core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.binary.linux.release-247 r247 2020.08+release.cb1caba cb1cabafd7463ab703f6abf5efa33d2707b85924 https://www.rosettacommons.org 2020-02-21T14:46:08.581859 core.init: command: /opt/rosetta/main/source/bin/rosetta_scripts @options.txt -nstruct 5 basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1575522402 seed_offset=0 real_seed=-1575522402 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1575522402 RG_type=mt19937 core.init: found database environment variable ROSETTA3_DB: /opt/rosetta/main/database protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed 4K8F_A_HEM.pdb nstruct indices 1 - 5 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB 4K8F_A_HEM.pdb core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 75 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.08 seconds. core.import_pose.import_pose: File '4K8F_A_HEM.pdb' automatically determined to be of type PDB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: pre_talaris_2013_standard.wts core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4 core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/opt/rosetta/main/database/rotamer/bbdep02.May.sortlib.Dunbrack02.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack library took 0.05 seconds to load from binary core.pack.rotamers.SingleLigandRotamerLibrary: Read in 99 rotamers from HEM_conformers.pdb ! core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 363 rotamers at 133 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 179.985 chino= 2 position: 12 SER SER core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 160.006 chino= 2 position: 17 THR THR core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 160.033 chino= 2 position: 24 SER SER core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 179.992 chino= 2 position: 31 SER SER core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 20.022 chino= 2 position: 34 CYS CYS core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 159.995 chino= 2 position: 35 THR THR core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 179.987 chino= 3 position: 54 TYR TYR core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 160.003 chino= 2 position: 63 SER SER core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 40.020 chino= 2 position: 68 THR THR core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 39.988 chino= 2 position: 69 SER SER core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 99.981 chino= 2 position: 74 CYS CYS core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 59.966 chino= 2 position: 77 SER SER core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 20.019 chino= 2 position: 79 CYS CYS core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 39.998 chino= 2 position: 84 THR THR core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 160.033 chino= 2 position: 87 THR THR core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 79.990 chino= 2 position: 96 THR THR core.io.pdb.file_data: [ WARNING ] OPT-H: heavyatom chi angle change: chidev= 180.000 chino= 3 position: 99 GLN GLN core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 160.002 chino= 2 position: 103 THR THR core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 140.007 chino= 2 position: 104 CYS CYS core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 179.969 chino= 2 position: 106 SER SER core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 160.023 chino= 2 position: 120 THR THR core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 159.985 chino= 2 position: 121 SER SER core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 20.001 chino= 2 position: 122 CYS CYS core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 159.988 chino= 2 position: 125 THR THR core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 28.321 chino= 1 position: 133 HEM HEM core.io.pdb.file_data: [ WARNING ] OPT-H: proton chi angle change: chidev= 176.093 chino= 2 position: 133 HEM HEM protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=dock.xml protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Validating input script... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Parsed script: core.scoring.ScoreFunctionFactory: SCOREFUNCTION: pre_talaris_2013_standard.wts core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12 core.scoring.etable: Using alternate parameters: LJ_RADIUS_SOFT in Etable construction. core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt protocols.jd2.parser.ScoreFunctionLoader: defined score function "ligand_soft_rep" with weights "ligand_soft_rep" protocols.jd2.parser.ScoreFunctionLoader: defined score function "hard_rep" with weights "ligand" protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "start_from" of type StartFrom protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "transform" of type Transform protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "high_res_docker" of type HighResDocker protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "final" of type FinalMinimizer core.import_pose.import_pose: File 'crystal_complex_4K8F.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 43 atoms at position 133 in file crystal_complex_4K8F.pdb. Best match rsd_type: HEM Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job '4K8F_A_HEM_0001' Error: [ ERROR ] Treating failure as bad input; canceling similar jobs protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: 4K8F_A_HEM_0001 protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 5 jobs considered, 1 jobs attempted in 21 seconds