core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.binary.mac.release-247 r247 2020.08+release.cb1cabafd74 cb1cabafd7463ab703f6abf5efa33d2707b85924 https://www.rosettacommons.org 2020-02-22T06:57:31.821199 core.init: command: /Users/sug82/Downloads/Rosetta/rosetta_bin_mac_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.macosclangrelease -cst_fa_file myconstraint.cst @docking.options basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-662015701 seed_offset=0 real_seed=-662015701 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-662015701 RG_type=mt19937 core.init: Resolved executable path: /Users/sug82/Downloads/Rosetta/rosetta_bin_mac_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.macosclangrelease core.init: Looking for database based on location of executable: /Users/sug82/Downloads/Rosetta/rosetta_bin_mac_2020.08.61146_bundle/main/database/ protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed ./input_files/complex_8_repacked_renumber.pdb nstruct indices 1 - 500 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB ./input_files/complex_8_repacked_renumber.pdb core.chemical: [ WARNING ] protein residue SPC is not explicitly listed as either L or D in its params file. core.chemical: [ WARNING ] To avoid seeing this warning in the future, add "L_AA", "D_AA", or "ACHIRAL_BACKBONE" to the "PROPERTIES" line of the params file. core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 982 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.71037 seconds. core.import_pose.import_pose: File './input_files/complex_8_repacked_renumber.pdb' automatically determined to be of type PDB protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=docking_full.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: ref2015.wts 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/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt 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 core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop 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/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 core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "ifcl" of type InitializeFromCommandline protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "rtr" of type RestrictToRepacking protocols.relax.RelaxScriptManager: Reading relax scripts list from database. core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015.wts protocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt protocols.relax.RelaxScriptManager: ================== Reading script file: /Users/sug82/Downloads/Rosetta/rosetta_bin_mac_2020.08.61146_bundle/main/database/sampling/relax_scripts/MonomerRelax2019.txt ================== protocols.relax.RelaxScriptManager: repeat %%nrepeats%% protocols.relax.RelaxScriptManager: coord_cst_weight 1.0 protocols.relax.RelaxScriptManager: scale:fa_rep 0.040 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: scale:fa_rep 0.051 protocols.relax.RelaxScriptManager: min 0.01 protocols.relax.RelaxScriptManager: coord_cst_weight 0.5 protocols.relax.RelaxScriptManager: scale:fa_rep 0.265 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: scale:fa_rep 0.280 protocols.relax.RelaxScriptManager: min 0.01 protocols.relax.RelaxScriptManager: coord_cst_weight 0.0 protocols.relax.RelaxScriptManager: scale:fa_rep 0.559 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: scale:fa_rep 0.581 protocols.relax.RelaxScriptManager: min 0.01 protocols.relax.RelaxScriptManager: coord_cst_weight 0.0 protocols.relax.RelaxScriptManager: scale:fa_rep 1 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: min 0.00001 protocols.relax.RelaxScriptManager: accept_to_best protocols.relax.RelaxScriptManager: endrepeat core.pack.task.xml_util: Object minimize_interface reading the following task_operations: Adding the following task operations ifcl rtr protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "minimize_interface" of type FastRelax core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015.wts protocols.docking.DockingInitialPerturbation: Reading options... core.pack.task.xml_util: Object dock_low reading the following task_operations: Adding the following task operations ifcl protocols.protein_interface_design.movers.DockAndRetrieveSidechains: docking mover with parameters low_res_protocol_only_ 1 local_refine 0 view 0 lowres_scorefxn= score_docking_low highres_scorefxn= REF2015 over rb_jumps 1, optimize fold tree=1 protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "dock_low" of type Docking core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015.wts core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015.wts core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015.wts core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015.wts core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015.wts core.pack.task.xml_util: Object dock_high reading the following task_operations: Adding the following task operations ifcl protocols.protein_interface_design.movers.DockAndRetrieveSidechains: docking mover with parameters low_res_protocol_only_ 0 local_refine 1 view 0 lowres_scorefxn= score_docking_low highres_scorefxn= REF2015 over rb_jumps 1, optimize fold tree=1 protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "dock_high" of type Docking protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "srsc" of type SaveAndRetrieveSidechains protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters protocols.rosetta_scripts.ParsedProtocol: added mover "dock_low" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "srsc" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "dock_high" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "minimize_interface" with filter "true_filter" protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy ./input_files/complex_8_repacked_renumber.pdb protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Docking - dock_low======================= protocols.docking.DockingProtocol: Setting docking foldtree protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 276 -1 EDGE 1 277 1 EDGE 277 353 -1 protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 80 -1 EDGE 80 276 -1 EDGE 80 344 1 EDGE 344 277 -1 EDGE 344 353 -1 protocols.docking.DockingProtocol: setting up the constraint set mover protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol: File: src/protocols/constraint_movers/ConstraintSetMover.cc:124 [ ERROR ] UtilityExitException ERROR: Can't read constraints from empty file! protocols.jd2.JobDistributor: [ ERROR ] [ERROR] Exception caught by JobDistributor for job complex_8_repacked_renumber_docked_0001 protocols.jd2.JobDistributor: [ WARNING ] complex_8_repacked_renumber_docked_0001 reported failure and will NOT retry protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy ./input_files/complex_8_repacked_renumber.pdb protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy ./input_files/complex_8_repacked_renumber.pdb protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Docking - dock_low======================= protocols.docking.DockingProtocol: Setting docking foldtree protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 276 -1 EDGE 1 277 1 EDGE 277 353 -1 protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 80 -1 EDGE 80 276 -1 EDGE 80 344 1 EDGE 344 277 -1 EDGE 344 353 -1 protocols.docking.DockingProtocol: setting up the constraint set mover protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol: File: src/protocols/constraint_movers/ConstraintSetMover.cc:124 [ ERROR ] UtilityExitException ERROR: Can't read constraints from empty file! protocols.jd2.JobDistributor: [ ERROR ] [ERROR] Exception caught by JobDistributor for job complex_8_repacked_renumber_docked_0002 protocols.jd2.JobDistributor: [ WARNING ] complex_8_repacked_renumber_docked_0002 reported failure and will NOT retry protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy ./input_files/complex_8_repacked_renumber.pdb protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy ./input_files/complex_8_repacked_renumber.pdb protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Docking - dock_low======================= protocols.docking.DockingProtocol: Setting docking foldtree protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 276 -1 EDGE 1 277 1 EDGE 277 353 -1 protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 80 -1 EDGE 80 276 -1 EDGE 80 344 1 EDGE 344 277 -1 EDGE 344 353 -1 protocols.docking.DockingProtocol: setting up the constraint set mover protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol: File: src/protocols/constraint_movers/ConstraintSetMover.cc:124 [ ERROR ] UtilityExitException ERROR: Can't read constraints from empty file! protocols.jd2.JobDistributor: [ ERROR ] [ERROR] Exception caught by JobDistributor for job complex_8_repacked_renumber_docked_0003 protocols.jd2.JobDistributor: [ WARNING ] complex_8_repacked_renumber_docked_0003 reported failure and will NOT retry protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy ./input_files/complex_8_repacked_renumber.pdb protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy ./input_files/complex_8_repacked_renumber.pdb protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Docking - dock_low======================= protocols.docking.DockingProtocol: Setting docking foldtree protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 276 -1 EDGE 1 277 1 EDGE 277 353 -1 protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 80 -1 EDGE 80 276 -1 EDGE 80 344 1 EDGE 344 277 -1 EDGE 344 353 -1 protocols.docking.DockingProtocol: setting up the constraint set mover protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol: File: src/protocols/constraint_movers/ConstraintSetMover.cc:124 [ ERROR ] UtilityExitException ERROR: Can't read constraints from empty file! protocols.jd2.JobDistributor: [ ERROR ] [ERROR] Exception caught by JobDistributor for job complex_8_repacked_renumber_docked_0004 protocols.jd2.JobDistributor: [ WARNING ] complex_8_repacked_renumber_docked_0004 reported failure and will NOT retry protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy ./input_files/complex_8_repacked_renumber.pdb protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy ./input_files/complex_8_repacked_renumber.pdb protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Docking - dock_low======================= protocols.docking.DockingProtocol: Setting docking foldtree protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 276 -1 EDGE 1 277 1 EDGE 277 353 -1 protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 80 -1 EDGE 80 276 -1 EDGE 80 344 1 EDGE 344 277 -1 EDGE 344 353 -1 protocols.docking.DockingProtocol: setting up the constraint set mover protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol: File: src/protocols/constraint_movers/ConstraintSetMover.cc:124 [ ERROR ] UtilityExitException ERROR: Can't read constraints from empty file! protocols.jd2.JobDistributor: [ ERROR ] [ERROR] Exception caught by JobDistributor for job complex_8_repacked_renumber_docked_0005