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_build_rna_helices\tst_build_rna_helices.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_copy_extra\tst_copy_extra.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_cross_gvp\tst_cross_gvp.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_cross_mismatch\tst_cross_mismatch.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_delete_bad\tst_delete_bad.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_get_cc_mtz_pdb\tst_get_cc_mtz_pdb.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_parallel_autobuild\tst_parallel_autobuild.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_phase_and_build\tst_phase_and_build.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_phase_and_build_perfect\tst_phase_and_build_perfect.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_phase_and_build_rs\tst_phase_and_build_rs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_find_all_ligands\tst_find_all_ligands.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_in_memory\tst_ligand_in_memory.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_library\tst_ligand_library.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_list\tst_ligand_list.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_ncs\tst_ligand_ncs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_refine\tst_ligand_refine.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_se_lig_in_refine\tst_se_lig_in_refine.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_loops_tests\test_alt_conf_loops\tst_alt_conf_loops.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_loops_tests\test_alt_conf_loop_lib\tst_alt_conf_loop_lib.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_loops_tests\test_fit_loops\tst_fit_loops.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_loops_tests\test_fit_loops_offset\tst_fit_loops_offset.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_loops_tests\test_loop_lib\tst_loop_lib.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_loops_tests\test_loop_lib_split\tst_loop_lib_split.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_build_rna_helices\tst_build_rna_helices.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_iterative_ss_refine\tst_iterative_ss_refine.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_map_to_model_helices\tst_map_to_model_helices.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_map_to_model_map_box\tst_map_to_model_map_box.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_map_to_model_overall\tst_map_to_model_overall.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_map_to_model_quick\tst_map_to_model_quick.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_map_to_model_sg\tst_map_to_model_sg.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_remove_poor_fragments\tst_remove_poor_fragments.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_segment\tst_segment.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_aniso_from_coords\tst_aniso_from_coords.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_anomalous_signal\tst_anomalous_signal.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_autosol_classic_denmod\tst_autosol_classic_denmod.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_average_map_coeffs\tst_average_map_coeffs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_backslash\tst_backslash.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_bayesian_estimator\tst_bayesian_estimator.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_cc_ano\tst_cc_ano.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_cc_mtz_pdb\tst_cc_mtz_pdb.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_cif\tst_cif.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_dano_labels\tst_dano_labels.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_denmod_iter\tst_denmod_iter.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_dos\tst_dos.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_erraser\tst_erraser.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_get_ca_segments\tst_get_ca_segments.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_guess_ncs_and_sites\tst_guess_ncs_and_sites.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_hyss\tst_hyss.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_import_and_add_free\tst_import_and_add_free.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_keep_atom_types\tst_keep_atom_types.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_map_to_object_and_sort_hetatms\tst_map_to_object_and_sort_hetatms.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_md\tst_md.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_merge_mtz\tst_merge_mtz.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_patterson_skew\tst_patterson_skew.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_phaser\tst_phaser.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_phaser_asu\tst_phaser_asu.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_plan_sad_experiment\tst_plan_sad_experiment.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_ps_in_rebuild\tst_ps_in_rebuild.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_ramalyze\tst_ramalyze.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_run_phenix_refine\tst_run_phenix_refine.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_sad_data_from_pdb\tst_sad_data_from_pdb.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_scale_and_merge\tst_scale_and_merge.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_set_sg\tst_set_sg.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_solvent_fraction\tst_solvent_fraction.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_special_pos\tst_special_pos.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_two_fofc_denmod_in_rebuild\tst_two_fofc_denmod_in_rebuild.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_two_fofc_in_rebuild\tst_two_fofc_in_rebuild.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_apply_ncs\tst_apply_ncs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_edit_chains\tst_edit_chains.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_euler\tst_euler.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_find_ncs\tst_find_ncs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_find_ncs_from_density\tst_find_ncs_from_density.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_magnification\tst_magnification.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_multi_ha\tst_multi_ha.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_ncs_change_of_basis\tst_ncs_change_of_basis.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_ncs_change_of_basis_offset\tst_ncs_change_of_basis_offset.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_offset\tst_offset.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_change_sg\tst_change_sg.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_cluster\tst_cluster.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_inv_sg\tst_inv_sg.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_long_file_names\tst_long_file_names.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_non_standard_sg\tst_non_standard_sg.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_part_map_coeffs\tst_part_map_coeffs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_zero_fom\tst_zero_fom.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_omit_tests\test_omit_selection\tst_omit_selection.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_build_in_memory\tst_build_in_memory.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_cutout\tst_cutout.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_density_modification\tst_density_modification.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_morph_model_in_memory\tst_morph_model_in_memory.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_ncs_average\tst_ncs_average.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_ncs_average_from_map_file\tst_ncs_average_from_map_file.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_denmod_memory\tst_resolve_denmod_memory.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_denmod_pdb_memory\tst_resolve_denmod_pdb_memory.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_map_likelihood\tst_resolve_map_likelihood.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_memory\tst_resolve_memory.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_ncs_in_memory\tst_resolve_ncs_in_memory.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_ncs_map_memory\tst_resolve_ncs_map_memory.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_ncs_memory\tst_resolve_ncs_memory.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_ncs_nomemory\tst_resolve_ncs_nomemory.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_pdb_memory\tst_resolve_pdb_memory.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_autobuild\tst_autobuild.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_autobuild_double\tst_autobuild_double.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_average\tst_average.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_average_double\tst_average_double.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_denmod_refine_after_mr\tst_denmod_refine_after_mr.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_denmod_refine_after_mr_double\tst_denmod_refine_after_mr_double.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_fixed_model\tst_fixed_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_hhr\tst_hhr.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_mr_rescoring\tst_mr_rescoring.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_mr_rescoring_double\tst_mr_rescoring_double.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_place_model\tst_place_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_place_model_double\tst_place_model_double.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_place_model_ps\tst_place_model_ps.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_prerefine\tst_prerefine.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_prerefine_double\tst_prerefine_double.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_prerefine_no_data\tst_prerefine_no_data.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_real_space\tst_real_space.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_refine_after_mr\tst_refine_after_mr.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_refine_after_mr_double\tst_refine_after_mr_double.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_refine_top_models\tst_refine_top_models.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_refine_top_models_double\tst_refine_top_models_double.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_assign_sequence\tst_assign_sequence.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_combine_models\tst_combine_models.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_commands\tst_commands.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_connect_all_segments\tst_connect_all_segments.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_density_outside_model\tst_density_outside_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_find_helices_strands\tst_find_helices_strands.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_morph_model\tst_morph_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_morph_model_hl\tst_morph_model_hl.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_phaser_denmod\tst_phaser_denmod.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_remove_free_from_map\tst_remove_free_from_map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_replace_side_chains\tst_replace_side_chains.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_r_free_flag\tst_r_free_flag.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_unmerged_mir\tst_unmerged_mir.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_trace_tests\test_fit_gap_trace\tst_fit_gap_trace.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_trace_tests\test_fit_loops_trace\tst_fit_loops_trace.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_trace_tests\test_trace\tst_trace.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_wizards_tests\test_autosol_test_flag\tst_autosol_test_flag.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_wizards_tests\test_find_ca_from_map\tst_find_ca_from_map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_wizards_tests\test_map_to_model\tst_map_to_model.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\extract_segment_pair_tests\test_protein\tst_protein.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\extract_segment_pair_tests\test_rna\tst_rna.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\extract_segment_tests\test_helix\tst_helix.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\extract_segment_tests\test_strand\tst_strand.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\help_tests\test_help\tst_help.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\input_files_tests\test_input_files\tst_input_files.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\labels_tests\test_labels\tst_labels.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_builder\tst_LigandFit_builder.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_cif\tst_LigandFit_cif.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_lc\tst_LigandFit_lc.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_std\tst_LigandFit_std.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\maps_only_tests\test_maps_only\tst_maps_only.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\map_to_object_tests\test_map_to_object\tst_map_to_object.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\misc_methods_tests\test_misc_methods\tst_misc_methods.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\missing_data_tests\test_missing_data\tst_missing_data.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\multi_tests\test_multi\tst_multi.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\mult_tests\test_mult\tst_mult.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\ncs_in_phenix_refine_tests\test_ncs_in_phenix_refine\tst_ncs_in_phenix_refine.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\ncs_tests\test_ncs\tst_ncs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\omit_lig_tests\test_omit_lig\tst_omit_lig.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\omit_tests\test_omit\tst_omit.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resno_tests\test_resno\tst_resno.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_extra\tst_extra.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_index_file\tst_index_file.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_local_pattern_2\tst_local_pattern_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_local_pattern_3\tst_local_pattern_3.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_pdb_in\tst_pdb_in.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_read_hist\tst_read_hist.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_read_pattern\tst_read_pattern.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_resolve_pattern\tst_resolve_pattern.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_setup\tst_setup.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_align_bases\tst_align_bases.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_background_map\tst_background_map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_bad\tst_bad.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build\tst_build.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build_1\tst_build_1.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build_image\tst_build_image.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build_repeat\tst_build_repeat.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build_se\tst_build_se.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_cc\tst_cc.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_cc_mask\tst_cc_mask.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_chain_name\tst_chain_name.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_combine\tst_combine.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_combine_maps\tst_combine_maps.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_compare\tst_compare.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_composite_pdb\tst_composite_pdb.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_connect\tst_connect.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_create_hist\tst_create_hist.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_cross\tst_cross.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_diff_map\tst_diff_map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_dump_frags\tst_dump_frags.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_dump_mask\tst_dump_mask.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_dump_relat\tst_dump_relat.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_extend_rna\tst_extend_rna.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_find_ncs\tst_find_ncs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_find_ncs_mlt\tst_find_ncs_mlt.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_find_strands\tst_find_strands.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_fit\tst_fit.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_fit_start\tst_fit_start.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_free\tst_free.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_getdir_solve_only\tst_getdir_solve_only.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_get_histograms\tst_get_histograms.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_get_inputs\tst_get_inputs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_helices_find\tst_helices_find.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_helices_trace\tst_helices_trace.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_helix_trace\tst_helix_trace.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_highest_mask\tst_highest_mask.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_high_pass\tst_high_pass.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_hist\tst_hist.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_image\tst_image.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_just_box\tst_just_box.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_fit\tst_ligand_fit.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_fit_distance\tst_ligand_fit_distance.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_group\tst_ligand_group.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_large\tst_ligand_large.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_relat\tst_ligand_relat.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_rot_trans\tst_ligand_rot_trans.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_volume\tst_ligand_volume.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_link_prob\tst_link_prob.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_local_hist\tst_local_hist.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_main_map\tst_main_map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_maps\tst_maps.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_masks\tst_masks.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_mask_image\tst_mask_image.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_mask_s_p\tst_mask_s_p.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_misc\tst_misc.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_modify_hist\tst_modify_hist.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_modify_ncs\tst_modify_ncs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_morph\tst_morph.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_mp_file\tst_mp_file.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ncs_groups\tst_ncs_groups.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_no_erase_protein\tst_no_erase_protein.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_n_model_create\tst_n_model_create.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_offset\tst_offset.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_offset_pdb\tst_offset_pdb.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_omit_box_id\tst_omit_box_id.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_omit_mask\tst_omit_mask.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_omit_region\tst_omit_region.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_opt_ncs\tst_opt_ncs.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_outside\tst_outside.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_planar_rings\tst_planar_rings.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_prime_and_switch\tst_prime_and_switch.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ps_edit\tst_ps_edit.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_q\tst_q.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_randomize_denmod\tst_randomize_denmod.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_randomize_side\tst_randomize_side.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_random_map\tst_random_map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_read_peaks\tst_read_peaks.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_rebuild\tst_rebuild.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_rebuild_side\tst_rebuild_side.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_resolve_multi\tst_resolve_multi.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_resolve_multi_b\tst_resolve_multi_b.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_resolve_multi_c\tst_resolve_multi_c.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_scores\tst_scores.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_score_tert\tst_score_tert.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_search_center\tst_search_center.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_set_fract\tst_set_fract.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_set_hist\tst_set_hist.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_sharpen\tst_sharpen.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_solvent_prob_min\tst_solvent_prob_min.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_special\tst_special.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_trace\tst_trace.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_trace_analyze\tst_trace_analyze.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_unit_tests\tst_unit_tests.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_update_proxy\tst_update_proxy.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_write_ca\tst_write_ca.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_write_ezd\tst_write_ezd.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_write_pdb_occ\tst_write_pdb_occ.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_zero_hl\tst_zero_hl.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\segment_library_tests\test_segment_library\tst_segment_library.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\short_seq_tests\test_short_seq\tst_short_seq.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\side_chains_tests\test_clusters\tst_clusters.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\side_chains_tests\test_use_clusters\tst_use_clusters.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\side_chains_tests\test_write_map\tst_write_map.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\side_chains_update_tests\test_update\tst_update.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_addseed\tst_addseed.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_avg_omit\tst_avg_omit.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_btof\tst_btof.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_cart_to_fract\tst_cart_to_fract.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_cc\tst_cc.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_cluster\tst_cluster.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_combine\tst_combine.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_compare_soln\tst_compare_soln.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_extra\tst_extra.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_fdiff\tst_fdiff.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_generate_mad\tst_generate_mad.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_generate_mir\tst_generate_mir.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_hassp\tst_hassp.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mad\tst_mad.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mad_mtz\tst_mad_mtz.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_maps\tst_maps.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_map_to_asym\tst_map_to_asym.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_math\tst_math.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mir\tst_mir.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mirror\tst_mirror.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mir_mtz\tst_mir_mtz.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_pdb_xyz_in\tst_pdb_xyz_in.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_phases_mtz\tst_phases_mtz.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_question\tst_question.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_read_ano\tst_read_ano.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_rho\tst_rho.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_scale\tst_scale.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_sites_from_phases\tst_sites_from_phases.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_solve\tst_solve.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_sym\tst_sym.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_systematic\tst_systematic.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_weights\tst_weights.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\ampl_int_autobuild_tests\test_ampl_int_autobuild\tst_ampl_int_autobuild.py" [OK] 35.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_gap\tst_AutoBuild_gap.py" [OK] 612.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_extend\tst_AutoBuild_extend.py" [OK] 815.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_lig\tst_AutoBuild_lig.py" [OK] 908.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_omit\tst_AutoBuild_omit.py" [OK] 535.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_outside\tst_AutoBuild_outside.py" [OK] 678.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_ncs\tst_AutoBuild_ncs.py" [OK] 1899.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_truncate\tst_AutoBuild_truncate.py" [OK] 951.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_A001\tst_AutoBuild_A001.py" [OK] 4687.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_hires\tst_AutoBuild_hires.py" [OK] 4754.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_phaser_mr\tst_AutoSol_phaser_mr.py" [FAIL] 168.2s Time: 168.15 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ Test test_AutoSol_phaser_mr FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_std\tst_AutoBuild_std.py" [OK] 4431.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoMR_tests\test_AutoMR_std\tst_AutoMR_std.py" [OK] 4290.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_mult\tst_AutoBuild_mult.py" [FAIL] 5800.3s Time: 5800.35 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\autosol_unmerged_tests\test_autosol_unmerged\tst_autosol_unmerged.py" [FAIL] 510.3s Time: 510.28 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ Test test_autosol_unmerged FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\commands_in_doc_tests\test_commands_in_doc\tst_commands_in_doc.py" [OK] 482.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_autobuild_quick\tst_autobuild_quick.py" [OK] 1043.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_automr_remark\tst_automr_remark.py" [OK] 29.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_build\tst_AutoBuild_build.py" [OK] 8063.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_build_rna_helices\tst_build_rna_helices.py" [OK] 60.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_copy_extra\tst_copy_extra.py" [OK] 59.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_cross_gvp\tst_cross_gvp.py" [OK] 24.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_cross_mismatch\tst_cross_mismatch.py" [OK] 119.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_delete_bad\tst_delete_bad.py" [OK] 202.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_get_cc_mtz_pdb\tst_get_cc_mtz_pdb.py" [OK] 35.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_parallel_autobuild\tst_parallel_autobuild.py" [OK] 38.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_build_one_model\tst_build_one_model.py" [OK] 879.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mir\tst_AutoSol_mir.py" [FAIL] 6791.2s Time: 6791.21 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_phase_and_build_rs\tst_phase_and_build_rs.py" [OK] 667.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_find_all_ligands\tst_find_all_ligands.py" [OK] 31.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mad\tst_AutoSol_mad.py" [FAIL] 7714.3s Time: 7714.26 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_in_memory\tst_ligand_in_memory.py" [OK] 74.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_list\tst_ligand_list.py" [FAIL] 135.3s Time: 135.32 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_list\tst_ligand_list.py", line 56, in run_wizard_test(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix_regression\wizards\run_wizard_test.py", line 184, in run_wizard_test module.run(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.wizards.test_all_parallel\command_line_ligands_tests\test_ligand_list\tst_ligand_list.py", line 26, in run run_ligandfit(args=args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 564, in __init__ self.RunWizard() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 1001, in RunWizard self.runWizard.run() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 836, in Run self.DoNextMethod() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1004, in DoNextMethod raise AssertionError, line AssertionError: Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\LigandFit.py", line 2044, in LigandFit_fit_ligand r.run(out=sys.stdout) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\run_group_of_wizards_win32.py", line 41, in run pool = multiprocessing.Pool(processes=self.nproc) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\__init__.py", line 232, in Pool return Pool(processes, initializer, initargs, maxtasksperchild) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\pool.py", line 161, in __init__ self._repopulate_pool() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\pool.py", line 225, in _repopulate_pool w.start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\process.py", line 130, in start self._popen = Popen(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 272, in __init__ prep_data = get_preparation_data(process_obj._name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 409, in get_preparation_data not d['sys_argv'][0].lower().endswith('pythonservice.exe'): IndexError: list index out of range Traceback (most recent call last): File "", line 1, in File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 379, in main preparation_data = load(from_parent) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 1384, in load return Unpickler(file).load() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 864, in load dispatch[key](self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 886, in load_eof raise EOFError EOFError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_phase_and_build_perfect\tst_phase_and_build_perfect.py" [OK] 1460.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_library\tst_ligand_library.py" [OK] 1035.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_se_lig_in_refine\tst_se_lig_in_refine.py" [OK] 244.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_loops_tests\test_alt_conf_loops\tst_alt_conf_loops.py" [OK] 65.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_loops_tests\test_alt_conf_loop_lib\tst_alt_conf_loop_lib.py" [OK] 122.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_loops_tests\test_fit_loops\tst_fit_loops.py" [OK] 58.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_loops_tests\test_fit_loops_offset\tst_fit_loops_offset.py" [OK] 70.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_loops_tests\test_loop_lib\tst_loop_lib.py" [OK] 362.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_loops_tests\test_loop_lib_split\tst_loop_lib_split.py" [OK] 43.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_build_rna_helices\tst_build_rna_helices.py" [OK] 82.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_phaser\tst_AutoSol_phaser.py" [FAIL] 7168.7s Time: 7168.71 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_map_to_model_helices\tst_map_to_model_helices.py" [OK] 86.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_map_to_model_map_box\tst_map_to_model_map_box.py" [OK] 62.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_rna\tst_AutoSol_rna.py" [OK] 7090.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_map_to_model_quick\tst_map_to_model_quick.py" [OK] 76.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_map_to_model_sg\tst_map_to_model_sg.py" [OK] 33.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_map_to_model_overall\tst_map_to_model_overall.py" [OK] 198.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_remove_poor_fragments\tst_remove_poor_fragments.py" [OK] 107.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_refine\tst_ligand_refine.py" [OK] 2184.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_segment\tst_segment.py" [OK] 195.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_anomalous_signal\tst_anomalous_signal.py" [OK] 26.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_average_map_coeffs\tst_average_map_coeffs.py" [OK] 28.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_backslash\tst_backslash.py" [OK] 24.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_autosol_classic_denmod\tst_autosol_classic_denmod.py" [OK] 80.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_aniso_from_coords\tst_aniso_from_coords.py" [OK] 258.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_cc_ano\tst_cc_ano.py" [OK] 48.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_cif\tst_cif.py" [OK] 27.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_cc_mtz_pdb\tst_cc_mtz_pdb.py" [OK] 123.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_denmod_iter\tst_denmod_iter.py" [OK] 36.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_bayesian_estimator\tst_bayesian_estimator.py" [OK] 192.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_erraser\tst_erraser.py" [OK] 24.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_get_ca_segments\tst_get_ca_segments.py" [OK] 53.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_guess_ncs_and_sites\tst_guess_ncs_and_sites.py" [OK] 81.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_dos\tst_dos.py" [FAIL] 252.9s Time: 252.94 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ Test test_dos FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_import_and_add_free\tst_import_and_add_free.py" [OK] 54.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_hyss\tst_hyss.py" [OK] 148.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_iterative_ss_refine\tst_iterative_ss_refine.py" [OK] 1294.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_keep_atom_types\tst_keep_atom_types.py" [OK] 93.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_ncs\tst_ligand_ncs.py" [OK] 3254.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_patterson_skew\tst_patterson_skew.py" [OK] 17.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_md\tst_md.py" [OK] 45.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_dano_labels\tst_dano_labels.py" [FAIL] 564.9s Time: 564.95 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 41 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 41 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 41 differ FAILED...numbers 21 and 41 differ FAILED...numbers 21 and 41 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 2 and 1 differ Test test_dano_labels FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_phaser_asu\tst_phaser_asu.py" [OK] 88.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_merge_mtz\tst_merge_mtz.py" [OK] 124.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_plan_sad_experiment\tst_plan_sad_experiment.py" [OK] 74.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_ramalyze\tst_ramalyze.py" [OK] 19.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_sad_data_from_pdb\tst_sad_data_from_pdb.py" [OK] 20.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_phaser\tst_phaser.py" [FAIL] 158.1s Time: 158.14 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ Test test_phaser FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_ps_in_rebuild\tst_ps_in_rebuild.py" [OK] 276.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_solvent_fraction\tst_solvent_fraction.py" [OK] 116.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_special_pos\tst_special_pos.py" [OK] 162.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_two_fofc_denmod_in_rebuild\tst_two_fofc_denmod_in_rebuild.py" [OK] 303.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_map_to_object_and_sort_hetatms\tst_map_to_object_and_sort_hetatms.py" [OK] 1190.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_apply_ncs\tst_apply_ncs.py" [OK] 72.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_set_sg\tst_set_sg.py" [OK] 1007.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_two_fofc_in_rebuild\tst_two_fofc_in_rebuild.py" [OK] 298.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_edit_chains\tst_edit_chains.py" [OK] 112.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_euler\tst_euler.py" [OK] 115.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_find_ncs_from_density\tst_find_ncs_from_density.py" [OK] 69.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_magnification\tst_magnification.py" [OK] 69.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_multi_ha\tst_multi_ha.py" [OK] 121.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_find_ncs\tst_find_ncs.py" [OK] 281.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_ncs_change_of_basis_offset\tst_ncs_change_of_basis_offset.py" [OK] 136.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_offset\tst_offset.py" [OK] 124.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_ncs_change_of_basis\tst_ncs_change_of_basis.py" [OK] 412.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_scale_and_merge\tst_scale_and_merge.py" [OK] 2208.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_long_file_names\tst_long_file_names.py" [OK] 46.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_phase_and_build\tst_phase_and_build.py" [OK] 7066.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_part_map_coeffs\tst_part_map_coeffs.py" [OK] 155.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_zero_fom\tst_zero_fom.py" [OK] 252.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_run_phenix_refine\tst_run_phenix_refine.py" [OK] 3008.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_omit_tests\test_omit_selection\tst_omit_selection.py" [OK] 188.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_cutout\tst_cutout.py" [OK] 56.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_density_modification\tst_density_modification.py" [FAIL] 153.1s Time: 153.08 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 0.359 and 0.361 differ FAILED...numbers 2.530 and 2.525 differ FAILED...numbers 0.16 and 0.15 differ FAILED...numbers 1.42 and 1.41 differ FAILED...numbers 0.424 and 0.425 differ FAILED...numbers 0.71 and 0.72 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 1.23 and 1.22 differ FAILED...numbers 4.885 and 4.886 differ FAILED...numbers 0.25 and 0.24 differ FAILED...numbers 0.12 and 0.13 differ FAILED...numbers 0.14 and 0.15 differ FAILED...numbers 0.34 and 0.33 differ FAILED...numbers 0.17392889504890346 and 0.17284358043114709 differ FAILED...numbers 0.39 and 0.38 differ FAILED...numbers 0.26 and 0.25 differ FAILED...numbers 0.56277425327518105 and 0.56030388499260697 differ FAILED...numbers 1.282 and 1.309 differ FAILED...numbers 0.7771232 and 0.7752666 differ FAILED...numbers 4.8085 and 4.8049 differ FAILED...numbers -8.35 and -8.36 differ FAILED...numbers -0.2174 and -0.2152 differ FAILED...numbers -0.2174 and -0.2152 differ FAILED...numbers 12.23638 and 12.24053 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 0.196 and 0.197 differ FAILED...numbers 3317 and 3307 differ FAILED...numbers 5981 and 5959 differ FAILED...numbers 0.04 and 0.05 differ FAILED...numbers 0.27 and 0.28 differ FAILED...numbers 0.03 and 0.05 differ FAILED...numbers 0.22 and 0.25 differ FAILED...numbers 4.10222244511827747E-02 and 3.32653811599860420E-002 differ FAILED...numbers 228.872 and 225.091 differ FAILED...numbers 0.24 and 0.23 differ FAILED...numbers 0.15 and 0.14 differ FAILED...numbers 4.8085 and 4.8049 differ FAILED...numbers -8.35 and -8.36 differ FAILED...numbers -0.2174 and -0.2152 differ FAILED...numbers -0.2174 and -0.2152 differ FAILED...numbers 12.23638 and 12.24053 differ FAILED...numbers 0.15 and 0.14 differ FAILED...numbers 0.43 and 0.44 differ FAILED...numbers 12.2 and 12.3 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 0.84 and 0.83 differ FAILED...numbers 0.53 and 0.51 differ FAILED...numbers 0.34 and 0.35 differ FAILED...numbers 0.32 and 0.33 differ FAILED...numbers 0.32 and 0.33 differ FAILED...numbers 0.53 and 0.51 differ FAILED...numbers 0.34 and 0.35 differ FAILED...numbers 0.32 and 0.33 differ FAILED...numbers 0.32 and 0.33 differ FAILED...numbers 0.52301972220232196 and 0.52540002738708980 differ FAILED...numbers 1.400 and 1.435 differ FAILED...numbers 0.53 and 0.51 differ Test test_density_modification FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_build_in_memory\tst_build_in_memory.py" [OK] 321.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_ncs_average\tst_ncs_average.py" [OK] 24.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_ncs_average_from_map_file\tst_ncs_average_from_map_file.py" [OK] 109.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_morph_model_in_memory\tst_morph_model_in_memory.py" [OK] 332.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_denmod_memory\tst_resolve_denmod_memory.py" [OK] 264.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_denmod_pdb_memory\tst_resolve_denmod_pdb_memory.py" [FAIL] 267.2s Time: 267.17 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers -0.57 and -0.56 differ FAILED...numbers 0.60 and 0.61 differ FAILED...numbers 5.71 and 5.72 differ FAILED...numbers 1.442 and 1.432 differ FAILED...numbers 6553 and 6556 differ FAILED...numbers 0.67624596307400620 and 0.67725417442606084 differ FAILED...numbers 5752 and 5754 differ FAILED...numbers 0.723 and 0.724 differ FAILED...numbers 0.34 and 0.35 differ FAILED...numbers 0.74991903427078965 and 0.75164617882000184 differ FAILED...numbers 0.34412563867733209 and 0.34530512242051420 differ FAILED...numbers 5752 and 5754 differ FAILED...numbers 0.41 and 0.40 differ FAILED...numbers 0.41 and 0.40 differ FAILED...numbers 0.48 and 0.47 differ FAILED...numbers 0.41 and 0.40 differ FAILED...numbers 0.74924231570536692 and 0.75085512409060018 differ FAILED...numbers 0.47422510307404170 and 0.47290034020940463 differ FAILED...numbers 5752 and 5754 differ FAILED...numbers -0.65 and -0.64 differ FAILED...numbers 0.74 and 0.75 differ FAILED...numbers 4.96 and 4.97 differ FAILED...numbers 0.47808014217793471 and 0.47669974542039584 differ FAILED...numbers 3.990 and 3.995 differ FAILED...numbers 0.83 and 0.82 differ FAILED...numbers 0.694 and 0.693 differ FAILED...numbers 0.59393650959795852 and 0.59283257281686375 differ FAILED...numbers 0.61231847926387639 and 0.61355273873787231 differ FAILED...numbers 0.30 and 0.29 differ FAILED...numbers 0.47 and 0.46 differ FAILED...numbers 0.47 and 0.46 differ FAILED...numbers 0.46 and 0.45 differ Test test_resolve_denmod_pdb_memory FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_map_likelihood\tst_resolve_map_likelihood.py" [OK] 309.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_ncs_in_memory\tst_resolve_ncs_in_memory.py" [OK] 176.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_ncs_map_memory\tst_resolve_ncs_map_memory.py" [OK] 162.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_memory\tst_resolve_memory.py" [OK] 630.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_ncs_memory\tst_resolve_ncs_memory.py" [OK] 178.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_ncs_nomemory\tst_resolve_ncs_nomemory.py" [OK] 241.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_pdb_memory\tst_resolve_pdb_memory.py" [OK] 211.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_autobuild\tst_autobuild.py" [OK] 68.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_autobuild_double\tst_autobuild_double.py" [OK] 61.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_average\tst_average.py" [OK] 24.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_average_double\tst_average_double.py" [OK] 23.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_denmod_refine_after_mr\tst_denmod_refine_after_mr.py" [OK] 15.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_denmod_refine_after_mr_double\tst_denmod_refine_after_mr_double.py" [OK] 15.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_fixed_model\tst_fixed_model.py" [OK] 16.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_hhr\tst_hhr.py" [OK] 17.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_mr_rescoring\tst_mr_rescoring.py" [OK] 12.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_mr_rescoring_double\tst_mr_rescoring_double.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_place_model\tst_place_model.py" [OK] 24.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_place_model_double\tst_place_model_double.py" [OK] 19.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_place_model_ps\tst_place_model_ps.py" [OK] 15.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_prerefine\tst_prerefine.py" [OK] 16.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_prerefine_double\tst_prerefine_double.py" [OK] 13.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_prerefine_no_data\tst_prerefine_no_data.py" [OK] 11.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_real_space\tst_real_space.py" [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_refine_after_mr\tst_refine_after_mr.py" [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_refine_after_mr_double\tst_refine_after_mr_double.py" [OK] 19.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_refine_top_models\tst_refine_top_models.py" [OK] 22.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_refine_top_models_double\tst_refine_top_models_double.py" [OK] 22.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_combine_models\tst_combine_models.py" [OK] 113.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_commands\tst_commands.py" [OK] 91.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_connect_all_segments\tst_connect_all_segments.py" [OK] 41.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_density_outside_model\tst_density_outside_model.py" [OK] 55.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_find_helices_strands\tst_find_helices_strands.py" [OK] 87.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_assign_sequence\tst_assign_sequence.py" [FAIL] 445.2s Time: 445.24 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 4 and 2 differ FAILED...numbers 11.1759039048 and 13.6364398947 differ FAILED...numbers 4 and 2 differ FAILED...numbers 11.1759039048 and 13.6364398947 differ FAILED...numbers 4 and 2 differ FAILED...numbers 11.1759039048 and 13.6364398947 differ FAILED...numbers 11.1759039048 and 13.6364398947 differ FAILED...numbers 11.1759039048 and 13.6364398947 differ FAILED...numbers 11.1759039048 and 13.6364398947 differ FAILED...numbers 75.1598149457 and 54.0527939614 differ Test test_assign_sequence FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_cluster\tst_cluster.py" [FAIL] 4687.0s Time: 4687.03 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_phaser_denmod\tst_phaser_denmod.py" [FAIL] 195.3s Time: 195.30 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 0.04 and 0.03 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ Test test_phaser_denmod FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_std\tst_AutoSol_std.py" [FAIL] 13831.5s Time: 13831.52 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_replace_side_chains\tst_replace_side_chains.py" [OK] 85.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_remove_free_from_map\tst_remove_free_from_map.py" [OK] 138.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_r_free_flag\tst_r_free_flag.py" [OK] 354.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_unmerged_mir\tst_unmerged_mir.py" [OK] 677.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_morph_model\tst_morph_model.py" [OK] 1869.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_change_sg\tst_change_sg.py" [OK] 5811.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_trace_tests\test_fit_loops_trace\tst_fit_loops_trace.py" [OK] 87.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_inv_sg\tst_inv_sg.py" [FAIL] 5685.8s Time: 5685.78 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_wizards_tests\test_find_ca_from_map\tst_find_ca_from_map.py" [OK] 216.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_trace_tests\test_trace\tst_trace.py" [FAIL] 335.9s Time: 335.91 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 5756 and 5759 differ FAILED...numbers 5.983623 and 6.019765 differ Test test_trace FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_trace_tests\test_fit_gap_trace\tst_fit_gap_trace.py" [OK] 803.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\extract_segment_pair_tests\test_rna\tst_rna.py" [OK] 77.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\extract_segment_pair_tests\test_protein\tst_protein.py" [OK] 195.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\help_tests\test_help\tst_help.py" [OK] 17.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\extract_segment_tests\test_helix\tst_helix.py" [OK] 82.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\extract_segment_tests\test_strand\tst_strand.py" [OK] 75.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_builder\tst_LigandFit_builder.py" [FAIL] 61.9s Time: 61.91 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_builder\tst_LigandFit_builder.py", line 56, in run_wizard_test(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix_regression\wizards\run_wizard_test.py", line 184, in run_wizard_test module.run(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.wizards.test_all_parallel\LigandFit_tests\test_LigandFit_builder\tst_LigandFit_builder.py", line 26, in run run_ligandfit(args=args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 564, in __init__ self.RunWizard() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 1001, in RunWizard self.runWizard.run() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 836, in Run self.DoNextMethod() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1004, in DoNextMethod raise AssertionError, line AssertionError: Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\LigandFit.py", line 2044, in LigandFit_fit_ligand r.run(out=sys.stdout) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\run_group_of_wizards_win32.py", line 41, in run pool = multiprocessing.Pool(processes=self.nproc) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\__init__.py", line 232, in Pool return Pool(processes, initializer, initargs, maxtasksperchild) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\pool.py", line 161, in __init__ self._repopulate_pool() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\pool.py", line 225, in _repopulate_pool w.start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\process.py", line 130, in start self._popen = Popen(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 272, in __init__ prep_data = get_preparation_data(process_obj._name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 409, in get_preparation_data not d['sys_argv'][0].lower().endswith('pythonservice.exe'): IndexError: list index out of range Traceback (most recent call last): File "", line 1, in File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 379, in main preparation_data = load(from_parent) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 1384, in load return Unpickler(file).load() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 864, in load dispatch[key](self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 886, in load_eof raise EOFError EOFError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\labels_tests\test_labels\tst_labels.py" [OK] 329.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_morph_model_hl\tst_morph_model_hl.py" [OK] 3354.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\input_files_tests\test_input_files\tst_input_files.py" [OK] 1043.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_sir_sad\tst_AutoSol_sir_sad.py" [FAIL] 17303.5s Time: 17303.53 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\map_to_object_tests\test_map_to_object\tst_map_to_object.py" [OK] 27.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\misc_methods_tests\test_misc_methods\tst_misc_methods.py" [OK] 105.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\missing_data_tests\test_missing_data\tst_missing_data.py" [OK] 126.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_wizards_tests\test_map_to_model\tst_map_to_model.py" [OK] 2429.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\multi_tests\test_multi\tst_multi.py" [OK] 64.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_std\tst_LigandFit_std.py" [OK] 1193.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\ncs_tests\test_ncs\tst_ncs.py" [OK] 193.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\ncs_in_phenix_refine_tests\test_ncs_in_phenix_refine\tst_ncs_in_phenix_refine.py" [OK] 744.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_wizards_tests\test_autosol_test_flag\tst_autosol_test_flag.py" [FAIL] 3375.4s Time: 3375.36 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_wizards_tests\test_autosol_test_flag\tst_autosol_test_flag.py", line 56, in run_wizard_test(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix_regression\wizards\run_wizard_test.py", line 184, in run_wizard_test module.run(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.wizards.test_all_parallel\command_line_wizards_tests\test_autosol_test_flag\tst_autosol_test_flag.py", line 26, in run run_autosol(args=args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 564, in __init__ self.RunWizard() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 1001, in RunWizard self.runWizard.run() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 836, in Run self.DoNextMethod() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1004, in DoNextMethod raise AssertionError, line AssertionError: Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 10679, in AutoSol_build self.Build_with_phase_and_build() # use phase_and_build routines File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 11120, in Build_with_phase_and_build b=phase_and_build(args,resolve_libs=resolve_libs) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\phase_and_build.py", line 580, in __init__ self.run(out=out) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\phase_and_build.py", line 761, in run self.run_phase_improvement_cycles(out=out) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\phase_and_build.py", line 1005, in run_phase_improvement_cycles ncs_info_file=self.ncs_info_file) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\phase_and_build.py", line 1647, in run_autobuild_maps_only "ERROR MESSAGE: \n"+line) Sorry: Failed to run density modification in phase_and_build ERROR MESSAGE: local variable 'overall_offset_list' referenced before assignment libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_non_standard_sg\tst_non_standard_sg.py" [OK] 8663.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\maps_only_tests\test_maps_only\tst_maps_only.py" [OK] 2180.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_extra\tst_extra.py" [OK] 69.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_cif\tst_LigandFit_cif.py" [OK] 3208.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\omit_lig_tests\test_omit_lig\tst_omit_lig.py" [OK] 890.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_local_pattern_2\tst_local_pattern_2.py" [OK] 118.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_local_pattern_3\tst_local_pattern_3.py" [OK] 123.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_index_file\tst_index_file.py" [OK] 178.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_pdb_in\tst_pdb_in.py" [OK] 122.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_resolve_pattern\tst_resolve_pattern.py" [OK] 61.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_read_hist\tst_read_hist.py" [OK] 90.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_lc\tst_LigandFit_lc.py" [OK] 3155.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_read_pattern\tst_read_pattern.py" [OK] 86.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_setup\tst_setup.py" [OK] 65.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_align_bases\tst_align_bases.py" [OK] 70.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_bad\tst_bad.py" [OK] 79.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build\tst_build.py" [OK] 88.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build_1\tst_build_1.py" [OK] 81.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_background_map\tst_background_map.py" [OK] 140.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build_repeat\tst_build_repeat.py" [OK] 97.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build_se\tst_build_se.py" [OK] 86.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_cc\tst_cc.py" [OK] 76.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build_image\tst_build_image.py" [OK] 136.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_cc_mask\tst_cc_mask.py" [OK] 83.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_chain_name\tst_chain_name.py" [OK] 84.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_composite_pdb\tst_composite_pdb.py" [OK] 71.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_combine\tst_combine.py" [OK] 133.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_connect\tst_connect.py" [OK] 73.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_create_hist\tst_create_hist.py" [OK] 67.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_combine_maps\tst_combine_maps.py" [OK] 184.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_cross\tst_cross.py" [OK] 79.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_compare\tst_compare.py" [OK] 241.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_dump_frags\tst_dump_frags.py" [OK] 84.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_dump_mask\tst_dump_mask.py" [OK] 69.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_extend_rna\tst_extend_rna.py" [OK] 84.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_dump_relat\tst_dump_relat.py" [OK] 134.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_find_ncs\tst_find_ncs.py" [OK] 96.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_find_ncs_mlt\tst_find_ncs_mlt.py" [OK] 97.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_diff_map\tst_diff_map.py" [OK] 240.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_find_strands\tst_find_strands.py" [OK] 92.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_fit\tst_fit.py" [OK] 82.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_fit_start\tst_fit_start.py" [OK] 85.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_free\tst_free.py" [OK] 87.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_getdir_solve_only\tst_getdir_solve_only.py" [OK] 71.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_get_histograms\tst_get_histograms.py" [OK] 70.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_get_inputs\tst_get_inputs.py" [OK] 69.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_helices_find\tst_helices_find.py" [OK] 68.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_helices_trace\tst_helices_trace.py" [OK] 71.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_helix_trace\tst_helix_trace.py" [FAIL] 75.7s Time: 75.69 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 13 and 11 differ FAILED...numbers 11 and 10 differ FAILED...numbers 11 and 10 differ Test test_helix_trace FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_highest_mask\tst_highest_mask.py" [OK] 94.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_high_pass\tst_high_pass.py" [OK] 96.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_hist\tst_hist.py" [OK] 95.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_just_box\tst_just_box.py" [OK] 97.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_fit\tst_ligand_fit.py" [OK] 64.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_fit_distance\tst_ligand_fit_distance.py" [OK] 61.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_image\tst_image.py" [OK] 182.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_group\tst_ligand_group.py" [OK] 115.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_relat\tst_ligand_relat.py" [OK] 81.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_rot_trans\tst_ligand_rot_trans.py" [OK] 81.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_volume\tst_ligand_volume.py" [OK] 80.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_link_prob\tst_link_prob.py" [OK] 79.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_local_hist\tst_local_hist.py" [OK] 72.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_main_map\tst_main_map.py" [OK] 77.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_large\tst_ligand_large.py" [OK] 182.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_mask_s_p\tst_mask_s_p.py" [OK] 139.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_misc\tst_misc.py" [OK] 137.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_modify_hist\tst_modify_hist.py" [OK] 69.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_modify_ncs\tst_modify_ncs.py" [OK] 72.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_mask_image\tst_mask_image.py" [OK] 232.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_morph\tst_morph.py" [OK] 59.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_mp_file\tst_mp_file.py" [OK] 62.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ncs_groups\tst_ncs_groups.py" [OK] 66.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_masks\tst_masks.py" [OK] 329.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_n_model_create\tst_n_model_create.py" [OK] 69.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_offset\tst_offset.py" [OK] 63.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_offset_pdb\tst_offset_pdb.py" [OK] 61.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_no_erase_protein\tst_no_erase_protein.py" [OK] 108.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_maps\tst_maps.py" [OK] 423.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_omit_box_id\tst_omit_box_id.py" [OK] 62.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_opt_ncs\tst_opt_ncs.py" [OK] 58.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resno_tests\test_resno\tst_resno.py" [FAIL] 2006.6s Time: 2006.65 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_outside\tst_outside.py" [OK] 65.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_omit_mask\tst_omit_mask.py" [OK] 101.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_omit_region\tst_omit_region.py" [OK] 94.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ps_edit\tst_ps_edit.py" [OK] 56.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_q\tst_q.py" [OK] 61.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_randomize_side\tst_randomize_side.py" [OK] 67.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_planar_rings\tst_planar_rings.py" [OK] 143.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_randomize_denmod\tst_randomize_denmod.py" [OK] 99.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_random_map\tst_random_map.py" [OK] 64.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_read_peaks\tst_read_peaks.py" [OK] 79.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_rebuild\tst_rebuild.py" [OK] 62.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_prime_and_switch\tst_prime_and_switch.py" [OK] 177.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_resolve_multi\tst_resolve_multi.py" [OK] 57.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_rebuild_side\tst_rebuild_side.py" [OK] 59.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_resolve_multi_b\tst_resolve_multi_b.py" [OK] 58.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_resolve_multi_c\tst_resolve_multi_c.py" [OK] 100.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_scores\tst_scores.py" [OK] 105.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_score_tert\tst_score_tert.py" [OK] 101.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_search_center\tst_search_center.py" [OK] 104.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_set_fract\tst_set_fract.py" [FAIL] 114.3s Time: 114.28 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 23.262 and 23.128 differ FAILED...numbers 1.10 and 1.11 differ FAILED...numbers 7.227 and 7.134 differ FAILED...numbers 0.727 and 0.729 differ FAILED...numbers 13.186 and 13.155 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 4.236 and 4.250 differ FAILED...numbers 0.733 and 0.732 differ FAILED...numbers -12.071 and -12.078 differ FAILED...numbers 1.18 and 1.17 differ FAILED...numbers 1.12 and 1.11 differ FAILED...numbers 0.22 and 0.21 differ FAILED...numbers 1.31 and 1.32 differ FAILED...numbers -0.44 and -0.43 differ FAILED...numbers 6.348 and 6.375 differ FAILED...numbers 1.20 and 1.19 differ FAILED...numbers 0.31 and 0.32 differ FAILED...numbers 1.71 and 1.72 differ FAILED...numbers -0.49 and -0.50 differ FAILED...numbers 1.19 and 1.18 differ Test test_set_fract FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_set_hist\tst_set_hist.py" [FAIL] 106.9s Time: 106.89 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 0.642 and 0.643 differ FAILED...numbers 0.515 and 0.514 differ FAILED...numbers 0.513 and 0.514 differ FAILED...numbers 0.490 and 0.491 differ FAILED...numbers 0.563 and 0.564 differ FAILED...numbers 0.468 and 0.461 differ FAILED...numbers 0.599 and 0.597 differ FAILED...numbers 0.569 and 0.571 differ FAILED...numbers 0.513 and 0.514 differ FAILED...numbers 19.826 and 19.784 differ Test test_set_hist FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_trace\tst_trace.py" [FAIL] 63.2s Time: 63.19 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 32 and 25 differ Test test_trace FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_trace_analyze\tst_trace_analyze.py" [OK] 61.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_unit_tests\tst_unit_tests.py" [OK] 60.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_sharpen\tst_sharpen.py" [OK] 109.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_solvent_prob_min\tst_solvent_prob_min.py" [OK] 106.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_special\tst_special.py" [OK] 100.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_update_proxy\tst_update_proxy.py" [OK] 59.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_write_ezd\tst_write_ezd.py" [OK] 56.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_write_pdb_occ\tst_write_pdb_occ.py" [OK] 57.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_write_ca\tst_write_ca.py" [OK] 70.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_zero_hl\tst_zero_hl.py" [OK] 62.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\short_seq_tests\test_short_seq\tst_short_seq.py" [OK] 27.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\segment_library_tests\test_segment_library\tst_segment_library.py" [OK] 109.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\side_chains_tests\test_clusters\tst_clusters.py" [OK] 122.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\side_chains_tests\test_use_clusters\tst_use_clusters.py" [OK] 116.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\side_chains_tests\test_write_map\tst_write_map.py" [OK] 119.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\side_chains_update_tests\test_update\tst_update.py" [OK] 114.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_avg_omit\tst_avg_omit.py" [OK] 71.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_addseed\tst_addseed.py" [OK] 126.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_btof\tst_btof.py" [OK] 90.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_cart_to_fract\tst_cart_to_fract.py" [OK] 95.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_cluster\tst_cluster.py" [OK] 99.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_compare_soln\tst_compare_soln.py" [OK] 96.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_combine\tst_combine.py" [OK] 111.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_cc\tst_cc.py" [OK] 166.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_fdiff\tst_fdiff.py" [OK] 94.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_generate_mad\tst_generate_mad.py" [OK] 92.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_generate_mir\tst_generate_mir.py" [OK] 95.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_hassp\tst_hassp.py" [OK] 95.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mad\tst_mad.py" [OK] 84.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mad_mtz\tst_mad_mtz.py" [OK] 107.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_maps\tst_maps.py" [OK] 108.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_extra\tst_extra.py" [OK] 228.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_map_to_asym\tst_map_to_asym.py" [OK] 108.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_math\tst_math.py" [OK] 110.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mir\tst_mir.py" [OK] 112.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mir_mtz\tst_mir_mtz.py" [OK] 80.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_pdb_xyz_in\tst_pdb_xyz_in.py" [OK] 75.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mirror\tst_mirror.py" [OK] 92.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_phases_mtz\tst_phases_mtz.py" [OK] 76.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_question\tst_question.py" [OK] 68.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_read_ano\tst_read_ano.py" [OK] 94.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_rho\tst_rho.py" [OK] 101.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_scale\tst_scale.py" [OK] 114.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_sites_from_phases\tst_sites_from_phases.py" [OK] 121.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_solve\tst_solve.py" [OK] 127.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_sym\tst_sym.py" [OK] 123.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_systematic\tst_systematic.py" [OK] 83.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_weights\tst_weights.py" [OK] 61.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\omit_tests\test_omit\tst_omit.py" [OK] 3539.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\mult_tests\test_mult\tst_mult.py" [OK] 4440.6s ================================================================================ Tests finished. Elapsed time: 27404.41s Distribution of test runtimes: 11.3s - 1740.6s: 301 1740.6s - 3469.8s: 13 3469.8s - 5199.0s: 7 5199.0s - 6928.2s: 4 6928.2s - 8657.4s: 5 8657.4s - 10386.7s: 1 10386.7s - 12115.9s: 0 12115.9s - 13845.1s: 1 13845.1s - 15574.3s: 0 15574.3s - 17303.5s: 1 Warning: the following jobs took at least 180 seconds: libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_image\tst_image.py": 182.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_large\tst_ligand_large.py": 182.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_combine_maps\tst_combine_maps.py": 184.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_omit_tests\test_omit_selection\tst_omit_selection.py": 188.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_bayesian_estimator\tst_bayesian_estimator.py": 192.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\ncs_tests\test_ncs\tst_ncs.py": 193.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\extract_segment_pair_tests\test_protein\tst_protein.py": 195.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_phaser_denmod\tst_phaser_denmod.py": 195.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_segment\tst_segment.py": 195.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_map_to_model_overall\tst_map_to_model_overall.py": 198.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_delete_bad\tst_delete_bad.py": 202.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_pdb_memory\tst_resolve_pdb_memory.py": 211.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_wizards_tests\test_find_ca_from_map\tst_find_ca_from_map.py": 216.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_extra\tst_extra.py": 228.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_mask_image\tst_mask_image.py": 232.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_diff_map\tst_diff_map.py": 240.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_compare\tst_compare.py": 241.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_ncs_nomemory\tst_resolve_ncs_nomemory.py": 241.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_se_lig_in_refine\tst_se_lig_in_refine.py": 244.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_zero_fom\tst_zero_fom.py": 252.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_dos\tst_dos.py": 252.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_aniso_from_coords\tst_aniso_from_coords.py": 258.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_denmod_memory\tst_resolve_denmod_memory.py": 264.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_denmod_pdb_memory\tst_resolve_denmod_pdb_memory.py": 267.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_ps_in_rebuild\tst_ps_in_rebuild.py": 276.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_find_ncs\tst_find_ncs.py": 281.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_two_fofc_in_rebuild\tst_two_fofc_in_rebuild.py": 298.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_two_fofc_denmod_in_rebuild\tst_two_fofc_denmod_in_rebuild.py": 303.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_map_likelihood\tst_resolve_map_likelihood.py": 309.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_build_in_memory\tst_build_in_memory.py": 321.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_masks\tst_masks.py": 329.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\labels_tests\test_labels\tst_labels.py": 329.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_morph_model_in_memory\tst_morph_model_in_memory.py": 332.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_trace_tests\test_trace\tst_trace.py": 335.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_r_free_flag\tst_r_free_flag.py": 354.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_loops_tests\test_loop_lib\tst_loop_lib.py": 362.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_ncs_change_of_basis\tst_ncs_change_of_basis.py": 412.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_maps\tst_maps.py": 423.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_assign_sequence\tst_assign_sequence.py": 445.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\commands_in_doc_tests\test_commands_in_doc\tst_commands_in_doc.py": 482.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\autosol_unmerged_tests\test_autosol_unmerged\tst_autosol_unmerged.py": 510.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_omit\tst_AutoBuild_omit.py": 535.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_dano_labels\tst_dano_labels.py": 564.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_gap\tst_AutoBuild_gap.py": 612.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_memory\tst_resolve_memory.py": 630.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_phase_and_build_rs\tst_phase_and_build_rs.py": 667.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_unmerged_mir\tst_unmerged_mir.py": 677.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_outside\tst_AutoBuild_outside.py": 678.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\ncs_in_phenix_refine_tests\test_ncs_in_phenix_refine\tst_ncs_in_phenix_refine.py": 744.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_trace_tests\test_fit_gap_trace\tst_fit_gap_trace.py": 803.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_extend\tst_AutoBuild_extend.py": 815.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_build_one_model\tst_build_one_model.py": 879.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\omit_lig_tests\test_omit_lig\tst_omit_lig.py": 890.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_lig\tst_AutoBuild_lig.py": 908.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_truncate\tst_AutoBuild_truncate.py": 951.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_set_sg\tst_set_sg.py": 1007.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_library\tst_ligand_library.py": 1035.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_autobuild_quick\tst_autobuild_quick.py": 1043.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\input_files_tests\test_input_files\tst_input_files.py": 1043.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_map_to_object_and_sort_hetatms\tst_map_to_object_and_sort_hetatms.py": 1190.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_std\tst_LigandFit_std.py": 1193.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_map_to_model_tests\test_iterative_ss_refine\tst_iterative_ss_refine.py": 1294.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_phase_and_build_perfect\tst_phase_and_build_perfect.py": 1460.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_morph_model\tst_morph_model.py": 1869.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_ncs\tst_AutoBuild_ncs.py": 1899.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resno_tests\test_resno\tst_resno.py": 2006.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\maps_only_tests\test_maps_only\tst_maps_only.py": 2180.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_refine\tst_ligand_refine.py": 2184.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_scale_and_merge\tst_scale_and_merge.py": 2208.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_wizards_tests\test_map_to_model\tst_map_to_model.py": 2429.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_run_phenix_refine\tst_run_phenix_refine.py": 3008.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_lc\tst_LigandFit_lc.py": 3155.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_cif\tst_LigandFit_cif.py": 3208.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_ncs\tst_ligand_ncs.py": 3254.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_morph_model_hl\tst_morph_model_hl.py": 3354.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_wizards_tests\test_autosol_test_flag\tst_autosol_test_flag.py": 3375.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\omit_tests\test_omit\tst_omit.py": 3539.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoMR_tests\test_AutoMR_std\tst_AutoMR_std.py": 4290.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_std\tst_AutoBuild_std.py": 4431.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\mult_tests\test_mult\tst_mult.py": 4440.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_cluster\tst_cluster.py": 4687.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_A001\tst_AutoBuild_A001.py": 4687.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_hires\tst_AutoBuild_hires.py": 4754.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_inv_sg\tst_inv_sg.py": 5685.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_mult\tst_AutoBuild_mult.py": 5800.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_change_sg\tst_change_sg.py": 5811.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mir\tst_AutoSol_mir.py": 6791.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_phase_and_build\tst_phase_and_build.py": 7066.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_rna\tst_AutoSol_rna.py": 7090.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_phaser\tst_AutoSol_phaser.py": 7168.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mad\tst_AutoSol_mad.py": 7714.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_build\tst_AutoBuild_build.py": 8063.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_non_standard_sg\tst_non_standard_sg.py": 8663.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_std\tst_AutoSol_std.py": 13831.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_sir_sad\tst_AutoSol_sir_sad.py": 17303.5s Please try to reduce overall runtime - consider splitting up these tests. Error: the following jobs returned non-zero exit codes or suspicious stderr output: libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_phaser_mr\tst_AutoSol_phaser_mr.py" [FAIL] 168.2s Time: 168.15 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ Test test_AutoSol_phaser_mr FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_mult\tst_AutoBuild_mult.py" [FAIL] 5800.3s Time: 5800.35 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\autosol_unmerged_tests\test_autosol_unmerged\tst_autosol_unmerged.py" [FAIL] 510.3s Time: 510.28 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ FAILED...numbers 2 and 6 differ Test test_autosol_unmerged FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mir\tst_AutoSol_mir.py" [FAIL] 6791.2s Time: 6791.21 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mad\tst_AutoSol_mad.py" [FAIL] 7714.3s Time: 7714.26 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_list\tst_ligand_list.py" [FAIL] 135.3s Time: 135.32 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_list\tst_ligand_list.py", line 56, in run_wizard_test(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix_regression\wizards\run_wizard_test.py", line 184, in run_wizard_test module.run(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.wizards.test_all_parallel\command_line_ligands_tests\test_ligand_list\tst_ligand_list.py", line 26, in run run_ligandfit(args=args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 564, in __init__ self.RunWizard() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 1001, in RunWizard self.runWizard.run() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 836, in Run self.DoNextMethod() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1004, in DoNextMethod raise AssertionError, line AssertionError: Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\LigandFit.py", line 2044, in LigandFit_fit_ligand r.run(out=sys.stdout) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\run_group_of_wizards_win32.py", line 41, in run pool = multiprocessing.Pool(processes=self.nproc) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\__init__.py", line 232, in Pool return Pool(processes, initializer, initargs, maxtasksperchild) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\pool.py", line 161, in __init__ self._repopulate_pool() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\pool.py", line 225, in _repopulate_pool w.start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\process.py", line 130, in start self._popen = Popen(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 272, in __init__ prep_data = get_preparation_data(process_obj._name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 409, in get_preparation_data not d['sys_argv'][0].lower().endswith('pythonservice.exe'): IndexError: list index out of range Traceback (most recent call last): File "", line 1, in File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 379, in main preparation_data = load(from_parent) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 1384, in load return Unpickler(file).load() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 864, in load dispatch[key](self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 886, in load_eof raise EOFError EOFError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_phaser\tst_AutoSol_phaser.py" [FAIL] 7168.7s Time: 7168.71 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_dos\tst_dos.py" [FAIL] 252.9s Time: 252.94 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ Test test_dos FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_dano_labels\tst_dano_labels.py" [FAIL] 564.9s Time: 564.95 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 41 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 41 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 41 differ FAILED...numbers 21 and 41 differ FAILED...numbers 21 and 41 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 2 and 1 differ Test test_dano_labels FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_phaser\tst_phaser.py" [FAIL] 158.1s Time: 158.14 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ FAILED...numbers 21 and 1 differ Test test_phaser FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_density_modification\tst_density_modification.py" [FAIL] 153.1s Time: 153.08 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 0.359 and 0.361 differ FAILED...numbers 2.530 and 2.525 differ FAILED...numbers 0.16 and 0.15 differ FAILED...numbers 1.42 and 1.41 differ FAILED...numbers 0.424 and 0.425 differ FAILED...numbers 0.71 and 0.72 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 1.23 and 1.22 differ FAILED...numbers 4.885 and 4.886 differ FAILED...numbers 0.25 and 0.24 differ FAILED...numbers 0.12 and 0.13 differ FAILED...numbers 0.14 and 0.15 differ FAILED...numbers 0.34 and 0.33 differ FAILED...numbers 0.17392889504890346 and 0.17284358043114709 differ FAILED...numbers 0.39 and 0.38 differ FAILED...numbers 0.26 and 0.25 differ FAILED...numbers 0.56277425327518105 and 0.56030388499260697 differ FAILED...numbers 1.282 and 1.309 differ FAILED...numbers 0.7771232 and 0.7752666 differ FAILED...numbers 4.8085 and 4.8049 differ FAILED...numbers -8.35 and -8.36 differ FAILED...numbers -0.2174 and -0.2152 differ FAILED...numbers -0.2174 and -0.2152 differ FAILED...numbers 12.23638 and 12.24053 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 0.196 and 0.197 differ FAILED...numbers 3317 and 3307 differ FAILED...numbers 5981 and 5959 differ FAILED...numbers 0.04 and 0.05 differ FAILED...numbers 0.27 and 0.28 differ FAILED...numbers 0.03 and 0.05 differ FAILED...numbers 0.22 and 0.25 differ FAILED...numbers 4.10222244511827747E-02 and 3.32653811599860420E-002 differ FAILED...numbers 228.872 and 225.091 differ FAILED...numbers 0.24 and 0.23 differ FAILED...numbers 0.15 and 0.14 differ FAILED...numbers 4.8085 and 4.8049 differ FAILED...numbers -8.35 and -8.36 differ FAILED...numbers -0.2174 and -0.2152 differ FAILED...numbers -0.2174 and -0.2152 differ FAILED...numbers 12.23638 and 12.24053 differ FAILED...numbers 0.15 and 0.14 differ FAILED...numbers 0.43 and 0.44 differ FAILED...numbers 12.2 and 12.3 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 0.84 and 0.83 differ FAILED...numbers 0.53 and 0.51 differ FAILED...numbers 0.34 and 0.35 differ FAILED...numbers 0.32 and 0.33 differ FAILED...numbers 0.32 and 0.33 differ FAILED...numbers 0.53 and 0.51 differ FAILED...numbers 0.34 and 0.35 differ FAILED...numbers 0.32 and 0.33 differ FAILED...numbers 0.32 and 0.33 differ FAILED...numbers 0.52301972220232196 and 0.52540002738708980 differ FAILED...numbers 1.400 and 1.435 differ FAILED...numbers 0.53 and 0.51 differ Test test_density_modification FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_resolve_denmod_pdb_memory\tst_resolve_denmod_pdb_memory.py" [FAIL] 267.2s Time: 267.17 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers -0.57 and -0.56 differ FAILED...numbers 0.60 and 0.61 differ FAILED...numbers 5.71 and 5.72 differ FAILED...numbers 1.442 and 1.432 differ FAILED...numbers 6553 and 6556 differ FAILED...numbers 0.67624596307400620 and 0.67725417442606084 differ FAILED...numbers 5752 and 5754 differ FAILED...numbers 0.723 and 0.724 differ FAILED...numbers 0.34 and 0.35 differ FAILED...numbers 0.74991903427078965 and 0.75164617882000184 differ FAILED...numbers 0.34412563867733209 and 0.34530512242051420 differ FAILED...numbers 5752 and 5754 differ FAILED...numbers 0.41 and 0.40 differ FAILED...numbers 0.41 and 0.40 differ FAILED...numbers 0.48 and 0.47 differ FAILED...numbers 0.41 and 0.40 differ FAILED...numbers 0.74924231570536692 and 0.75085512409060018 differ FAILED...numbers 0.47422510307404170 and 0.47290034020940463 differ FAILED...numbers 5752 and 5754 differ FAILED...numbers -0.65 and -0.64 differ FAILED...numbers 0.74 and 0.75 differ FAILED...numbers 4.96 and 4.97 differ FAILED...numbers 0.47808014217793471 and 0.47669974542039584 differ FAILED...numbers 3.990 and 3.995 differ FAILED...numbers 0.83 and 0.82 differ FAILED...numbers 0.694 and 0.693 differ FAILED...numbers 0.59393650959795852 and 0.59283257281686375 differ FAILED...numbers 0.61231847926387639 and 0.61355273873787231 differ FAILED...numbers 0.30 and 0.29 differ FAILED...numbers 0.47 and 0.46 differ FAILED...numbers 0.47 and 0.46 differ FAILED...numbers 0.46 and 0.45 differ Test test_resolve_denmod_pdb_memory FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_assign_sequence\tst_assign_sequence.py" [FAIL] 445.2s Time: 445.24 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 4 and 2 differ FAILED...numbers 11.1759039048 and 13.6364398947 differ FAILED...numbers 4 and 2 differ FAILED...numbers 11.1759039048 and 13.6364398947 differ FAILED...numbers 4 and 2 differ FAILED...numbers 11.1759039048 and 13.6364398947 differ FAILED...numbers 11.1759039048 and 13.6364398947 differ FAILED...numbers 11.1759039048 and 13.6364398947 differ FAILED...numbers 11.1759039048 and 13.6364398947 differ FAILED...numbers 75.1598149457 and 54.0527939614 differ Test test_assign_sequence FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_cluster\tst_cluster.py" [FAIL] 4687.0s Time: 4687.03 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_phaser_denmod\tst_phaser_denmod.py" [FAIL] 195.3s Time: 195.30 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 0.04 and 0.03 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ FAILED...numbers 21 and 43 differ Test test_phaser_denmod FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_std\tst_AutoSol_std.py" [FAIL] 13831.5s Time: 13831.52 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_inv_sg\tst_inv_sg.py" [FAIL] 5685.8s Time: 5685.78 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_trace_tests\test_trace\tst_trace.py" [FAIL] 335.9s Time: 335.91 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 5756 and 5759 differ FAILED...numbers 5.983623 and 6.019765 differ Test test_trace FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_builder\tst_LigandFit_builder.py" [FAIL] 61.9s Time: 61.91 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_builder\tst_LigandFit_builder.py", line 56, in run_wizard_test(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix_regression\wizards\run_wizard_test.py", line 184, in run_wizard_test module.run(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.wizards.test_all_parallel\LigandFit_tests\test_LigandFit_builder\tst_LigandFit_builder.py", line 26, in run run_ligandfit(args=args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 564, in __init__ self.RunWizard() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 1001, in RunWizard self.runWizard.run() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 836, in Run self.DoNextMethod() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1004, in DoNextMethod raise AssertionError, line AssertionError: Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\LigandFit.py", line 2044, in LigandFit_fit_ligand r.run(out=sys.stdout) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\run_group_of_wizards_win32.py", line 41, in run pool = multiprocessing.Pool(processes=self.nproc) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\__init__.py", line 232, in Pool return Pool(processes, initializer, initargs, maxtasksperchild) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\pool.py", line 161, in __init__ self._repopulate_pool() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\pool.py", line 225, in _repopulate_pool w.start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\process.py", line 130, in start self._popen = Popen(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 272, in __init__ prep_data = get_preparation_data(process_obj._name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 409, in get_preparation_data not d['sys_argv'][0].lower().endswith('pythonservice.exe'): IndexError: list index out of range Traceback (most recent call last): File "", line 1, in File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\multiprocessing\forking.py", line 379, in main preparation_data = load(from_parent) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 1384, in load return Unpickler(file).load() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 864, in load dispatch[key](self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\conda_base\lib\pickle.py", line 886, in load_eof raise EOFError EOFError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_sir_sad\tst_AutoSol_sir_sad.py" [FAIL] 17303.5s Time: 17303.53 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_wizards_tests\test_autosol_test_flag\tst_autosol_test_flag.py" [FAIL] 3375.4s Time: 3375.36 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_wizards_tests\test_autosol_test_flag\tst_autosol_test_flag.py", line 56, in run_wizard_test(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix_regression\wizards\run_wizard_test.py", line 184, in run_wizard_test module.run(args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.wizards.test_all_parallel\command_line_wizards_tests\test_autosol_test_flag\tst_autosol_test_flag.py", line 26, in run run_autosol(args=args) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 564, in __init__ self.RunWizard() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 1001, in RunWizard self.runWizard.run() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 836, in Run self.DoNextMethod() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1004, in DoNextMethod raise AssertionError, line AssertionError: Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 10679, in AutoSol_build self.Build_with_phase_and_build() # use phase_and_build routines File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 11120, in Build_with_phase_and_build b=phase_and_build(args,resolve_libs=resolve_libs) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\phase_and_build.py", line 580, in __init__ self.run(out=out) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\phase_and_build.py", line 761, in run self.run_phase_improvement_cycles(out=out) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\phase_and_build.py", line 1005, in run_phase_improvement_cycles ncs_info_file=self.ncs_info_file) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\phase_and_build.py", line 1647, in run_autobuild_maps_only "ERROR MESSAGE: \n"+line) Sorry: Failed to run density modification in phase_and_build ERROR MESSAGE: local variable 'overall_offset_list' referenced before assignment libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_helix_trace\tst_helix_trace.py" [FAIL] 75.7s Time: 75.69 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 13 and 11 differ FAILED...numbers 11 and 10 differ FAILED...numbers 11 and 10 differ Test test_helix_trace FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resno_tests\test_resno\tst_resno.py" [FAIL] 2006.6s Time: 2006.65 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_set_fract\tst_set_fract.py" [FAIL] 114.3s Time: 114.28 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 23.262 and 23.128 differ FAILED...numbers 1.10 and 1.11 differ FAILED...numbers 7.227 and 7.134 differ FAILED...numbers 0.727 and 0.729 differ FAILED...numbers 13.186 and 13.155 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 4.236 and 4.250 differ FAILED...numbers 0.733 and 0.732 differ FAILED...numbers -12.071 and -12.078 differ FAILED...numbers 1.18 and 1.17 differ FAILED...numbers 1.12 and 1.11 differ FAILED...numbers 0.22 and 0.21 differ FAILED...numbers 1.31 and 1.32 differ FAILED...numbers -0.44 and -0.43 differ FAILED...numbers 6.348 and 6.375 differ FAILED...numbers 1.20 and 1.19 differ FAILED...numbers 0.31 and 0.32 differ FAILED...numbers 1.71 and 1.72 differ FAILED...numbers -0.49 and -0.50 differ FAILED...numbers 1.19 and 1.18 differ Test test_set_fract FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_set_hist\tst_set_hist.py" [FAIL] 106.9s Time: 106.89 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 0.642 and 0.643 differ FAILED...numbers 0.515 and 0.514 differ FAILED...numbers 0.513 and 0.514 differ FAILED...numbers 0.490 and 0.491 differ FAILED...numbers 0.563 and 0.564 differ FAILED...numbers 0.468 and 0.461 differ FAILED...numbers 0.599 and 0.597 differ FAILED...numbers 0.569 and 0.571 differ FAILED...numbers 0.513 and 0.514 differ FAILED...numbers 19.826 and 19.784 differ Test test_set_hist FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_trace\tst_trace.py" [FAIL] 63.2s Time: 63.19 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 32 and 25 differ Test test_trace FAILED Please verify these tests manually. Summary: Tests run : 333 Failures : 26 Warnings (possible failures) : 0 Known Failures ( 0) : 0 Known Unstable ( 0) : 0 Stderr output (discouraged) : 17 See run_tests_parallel_zlog for full output. ******************************************************************************** ERROR: 26 TEST FAILURES. PLEASE FIX BEFORE COMMITTING CODE. ******************************************************************************** Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\phenix_regression\wizards\test_all_parallel.py", line 40, in run(sys.argv[1:]) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\phenix_regression\wizards\test_all_parallel.py", line 36, in run raise AssertionError,"AT LEAST ONE TEST FAILED" AssertionError: AT LEAST ONE TEST FAILED Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\cctbx_project\libtbx\command_line\run_tests_parallel.py", line 162, in if (run(sys.argv[1:]) > 0): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\cctbx_project\libtbx\command_line\run_tests_parallel.py", line 93, in run python_keyword_text=python_keyword_text) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\test_utils\parallel.py", line 69, in get_module_tests python_keyword_text=python_keyword_text) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\test_utils\parallel.py", line 47, in get_test_list where_str="").object) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\utils.py", line 1604, in __init__ error_prefix, module_path, where_str, module_path)) ImportError: no module dials.run_tests or possibly import errors in module dials.run_tests Performing actions: tests ===== Running in .: deleting dist, tests, tmp removing .pyc files in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules, walk? True removed 281 files ===== Running in tests\libtbx.import_all_ext: test libtbx.import_all_ext ===== Running in tests\cctbx_regression.test_nightly: test cctbx_regression.test_nightly ===== Running in tests\phenix_regression.test_nightly_windows: test phenix_regression.test_nightly_windows ===== Running in tests\elbow: test elbow ===== Running in build: phenix_html.rebuild_docs.bat ===== Running in tests\phenix_regression.run_p9_sad_benchmark: test p9 sad ===== Running in tests\phenix_regression.run_hipip_refine_benchmark: test hipip ===== Running in tests\phenix_regression.wizards.test_all_parallel: test wizards ===== Running in tests\dials: test dials Bootstrap success: tests 01/05/2020 17:05:43.66