06/10/2019 6:31:29.76 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.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.masks smtbx.refinement smtbx.refinement.constraints smtbx.refinement.constraints.geometrical smtbx.refinement.constraints.tests smtbx.refinement.restraints 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.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.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.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.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 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 File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\xfel\merging\algorithms\error_model\__init__.py", line 3, in ext = boost.python.import_ext("xfel_sdfac_refine_ext") File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\boost\python.py", line 42, in import_ext + [" "+p for p in sys.path])) ImportError: __import__("xfel_sdfac_refine_ext"): DLL load failed: The specified module could not be found. sys.path: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\site-packages C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\command_line C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\reel C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phaser C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\tntbx C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\elbow C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\PyQuante C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\lib C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\site-packages C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\libtbx.import_all_ext C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\python27.zip C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\DLLs C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\plat-win C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\lib-tk c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\site-packages\win32 C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\site-packages\win32\lib C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\site-packages\Pythonwin C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\site-packages\wx-3.0-msw 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: __import__("xfel_sdfac_refine_ext"): DLL load failed: The specified module could not be found. sys.path: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\site-packages C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\command_line C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\reel C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phaser C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\tntbx C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\elbow C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\PyQuante C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\lib C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\site-packages C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\libtbx.import_all_ext C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\python27.zip C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\DLLs C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\plat-win C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\lib-tk c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\site-packages\win32 C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\site-packages\win32\lib C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\site-packages\Pythonwin C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\site-packages\wx-3.0-msw 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 832 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_python3_regression.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_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" 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"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 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"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\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_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_mtz_as_cif.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\pdb\tst_pdb.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_least_squares.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 -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\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_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\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 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_validate_H.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_connectivity.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_coefficients.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_manager.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_1.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_3.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_4.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_5.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_6.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_7.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_8.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_1.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_3.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_4.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_5.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_minimize.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\max_lik\tst_maxlik.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\masks\tst_masks.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\masks\tst_asu_mask.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\max_lik\tst_max_lik.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\dynamics\tst_cartesian_dynamics.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\dynamics\tst_sa.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\examples\f_model_manager.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_bulk_solvent_and_scaling.py" libtbx.python "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_pH_mechanism.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_find_ss_structure.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fix_rotamer_outliers.py" libtbx.python "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 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_1H.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_3.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_4.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_5.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_6.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_1.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_1H.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_2.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_3.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_4.py" libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_5.py" libtbx.python "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\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\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\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] 2.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\queuing_system_utils\pbs_utils.py" [OK] 2.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\queuing_system_utils\sge_utils.py" [OK] 2.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\introspection.py" [OK] 3.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_containers.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\table_utils.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_easy_pickle.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\phil\tst_tokenizer.py" [OK] 3.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\phil\tst_experimental.py" [OK] 3.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\find_reference_cycles.py" [OK] 1.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_path.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\test_utils\__init__.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_easy_mp.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_fully_buffered_timeout.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_str_utils.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_math_utils.py" [OK] 4.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_easy_mp_state.py" [OK] 4.7s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\boost_adaptbx\tests\tst_optional_copy" [OK] 0.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\phil\tst.py" [OK] 4.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\assert_utils.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_binary_search.py" [OK] 3.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_representation.py" [OK] 1.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_object_oriented_patterns.py" [OK] 3.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_dlite.py" [OK] 5.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_topological_sort.py" [OK] 3.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\clusterTests.py" [OK] 3.5s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_1" [OK] 0.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_python_code_parsing.py" [OK] 3.1s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_2" [OK] 0.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_libc_backtrace.py" [OK] 3.1s 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) "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_4" [OK] 0.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_find_unused_imports.py" [OK] 3.5s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_3" [OK] 0.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_citations.py" [OK] 4.2s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_af_5" [OK] 0.6s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_vec3" [OK] 0.5s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_mat3" [OK] 0.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_program_template.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_python3_regression.py" [OK] 4.1s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_unsigned_float_arithmetic" [OK] 0.6s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_sym_mat3" [OK] 0.6s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_ref_matrix_facet" [OK] 0.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_tuple.py" [OK] 3.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_xmlrpc_utils.py" [EXPECTED FAIL] 4.3s Time: 4.34 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_stderr_stdout.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_rational.py" [OK] 3.9s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_accessors" [OK] 0.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_optional.py" [OK] 3.8s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_rectangular_full_packed" [OK] 0.7s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\array_family\tst_optional_copy" [OK] 0.8s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\math\tests\tst" [OK] 0.6s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\matrix\tests\tst_givens" [OK] 0.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_std_pair.py" [OK] 4.1s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\matrix\tests\tst_householder" [OK] 0.7s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\serialization\tst_base_256" [OK] 1.0s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\matrix\tests\tst_svd" [OK] 0.7s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\matrix\tests\tst_cholesky" [OK] 0.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\tst_smoothing.py" [OK] 5.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_stdout.py" [OK] 6.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\matrix\tests\tst_row_echelon.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\stl\tst_map.py" [OK] 2.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_flex_argument_passing.py" [OK] 4.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\error\tst_error.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_gaussian_fit_1d_analytical.py" [OK] 5.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\boost_adaptbx\tests\tst_python_streambuf.py" [OK] 7.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_minimum_covering_ellipsoid.py" [OK] 5.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_cubic_equation.py" [OK] 5.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\matrix\tests\tst_householder.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\linalg\tests\tst_matrix.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\stl\tst_set.py" [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\linalg\tests\tst_lapack_svd.py" [OK] 5.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\linalg\tests\tst_lapack_dsyev.py" [OK] 5.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\linalg\tests\tst_eigensystem.py" [OK] 5.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\stl\tst_vector.py" [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\linalg\tests\tst_cholesky.py" [OK] 7.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_utils.py" [OK] 16.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\regression_test.py" [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\python_utils\tst_graph.py" [OK] 3.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_numpy_bridge.py" [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_smart_selection.py" [OK] 4.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\tst_cubicle_neighbors.py" [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_shared.py" [OK] 4.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\tst_r3_utils.py" [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\python_utils\tst_robust.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\phil\tst_interface.py" [OK] 18.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\matrix\__init__.py" [OK] 4.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\tst_regular_grid_on_unit_sphere.py" [OK] 5.4s 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] 5.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_runtime_utils.py" [EXPECTED FAIL] 15.2s Time: 15.20 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 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\linalg\tests\tst_svd.py" [OK] 11.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\superpose.py" [OK] 5.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\python_utils\tst_random_transform.py" [OK] 6.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_flex.py" [OK] 8.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\incremental_SO3_sampling.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_similarity_indices.py" [OK] 4.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_weighted_correlation.py" [OK] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_exp_functions.py" [OK] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_fit_quadratic_function.py" [OK] 5.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\easy_run.py" [OK] 22.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_gcd.py" [OK] 5.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_resample.py" [OK] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_line_search.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\sieve_of_eratosthenes.py" [OK] 1.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_bessel.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_quadrature.py" [OK] 5.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\besselk.py" [OK] 2.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_halton.py" [OK] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_uniform_rotation_matrix.py" [OK] 4.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_superpose.py" [OK] 5.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tst_zernike_mom.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\spe.py" [OK] 9.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\tst_basic.py" [OK] 20.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_math.py" [OK] 8.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_clustering.py" [OK] 3.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_fit_peak.py" [OK] 4.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_euler_angles.py" [OK] 7.3s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\scitbx\lbfgs\tst_lbfgs" [OK] 0.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_orthonormal_basis.py" [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_g_function.py" [OK] 4.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_angle_derivative.py" [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_periodogram.py" [OK] 4.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tst_undirected_graph.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tst_so3_lie_algebra.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_tetrahedron.py" [OK] 4.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\minpack\tst.py" [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lbfgs\tst_ext.py" [OK] 3.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\array_family\boost_python\tst_integer_offsets_vs_pointers.py" [OK] 16.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lbfgs\tst_func_free_line_search.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\flex_grid.py" [OK] 3.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lbfgs\tst_curvatures.py" [OK] 5.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\flex_array_loops.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\lbfgs_recipe.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\principal_axes_of_inertia.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lbfgsb\boost_python\tst_lbfgsb.py" [OK] 4.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\tst_utils.py" [OK] 2.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\lbfgs_linear_least_squares_fit.py" [OK] 3.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\fftpack\boost_python\tst_fftpack.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\rigidity.py" [OK] 1.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_r3_rotation.py" [OK] 14.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\rigid_body_refinement_core.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tst_zernike.py" [OK] 12.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\chebyshev_lsq_example.py" [OK] 4.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_thread_utils.py" [OK] 33.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\test_cases_tardy_pdb.py" [OK] 2.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\tst_rigidity.py" [OK] 3.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\integrating_a_weighted_sinc_function.py" [OK] 5.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_error_propagation_matrix_inverse.py" [OK] 10.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_curve_fitting.py" [OK] 17.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\free_motion_reference_impl.py" [OK] 2.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\essence\tst_basic.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\tst_tardy_tree.py" [OK] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_featherstone.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\rigidity_matrix_symbolic.py" [OK] 5.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\essence\tst_energy_plots.py" [OK] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_free_motion.py" [OK] 4.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\golden_section_search.py" [OK] 1.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\sparse\tests\tst_lu_factorization.py" [OK] 3.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\sparse\tests\tst_sparse.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\differential_evolution.py" [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_joint_lib.py" [OK] 5.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_free_motion_hard.py" [OK] 5.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_spherical_refinement.py" [OK] 4.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\simplex.py" [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lstbx\tests\test_problems.py" [OK] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lstbx\tests\tst_normal_equations.py" [OK] 2.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\suffixtree\test\tst_single.py" [WARNING] 1.9s Time: 1.88 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 0.031s FAILED (failures=2) libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\tst.py" [OK] 7.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\glmtbx\tests\tst.py" [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\omz\tst_bfgs.py" [OK] 3.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_molecules.py" [OK] 7.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\graph\tst_tardy_tree_find_paths.py" [OK] 10.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\miller\tst_map_to_asu_isym.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\miller\tst_reindexing.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_double_step_filtration.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\random\tests\tst_random.py" [OK] 5.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\omz\tst_dev.py" P31 [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\proto\tst_singular.py" [OK] 9.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\covariance\tests\tst_covariance.py" [OK] 3.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry\tests\tst_geometry.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\libtbx\tst_scheduling.py" [OK] 44.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\math\boost_python\tst_math.py" [OK] 2.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\targets\tst_r1.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\uctbx\boost_python\tst_crystal_orientation.py" [OK] 3.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\targets\tst_shelxl_wght_ls.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\array_family\boost_python\tst_flex.py" [OK] 3.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\uctbx\boost_python\tst_uctbx.py" [OK] 3.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\boost_python\tst_targets_fd.py" [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\boost_python\tst_N_fold_rot.py" [OK] 2.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_adp_aniso_restraints.py" [OK] 6.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\crystal\tst_distance_based_connectivity.py" [OK] 3.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\tests\direct_search_simulated_annealing.py" [OK] 10.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\boost_python\tst_f_model.py" [OK] 5.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\crystal\tst_ext.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_chemical_elements.py" [OK] 2.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\immoptibox_ports.py" [OK] 19.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_henke.py" [OK] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\adptbx\boost_python\tst_adptbx.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\iso_surface\tst_iso_surface.py" [OK] 13.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\boost_python\tst_sgtbx.py" [OK] 5.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_icsd_radii.py" [OK] 2.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_neutron.py" [OK] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_covalent_radii.py" [OK] 2.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_sasaki.py" [OK] 2.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\examples\minimizer_comparisons.py" [OK] 20.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_xray_scattering.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\miller\boost_python\tst_miller.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_tiny_pse.py" [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_wavelengths.py" [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\scale_curves.py" [OK] 28.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_attenuation_coefficient.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\eltbx\tests\tst_formula.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\symmetry_search\tests\tst_from_map.py" P312 [OK] 12.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\dmtbx\boost_python\tst_dmtbx.py" [OK] 4.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_math_module.py" [OK] 3.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\translation_search\boost_python\tst_translation_search.py" [OK] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_proxy_registry.py" [OK] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_motif.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_angle_derivs.py" [WARNING] 5.6s Time: 5.56 Return code: 0 OKs: 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_itvb_2001_table_a1427_hall_symbols.py" [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\adp_restraints\tst_ext.py" [OK] 5.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_denominators.py" P31 [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\rigid_body\essence\tst_tardy.py" [OK] 23.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_subgroups.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_space_group_type_tidy_cb_op_t.py" [OK] 6.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_adp_constraints.py" P3 [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_adp_constraints_cartesian.py" [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\symbol_confidence.py" [OK] 2.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_krivy_gruber.py" --Quick [OK] 7.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_harker.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx.py" [OK] 7.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\bravais_types.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_special_op_simplifier.py" [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\math\tests\tst_gaussian.py" [OK] 39.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_ext.py" [OK] 10.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_lookup_utils.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\boost_python\tst_maptbx.py" [OK] 12.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_crystal.py" I41/acd [OK] 4.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_reflection_statistics.py" [OK] 7.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_site_constraints.py" [OK] 7.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_crystal_asu_clusters.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_fourier_transform_real_part_at_x.py" P31 [OK] 5.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_reciprocal_space_asu.py" P312 [OK] 4.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_pair_asu_table.py" [OK] 6.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_triplet_generator.py" P41 [OK] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_crystal_close_packing.py" R-3mr [OK] 6.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_expand_to_p1.py" P31 [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_change_basis.py" P31 [OK] 4.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_coordination_sequences.py" [OK] 7.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\symmetry_search\tests\tst_goodness_of_symmetry.py" [OK] 24.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_wilson_plot.py" P31 [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_lattice_symmetry.py" [OK] 14.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_data_manipulation.py" [OK] 26.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray_fast_gradients.py" P31 [OK] 5.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_maptbx_structure_factors.py" P31 [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray_derivatives.py" P31 [OK] 6.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_map_weights_for_symmetry_summation.py" Pmmm [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_emma.py" P31 [OK] 9.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_grouped_data.py" P31 [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_merge_equivalents.py" P31 [OK] 4.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_real_space_refinement_simple.py" [OK] 5.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_fast_nv1995.py" F222 [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_mem_2.py" [OK] 12.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray_minimization.py" --F_sq P31 [OK] 8.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_fft_map.py" P31 [OK] 5.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sampled_model_density.py" P31 [OK] 5.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_geometry_restraints.py" [OK] 5.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_loc_res.py" [OK] 7.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\development\make_cns_input.py" P31 [OK] 3.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_geometry_restraints_lbfgs.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\development\tst_cns_epsilon.py" P31 [OK] 3.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\development\tst_cns_hl.py" P31 [OK] 3.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\development\run_shelx76.py" P31 [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\sub_lattice_tools.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray_minimization.py" --F P31 [OK] 14.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_find_best_cell.py" [OK] 2.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_amplitude_normalisation.py" [OK] 3.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_pointgroup_tools.py" [OK] 5.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\cosets.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\reticular_pg_tools.py" [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_web_change_basis.py" [OK] 2.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_geometry_restraints_2.py" [OK] 9.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_target_and_gradients.py" [OK] 13.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\masks\tests\tst_flood_fill.py" [OK] 2.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sgtbx_tidy_pickling.py" [OK] 3.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\observations\tst_observations.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_statistics_graphs.py" [OK] 5.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_french_wilson.py" [OK] 11.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_mask.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_grm_pickling.py" [OK] 13.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_direct_space_asu.py" I41/acd [OK] 25.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_ccp.py" [OK] 6.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\rational_matrices_point_groups.py" [OK] 13.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_get_percentile_cutoffs.py" [OK] 5.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\merging\brehm_diederichs.py" [OK] 2.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_statistics.py" [FAIL] 4.4s Time: 4.36 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_statistics.py", line 114, in exercise() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_statistics.py", line 22, in exercise i_obs = hkl_in.file_server.miller_arrays[0] File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\file_reader.py", line 337, in file_server err=sys.stderr) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\reflection_file_utils.py", line 484, in __init__ force_symmetry=self.force_symmetry)) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\reflection_file_reader.py", line 313, in as_miller_arrays anomalous=anomalous, TypeError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_map_peak_3d_as_2d.py" [OK] 8.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_peak_volume_estimate.py" [OK] 7.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_sphericity.py" [OK] 6.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_wildcard.py" [OK] 1.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_simple_parser.py" [OK] 1.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_r_free_utils.py" [OK] 11.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\xray\boost_python\tst_xray.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\ranges.py" [OK] 0.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\multipolar\regression\tst_multipolar.py" [OK] 6.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_connectivity.py" [OK] 6.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_phil.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_pdb_cif_inputs.py" [OK] 3.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_diffuse.py" [OK] 6.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_poscar.py" [OK] 3.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_crystal_symmetry_from_any.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_geometry.py" [OK] 2.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_model.py" [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_grm_modifications.py" [OK] 8.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_lex_parse_build.py" [OK] 3.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_restraints.py" [OK] 3.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_xray.py" I41/acd [OK] 9.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_parser.py" [OK] 2.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_atom_radius_as_central_peak_width.py" [OK] 16.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_citations.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\kriber\tst_strudat.py" [OK] 7.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\shelx\tst_hklf.py" [OK] 3.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\shelx\tst_lex_parse_build.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_validation.py" [OK] 5.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\shelx\tst_writer.py" [OK] 3.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\hybrid_36.py" exercise [OK] 1.3s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\iotbx\pdb\hybrid_36_fem" [OK] 1.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\shelx\tst_fvar_encoding.py" [OK] 3.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_mmcif.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\reticular_twin_laws.py" [OK] 26.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\modified_aa_names.py" [OK] 0.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_hierarchy_atom_sort.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_atom_name_interpretation.py" [OK] 3.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_rna_dna_atom_names.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\modified_rna_dna_names.py" [OK] 0.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_atom_selection.py" [OK] 3.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_twin_target.py" [OK] 47.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_hierarchy.py" [OK] 5.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_extract_rfactors_resolutions_sigma.py" [OK] 3.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_ext.py" [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\secondary_structure\tst_sheet.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\secondary_structure.py" [OK] 3.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_atom_selection_string.py" [OK] 3.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_process_nonbonded_proxies.py" [OK] 55.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_utils.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\sgtbx\direct_space_asu\proto\tst_asu.py" [OK] 30.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\examples\pdb_to_map_simple.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\examples\pdb_truncate_to_ala\tst.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_data_manager.py" [OK] 18.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_secondary_structure_2.py" [OK] 3.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cns\space_group_symbols.py" [OK] 2.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_secondary_structure.py" [OK] 5.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cif\tests\tst_ucif_examples_compilation.py" [OK] 15.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\examples\pdb_tardy_conf_sampling_simple.py" [OK] 3.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\scalepack\tst_merge.py" P31 [OK] 3.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_resolution_from_map_and_model.py" [OK] 29.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\scalepack\no_merge_original_index.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\secondary_structure\tst_annotation.py" [OK] 7.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_dano.py" [OK] 3.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_miller_dict.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\ccp4_map\tst.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\cns\tst_cns.py" [OK] 4.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_ext.py" [OK] 4.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\detectors\tst_detectors.py" [OK] 1.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_interpolation_2.py" [OK] 45.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_unmerged.py" [OK] 3.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_tls.py" [OK] 14.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_data_plots.py" [OK] 2.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst_extract_from_symmetry_lib.py" [OK] 6.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller.py" P31 [OK] 53.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\mtz\tst.py" P31 [OK] 4.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\detectors\tst_adsc.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xplor\tst_xplormap.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_bioinformatics.py" [OK] 2.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\examples\tst_mtz_free_flipper.py" [OK] 5.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_phases.py" P31 [OK] 4.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reflection_file_utils.py" [OK] 5.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_csv_utils.py" [OK] 3.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_mmcif_hierarchy.py" [OK] 17.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_symmetry.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xds\tests\tst_xparm.py" [OK] 2.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_mem.py" [OK] 58.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xds\tests\tst_xds_inp.py" [OK] 2.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_pdbx_mmcif_tutorial.py" [OK] 8.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_add_conformations.py" [OK] 5.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reindex.py" [OK] 5.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_pdb_as_fasta.py" [OK] 5.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_mmcif_segids.py" [OK] 6.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reflection_statistics.py" Fdd2 P31m [OK] 8.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xds\tests\tst_spots_xds.py" [OK] 2.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_box_around_molecule.py" [OK] 10.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\xds\tests\tst_integrate_hkl.py" [OK] 5.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\scalepack\tst_no_merge_original_index.py" [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\dsn6\tst.py" P31 [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_export_scalepack_unmerged.py" [OK] 5.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_split_models.py" [OK] 10.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_search_ligs.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_file_reader.py" [OK] 12.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_search_broken_chain.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_sort_atoms.py" [OK] 10.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_input.py" [OK] 5.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\bioinformatics\test\tst_alignment_as_hsearch.py" [OK] 2.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\bioinformatics\test\tst_ebi_wu_blast_xml.py" [OK] 2.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\bioinformatics\test\tst_ncbi_blast_xml.py" [OK] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_groups_preprocessing.py" [OK] 7.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_mtz_as_cif.py" [OK] 15.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs_user_selections.py" [OK] 5.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_miller_sort_asu.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_show_systematic_absences.py" [OK] 5.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reflection_file_reader.py" [OK] 5.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_read_mtrix_records_from_cif.py" [OK] 7.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_ncs.py" [OK] 7.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\detectors\tst_debug_write.py" [EXPECTED FAIL] 3.2s Time: 3.17 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 "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\smtbx\refinement\constraints\tests\tst_reparametrisation" [OK] 0.5s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\smtbx\refinement\constraints\tests\tst_geometrical_hydrogens" [OK] 0.5s "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\build\smtbx\refinement\constraints\tests\tst_special_position" [OK] 0.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_xray_scale.py" [OK] 7.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\ab_initio\tests\tst_ab_initio_ext.py" [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_cif_as_pdb_1atom.py" [OK] 6.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\pdb\tst_pdb.py" [OK] 6.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_pdb_as_cif.py" [OK] 15.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\tst_reparametrisation.py" [OK] 3.4s 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] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_reflection_file_editor.py" [OK] 22.1s 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] 4.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_asymmetric_map.py" [OK] 56.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_lattice_symmetry.py" [OK] 26.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_simple_map_coefficients.py" [OK] 24.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\tests\tst_weighting_schemes.py" --fix_random_seeds [OK] 9.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\absolute_structure\tests\tst_absolute_structure.py" --fix_random_seeds [OK] 13.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\constraints\tests\tst_lbfgs.py" [OK] 11.3s 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] 9.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\tst_merging_statistics.py" [OK] 27.6s 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] 14.5s 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] 10.2s 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] 9.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\masks\tests\tst_masks.py" [OK] 14.7s 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] 10.1s 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] 9.6s 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] 10.0s 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] 9.6s 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] 10.0s 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] 9.9s 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] 9.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\svm\tst_classifier.py" [OK] 4.1s 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] 9.4s 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] 9.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_ca_svm.py" [OK] 3.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_validate_ca.py" [OK] 1.6s 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] 10.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\refinement\tests\tst_least_squares.py" [OK] 23.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\smtbx\structure_factors\direct\tests\tst_standard_xray.py" [OK] 25.0s 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] 12.4s 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] 12.2s 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] 13.8s 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] 12.8s 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] 12.8s 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] 12.4s 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] 12.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_atom_curves.py" [OK] 74.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_utils.py" [OK] 5.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_optimise_amplitudes.py" [FAIL] 5.3s Time: 5.30 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\tls\tst_tls_optimise_amplitudes.py", line 661, 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 204, 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 37, in run self._optimise() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\tls\optimise_amplitudes.py", line 50, in _optimise residual_uijs = self.residual_uijs, ValueError: invalid selection in base_atom_indices (9799982684676663651): 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_utils.py" [OK] 6.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_03.py" [OK] 8.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_02.py" [OK] 9.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\iotbx\regression\ncs\tst_mtrix_biomt_cmdl.py" [OK] 49.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_analysis.py" [OK] 19.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\rotamer\tst_geostd_vs_sidechain_angles_props.py" [OK] 3.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls.py" [OK] 21.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\rotamer\tst_rotamer_eval.py" [OK] 11.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_parameters.py" [OK] 30.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_idealized_aa.py" [OK] 6.5s 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] 36.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_as_xyz.py" [OK] 23.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_map_type_parser.py" [OK] 1.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_ml_estimate.py" [OK] 8.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_manager.py" [OK] 5.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\chemical_components\tst.py" [OK] 1.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\polygon\tst_gui.py" [OK] 6.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\rotamer\rotamer_eval.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_mg.py" [OK] 41.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\wwpdb\tst_standard_geometry_cif.py" [OK] 1.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_validate_mg.py" [OK] 40.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\polygon\tst.py" [OK] 10.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_fit_rotamers.py" [OK] 1.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_add_h_to_water.py" [OK] 9.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_anomalous_scatterer_groups.py" P3 [OK] 3.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_01.py" [OK] 38.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\rsr\tst.py" [OK] 15.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_refinement_flags.py" [OK] 2.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_04.py" [OK] 40.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_rigid_body_groups_from_pdb_chains.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\scitbx\lbfgs\tst_lbfgs_fem.py" [OK] 168.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_biomt_mtrix.py" [OK] 4.7s 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] 41.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ias\tst_ias.py" [OK] 13.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_get_t_scheme.py" [OK] 48.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_neutralize_scatterers.py" [OK] 5.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_mtrix.py" [OK] 8.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_remove_alternative_conformations.py" [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_get_vdw_radii.py" [OK] 5.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_alignment.py" [OK] 3.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_2.py" [OK] 13.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_u_tls_vs_u_ens_00.py" [OK] 55.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model_ligands.py" [FAIL] 16.7s Time: 16.72 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 551, 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 540, 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\ions\tst_symmetry_axis.py" [OK] 63.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_tors_ref_restraints.py" [OK] 13.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model_cart_ref_restraints.py" [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_ncs_utils.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_ncs_restraints_group_list.py" [OK] 3.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel_fd.py" P31 [OK] 9.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_utils.py" [OK] 14.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\maps\tst_composite_omit_map_2.py" [OK] 10.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_ncs_search.py" [OK] 3.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ncs\ncs.py" exercise [OK] 1.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_restraints.py" [OK] 4.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_angle.py" [OK] 59.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_adp_restraints.py" [OK] 4.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_outlier.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_ncs_search_flips.py" [OK] 8.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_metal_link_1.py" [OK] 5.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\density_modification\tst_density_modification.py" [OK] 53.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\matthews.py" [OK] 2.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_absences.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\absence_likelihood.py" [OK] 2.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\twinning\probabalistic_detwinning.py" [OK] 1.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_rna_sugar_pucker_analysis.py" [OK] 1.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\thorough_outlier_test.py" P21 [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_geometry_minimization.py" [OK] 12.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_cif_types.py" [OK] 2.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_xtriage_twin_analyses.py" [OK] 6.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_cif_triage.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_motif.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_selection.py" [OK] 5.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_tyr_from_gly_and_bnz.py" [OK] 6.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_rna_dna_interpretation.py" [OK] 5.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_rotamer_utils.py" [OK] 9.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\maps\tst_correlation.py" [OK] 29.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_pdb_interpretation_ncs_processing.py" [OK] 5.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\real_space\tst.py" [OK] 54.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_geo_reduce_for_tardy.py" [OK] 5.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_scaling.py" [OK] 22.5s 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] 86.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_protein_interpretation.py" [OK] 13.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_nonbonded_overlaps.py" [OK] 198.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_interpolation.py" [OK] 183.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_coefficients.py" [OK] 0.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_ramachandran.py" [OK] 75.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen_2.py" [OK] 8.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_connectivity.py" [OK] 5.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_neutron_distance.py" [OK] 13.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_rigid_body.py" [OK] 64.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst.py" [OK] 13.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pickle.py" [OK] 110.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_manager.py" [OK] 7.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_1.py" [OK] 7.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_2.py" [OK] 6.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_approx_zn.py" [OK] 110.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_5.py" [OK] 8.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_7.py" [OK] 7.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_8.py" [OK] 7.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_6.py" [OK] 9.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_3.py" [OK] 12.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_3.py" [OK] 8.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\build_hydrogens.py" [OK] 25.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_4.py" [OK] 10.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_minimize.py" [OK] 6.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model.py" [OK] 75.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\masks\tst_masks.py" [OK] 7.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_add_hydrogen.py" [OK] 29.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\examples\f_model_manager.py" [OK] 3.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_parameterization_4.py" [OK] 21.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\dynamics\tst_cartesian_dynamics.py" [OK] 6.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_pdb_interpretation.py" [OK] 42.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_ca.py" [OK] 129.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_fit_kexpb_to_ktotal.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\invariant_domain.py" [OK] 2.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_kb_sol_u_star_fd.py" [OK] 4.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_psi_phi_extraction.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_scaler.py" [OK] 6.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\max_lik\tst_maxlik.py" [OK] 15.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_flat_nonuniform.py" [OK] 6.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_validate_H.py" [OK] 34.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\tst_insertion_codes.py" [OK] 4.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\tst.py" [FAIL] 5.9s Time: 5.94 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\tst.py", line 1177, in exercise_sheet_ends() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\tst.py", line 218, in exercise_sheet_ends assert proxies.size() == 12, proxies.size() AssertionError: 14 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_5.py" [OK] 21.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_c_beta_restraints.py" [OK] 6.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\maps\tst_composite_omit_map_3.py" [OK] 76.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\maps\tst_composite_omit_map.py" [OK] 78.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_cdl_esd.py" [OK] 6.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\tst_segid.py" [OK] 10.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_aniso_scaler.py" [OK] 17.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_2.py" [OK] 33.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_chain_comparison.py" [OK] 6.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_reference_coordinate.py" [OK] 16.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_find_ss_structure.py" [OK] 7.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_sequence_validation.py" [OK] 1.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\hydrogens\tst_riding_fd_1.py" [OK] 38.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_torsion_ncs.py" [OK] 18.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\max_lik\tst_max_lik.py" [OK] 31.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_sort_hetatms.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_cdl.py" [OK] 19.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_hpdl.py" [OK] 18.3s 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] 147.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_prune_model.py" [OK] 7.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_examples.py" [OK] 7.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_pH_mechanism.py" [OK] 17.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\tst_reference_coordinate2.py" [OK] 24.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_rdl.py" [OK] 22.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_real_space_correlation.py" [OK] 10.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_aa_residue_axes_and_clusters.py" [OK] 8.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_xtriage.py" [OK] 83.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fix_rotamer_outliers.py" [OK] 22.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_0.py" [OK] 12.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_find_ncs.py" [OK] 20.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_0H.py" [OK] 12.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_4.py" [OK] 14.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_regularize_from_pdb.py" [OK] 28.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_3.py" [FAIL] 15.2s Time: 15.20 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_3.py", line 94, in exercise() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_3.py", line 90, in exercise tol = 0.1) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\refinement\real_space\__init__.py", line 87, in check_sites_match assert dist < tol, [dist, tol] AssertionError: [0.14822425599000846, 0.1] libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_6.py" [OK] 15.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_2.py" [OK] 13.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\masks\tst_asu_mask.py" [OK] 55.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_4.py" [OK] 13.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_5.py" [OK] 20.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_altloc_remediate.py" [OK] 84.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_flipbase.py" [OK] 8.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_6.py" [OK] 15.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_1H.py" [FAIL] 25.7s Time: 25.72 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_1H.py", line 191, in i_pdb = i_pdb) File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_1H.py", line 183, in exercise tol = 0.15) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\refinement\real_space\__init__.py", line 87, in check_sites_match assert dist < tol, [dist, tol] AssertionError: [0.29898084676232684, 0.15] libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_monitor.py" [OK] 7.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_individual_sites_3.py" [OK] 9.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_3.py" [OK] 21.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_rigid_body.py" [OK] 7.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cablam.py" [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_1.py" [OK] 27.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_5.py" [OK] 24.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_chg.py" [OK] 95.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_individual_sites_2.py" [OK] 16.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_2.py" [OK] 34.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ligands\tst_xtal_screens.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_selection.py" [OK] 27.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_water.py" [OK] 24.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_dssp.py" [OK] 16.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ringer\tst_em_rscc.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_1.py" [OK] 42.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_dynamics_cli.py" [OK] 10.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ringer\tst_emringer.py" [OK] 8.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel_no_cryst1.py" [OK] 14.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_map_coeffs_simple.py" [OK] 20.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_ramalyze.py" [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_ramalyze2.py" [OK] 4.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_anomalous_substructure.py" [OK] 22.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_minimize_chain.py" [OK] 60.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_mp_geo.py" [OK] 8.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_omegalyze.py" [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_weight.py" [OK] 31.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_rotalyze.py" [OK] 14.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_waters.py" [OK] 17.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_model_properties.py" [OK] 9.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_mtz2map.py" [OK] 26.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_restraints.py" [OK] 11.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_find_region_max_value.py" [OK] 3.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_hydrogen_addition_clashscore.py" [OK] 9.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residues_1H.py" [OK] 61.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel_misc.py" [OK] 35.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_symmetry_SS.py" [OK] 8.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_helix_sheet_recs_as_pdb_files.py" [OK] 7.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_ringer.py" [OK] 36.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_individual_sites_1.py" [OK] 55.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_rna_validate.py" [OK] 23.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\idealized_aa_residues\tst.py" [OK] 50.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cif_as_mtz_wavelengths.py" [OK] 8.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\tst_extend_sidechains_2.py" [OK] 8.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\disorder\tst.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_do_flips_clashscore.py" [OK] 17.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\disorder\tst_backbone.py" [OK] 3.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_select_best_starting_model.py" [OK] 19.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_group_2.py" [OK] 5.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_group.py" [OK] 8.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_io.py" [OK] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\alternate_conformations\tst_partial_omit_map.py" [OK] 16.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_clashscore.py" [OK] 41.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\tst_extend_sidechains.py" [OK] 25.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\alternate_conformations\tst_shear_conformers.py" [OK] 21.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\disorder\tst_analyze_model.py" [OK] 19.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_1.py" [OK] 18.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\dynamics\tst_sa.py" [OK] 128.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_keep_hydrogens.py" [OK] 59.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\alternate_conformations\tst_backrub_conformers.py" [OK] 35.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_3.py" [OK] 58.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_loop_closure.py" [OK] 27.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_3.py" [OK] 36.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validation_summary.py" [OK] 91.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_isomorphous_difference_misc.py" [OK] 95.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_maps_misc.py" [OK] 100.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\utils\tst_switch_rotamers.py" [OK] 11.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_refine_anomalous_substructure.py" [OK] 82.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel.py" [OK] 253.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints.py" [FAIL] 19.0s Time: 18.97 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 288, 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 256, 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 181, 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] 3.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_command_line_input.py" [OK] 95.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints_real_space.py" [OK] 6.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_plan_sad_experiment.py" [OK] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints2.py" [OK] 29.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tncs\tst_pair.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_models_to_from_chains.py" [OK] 10.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_occupancy_selections.py" [OK] 57.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_correct_hydrogens.py" [OK] 34.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_02.py" [OK] 103.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tncs\tst_fd.py" [OK] 17.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tncs\tst_moments.py" [OK] 10.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder.py" [FAIL] 4.6s Time: 4.62 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_rank_scale_map.py" [OK] 6.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_2.py" [FAIL] 4.6s Time: 4.61 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\bulk_solvent\tst_bulk_solvent_and_scaling.py" [OK] 232.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_06.py" [OK] 93.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tncs\tst_epsfac_and_radius.py" [OK] 30.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_superpose_ideal.py" [OK] 56.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_model_map.py" [OK] 10.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_2.py" [OK] 168.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_arguments.py" [OK] 180.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_ccs.py" [OK] 21.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_box.py" [OK] 22.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_multi_residue_class.py" [OK] 7.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_ss_id_ncs.py" [OK] 143.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_03.py" [OK] 135.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_altloc.py" [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_04.py" [OK] 136.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_clash.py" [OK] 3.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_indexing.py" [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_shared_types.py" [OK] 2.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_sphere_surface_sampling.py" [OK] 2.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_03.py" [OK] 137.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_topology.py" [OK] 3.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry\tests\tst_asa.py" [OK] 8.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_05.py" [OK] 129.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_04.py" [OK] 134.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_3.py" [OK] 39.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_misc.py" [OK] 3.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_mean_f_rms_f.py" [OK] 2.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_polder_1.py" [OK] 47.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_apply_cif_restraints.py" [OK] 27.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_massage_data.py" [OK] 3.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_pick_k.py" [OK] 1.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_sigmaa.py" [OK] 5.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\wwpdb\tst_rcsb_web_services.py" [OK] 12.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_table_one.py" [OK] 5.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_build_alt_confs.py" [OK] 4.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_msa.py" [OK] 5.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_all_cif_files.py" [OK] 15.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\wwpdb\tst_utils.py" [OK] 18.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\tst_real_space_simple.py" [OK] 18.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cablam.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py" [FAIL] 49.6s Time: 49.58 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py", line 426, in run() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py", line 420, in run run_test1() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py", line 327, 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 715, 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\base\bin\python\lib\multiprocessing\process.py", line 130, in start self._popen = Popen(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\forking.py", line 277, in __init__ dump(process_obj, to_child, HIGHEST_PROTOCOL) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\forking.py", line 199, in dump ForkingPickler(file, protocol).dump(obj) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 224, in dump self.save(obj) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 331, in save self.save_reduce(obj=obj, *rv) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 425, in save_reduce save(state) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 655, in save_dict self._batch_setitems(obj.iteritems()) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 687, in _batch_setitems save(v) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 568, in save_tuple save(element) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\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\base\bin\python\lib\multiprocessing\forking.py", line 381, in main self = load(from_parent) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 1384, in load return Unpickler(file).load() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 864, in load dispatch[key](self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 886, in load_eof raise EOFError EOFError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_server.py" [OK] 35.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\building\tst_make_library.py" [OK] 5.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_nomap_01.py" [OK] 168.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cc_star.py" [OK] 8.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\nci\tst_hbond.py" [OK] 25.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_rigid_bond_test.py" [OK] 7.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_scattering_type_registry.py" [OK] 6.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\conformation_dependent_library\tst_omega_cdl.py" [OK] 9.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\fix_cablam\tst_insertion_codes.py" [OK] 8.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\fix_cablam\tst_one_resid_rotation.py" [OK] 11.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\fix_cablam\tst_single_outliers_surroundings.py" [OK] 12.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits.py" [FAIL] 12.6s Time: 12.56 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\model_idealization\tst_withmap_02.py" [OK] 177.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_reduce_timeout.py" [OK] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cbetadev.py" [OK] 3.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_add_arrows_on_plot.py" [FAIL] 12.2s Time: 12.18 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_add_arrows_on_plot.py", line 75, in exercise_1() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_add_arrows_on_plot.py", line 72, in exercise_1 assert fhash == reference_md5, "%s != %s" % (fhash, reference_md5) AssertionError: f5164b74c12a7c2e0176b31cdd4a9cbf != f603dae282f5748e737b0a9572b768f5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel_2.py" [OK] 27.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_geometries.py" [OK] 35.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\ions\tst_environment.py" [OK] 35.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_ligands.py" [OK] 167.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_ext_map_01.py" [OK] 164.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_map_model_cc.py" [OK] 84.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\real_space_refine_chain\tst_00.py" [OK] 32.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\real_space_refine_chain\tst_01.py" [OK] 31.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_altloc_chain_break.py" [OK] 18.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_01.py" [OK] 199.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_geo_min_restraints_phil.py" [OK] 20.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_clashes.py" [OK] 26.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_superpose.py" [OK] 79.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_statistics_output.py" [OK] 25.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_nqh_minimize.py" [OK] 23.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_4.py" [OK] 23.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_experimental.py" [OK] 26.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\fix_cablam\tst_basic_cl_operations.py" [OK] 54.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_model_vs_map.py" [OK] 52.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_flip_symmetric.py" [OK] 109.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 2 [OK] 39.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 3 [OK] 37.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits_actions.py" [WARNING] 74.7s Time: 74.70 Return code: 0 OKs: 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 4 [OK] 41.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 5 [OK] 40.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 7 [OK] 41.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 6 [OK] 41.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 8 [OK] 40.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 9 [OK] 41.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_geometry_minimization_ncs_constraints.py" [OK] 81.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 10 [OK] 41.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_2.py" [OK] 282.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 1 [OK] 75.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_metal_coordination.py" 2 [OK] 83.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 12 [OK] 41.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_metal_coordination.py" 1 [OK] 86.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 11 [OK] 42.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 13 [OK] 40.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 14 [OK] 38.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cablam_2.py" [FAIL] 88.9s Time: 88.92 Return code: 1 OKs: 0 Standard error: Starting phenix.cablam.bat on Sun Oct 6 06:42:34 2019 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 803, 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 525, 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\monomer_library\tst_linking.py" 16 [OK] 39.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 15 [OK] 43.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model\tst_model.py" [OK] 117.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 17 [OK] 44.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 19 [OK] 42.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 18 [OK] 43.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 20 [OK] 41.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 21 [OK] 38.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 22 [OK] 38.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 23 [OK] 38.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 24 [OK] 36.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 25 [OK] 34.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_with_mtz.py" [OK] 282.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_pdbtools.py" [OK] 514.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 26 [OK] 31.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_1.py" [OK] 125.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 29 [OK] 31.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 30 [OK] 31.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 28 [OK] 32.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 27 [OK] 32.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 32 [OK] 31.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\monomer_library\tst_linking.py" 31 [OK] 31.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cis_trans_peptide_link.py" [OK] 197.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_bayesian_estimator.py" [OK] 209.3s ================================================================================ Tests finished. Elapsed time: 747.55s Distribution of test runtimes: 0.5s - 51.9s: 757 51.9s - 103.4s: 44 103.4s - 154.8s: 14 154.8s - 206.3s: 11 206.3s - 257.7s: 3 257.7s - 309.1s: 2 309.1s - 360.6s: 0 360.6s - 412.0s: 0 412.0s - 463.5s: 0 463.5s - 514.9s: 1 Warning: the following jobs took at least 180 seconds: libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_molprobity_arguments.py": 180.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\maptbx\tst_interpolation.py": 183.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_cis_trans_peptide_link.py": 197.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_nonbonded_overlaps.py": 198.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_withmap_01.py": 199.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\scaling\tst_bayesian_estimator.py": 209.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\bulk_solvent\tst_bulk_solvent_and_scaling.py": 232.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_fmodel.py": 253.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\model_idealization\tst_with_mtz.py": 282.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\build\tst_2.py": 282.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_pdbtools.py": 514.9s 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] 1.9s Time: 1.88 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 0.031s FAILED (failures=2) libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\geometry_restraints\tst_angle_derivs.py" [WARNING] 5.6s Time: 5.56 Return code: 0 OKs: 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\pdb_interpretation\tst_edits_actions.py" [WARNING] 74.7s Time: 74.70 Return code: 0 OKs: 1 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_statistics.py" [FAIL] 4.4s Time: 4.36 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_statistics.py", line 114, in exercise() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\cctbx\regression\tst_miller_statistics.py", line 22, in exercise i_obs = hkl_in.file_server.miller_arrays[0] File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\file_reader.py", line 337, in file_server err=sys.stderr) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\reflection_file_utils.py", line 484, in __init__ force_symmetry=self.force_symmetry)) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\reflection_file_reader.py", line 313, in as_miller_arrays anomalous=anomalous, TypeError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tls\tst_tls_optimise_amplitudes.py" [FAIL] 5.3s Time: 5.30 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\tls\tst_tls_optimise_amplitudes.py", line 661, 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 204, 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 37, in run self._optimise() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\tls\optimise_amplitudes.py", line 50, in _optimise residual_uijs = self.residual_uijs, ValueError: invalid selection in base_atom_indices (9799982684676663651): attempting to select atom outside of array (size 10) libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\geometry_restraints\torsion_restraints\tst_reference_model_ligands.py" [FAIL] 16.7s Time: 16.72 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 551, 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 540, 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\secondary_structure\tst.py" [FAIL] 5.9s Time: 5.94 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\tst.py", line 1177, in exercise_sheet_ends() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\secondary_structure\tst.py", line 218, in exercise_sheet_ends assert proxies.size() == 12, proxies.size() AssertionError: 14 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_3.py" [FAIL] 15.2s Time: 15.20 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_3.py", line 94, in exercise() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_3.py", line 90, in exercise tol = 0.1) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\refinement\real_space\__init__.py", line 87, in check_sites_match assert dist < tol, [dist, tol] AssertionError: [0.14822425599000846, 0.1] libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_1H.py" [FAIL] 25.7s Time: 25.72 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_1H.py", line 191, in i_pdb = i_pdb) File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\refinement\real_space\tst_fit_residue_1H.py", line 183, in exercise tol = 0.15) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\mmtbx\refinement\real_space\__init__.py", line 87, in check_sites_match assert dist < tol, [dist, tol] AssertionError: [0.29898084676232684, 0.15] libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\ncs\tst_minimization_ncs_constraints.py" [FAIL] 19.0s Time: 18.97 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 288, 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 256, 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 181, 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] 4.6s Time: 4.62 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] 4.6s Time: 4.61 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] 49.6s Time: 49.58 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py", line 426, in run() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py", line 420, in run run_test1() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_validate_ligands.py", line 327, 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 715, 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\base\bin\python\lib\multiprocessing\process.py", line 130, in start self._popen = Popen(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\forking.py", line 277, in __init__ dump(process_obj, to_child, HIGHEST_PROTOCOL) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\forking.py", line 199, in dump ForkingPickler(file, protocol).dump(obj) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 224, in dump self.save(obj) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 331, in save self.save_reduce(obj=obj, *rv) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 425, in save_reduce save(state) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 655, in save_dict self._batch_setitems(obj.iteritems()) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 687, in _batch_setitems save(v) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 568, in save_tuple save(element) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\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\base\bin\python\lib\multiprocessing\forking.py", line 381, in main self = load(from_parent) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 1384, in load return Unpickler(file).load() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 864, in load dispatch[key](self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\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] 12.6s Time: 12.56 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_add_arrows_on_plot.py" [FAIL] 12.2s Time: 12.18 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_add_arrows_on_plot.py", line 75, in exercise_1() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\regression\tst_add_arrows_on_plot.py", line 72, in exercise_1 assert fhash == reference_md5, "%s != %s" % (fhash, reference_md5) AssertionError: f5164b74c12a7c2e0176b31cdd4a9cbf != f603dae282f5748e737b0a9572b768f5 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\cctbx_project\mmtbx\validation\regression\tst_cablam_2.py" [FAIL] 88.9s Time: 88.92 Return code: 1 OKs: 0 Standard error: Starting phenix.cablam.bat on Sun Oct 6 06:42:34 2019 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 803, 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 525, 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 : 832 Failures : 13 Warnings (possible failures) : 3 Known Failures ( 3) : 3 Known Unstable ( 0) : 0 Stderr output (discouraged) : 18 See run_tests_parallel_zlog for full output. ******************************************************************************** ERROR: 13 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\..\base\bin\python\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\..\base\bin\python\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" Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\gui\tst_hyss_gui.py", line 38, in exercise() File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\gui\tst_hyss_gui.py", line 28, in exercise result = launcher() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\runtime_utils.py", line 76, in __call__ result = self.run() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\hyss.py", line 2750, in run result = run(args=self.args, out=sys.stdout) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\hyss.py", line 619, in run space_group_info=params.space_group,out=out) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\hyss.py", line 2610, in prompt_for_symmetry_if_necessary for input_array in reflection_file.as_miller_arrays(): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\reflection_file_reader.py", line 313, in as_miller_arrays anomalous=anomalous, TypeError: as_miller_arrays() got an unexpected keyword argument 'anomalous' ################################################################################ # 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] 10.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 5 [OK] 10.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_benzene_sdf.py" 1 [OK] 10.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 6 [OK] 10.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 10 [OK] 11.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 9 [OK] 11.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 7 [OK] 1.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 1 [OK] 18.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cis_trans_enumerate.py" 1 [OK] 19.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 3 [OK] 1.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 1 [OK] 23.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 9 [OK] 20.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 4 [OK] 36.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 1 [OK] 55.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 1 [OK] 5.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_enumerate.py" 2 [OK] 62.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sulfur_chiral.py" 2 [OK] 64.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 2 [OK] 71.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 5 [OK] 73.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\tst_am1_ext.py" [OK] 2.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 1 [OK] 75.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\tst_am1_forces.py" [OK] 5.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 8 [OK] 78.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 4 [OK] 79.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 3 [OK] 87.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 6 [OK] 76.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 1 [OK] 26.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_generic_ringise.py" [OK] 17.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_amino_acid_switch.py" 1 [OK] 69.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_libtbx_memory.py" [OK] 1.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 7 [OK] 99.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_enumerate.py" 2 [OK] 99.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sulfur_chiral.py" 1 [OK] 103.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_planar.py" [OK] 5.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 3 [OK] 110.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_enumerate.py" 1 [OK] 101.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_assign.py" [OK] 8.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_link_edits.py" [OK] 4.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zmatrix_order.py" [OK] 44.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_bad_pdb_files.py" [OK] 38.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 2 [OK] 114.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zinc_smiles.py" 1 [OK] 71.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cif_writer.py" [OK] 59.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 4 [OK] 140.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_all_am1_elements.py" [OK] 2.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_hydrogenise.py" [OK] 28.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 1 [OK] 113.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_alternative_location.py" [OK] 33.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 1 [OK] 127.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_dna_pdb_input.py" 1 [OK] 152.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_synonyms.py" [OK] 10.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_initial_final.py" [OK] 61.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 5 [OK] 151.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_peptide_class.py" [OK] 71.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_bond_valence.py" [OK] 53.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_boron_geometry.py" [OK] 30.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sugar.py" [OK] 25.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_unusual_pdb.py" [OK] 27.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_multi_cif.py" [OK] 4.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_linear_angle.py" [OK] 93.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_3_ring_mol.py" [OK] 15.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ligand_linking.py" [OK] 4.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_planar_radial_hydrogens.py" [OK] 4.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_am1_extended.py" [OK] 39.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_xml.py" [OK] 8.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\tst_lzw.py" [OK] 0.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_atom_naming_polish.py" [OK] 80.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pass_throughs.py" [OK] 15.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_chiral.py" [OK] 25.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_lots_main.py" [OK] 103.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_heavy_hydrogen.py" [OK] 61.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_aromatic_sulphur.py" [OK] 108.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zinc_smiles.py" 2 [OK] 30.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 1 [OK] 153.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 2 [OK] 26.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 3 [OK] 28.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_aromatic_nitrogens.py" [OK] 61.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_conformations_ext.py" [OK] 83.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 4 [OK] 33.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chiral_zmatrix.py" [OK] 100.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zinc_smiles.py" 3 [OK] 48.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 6 [OK] 27.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_elbow_generate_all.py" [OK] 60.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zinc_smiles.py" 4 [OK] 52.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_not_planar.py" [OK] 65.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 9 [OK] 24.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 3 [FAIL] 8.4s Time: 8.38 Return code: -1073741819 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_molfile_chiral.py" [OK] 94.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 4 [FAIL] 8.0s Time: 8.05 Return code: -1073741819 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 7 [OK] 32.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 8 [OK] 240.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 2 [OK] 5.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 5 [OK] 60.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 3 [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 11 [OK] 35.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 10 [OK] 42.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 12 [OK] 37.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 13 [OK] 36.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_atom_ordering.py" [OK] 193.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 5 [OK] 9.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_geo_parser.py" [OK] 95.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 14 [OK] 41.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_sdf_aromatic.py" 8 [OK] 59.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 11 [OK] 8.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_peptide_planar_conform.py" [OK] 125.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 7 [OK] 27.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_chirals_more.py" [OK] 122.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 6 [OK] 31.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 8 [OK] 30.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 9 [OK] 28.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 12 [OK] 27.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_elbow_general.py" 2 [OK] 8.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 16 [OK] 9.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 13 [OK] 27.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 5 [OK] 63.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 14 [OK] 27.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 3 [OK] 9.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 15 [OK] 29.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 6 [OK] 64.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 11 [OK] 4.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 7 [OK] 8.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 7 [OK] 62.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 9 [OK] 62.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 8 [OK] 62.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 10 [OK] 62.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 12 [OK] 1.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 13 [OK] 1.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 15 [OK] 1.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 9 [OK] 9.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 5 [OK] 17.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 4 [OK] 20.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 10 [OK] 49.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 10 [OK] 21.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 4 [OK] 17.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 2 [OK] 19.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 10 [OK] 22.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 11 [OK] 22.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_elbow_general.py" 1 [OK] 284.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 6 [OK] 33.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 2 [OK] 41.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 14 [OK] 23.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_r_s_chiral.py" [OK] 172.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 5 [OK] 20.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\test\test_commandline_scripts.py" 4 [OK] 80.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 13 [OK] 5.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 14 [OK] 5.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 6 [OK] 24.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 5 [OK] 10.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 8 [OK] 20.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 11 [OK] 15.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 7 [OK] 10.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 7 [OK] 36.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 12 [OK] 23.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 9 [OK] 25.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 10 [OK] 28.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_nitrogen_types.py" 3 [OK] 48.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_amino_acid_switch.py" 2 [OK] 65.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_amino_acid_switch.py" 5 [OK] 62.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_amino_acid_switch.py" 4 [OK] 64.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_amino_acid_switch.py" 3 [OK] 64.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 3 [OK] 37.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 7 [OK] 15.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 9 [OK] 12.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 8 [OK] 16.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_library.py" [OK] 244.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_file_reading.py" 8 [OK] 75.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 2 [OK] 46.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 10 [OK] 12.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 11 [OK] 11.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 6 [OK] 28.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 8 [OK] 45.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 14 [OK] 13.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 13 [OK] 13.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 12 [OK] 18.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 3 [OK] 42.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 5 [OK] 38.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 15 [OK] 22.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 16 [OK] 21.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cis_trans_enumerate.py" 4 [OK] 25.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cis_trans_enumerate.py" 3 [OK] 25.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_cis_trans_enumerate.py" 2 [OK] 30.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 4 [OK] 72.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 4 [OK] 58.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pH.py" 2 [OK] 67.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_zmatrix_construction.py" 2 [OK] 77.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_2d_writer.py" [OK] 280.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 9 [OK] 91.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_phenix_refine.py" 6 [OK] 136.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_tripos_writer.py" [OK] 408.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 2 [OK] 252.8s ================================================================================ Tests finished. Elapsed time: 493.45s Distribution of test runtimes: 0.8s - 41.6s: 110 41.6s - 82.3s: 48 82.3s - 123.1s: 17 123.1s - 163.9s: 7 163.9s - 204.7s: 2 204.7s - 245.4s: 2 245.4s - 286.2s: 3 286.2s - 327.0s: 0 327.0s - 367.7s: 0 367.7s - 408.5s: 1 Warning: the following jobs took at least 180 seconds: libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_atom_ordering.py": 193.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_ready_set.py" 8: 240.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pdb_library.py": 244.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 2: 252.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_2d_writer.py": 280.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_elbow_general.py" 1: 284.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_tripos_writer.py": 408.5s 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\elbow\elbow\regression\test_pucker_define.py" 3 [FAIL] 8.4s Time: 8.38 Return code: -1073741819 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\elbow\elbow\regression\test_pucker_define.py" 4 [FAIL] 8.0s Time: 8.05 Return code: -1073741819 OKs: 0 Please verify these tests manually. Summary: Tests run : 190 Failures : 2 Warnings (possible failures) : 0 Known Failures ( 0) : 0 Known Unstable ( 0) : 0 Stderr output (discouraged) : 0 See run_tests_parallel_zlog for full output. ******************************************************************************** ERROR: 2 TEST FAILURES. PLEASE FIX BEFORE COMMITTING CODE. ******************************************************************************** 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 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 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 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 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 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 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\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 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 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\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 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_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_fit_cmdline.txt to c:\users\phaserbuilder\nightlybuilds\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\tutoria:3: (WARNING/2) Duplicate explicit target name: "here". ls\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 Sun Oct 6 06:53:52 2019 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 = 10564 ************************************************************ PHENIX AutoSol Sun Oct 6 06:53:52 2019 ************************************************************ 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 Sun Oct 6 06:53:53 2019 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'] Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\phenix\phenix\command_line\autosol.py", line 719, in run_autosol=run_autosol(args=sys.argv[1:]) 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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' Traceback (most recent call last): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\phenix_regression\command_line\run_p9_sad_benchmark.py", line 32, in run() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\phenix_regression\command_line\run_p9_sad_benchmark.py", line 27, in run assert easy_run.call(" ".join(args)) == 0 AssertionError 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 Correct metals Generate metal coordination OUTPUT Writing metal edits to hipip.metal.edits 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 2019-10-06 Time 06:54:12 GMT Daylight Time +0100 (1570341252.54 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 = 35780 ------------------------------------------------------------------------------- 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% 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: 0.59, per 1000 atoms: 0.45 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. No array of experimental phases found. ============================== 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. ==================== Fixing bad ADP in input model (if any) =================== ========================== 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: 0.41 Conformation dependent library (CDL) restraints added in 109.0 milliseconds Time building geometry restraints manager: 0.47 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. ======================== Summary of geometry restraints ======================= ====================== Modifying start model if requested ===================== 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 ******************************************************************************* Automatic adjustment: hydrogens.refine=individual ******************************************************************************* ==================== Process input NCS or/and find new NCS ==================== Using existing and finding new NCS is disabled. Use ncs_search.enabled=true to activate it. Look at refinement.ncs for more NCS related parameters. =================== Write initial parameters into .eff file =================== Writing effective parameters to file: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_hipip_refine_benchmark\hipip.updated_refine_001.eff Writing geometry restraints to file: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_hipip_refine_benchmark\hipip.updated_refine_001.geo CPU time processing inputs: 9.17 ============================ 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__ =============================== 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 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.925602 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.105686 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 22.35 22.18 -0.17 0.016 1.7 7.4 0.0 0.0 0 none 0.056 0.0824 22.23 22.77 0.53 0.007 0.9 5.7 0.0 0.0 0 9.463 0.053 0.0272 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 22.23 22.77 0.53 1.536 7.578 0.106 0.053 23.29 23.90 0.61 1.294 8.061 0.106 0.057 min max mean iso aniso Overall: 2.06 65.47 8.60 1.47 728 0 Protein: 2.81 47.63 6.62 1.39 616 0 Water: 4.45 65.47 21.05 N/A 93 0 Other: 2.06 20.15 11.70 N/A 19 0 Chain A: 2.06 47.63 6.59 N/A 620 0 Chain : 4.45 65.47 20.09 N/A 108 0 Histogram: Values Number of atoms 2.06 - 8.40 547 8.40 - 14.74 103 14.74 - 21.08 34 21.08 - 27.42 14 27.42 - 33.76 15 33.76 - 40.11 6 40.11 - 46.45 3 46.45 - 52.79 2 52.79 - 59.13 3 59.13 - 65.47 1 =========================== ADP refinement (H only) =========================== |- start----------------------------------------------------------------------| | target_work(ls_wunit_k1) = 0.0566314 r_work = 0.2329 r_free = 0.2390 | |-----------------------------------------------------------------------------| |- final----------------------------------------------------------------------| | target_work(ls_wunit_k1) = 0.0552506 r_work = 0.2315 r_free = 0.2407 | |-----------------------------------------------------------------------------| ======================== Occupancy refinement (H only) ======================== |- start----------------------------------------------------------------------| | target_work(ls_wunit_k1) = 0.0552506 r_work = 0.2315 r_free = 0.2407 | |-----------------------------------------------------------------------------| |- final----------------------------------------------------------------------| | target_work(ls_wunit_k1) = 0.0531919 r_work = 0.2308 r_free = 0.2411 | |-----------------------------------------------------------------------------| ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2308 r_free = 0.2411 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2298 r_free = 0.2388 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 0.80 - 14.96 A, n_refl.=61781 (all), 5.02 % free)------------| | | | r_work= 0.2298 r_free= 0.2388 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.053240 | | target function (ls_wunit_k1) not normalized (work): 3124.110437 | | target function (ls_wunit_k1) not normalized (free): 179.125111 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2303 0.2298 0.2388 n_refl.: 61781 re-set all scales: r(all,work,free)=0.2493 0.2487 0.2610 n_refl.: 61781 remove outliers: r(all,work,free)=0.2493 0.2487 0.2610 n_refl.: 61781 overall B=-0.00 to atoms: r(all,work,free)=0.2493 0.2487 0.2610 n_refl.: 61781 bulk-solvent and scaling: r(all,work,free)=0.2286 0.2282 0.2372 n_refl.: 61781 remove outliers: r(all,work,free)=0.2286 0.2282 0.2372 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 0.2416 260.484 248.093 0.921 0.998 0.400 7.246-5.773 99.01 98 2 0.2176 263.466 250.002 0.937 0.999 0.330 5.768-4.607 98.95 180 9 0.1796 278.149 267.820 0.939 0.999 0.304 4.593-3.659 92.73 341 16 0.1478 311.805 304.291 0.937 1.003 0.278 3.656-2.912 98.75 675 36 0.1757 248.143 242.136 0.953 0.999 0.173 2.911-2.318 100.00 1343 59 0.2048 183.341 178.655 0.926 0.999 0.000 2.318-1.845 100.00 2587 143 0.1730 161.888 158.652 0.980 0.999 0.000 1.845-1.469 99.85 5060 262 0.2186 104.432 100.757 1.014 0.999 0.000 1.469-1.169 99.19 9852 508 0.2328 71.754 68.462 0.970 1.001 0.000 1.169-0.931 96.65 18810 1002 0.2392 49.856 47.734 1.075 1.001 0.000 0.931-0.801 88.70 19639 1058 0.3035 27.107 25.421 0.982 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=-0.0200 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2282 r_free=0.2372 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2282 r_free=0.2372 ========================= Local real-space refinement ========================= Before: r_work=0.2282 r_free=0.2372 rotamer outliers: 0.00 % outliers start: 0 outliers after map fit: 0 tune up outliers final: 0 Did it for: 33 After: r_work=0.2285 r_free=0.2382 rotamer outliers: 0.00 % ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.812183 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.083595 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 22.85 23.82 0.97 0.007 0.9 6.5 0.0 0.0 0 none 4.099 0.0258 22.64 23.46 0.82 0.005 0.9 4.9 0.0 0.0 0 1.906 4.083 0.0233 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 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2264 r_free=0.2346 rotamer outliers: 0.00 % outliers start: 0 tune up outliers final: 0 Did it for: 0 After: r_work=0.2264 r_free=0.2346 rotamer outliers: 0.00 % ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.64 23.46 0.82 50.300 26.922 0.084 4.083 23.01 23.71 0.70 47.580 27.355 0.084 4.097 min max mean iso aniso Overall: 2.56 62.95 9.14 2.71 728 0 Protein: 2.71 46.94 7.13 2.62 616 0 Water: 4.84 62.95 22.01 N/A 93 0 Other: 2.56 20.35 11.47 N/A 19 0 Chain A: 2.56 46.94 7.10 N/A 620 0 Chain : 4.84 62.95 20.87 N/A 108 0 Histogram: Values Number of atoms 2.56 - 8.60 487 8.60 - 14.64 127 14.64 - 20.68 67 20.68 - 26.72 16 26.72 - 32.75 14 32.75 - 38.79 7 38.79 - 44.83 3 44.83 - 50.87 3 50.87 - 56.91 3 56.91 - 62.95 1 =========================== ADP refinement (H only) =========================== |- start----------------------------------------------------------------------| | target_work(ml) = 4.09697 r_work = 0.2301 r_free = 0.2371 | |-----------------------------------------------------------------------------| |- final----------------------------------------------------------------------| | target_work(ml) = 4.09573 r_work = 0.2296 r_free = 0.2374 | |-----------------------------------------------------------------------------| ======================== Occupancy refinement (H only) ======================== |- start----------------------------------------------------------------------| | target_work(ml) = 4.09573 r_work = 0.2296 r_free = 0.2374 | |-----------------------------------------------------------------------------| |- final----------------------------------------------------------------------| | target_work(ml) = 4.09421 r_work = 0.2286 r_free = 0.2382 | |-----------------------------------------------------------------------------| ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2286 r_free = 0.2382 target_work(ml) = 4.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2289 r_free = 0.2383 target_work(ml) = 4.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 0.80 - 14.96 A, n_refl.=61781 (all), 5.02 % free)------------| | | | r_work= 0.2289 r_free= 0.2383 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.094066 | | target function (ml) not normalized (work): 240239.772559 | | target function (ml) not normalized (free): 12793.408038 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2294 0.2289 0.2383 n_refl.: 61781 re-set all scales: r(all,work,free)=0.2506 0.2501 0.2618 n_refl.: 61781 remove outliers: r(all,work,free)=0.2506 0.2501 0.2618 n_refl.: 61781 overall B=-0.12 to atoms: r(all,work,free)=0.2492 0.2486 0.2600 n_refl.: 61781 bulk-solvent and scaling: r(all,work,free)=0.2293 0.2288 0.2380 n_refl.: 61781 remove outliers: r(all,work,free)=0.2293 0.2288 0.2380 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 0.2375 260.484 245.094 0.939 0.996 0.400 7.246-5.773 99.01 98 2 0.2132 263.466 250.343 0.937 0.998 0.370 5.768-4.607 98.95 180 9 0.1879 278.149 264.792 0.932 0.998 0.340 4.593-3.659 92.73 341 16 0.1478 311.805 303.014 0.936 1.003 0.341 3.656-2.912 98.75 675 36 0.1872 248.143 240.714 0.953 0.999 0.178 2.911-2.318 100.00 1343 59 0.2081 183.341 178.141 0.927 0.999 0.000 2.318-1.845 100.00 2587 143 0.1766 161.888 157.979 0.986 0.999 0.000 1.845-1.469 99.85 5060 262 0.2193 104.432 100.458 1.019 0.999 0.000 1.469-1.169 99.19 9852 508 0.2318 71.754 68.333 0.963 1.001 0.000 1.169-0.931 96.65 18810 1002 0.2389 49.856 47.653 1.053 1.001 0.000 0.931-0.801 88.70 19639 1058 0.3010 27.107 25.421 0.973 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0248 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2288 r_free=0.2380 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2288 r_free=0.2380 ========================= Local real-space refinement ========================= Before: r_work=0.2288 r_free=0.2380 rotamer outliers: 0.00 % outliers start: 0 outliers after map fit: 0 tune up outliers final: 0 Did it for: 37 After: r_work=0.2292 r_free=0.2382 rotamer outliers: 0.00 % ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.112314 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.143212 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 22.92 23.82 0.91 0.005 0.9 4.9 0.0 0.0 0 none 4.095 0.0249 22.82 23.79 0.97 0.005 0.9 5.7 0.0 0.0 0 2.056 4.092 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 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2282 r_free=0.2379 rotamer outliers: 0.00 % outliers start: 0 tune up outliers final: 0 Did it for: 0 After: r_work=0.2282 r_free=0.2379 rotamer outliers: 0.00 % ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.82 23.79 0.97 47.665 26.934 0.143 4.092 22.31 23.22 0.91 47.027 26.814 0.143 4.069 min max mean iso aniso Overall: 2.10 61.77 9.02 2.33 728 0 Protein: 2.10 46.34 7.03 2.29 616 0 Water: 5.05 61.77 21.72 N/A 93 0 Other: 2.62 21.00 11.46 N/A 19 0 Chain A: 2.10 46.34 7.00 N/A 620 0 Chain : 5.05 61.77 20.61 N/A 108 0 Histogram: Values Number of atoms 2.10 - 8.07 483 8.07 - 14.03 126 14.03 - 20.00 65 20.00 - 25.97 19 25.97 - 31.93 16 31.93 - 37.90 8 37.90 - 43.87 4 43.87 - 49.83 3 49.83 - 55.80 3 55.80 - 61.77 1 =========================== ADP refinement (H only) =========================== |- start----------------------------------------------------------------------| | target_work(ml) = 4.06923 r_work = 0.2231 r_free = 0.2322 | |-----------------------------------------------------------------------------| |- final----------------------------------------------------------------------| | target_work(ml) = 4.06846 r_work = 0.2228 r_free = 0.2331 | |-----------------------------------------------------------------------------| ======================== Occupancy refinement (H only) ======================== |- start----------------------------------------------------------------------| | target_work(ml) = 4.06846 r_work = 0.2228 r_free = 0.2331 | |-----------------------------------------------------------------------------| |- final----------------------------------------------------------------------| | target_work(ml) = 4.06722 r_work = 0.2218 r_free = 0.2328 | |-----------------------------------------------------------------------------| ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2218 r_free = 0.2328 target_work(ml) = 4.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2226 r_free = 0.2328 target_work(ml) = 4.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.80 - 14.96 A, n_refl.=61781 (all), 5.02 % free)------------| | | | r_work= 0.2226 r_free= 0.2328 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.067729 | | target function (ml) not normalized (work): 238694.311236 | | target function (ml) not normalized (free): 12711.013208 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1899 0.1876 5.3468 5.332| | 2: 2.24 - 1.78 1.00 2894 154 0.1760 0.1781 4.9317 4.914| | 3: 1.78 - 1.56 1.00 2872 149 0.2100 0.2212 4.7187 4.8016| | 4: 1.56 - 1.41 1.00 2838 163 0.2290 0.2598 4.5393 4.6039| | 5: 1.41 - 1.31 0.99 2796 154 0.2251 0.2370 4.3631 4.3828| | 6: 1.31 - 1.24 0.99 2808 132 0.2231 0.2375 4.2927 4.302| | 7: 1.24 - 1.17 0.99 2785 134 0.2222 0.2440 4.3009 4.4453| | 8: 1.17 - 1.12 0.99 2782 162 0.2160 0.1967 4.2521 4.2447| | 9: 1.12 - 1.08 0.98 2765 142 0.2264 0.2438 4.183 4.2746| | 10: 1.08 - 1.04 0.97 2717 145 0.2286 0.2513 4.0819 4.1363| | 11: 1.04 - 1.01 0.97 2687 162 0.2432 0.2494 3.9751 3.9795| | 12: 1.01 - 0.98 0.97 2697 136 0.2424 0.2882 3.8832 4.0242| | 13: 0.98 - 0.95 0.94 2653 138 0.2340 0.2378 3.8098 3.8548| | 14: 0.95 - 0.93 0.95 2661 125 0.2395 0.2551 3.7393 3.8193| | 15: 0.93 - 0.91 0.93 2594 146 0.2562 0.2904 3.6753 3.7094| | 16: 0.91 - 0.89 0.92 2562 132 0.2710 0.2800 3.672 3.8255| | 17: 0.89 - 0.87 0.92 2537 135 0.2783 0.2748 3.6232 3.644| | 18: 0.87 - 0.86 0.90 2482 149 0.2913 0.3170 3.5652 3.599| | 19: 0.86 - 0.84 0.89 2491 115 0.3112 0.3079 3.5261 3.3876| | 20: 0.84 - 0.83 0.87 2422 121 0.3201 0.3173 3.482 3.4467| | 21: 0.83 - 0.81 0.86 2379 130 0.3159 0.3029 3.3963 3.4917| | 22: 0.81 - 0.80 0.81 2245 131 0.3233 0.3622 3.4163 3.3619| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 16.75 0.99 1.17 5667.85| | 2: 2.24 - 1.78 2894 154 0.87 19.17 1.00 1.19 3397.69| | 3: 1.78 - 1.56 2872 149 0.87 20.11 1.02 1.16 1947.53| | 4: 1.56 - 1.41 2838 163 0.85 22.19 0.96 1.16 1447.09| | 5: 1.41 - 1.31 2796 154 0.84 23.21 0.97 1.12 1080.48| | 6: 1.31 - 1.24 2808 132 0.84 22.75 1.01 1.17 921.44| | 7: 1.24 - 1.17 2785 134 0.86 20.75 1.06 1.19 819.22| | 8: 1.17 - 1.12 2782 162 0.87 19.68 1.02 1.21 742.31| | 9: 1.12 - 1.08 2765 142 0.86 21.12 1.02 1.18 651.06| | 10: 1.08 - 1.04 2717 145 0.85 22.11 1.01 1.16 562.35| | 11: 1.04 - 1.01 2687 162 0.83 24.33 0.99 1.15 480.79| | 12: 1.01 - 0.98 2697 136 0.83 24.59 1.00 1.15 416.93| | 13: 0.98 - 0.95 2653 138 0.82 24.99 1.03 1.15 363.11| | 14: 0.95 - 0.93 2661 125 0.83 24.38 1.02 1.20 324.39| | 15: 0.93 - 0.91 2594 146 0.82 25.57 1.09 1.23 286.46| | 16: 0.91 - 0.89 2562 132 0.82 25.89 1.06 1.26 268.87| | 17: 0.89 - 0.87 2537 135 0.80 27.03 1.04 1.23 250.66| | 18: 0.87 - 0.86 2482 149 0.79 28.07 1.02 1.19 228.70| | 19: 0.86 - 0.84 2491 115 0.79 28.49 0.97 1.15 195.69| | 20: 0.84 - 0.83 2422 121 0.78 29.59 0.96 1.11 179.14| | 21: 0.83 - 0.81 2379 130 0.74 32.79 0.96 1.02 181.05| | 22: 0.81 - 0.80 2245 131 0.68 37.83 0.95 0.88 200.91| |alpha: min = 0.88 max = 1.26 mean = 1.16| |beta: min = 179.14 max = 5667.85 mean = 998.21| |figures of merit: min = 0.00 max = 1.00 mean = 0.83| |phase err.(work): min = 0.00 max = 90.00 mean = 24.30| |phase err.(test): min = 0.00 max = 90.00 mean = 24.29| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2231 0.2226 0.2328 n_refl.: 61781 re-set all scales: r(all,work,free)=0.2446 0.2440 0.2563 n_refl.: 61781 remove outliers: r(all,work,free)=0.2446 0.2440 0.2563 n_refl.: 61781 overall B=-0.00 to atoms: r(all,work,free)=0.2446 0.2440 0.2563 n_refl.: 61781 bulk-solvent and scaling: r(all,work,free)=0.2230 0.2225 0.2325 n_refl.: 61781 remove outliers: r(all,work,free)=0.2230 0.2225 0.2325 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 0.2431 260.484 245.482 0.948 0.996 0.400 7.246-5.773 99.01 98 2 0.2161 263.466 250.147 0.939 0.998 0.380 5.768-4.607 98.95 180 9 0.1850 278.149 264.967 0.935 0.998 0.319 4.593-3.659 92.73 341 16 0.1497 311.805 302.589 0.935 1.003 0.287 3.656-2.912 98.75 675 36 0.1842 248.143 240.845 0.955 0.999 0.190 2.911-2.318 100.00 1343 59 0.2061 183.341 178.160 0.932 0.999 0.000 2.318-1.845 100.00 2587 143 0.1725 161.888 158.162 0.991 0.999 0.000 1.845-1.469 99.85 5060 262 0.2146 104.432 100.623 1.026 0.999 0.000 1.469-1.169 99.19 9852 508 0.2233 71.754 68.528 0.978 1.001 0.000 1.169-0.931 96.65 18810 1002 0.2308 49.856 47.773 1.079 1.001 0.000 0.931-0.801 88.70 19639 1058 0.2911 27.107 25.536 1.007 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=-0.0760 ================= 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_weight: 0.2235 0.2218 0.016 1.703 2.5 70.5 8.6 93 0.000 1_fitrh: 0.2235 0.2218 0.016 1.703 2.5 70.5 8.6 93 0.000 1_xyzrec: 0.2223 0.2277 0.007 0.887 2.5 70.5 8.6 93 0.055 1_adp: 0.2329 0.2390 0.007 0.887 2.1 65.5 8.6 93 0.055 1_adph: 0.2315 0.2407 0.007 0.887 2.1 65.5 8.6 93 0.055 1_occh: 0.2308 0.2411 0.007 0.887 2.1 65.5 8.6 93 0.055 1_occ: 0.2298 0.2388 0.007 0.887 2.1 65.5 8.6 93 0.055 2_bss: 0.2282 0.2372 0.007 0.887 2.1 65.5 8.6 93 0.055 2_settarget: 0.2282 0.2372 0.007 0.887 2.1 65.5 8.6 93 0.055 2_updatecdl: 0.2282 0.2372 0.007 0.892 2.1 65.5 8.6 93 0.055 2_nqh: 0.2282 0.2372 0.007 0.892 2.1 65.5 8.6 93 0.055 2_realsrl: 0.2285 0.2382 0.007 0.906 2.1 65.5 8.6 93 0.074 2_weight: 0.2285 0.2382 0.007 0.906 2.1 65.5 8.6 93 0.074 2_fitrh: 0.2285 0.2382 0.007 0.906 2.1 65.5 8.6 93 0.074 2_xyzrec: 0.2264 0.2346 0.005 0.860 2.1 65.5 8.6 93 0.064 2_realsrl2: 0.2264 0.2346 0.005 0.860 2.1 65.5 8.6 93 0.064 2_adp: 0.2301 0.2371 0.005 0.860 2.6 62.9 9.1 93 0.064 2_adph: 0.2296 0.2374 0.005 0.860 2.6 62.9 9.1 93 0.064 2_occh: 0.2286 0.2382 0.005 0.860 2.6 62.9 9.1 93 0.064 2_occ: 0.2289 0.2383 0.005 0.860 2.6 62.9 9.1 93 0.064 3_bss: 0.2288 0.2380 0.005 0.860 2.4 62.8 9.0 93 0.064 3_settarget: 0.2288 0.2380 0.005 0.860 2.4 62.8 9.0 93 0.064 3_updatecdl: 0.2288 0.2380 0.005 0.858 2.4 62.8 9.0 93 0.064 3_nqh: 0.2288 0.2380 0.005 0.858 2.4 62.8 9.0 93 0.064 3_realsrl: 0.2292 0.2382 0.005 0.864 2.4 62.8 9.0 93 0.065 3_weight: 0.2292 0.2382 0.005 0.864 2.4 62.8 9.0 93 0.065 3_fitrh: 0.2292 0.2382 0.005 0.864 2.4 62.8 9.0 93 0.065 3_xyzrec: 0.2282 0.2379 0.005 0.870 2.4 62.8 9.0 93 0.065 3_realsrl2: 0.2282 0.2379 0.005 0.870 2.4 62.8 9.0 93 0.065 3_adp: 0.2231 0.2322 0.005 0.870 2.1 61.8 9.0 93 0.065 3_adph: 0.2228 0.2331 0.005 0.870 2.1 61.8 9.0 93 0.065 3_occh: 0.2218 0.2328 0.005 0.870 2.1 61.8 9.0 93 0.065 3_occ: 0.2226 0.2328 0.005 0.870 2.1 61.8 9.0 93 0.065 end: 0.2225 0.2325 0.005 0.870 2.1 61.8 9.0 93 0.065 ------------------------------------------------------------------------ CPU time actual refinement: 376.69 ============================== Exporting results ============================== Writing refined structure to PDB file: C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\tests\phenix_regression.run_hipip_refine_benchmark\hipip.updated_refine_001.pdb 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 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 =============================== Detailed timings ============================== Micro-tasks: mask = 0.00 f_calc = 0.00 alpha_beta = 1.02 target = 0.98 gradients_wrt_atomic_parameters = 0.00 fmodel = 0.00 r_factors = 1.53 phase_errors = 8.06 foms = 0.20 TOTAL for micro-tasks = 11.80 NUMBER OF MASK CALCS= 0 Total CPU time: 7.22 minutes from_scatterers_fft: 462 calls, 94.31 s gradients_fft: 388 calls, 97.05 s =========================== phenix.refine: finished =========================== # Date 2019-10-06 Time 07:01:58 GMT Daylight Time +0100 (1570341718.26 s) wall clock time: 467.06 s Start R-work = 0.2235, R-free = 0.2218 Final R-work = 0.2225, R-free = 0.2325 RUNTIME: 484.1s 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] 11.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_gap\tst_AutoBuild_gap.py" [OK] 79.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_extend\tst_AutoBuild_extend.py" [OK] 97.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_omit\tst_AutoBuild_omit.py" [OK] 89.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_outside\tst_AutoBuild_outside.py" [OK] 86.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_ncs\tst_AutoBuild_ncs.py" [OK] 235.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoMR_tests\test_AutoMR_std\tst_AutoMR_std.py" [FAIL] 3.3s Time: 3.33 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mad\tst_AutoSol_mad.py" [FAIL] 3.5s Time: 3.53 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mad\tst_AutoSol_mad.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\AutoSol_tests\test_AutoSol_mad\tst_AutoSol_mad.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mir\tst_AutoSol_mir.py" [FAIL] 3.4s Time: 3.44 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mir\tst_AutoSol_mir.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\AutoSol_tests\test_AutoSol_mir\tst_AutoSol_mir.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_phaser\tst_AutoSol_phaser.py" [FAIL] 3.7s Time: 3.70 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_phaser\tst_AutoSol_phaser.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\AutoSol_tests\test_AutoSol_phaser\tst_AutoSol_phaser.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 3.6s Time: 3.59 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_phaser_mr\tst_AutoSol_phaser_mr.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\AutoSol_tests\test_AutoSol_phaser_mr\tst_AutoSol_phaser_mr.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_rna\tst_AutoSol_rna.py" [FAIL] 3.7s Time: 3.69 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_rna\tst_AutoSol_rna.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\AutoSol_tests\test_AutoSol_rna\tst_AutoSol_rna.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 3.6s Time: 3.59 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_sir_sad\tst_AutoSol_sir_sad.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\AutoSol_tests\test_AutoSol_sir_sad\tst_AutoSol_sir_sad.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_std\tst_AutoSol_std.py" [FAIL] 3.5s Time: 3.53 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_std\tst_AutoSol_std.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\AutoSol_tests\test_AutoSol_std\tst_AutoSol_std.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_truncate\tst_AutoBuild_truncate.py" [OK] 140.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\autosol_unmerged_tests\test_autosol_unmerged\tst_autosol_unmerged.py" [FAIL] 51.5s Time: 51.53 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\autosol_unmerged_tests\test_autosol_unmerged\tst_autosol_unmerged.py", line 87, 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\autosol_unmerged_tests\test_autosol_unmerged\tst_autosol_unmerged.py", line 41, 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 3464, in AutoSol_scale_and_analyze_mad local_datafile_list,aniso_list,orig_list=self.copy_and_remove_aniso() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 4027, in copy_and_remove_aniso GetDataFile=GetDataFileInfo(os.path.join(self.Facts['temp_dir'],file_name)) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_autobuild_quick\tst_autobuild_quick.py" [FAIL] 3.5s Time: 3.52 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_automr_remark\tst_automr_remark.py" [FAIL] 3.3s Time: 3.33 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 15.2s 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] 30.5s 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] 1.9s 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] 14.0s 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] 7.9s 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] 89.3s 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] 43.3s 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] 0.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_A001\tst_AutoBuild_A001.py" [OK] 439.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_lig\tst_AutoBuild_lig.py" [OK] 453.4s 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] 33.4s 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] 0.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_hires\tst_AutoBuild_hires.py" [OK] 458.2s 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] 6.3s 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] 41.6s 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] 58.3s Time: 58.28 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 2042, 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\base\bin\python\lib\multiprocessing\__init__.py", line 232, in Pool return Pool(processes, initializer, initargs, maxtasksperchild) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\pool.py", line 161, in __init__ self._repopulate_pool() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\pool.py", line 225, in _repopulate_pool w.start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\process.py", line 130, in start self._popen = Popen(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\forking.py", line 272, in __init__ prep_data = get_preparation_data(process_obj._name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\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\base\bin\python\lib\multiprocessing\forking.py", line 379, in main preparation_data = load(from_parent) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 1384, in load return Unpickler(file).load() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 864, in load dispatch[key](self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 886, in load_eof raise EOFError EOFError libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_mult\tst_AutoBuild_mult.py" [OK] 541.6s 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] 109.6s 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] 17.8s 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] 114.8s 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] 41.8s 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] 102.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_std\tst_AutoBuild_std.py" [OK] 436.8s 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] 38.8s 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] 10.5s 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] 13.2s 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] 32.7s 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] 39.8s 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] 7.9s 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] 6.0s 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] 88.4s 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] 29.3s 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] 9.5s 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] 15.3s 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] 30.9s 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] 5.5s 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] 24.1s 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" [FAIL] 3.5s Time: 3.53 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_misc_tests\test_autosol_classic_denmod\tst_autosol_classic_denmod.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_misc_tests\test_autosol_classic_denmod\tst_autosol_classic_denmod.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_backslash\tst_backslash.py" [OK] 1.0s 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] 3.7s 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] 3.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_cif\tst_cif.py" [FAIL] 4.1s Time: 4.08 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_misc_tests\test_cif\tst_cif.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_misc_tests\test_cif\tst_cif.py", line 26, in run run_autobuild(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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\ImportRawData.py", line 352, in finish_ImportRawData_start pick_best_label=pick_best_label) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\read_hkl.py", line 153, in __init__ labels[0] in ['N','N(+)']: # skip N or N(+) which are counts not data IndexError: list index out of range 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" [FAIL] 71.6s Time: 71.63 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 80.0000 and 100.0000 differ FAILED...numbers 82.5000 and 87.5000 differ FAILED...numbers 0.5415 and 0.5425 differ FAILED...numbers 0.5293 and 0.5349 differ FAILED...numbers 0.5293 and 0.5349 differ FAILED...numbers 0.5292 and 0.5349 differ FAILED...numbers 0.0622 and 0.0655 differ FAILED...numbers 0.384 and 0.365 differ FAILED...numbers 3.364 and 3.352 differ FAILED...numbers 0.0622 and 0.0655 differ FAILED...numbers 0.384 and 0.365 differ FAILED...numbers 3.364 and 3.352 differ FAILED...numbers 357 and 355 differ FAILED...numbers 357 and 355 differ FAILED...numbers 357 and 355 differ FAILED...numbers 63 and 62 differ FAILED...numbers 231 and 230 differ FAILED...numbers 114 and 112 differ FAILED...numbers 370 and 368 differ FAILED...numbers 365 and 363 differ FAILED...numbers 94.89 and 94.88 differ FAILED...numbers 0.05 and 0.03 differ FAILED...numbers 193 and 192 differ FAILED...numbers 31 and 32 differ FAILED...numbers 2.63e+01 and 2.64e+01 differ FAILED...numbers 1.53e+01 and 1.52e+01 differ FAILED...numbers 66 and 65 differ FAILED...numbers -0.129 and -0.127 differ FAILED...numbers 0.126 and 0.124 differ FAILED...numbers 0.099 and 0.098 differ FAILED...numbers 63 and 62 differ FAILED...numbers 2.05 and 2.04 differ FAILED...numbers 691 and 680 differ FAILED...numbers 26 and 20 differ FAILED...numbers 1949 and 1938 differ FAILED...numbers 0.0625 and 0.0640 differ FAILED...numbers 370 and 368 differ FAILED...numbers 83.33 and 88.01 differ FAILED...numbers 2 and 1 differ FAILED...numbers 1 and 0 differ FAILED...numbers 0.5147 and 0.5078 differ FAILED...numbers 0.5027 and 0.5001 differ FAILED...numbers 0.5040 and 0.5010 differ FAILED...numbers -0.0199 and 0.0320 differ FAILED...numbers 0.037 and 0.048 differ FAILED...numbers 7.58 and 7.59 differ FAILED...numbers 25.58 and 16.28 differ FAILED...numbers -0.0199 and 0.0320 differ FAILED...numbers 0.037 and 0.048 differ FAILED...numbers 7.58 and 7.59 differ FAILED...numbers 25.58 and 16.28 differ FAILED...numbers 2.93 and 2.94 differ FAILED...numbers 2.93 and 2.94 differ Test test_iterative_ss_refine FAILED 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] 7.7s 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] 3.6s Time: 3.64 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_misc_tests\test_dano_labels\tst_dano_labels.py", line 251, 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_misc_tests\test_dano_labels\tst_dano_labels.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_erraser\tst_erraser.py" [OK] 1.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_dos\tst_dos.py" [FAIL] 3.6s Time: 3.56 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_misc_tests\test_dos\tst_dos.py", line 101, 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_misc_tests\test_dos\tst_dos.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_hyss\tst_hyss.py" [FAIL] 2.2s Time: 2.19 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_misc_tests\test_hyss\tst_hyss.py", line 125, 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_misc_tests\test_hyss\tst_hyss.py", line 21, in run run(args=args,out=log) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\hyss.py", line 619, in run space_group_info=params.space_group,out=out) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\hyss.py", line 2610, in prompt_for_symmetry_if_necessary for input_array in reflection_file.as_miller_arrays(): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\reflection_file_reader.py", line 313, in as_miller_arrays anomalous=anomalous, TypeError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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" [FAIL] 2.8s Time: 2.78 Return code: 1 OKs: 0 Standard error: Sorry: Failed to read the file native.sca 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] 13.0s 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] 8.0s 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" [FAIL] 3.4s Time: 3.44 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_misc_tests\test_keep_atom_types\tst_keep_atom_types.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_misc_tests\test_keep_atom_types\tst_keep_atom_types.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_md\tst_md.py" [OK] 6.7s 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] 4.0s 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] 11.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_phaser\tst_phaser.py" [FAIL] 3.1s Time: 3.09 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 3.4s 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] 3.8s 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" [FAIL] 3.2s Time: 3.20 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_ramalyze\tst_ramalyze.py" [OK] 3.2s 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] 11.9s 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" [FAIL] 4.8s Time: 4.83 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_misc_tests\test_scale_and_merge\tst_scale_and_merge.py", line 83, 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_misc_tests\test_scale_and_merge\tst_scale_and_merge.py", line 21, in run run(args=args,out=log) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\scale_and_merge.py", line 3381, in run sc=scale_and_merge(out=out,params=params) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\scale_and_merge.py", line 2223, in __init__ crystal_symmetry=crystal_symmetry,out=out) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\scale_and_merge.py", line 2341, in read_and_scale_datasets crystal_symmetry=crystal_symmetry,out=out) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\scale_and_merge.py", line 3205, in scale_datasets kw_list=kw_list) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\easy_mp.py", line 771, in run_parallel results.append(ra(i)) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\easy_mp.py", line 756, in __call__ return self.target_function(**kw) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\scale_and_merge.py", line 2084, in scale_one_dataset merge_equivalents=True)[0] File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\reflection_file_reader.py", line 313, in as_miller_arrays anomalous=anomalous, TypeError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_set_sg\tst_set_sg.py" [FAIL] 3.5s Time: 3.52 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_misc_tests\test_set_sg\tst_set_sg.py", line 176, 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_misc_tests\test_set_sg\tst_set_sg.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 234.6s 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" [OK] 126.7s 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" [FAIL] 3.4s Time: 3.42 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_special_pos\tst_special_pos.py" [FAIL] 3.5s Time: 3.52 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_misc_tests\test_special_pos\tst_special_pos.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_misc_tests\test_special_pos\tst_special_pos.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 3.4s 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" [FAIL] 3.4s Time: 3.44 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_euler\tst_euler.py" [OK] 3.0s 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] 3.3s 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] 26.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_magnification\tst_magnification.py" [OK] 4.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_find_ncs\tst_find_ncs.py" [OK] 13.0s 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] 14.0s 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] 4.8s 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] 34.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ncs_tests\test_offset\tst_offset.py" [OK] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_cluster\tst_cluster.py" [FAIL] 3.6s Time: 3.61 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_non_standard_tests\test_cluster\tst_cluster.py", line 86, 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_non_standard_tests\test_cluster\tst_cluster.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1362, in finish_AutoSol_start ok=self.AutoSol_check_data_files() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 2120, in AutoSol_check_data_files self.finish_AutoSol_start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1362, in finish_AutoSol_start ok=self.AutoSol_check_data_files() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1935, in AutoSol_check_data_files GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 3.4s Time: 3.41 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_non_standard_tests\test_inv_sg\tst_inv_sg.py", line 72, 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_non_standard_tests\test_inv_sg\tst_inv_sg.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 110.4s 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] 0.9s 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" [FAIL] 3.7s Time: 3.69 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_non_standard_tests\test_non_standard_sg\tst_non_standard_sg.py", line 71, 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_non_standard_tests\test_non_standard_sg\tst_non_standard_sg.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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" [FAIL] 3.6s Time: 3.62 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_non_standard_tests\test_part_map_coeffs\tst_part_map_coeffs.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_non_standard_tests\test_part_map_coeffs\tst_part_map_coeffs.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1362, in finish_AutoSol_start ok=self.AutoSol_check_data_files() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 2120, in AutoSol_check_data_files self.finish_AutoSol_start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1362, in finish_AutoSol_start ok=self.AutoSol_check_data_files() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1935, in AutoSol_check_data_files GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_omit_tests\test_omit_selection\tst_omit_selection.py" [FAIL] 3.2s Time: 3.22 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 145.0s 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] 53.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_resolve_memory_tests\test_cutout\tst_cutout.py" [OK] 4.7s 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] 28.2s 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] 5.2s 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] 21.2s 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] 3.8s 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] 39.0s 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" [OK] 9.8s 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] 7.0s 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] 15.6s 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] 4.1s 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] 5.3s 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] 4.3s 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] 5.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_autobuild\tst_autobuild.py" [OK] 1.1s 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] 1.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_average\tst_average.py" [OK] 0.9s 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] 15.8s 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] 1.0s 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] 0.9s 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] 0.9s 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] 0.9s 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] 159.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_hhr\tst_hhr.py" [OK] 1.0s 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] 1.0s 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] 1.1s 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] 1.0s 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] 1.0s 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" [OK] 8.0s 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] 1.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_rosetta_quick_tests\test_prerefine\tst_prerefine.py" [OK] 1.0s 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] 1.0s 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] 1.0s 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] 1.0s 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] 1.0s 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] 1.0s 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] 1.0s 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] 1.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_commands\tst_commands.py" [OK] 1.0s 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] 60.6s Time: 60.64 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 0.34 and 0.33 differ FAILED...numbers 0.23 and 0.22 differ FAILED...numbers 0.17 and 0.16 differ FAILED...numbers 0.17 and 0.16 differ FAILED...numbers 6.16509705647428491E-02 and 6.57551065270074040E-002 differ FAILED...numbers 7.431 and 7.612 differ FAILED...numbers 0.22873952571100287 and 0.22383430108447586 differ FAILED...numbers 0.28973519802093506 and 0.29308140277862549 differ FAILED...numbers 4.8088 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 12.23613 and 12.24053 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 4.09704655250958394E-02 and 3.32651507186891990E-002 differ FAILED...numbers 0.15 and 0.14 differ FAILED...numbers 4.8088 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 12.23613 and 12.24053 differ FAILED...numbers 5182 and 5223 differ FAILED...numbers 0.15 and 0.14 differ FAILED...numbers 12.19996 and 12.27342 differ FAILED...numbers 0.43 and 0.44 differ FAILED...numbers 12.2 and 12.3 differ FAILED...numbers 0.19928348064422607 and 0.19815889000892639 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 0.054 and 0.053 differ FAILED...numbers 5.89626075427985077E-02 and 5.63865282179515790E-002 differ FAILED...numbers 0.61 and 0.59 differ FAILED...numbers 0.52 and 0.55 differ FAILED...numbers -0.0963166 and -0.0978056 differ FAILED...numbers 0.62 and 0.64 differ Test test_density_modification FAILED 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] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_morph_model\tst_morph_model.py" [FAIL] 2.9s Time: 2.91 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 5.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_phaser_denmod\tst_phaser_denmod.py" [FAIL] 3.6s Time: 3.59 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_tests\test_phaser_denmod\tst_phaser_denmod.py", line 77, 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_tests\test_phaser_denmod\tst_phaser_denmod.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 17.4s 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] 5.8s 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] 32.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_build\tst_AutoBuild_build.py" [OK] 936.5s 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] 35.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_combine_models\tst_combine_models.py" [OK] 56.0s 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] 10.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_unmerged_mir\tst_unmerged_mir.py" [FAIL] 16.9s Time: 16.86 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_tests\test_unmerged_mir\tst_unmerged_mir.py", line 101, 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_tests\test_unmerged_mir\tst_unmerged_mir.py", line 41, 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 4127, in AutoSol_scale_and_analyze_mir local_datafile_list,aniso_list,orig_list=self.copy_and_remove_aniso() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 4027, in copy_and_remove_aniso GetDataFile=GetDataFileInfo(os.path.join(self.Facts['temp_dir'],file_name)) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 3.6s Time: 3.64 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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1362, in finish_AutoSol_start ok=self.AutoSol_check_data_files() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 2120, in AutoSol_check_data_files self.finish_AutoSol_start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1362, in finish_AutoSol_start ok=self.AutoSol_check_data_files() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1935, in AutoSol_check_data_files GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 5.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\extract_segment_pair_tests\test_protein\tst_protein.py" [OK] 9.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\extract_segment_pair_tests\test_rna\tst_rna.py" [OK] 0.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\extract_segment_tests\test_helix\tst_helix.py" [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\extract_segment_tests\test_strand\tst_strand.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_trace_tests\test_trace\tst_trace.py" [FAIL] 34.8s Time: 34.77 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\help_tests\test_help\tst_help.py" [OK] 1.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\input_files_tests\test_input_files\tst_input_files.py" [FAIL] 3.5s Time: 3.50 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\labels_tests\test_labels\tst_labels.py" [FAIL] 4.2s Time: 4.16 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_builder\tst_LigandFit_builder.py" [FAIL] 17.7s Time: 17.72 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 2042, 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\base\bin\python\lib\multiprocessing\__init__.py", line 232, in Pool return Pool(processes, initializer, initargs, maxtasksperchild) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\pool.py", line 161, in __init__ self._repopulate_pool() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\pool.py", line 225, in _repopulate_pool w.start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\process.py", line 130, in start self._popen = Popen(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\forking.py", line 272, in __init__ prep_data = get_preparation_data(process_obj._name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\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\base\bin\python\lib\multiprocessing\forking.py", line 379, in main preparation_data = load(from_parent) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 1384, in load return Unpickler(file).load() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 864, in load dispatch[key](self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\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\tst_phase_and_build.py" [OK] 578.4s 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] 95.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_std\tst_LigandFit_std.py" [OK] 33.2s 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] 2.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\misc_methods_tests\test_misc_methods\tst_misc_methods.py" [OK] 0.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\missing_data_tests\test_missing_data\tst_missing_data.py" [OK] 8.1s 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] 122.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_cif\tst_LigandFit_cif.py" [OK] 96.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\multi_tests\test_multi\tst_multi.py" [OK] 46.2s 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] 216.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_lc\tst_LigandFit_lc.py" [OK] 115.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\ncs_tests\test_ncs\tst_ncs.py" [OK] 4.2s 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] 36.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_extra\tst_extra.py" [OK] 2.9s 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] 357.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\maps_only_tests\test_maps_only\tst_maps_only.py" [OK] 135.5s 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] 20.7s 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] 25.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_pdb_in\tst_pdb_in.py" [OK] 39.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_read_hist\tst_read_hist.py" [OK] 38.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_resolve_pattern\tst_resolve_pattern.py" [OK] 14.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_read_pattern\tst_read_pattern.py" [OK] 39.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_index_file\tst_index_file.py" [OK] 146.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_align_bases\tst_align_bases.py" [OK] 6.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_background_map\tst_background_map.py" [OK] 4.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_bad\tst_bad.py" [OK] 3.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_pattern_tests\test_setup\tst_setup.py" [OK] 26.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build\tst_build.py" [OK] 7.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build_image\tst_build_image.py" [OK] 6.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build_1\tst_build_1.py" [OK] 9.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_cc\tst_cc.py" [OK] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_cc_mask\tst_cc_mask.py" [OK] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build_repeat\tst_build_repeat.py" [OK] 11.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_build_se\tst_build_se.py" [OK] 8.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_chain_name\tst_chain_name.py" [OK] 6.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_combine\tst_combine.py" [OK] 4.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_combine_maps\tst_combine_maps.py" [OK] 5.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_composite_pdb\tst_composite_pdb.py" [OK] 4.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_create_hist\tst_create_hist.py" [OK] 2.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_compare\tst_compare.py" [OK] 8.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_cross\tst_cross.py" [OK] 3.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_connect\tst_connect.py" [OK] 9.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_dump_mask\tst_dump_mask.py" [OK] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_diff_map\tst_diff_map.py" [OK] 7.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_dump_frags\tst_dump_frags.py" [OK] 7.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_dump_relat\tst_dump_relat.py" [OK] 6.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_extend_rna\tst_extend_rna.py" [OK] 5.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_assign_sequence\tst_assign_sequence.py" [FAIL] 433.4s Time: 433.43 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\resolve_tests\test_find_ncs_mlt\tst_find_ncs_mlt.py" [OK] 7.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_find_ncs\tst_find_ncs.py" [OK] 8.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_find_strands\tst_find_strands.py" [OK] 8.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_fit_start\tst_fit_start.py" [OK] 2.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_free\tst_free.py" [OK] 3.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_fit\tst_fit.py" [OK] 3.7s 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] 3.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_get_inputs\tst_get_inputs.py" [OK] 2.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_helices_find\tst_helices_find.py" [OK] 3.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_get_histograms\tst_get_histograms.py" [OK] 4.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_helices_trace\tst_helices_trace.py" [OK] 3.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_hist\tst_hist.py" [OK] 2.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_highest_mask\tst_highest_mask.py" [OK] 5.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_helix_trace\tst_helix_trace.py" [FAIL] 8.0s Time: 7.98 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 200805 and 200203 differ 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_just_box\tst_just_box.py" [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_high_pass\tst_high_pass.py" [OK] 8.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_fit\tst_ligand_fit.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_image\tst_image.py" [OK] 6.6s 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] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_group\tst_ligand_group.py" [OK] 4.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_relat\tst_ligand_relat.py" [OK] 4.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_volume\tst_ligand_volume.py" [OK] 2.5s 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] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ligand_large\tst_ligand_large.py" [OK] 8.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_local_hist\tst_local_hist.py" [OK] 3.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_link_prob\tst_link_prob.py" [OK] 8.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_main_map\tst_main_map.py" [OK] 8.4s 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] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_misc\tst_misc.py" [OK] 2.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_mask_image\tst_mask_image.py" [OK] 5.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_masks\tst_masks.py" [OK] 11.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_modify_hist\tst_modify_hist.py" [OK] 2.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_morph\tst_morph.py" [OK] 2.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_mp_file\tst_mp_file.py" [OK] 3.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_modify_ncs\tst_modify_ncs.py" [OK] 5.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ncs_groups\tst_ncs_groups.py" [OK] 6.4s 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] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_offset\tst_offset.py" [OK] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_offset_pdb\tst_offset_pdb.py" [OK] 2.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_maps\tst_maps.py" [OK] 25.3s 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] 3.2s 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] 9.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_omit_mask\tst_omit_mask.py" [OK] 5.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_opt_ncs\tst_opt_ncs.py" [OK] 2.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_omit_region\tst_omit_region.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_ps_edit\tst_ps_edit.py" [OK] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_q\tst_q.py" [OK] 3.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_outside\tst_outside.py" [OK] 9.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_planar_rings\tst_planar_rings.py" [OK] 9.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_randomize_denmod\tst_randomize_denmod.py" [OK] 4.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_random_map\tst_random_map.py" [OK] 2.5s 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] 13.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_randomize_side\tst_randomize_side.py" [OK] 8.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_resolve_multi\tst_resolve_multi.py" [OK] 2.2s 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] 2.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_rebuild_side\tst_rebuild_side.py" [OK] 6.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_rebuild\tst_rebuild.py" [OK] 9.2s 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] 2.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_scores\tst_scores.py" [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_score_tert\tst_score_tert.py" [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_search_center\tst_search_center.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_read_peaks\tst_read_peaks.py" [OK] 16.0s 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] 4.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_sharpen\tst_sharpen.py" [OK] 6.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_set_hist\tst_set_hist.py" [FAIL] 8.3s Time: 8.31 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 200805 and 200203 differ 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_special\tst_special.py" [OK] 3.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_trace_analyze\tst_trace_analyze.py" [OK] 3.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_trace\tst_trace.py" [FAIL] 4.6s Time: 4.62 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 200805 and 200203 differ FAILED...numbers 0.9625077 and 0.9637723 differ FAILED...numbers 81 and 77 differ FAILED...numbers 45 and 43 differ FAILED...numbers 45 and 43 differ FAILED...numbers 46 and 44 differ FAILED...numbers 47 and 45 differ 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_set_fract\tst_set_fract.py" [FAIL] 14.3s Time: 14.34 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 200805 and 200203 differ 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 3.615 and 3.613 differ FAILED...numbers 1.18 and 1.17 differ FAILED...numbers 13.970 and 14.066 differ FAILED...numbers 1.38 and 1.37 differ FAILED...numbers 3.964 and 4.003 differ FAILED...numbers 14.084 and 14.115 differ FAILED...numbers 1.34 and 1.33 differ FAILED...numbers 3.900 and 3.913 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 14.494 and 14.621 differ FAILED...numbers 3.933 and 3.964 differ FAILED...numbers 0.647 and 0.646 differ FAILED...numbers 16.562 and 16.565 differ FAILED...numbers 4.458 and 4.467 differ FAILED...numbers -20.497 and -20.505 differ FAILED...numbers 5.133 and 5.142 differ FAILED...numbers 0.435 and 0.434 differ FAILED...numbers 20.439 and 20.451 differ FAILED...numbers 5.899 and 5.910 differ FAILED...numbers 22.286 and 22.377 differ FAILED...numbers -0.44 and -0.43 differ FAILED...numbers 6.348 and 6.375 differ FAILED...numbers 29.909 and 29.877 differ FAILED...numbers 1.20 and 1.19 differ FAILED...numbers -0.56 and -0.55 differ FAILED...numbers 37.089 and 36.865 differ FAILED...numbers 0.31 and 0.32 differ FAILED...numbers 12.954 and 12.877 differ FAILED...numbers 0.547 and 0.548 differ FAILED...numbers 1.71 and 1.72 differ FAILED...numbers 42.382 and 42.788 differ FAILED...numbers 44.920 and 44.988 differ FAILED...numbers 24.561 and 24.581 differ FAILED...numbers 35.101 and 35.235 differ FAILED...numbers -0.49 and -0.50 differ FAILED...numbers 1.19 and 1.18 differ FAILED...numbers 25.253 and 25.309 differ FAILED...numbers 20.548 and 20.523 differ Test test_set_fract FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_unit_tests\tst_unit_tests.py" [OK] 2.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_update_proxy\tst_update_proxy.py" [OK] 2.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_write_ezd\tst_write_ezd.py" [OK] 2.6s 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] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_zero_hl\tst_zero_hl.py" [OK] 2.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resno_tests\test_resno\tst_resno.py" [FAIL] 302.4s Time: 302.38 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\segment_library_tests\test_segment_library\tst_segment_library.py" [OK] 2.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\short_seq_tests\test_short_seq\tst_short_seq.py" [FAIL] 3.9s Time: 3.88 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\side_chains_tests\test_clusters\tst_clusters.py" [OK] 3.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\side_chains_tests\test_write_map\tst_write_map.py" [OK] 3.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\side_chains_tests\test_use_clusters\tst_use_clusters.py" [OK] 4.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_avg_omit\tst_avg_omit.py" [OK] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_btof\tst_btof.py" [OK] 2.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\side_chains_update_tests\test_update\tst_update.py" [OK] 5.1s 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] 2.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_cc\tst_cc.py" [OK] 4.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resolve_tests\test_write_ca\tst_write_ca.py" [OK] 16.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_compare_soln\tst_compare_soln.py" [OK] 2.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_cluster\tst_cluster.py" [OK] 6.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_fdiff\tst_fdiff.py" [OK] 2.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_extra\tst_extra.py" [OK] 4.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_generate_mad\tst_generate_mad.py" [OK] 3.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_addseed\tst_addseed.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_generate_mir\tst_generate_mir.py" [OK] 3.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_hassp\tst_hassp.py" [OK] 2.8s 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] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_maps\tst_maps.py" [OK] 2.9s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_math\tst_math.py" [OK] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mad\tst_mad.py" [OK] 8.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mir_mtz\tst_mir_mtz.py" [OK] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mir\tst_mir.py" [OK] 6.9s 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] 2.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mad_mtz\tst_mad_mtz.py" [OK] 12.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_question\tst_question.py" [OK] 2.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_combine\tst_combine.py" [OK] 23.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_rho\tst_rho.py" [OK] 2.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_mirror\tst_mirror.py" [OK] 12.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_phases_mtz\tst_phases_mtz.py" [OK] 8.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_read_ano\tst_read_ano.py" [OK] 8.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_scale\tst_scale.py" [OK] 9.1s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_systematic\tst_systematic.py" [OK] 2.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_weights\tst_weights.py" [OK] 2.4s 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] 15.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_sym\tst_sym.py" [OK] 16.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\solve_tests\test_solve\tst_solve.py" [OK] 21.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\omit_tests\test_omit\tst_omit.py" [OK] 441.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\omit_lig_tests\test_omit_lig\tst_omit_lig.py" [OK] 445.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\mult_tests\test_mult\tst_mult.py" [OK] 529.3s ================================================================================ Tests finished. Elapsed time: 1605.35s Distribution of test runtimes: 0.8s - 94.4s: 302 94.4s - 188.0s: 15 188.0s - 281.5s: 3 281.5s - 375.1s: 2 375.1s - 468.7s: 7 468.7s - 562.2s: 2 562.2s - 655.8s: 1 655.8s - 749.4s: 0 749.4s - 842.9s: 0 842.9s - 936.5s: 1 Warning: the following jobs took at least 180 seconds: 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": 216.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_ligands_tests\test_ligand_refine\tst_ligand_refine.py": 234.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_ncs\tst_AutoBuild_ncs.py": 235.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resno_tests\test_resno\tst_resno.py": 302.4s 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": 357.7s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_assign_sequence\tst_assign_sequence.py": 433.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_std\tst_AutoBuild_std.py": 436.8s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_A001\tst_AutoBuild_A001.py": 439.5s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\omit_tests\test_omit\tst_omit.py": 441.0s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\omit_lig_tests\test_omit_lig\tst_omit_lig.py": 445.6s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_lig\tst_AutoBuild_lig.py": 453.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_hires\tst_AutoBuild_hires.py": 458.2s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\mult_tests\test_mult\tst_mult.py": 529.3s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_mult\tst_AutoBuild_mult.py": 541.6s 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": 578.4s libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoBuild_tests\test_AutoBuild_build\tst_AutoBuild_build.py": 936.5s 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\AutoMR_tests\test_AutoMR_std\tst_AutoMR_std.py" [FAIL] 3.3s Time: 3.33 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mad\tst_AutoSol_mad.py" [FAIL] 3.5s Time: 3.53 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mad\tst_AutoSol_mad.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\AutoSol_tests\test_AutoSol_mad\tst_AutoSol_mad.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mir\tst_AutoSol_mir.py" [FAIL] 3.4s Time: 3.44 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_mir\tst_AutoSol_mir.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\AutoSol_tests\test_AutoSol_mir\tst_AutoSol_mir.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_phaser\tst_AutoSol_phaser.py" [FAIL] 3.7s Time: 3.70 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_phaser\tst_AutoSol_phaser.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\AutoSol_tests\test_AutoSol_phaser\tst_AutoSol_phaser.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 3.6s Time: 3.59 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_phaser_mr\tst_AutoSol_phaser_mr.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\AutoSol_tests\test_AutoSol_phaser_mr\tst_AutoSol_phaser_mr.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_rna\tst_AutoSol_rna.py" [FAIL] 3.7s Time: 3.69 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_rna\tst_AutoSol_rna.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\AutoSol_tests\test_AutoSol_rna\tst_AutoSol_rna.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 3.6s Time: 3.59 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_sir_sad\tst_AutoSol_sir_sad.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\AutoSol_tests\test_AutoSol_sir_sad\tst_AutoSol_sir_sad.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_std\tst_AutoSol_std.py" [FAIL] 3.5s Time: 3.53 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\AutoSol_tests\test_AutoSol_std\tst_AutoSol_std.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\AutoSol_tests\test_AutoSol_std\tst_AutoSol_std.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\autosol_unmerged_tests\test_autosol_unmerged\tst_autosol_unmerged.py" [FAIL] 51.5s Time: 51.53 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\autosol_unmerged_tests\test_autosol_unmerged\tst_autosol_unmerged.py", line 87, 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\autosol_unmerged_tests\test_autosol_unmerged\tst_autosol_unmerged.py", line 41, 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 3464, in AutoSol_scale_and_analyze_mad local_datafile_list,aniso_list,orig_list=self.copy_and_remove_aniso() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 4027, in copy_and_remove_aniso GetDataFile=GetDataFileInfo(os.path.join(self.Facts['temp_dir'],file_name)) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_autobuild_quick\tst_autobuild_quick.py" [FAIL] 3.5s Time: 3.52 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_build_tests\test_automr_remark\tst_automr_remark.py" [FAIL] 3.3s Time: 3.33 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 58.3s Time: 58.28 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 2042, 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\base\bin\python\lib\multiprocessing\__init__.py", line 232, in Pool return Pool(processes, initializer, initargs, maxtasksperchild) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\pool.py", line 161, in __init__ self._repopulate_pool() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\pool.py", line 225, in _repopulate_pool w.start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\process.py", line 130, in start self._popen = Popen(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\forking.py", line 272, in __init__ prep_data = get_preparation_data(process_obj._name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\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\base\bin\python\lib\multiprocessing\forking.py", line 379, in main preparation_data = load(from_parent) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 1384, in load return Unpickler(file).load() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 864, in load dispatch[key](self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\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_misc_tests\test_autosol_classic_denmod\tst_autosol_classic_denmod.py" [FAIL] 3.5s Time: 3.53 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_misc_tests\test_autosol_classic_denmod\tst_autosol_classic_denmod.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_misc_tests\test_autosol_classic_denmod\tst_autosol_classic_denmod.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_cif\tst_cif.py" [FAIL] 4.1s Time: 4.08 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_misc_tests\test_cif\tst_cif.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_misc_tests\test_cif\tst_cif.py", line 26, in run run_autobuild(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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\ImportRawData.py", line 352, in finish_ImportRawData_start pick_best_label=pick_best_label) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\read_hkl.py", line 153, in __init__ labels[0] in ['N','N(+)']: # skip N or N(+) which are counts not data IndexError: list index out of range 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" [FAIL] 71.6s Time: 71.63 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 80.0000 and 100.0000 differ FAILED...numbers 82.5000 and 87.5000 differ FAILED...numbers 0.5415 and 0.5425 differ FAILED...numbers 0.5293 and 0.5349 differ FAILED...numbers 0.5293 and 0.5349 differ FAILED...numbers 0.5292 and 0.5349 differ FAILED...numbers 0.0622 and 0.0655 differ FAILED...numbers 0.384 and 0.365 differ FAILED...numbers 3.364 and 3.352 differ FAILED...numbers 0.0622 and 0.0655 differ FAILED...numbers 0.384 and 0.365 differ FAILED...numbers 3.364 and 3.352 differ FAILED...numbers 357 and 355 differ FAILED...numbers 357 and 355 differ FAILED...numbers 357 and 355 differ FAILED...numbers 63 and 62 differ FAILED...numbers 231 and 230 differ FAILED...numbers 114 and 112 differ FAILED...numbers 370 and 368 differ FAILED...numbers 365 and 363 differ FAILED...numbers 94.89 and 94.88 differ FAILED...numbers 0.05 and 0.03 differ FAILED...numbers 193 and 192 differ FAILED...numbers 31 and 32 differ FAILED...numbers 2.63e+01 and 2.64e+01 differ FAILED...numbers 1.53e+01 and 1.52e+01 differ FAILED...numbers 66 and 65 differ FAILED...numbers -0.129 and -0.127 differ FAILED...numbers 0.126 and 0.124 differ FAILED...numbers 0.099 and 0.098 differ FAILED...numbers 63 and 62 differ FAILED...numbers 2.05 and 2.04 differ FAILED...numbers 691 and 680 differ FAILED...numbers 26 and 20 differ FAILED...numbers 1949 and 1938 differ FAILED...numbers 0.0625 and 0.0640 differ FAILED...numbers 370 and 368 differ FAILED...numbers 83.33 and 88.01 differ FAILED...numbers 2 and 1 differ FAILED...numbers 1 and 0 differ FAILED...numbers 0.5147 and 0.5078 differ FAILED...numbers 0.5027 and 0.5001 differ FAILED...numbers 0.5040 and 0.5010 differ FAILED...numbers -0.0199 and 0.0320 differ FAILED...numbers 0.037 and 0.048 differ FAILED...numbers 7.58 and 7.59 differ FAILED...numbers 25.58 and 16.28 differ FAILED...numbers -0.0199 and 0.0320 differ FAILED...numbers 0.037 and 0.048 differ FAILED...numbers 7.58 and 7.59 differ FAILED...numbers 25.58 and 16.28 differ FAILED...numbers 2.93 and 2.94 differ FAILED...numbers 2.93 and 2.94 differ Test test_iterative_ss_refine 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] 3.6s Time: 3.64 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_misc_tests\test_dano_labels\tst_dano_labels.py", line 251, 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_misc_tests\test_dano_labels\tst_dano_labels.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_dos\tst_dos.py" [FAIL] 3.6s Time: 3.56 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_misc_tests\test_dos\tst_dos.py", line 101, 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_misc_tests\test_dos\tst_dos.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_hyss\tst_hyss.py" [FAIL] 2.2s Time: 2.19 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_misc_tests\test_hyss\tst_hyss.py", line 125, 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_misc_tests\test_hyss\tst_hyss.py", line 21, in run run(args=args,out=log) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\hyss.py", line 619, in run space_group_info=params.space_group,out=out) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\hyss.py", line 2610, in prompt_for_symmetry_if_necessary for input_array in reflection_file.as_miller_arrays(): File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\reflection_file_reader.py", line 313, in as_miller_arrays anomalous=anomalous, TypeError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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" [FAIL] 2.8s Time: 2.78 Return code: 1 OKs: 0 Standard error: Sorry: Failed to read the file native.sca 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" [FAIL] 3.4s Time: 3.44 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_misc_tests\test_keep_atom_types\tst_keep_atom_types.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_misc_tests\test_keep_atom_types\tst_keep_atom_types.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_phaser\tst_phaser.py" [FAIL] 3.1s Time: 3.09 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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" [FAIL] 3.2s Time: 3.20 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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" [FAIL] 4.8s Time: 4.83 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_misc_tests\test_scale_and_merge\tst_scale_and_merge.py", line 83, 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_misc_tests\test_scale_and_merge\tst_scale_and_merge.py", line 21, in run run(args=args,out=log) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\scale_and_merge.py", line 3381, in run sc=scale_and_merge(out=out,params=params) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\scale_and_merge.py", line 2223, in __init__ crystal_symmetry=crystal_symmetry,out=out) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\scale_and_merge.py", line 2341, in read_and_scale_datasets crystal_symmetry=crystal_symmetry,out=out) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\scale_and_merge.py", line 3205, in scale_datasets kw_list=kw_list) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\easy_mp.py", line 771, in run_parallel results.append(ra(i)) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\libtbx\easy_mp.py", line 756, in __call__ return self.target_function(**kw) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\command_line\scale_and_merge.py", line 2084, in scale_one_dataset merge_equivalents=True)[0] File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\cctbx_project\iotbx\reflection_file_reader.py", line 313, in as_miller_arrays anomalous=anomalous, TypeError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_set_sg\tst_set_sg.py" [FAIL] 3.5s Time: 3.52 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_misc_tests\test_set_sg\tst_set_sg.py", line 176, 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_misc_tests\test_set_sg\tst_set_sg.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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" [FAIL] 3.4s Time: 3.42 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_misc_tests\test_special_pos\tst_special_pos.py" [FAIL] 3.5s Time: 3.52 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_misc_tests\test_special_pos\tst_special_pos.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_misc_tests\test_special_pos\tst_special_pos.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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" [FAIL] 3.4s Time: 3.44 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_non_standard_tests\test_cluster\tst_cluster.py" [FAIL] 3.6s Time: 3.61 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_non_standard_tests\test_cluster\tst_cluster.py", line 86, 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_non_standard_tests\test_cluster\tst_cluster.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1362, in finish_AutoSol_start ok=self.AutoSol_check_data_files() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 2120, in AutoSol_check_data_files self.finish_AutoSol_start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1362, in finish_AutoSol_start ok=self.AutoSol_check_data_files() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1935, in AutoSol_check_data_files GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 3.4s Time: 3.41 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_non_standard_tests\test_inv_sg\tst_inv_sg.py", line 72, 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_non_standard_tests\test_inv_sg\tst_inv_sg.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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" [FAIL] 3.7s Time: 3.69 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_non_standard_tests\test_non_standard_sg\tst_non_standard_sg.py", line 71, 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_non_standard_tests\test_non_standard_sg\tst_non_standard_sg.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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" [FAIL] 3.6s Time: 3.62 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_non_standard_tests\test_part_map_coeffs\tst_part_map_coeffs.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_non_standard_tests\test_part_map_coeffs\tst_part_map_coeffs.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1362, in finish_AutoSol_start ok=self.AutoSol_check_data_files() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 2120, in AutoSol_check_data_files self.finish_AutoSol_start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1362, in finish_AutoSol_start ok=self.AutoSol_check_data_files() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1935, in AutoSol_check_data_files GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_omit_tests\test_omit_selection\tst_omit_selection.py" [FAIL] 3.2s Time: 3.22 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 60.6s Time: 60.64 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 0.34 and 0.33 differ FAILED...numbers 0.23 and 0.22 differ FAILED...numbers 0.17 and 0.16 differ FAILED...numbers 0.17 and 0.16 differ FAILED...numbers 6.16509705647428491E-02 and 6.57551065270074040E-002 differ FAILED...numbers 7.431 and 7.612 differ FAILED...numbers 0.22873952571100287 and 0.22383430108447586 differ FAILED...numbers 0.28973519802093506 and 0.29308140277862549 differ FAILED...numbers 4.8088 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 12.23613 and 12.24053 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 4.09704655250958394E-02 and 3.32651507186891990E-002 differ FAILED...numbers 0.15 and 0.14 differ FAILED...numbers 4.8088 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 12.23613 and 12.24053 differ FAILED...numbers 5182 and 5223 differ FAILED...numbers 0.15 and 0.14 differ FAILED...numbers 12.19996 and 12.27342 differ FAILED...numbers 0.43 and 0.44 differ FAILED...numbers 12.2 and 12.3 differ FAILED...numbers 0.19928348064422607 and 0.19815889000892639 differ FAILED...numbers 0.13 and 0.12 differ FAILED...numbers 0.054 and 0.053 differ FAILED...numbers 5.89626075427985077E-02 and 5.63865282179515790E-002 differ FAILED...numbers 0.61 and 0.59 differ FAILED...numbers 0.52 and 0.55 differ FAILED...numbers -0.0963166 and -0.0978056 differ FAILED...numbers 0.62 and 0.64 differ Test test_density_modification FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_morph_model\tst_morph_model.py" [FAIL] 2.9s Time: 2.91 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_phaser_denmod\tst_phaser_denmod.py" [FAIL] 3.6s Time: 3.59 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_tests\test_phaser_denmod\tst_phaser_denmod.py", line 77, 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_tests\test_phaser_denmod\tst_phaser_denmod.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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1357, in finish_AutoSol_start self.find_best_ref_file(self.Facts['input_file_list']) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1215, in find_best_ref_file GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_tests\test_unmerged_mir\tst_unmerged_mir.py" [FAIL] 16.9s Time: 16.86 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_tests\test_unmerged_mir\tst_unmerged_mir.py", line 101, 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_tests\test_unmerged_mir\tst_unmerged_mir.py", line 41, 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 4127, in AutoSol_scale_and_analyze_mir local_datafile_list,aniso_list,orig_list=self.copy_and_remove_aniso() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 4027, in copy_and_remove_aniso GetDataFile=GetDataFileInfo(os.path.join(self.Facts['temp_dir'],file_name)) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' 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] 3.6s Time: 3.64 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 815, in Run ok=self.CollectInputs()# raises AssertionError on failure File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1887, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1362, in finish_AutoSol_start ok=self.AutoSol_check_data_files() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 2120, in AutoSol_check_data_files self.finish_AutoSol_start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1362, in finish_AutoSol_start ok=self.AutoSol_check_data_files() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\wizards\AutoSol.py", line 1935, in AutoSol_check_data_files GetDataFile=GetDataFileInfo(file_name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules\phenix\phenix\autosol\GetDataFileInfo.py", line 82, in __init__ raise AssertionError, str(e) AssertionError: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\command_line_trace_tests\test_trace\tst_trace.py" [FAIL] 34.8s Time: 34.77 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\input_files_tests\test_input_files\tst_input_files.py" [FAIL] 3.5s Time: 3.50 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\labels_tests\test_labels\tst_labels.py" [FAIL] 4.2s Time: 4.16 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\LigandFit_tests\test_LigandFit_builder\tst_LigandFit_builder.py" [FAIL] 17.7s Time: 17.72 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 2042, 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\base\bin\python\lib\multiprocessing\__init__.py", line 232, in Pool return Pool(processes, initializer, initargs, maxtasksperchild) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\pool.py", line 161, in __init__ self._repopulate_pool() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\pool.py", line 225, in _repopulate_pool w.start() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\process.py", line 130, in start self._popen = Popen(self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\multiprocessing\forking.py", line 272, in __init__ prep_data = get_preparation_data(process_obj._name) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\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\base\bin\python\lib\multiprocessing\forking.py", line 379, in main preparation_data = load(from_parent) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 1384, in load return Unpickler(file).load() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\lib\pickle.py", line 864, in load dispatch[key](self) File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\base\bin\python\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_tests\test_assign_sequence\tst_assign_sequence.py" [FAIL] 433.4s Time: 433.43 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\resolve_tests\test_helix_trace\tst_helix_trace.py" [FAIL] 8.0s Time: 7.98 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 200805 and 200203 differ 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_set_hist\tst_set_hist.py" [FAIL] 8.3s Time: 8.31 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 200805 and 200203 differ 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] 4.6s Time: 4.62 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 200805 and 200203 differ FAILED...numbers 0.9625077 and 0.9637723 differ FAILED...numbers 81 and 77 differ FAILED...numbers 45 and 43 differ FAILED...numbers 45 and 43 differ FAILED...numbers 46 and 44 differ FAILED...numbers 47 and 45 differ 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_set_fract\tst_set_fract.py" [FAIL] 14.3s Time: 14.34 Return code: 1 OKs: 0 Standard error: Sorry: FAILED...numbers 200805 and 200203 differ 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 3.615 and 3.613 differ FAILED...numbers 1.18 and 1.17 differ FAILED...numbers 13.970 and 14.066 differ FAILED...numbers 1.38 and 1.37 differ FAILED...numbers 3.964 and 4.003 differ FAILED...numbers 14.084 and 14.115 differ FAILED...numbers 1.34 and 1.33 differ FAILED...numbers 3.900 and 3.913 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 14.494 and 14.621 differ FAILED...numbers 3.933 and 3.964 differ FAILED...numbers 0.647 and 0.646 differ FAILED...numbers 16.562 and 16.565 differ FAILED...numbers 4.458 and 4.467 differ FAILED...numbers -20.497 and -20.505 differ FAILED...numbers 5.133 and 5.142 differ FAILED...numbers 0.435 and 0.434 differ FAILED...numbers 20.439 and 20.451 differ FAILED...numbers 5.899 and 5.910 differ FAILED...numbers 22.286 and 22.377 differ FAILED...numbers -0.44 and -0.43 differ FAILED...numbers 6.348 and 6.375 differ FAILED...numbers 29.909 and 29.877 differ FAILED...numbers 1.20 and 1.19 differ FAILED...numbers -0.56 and -0.55 differ FAILED...numbers 37.089 and 36.865 differ FAILED...numbers 0.31 and 0.32 differ FAILED...numbers 12.954 and 12.877 differ FAILED...numbers 0.547 and 0.548 differ FAILED...numbers 1.71 and 1.72 differ FAILED...numbers 42.382 and 42.788 differ FAILED...numbers 44.920 and 44.988 differ FAILED...numbers 24.561 and 24.581 differ FAILED...numbers 35.101 and 35.235 differ FAILED...numbers -0.49 and -0.50 differ FAILED...numbers 1.19 and 1.18 differ FAILED...numbers 25.253 and 25.309 differ FAILED...numbers 20.548 and 20.523 differ Test test_set_fract FAILED libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\resno_tests\test_resno\tst_resno.py" [FAIL] 302.4s Time: 302.38 Return code: 1 OKs: 0 libtbx.python "c:\users\phaserbuilder\nightlybuilds\phenixvc2008\x64\current\modules\phenix_regression\wizards\short_seq_tests\test_short_seq\tst_short_seq.py" [FAIL] 3.9s Time: 3.88 Return code: 1 OKs: 0 Standard error: Sorry: as_miller_arrays() got an unexpected keyword argument 'anomalous' Please verify these tests manually. Summary: Tests run : 333 Failures : 48 Warnings (possible failures) : 0 Known Failures ( 0) : 0 Known Unstable ( 0) : 0 Stderr output (discouraged) : 47 See run_tests_parallel_zlog for full output. ******************************************************************************** ERROR: 48 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 25, in main() File "C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\build\..\modules\phenix_regression\wizards\test_all_parallel.py", line 19, in main raise AssertionError,"AT LEAST ONE TEST FAILED" AssertionError: AT LEAST ONE TEST FAILED To run dials tests please run 'pytest' inside the dials directory For more information see: https://github.com/dials/dials/wiki/pytest Performing actions: tests ===== Running in .: deleting dist, tests, tmp removing .pyc files in C:\Users\phaserbuilder\NightlyBuilds\PhenixVC2008\x64\Current\modules, walk? True removed 283 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 06/10/2019 7:28:46.76