core.init: Rosetta version unknown:exported  from http://www.rosettacommons.org
core.init: command: /app/biology/Rosetta_3.7/main/source/bin/rosetta_scripts.linuxgccrelease @options
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1673631492 seed_offset=0 real_seed=-1673631492
core.init.random: RandomGenerator:init: Normal mode, seed=-1673631492 RG_type=mt19937
core.init: Resolved executable path: /app/biology/Rosetta_3.7/main/source/build/src/release/linux/2.6/64/x86/gcc/4.4/default/rosetta_scripts.default.linuxgccrelease
core.init: Looking for database based on location of executable: /app/biology/Rosetta_3.7/main/database/
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed 3PBL_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed ETQ.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... 
protocols.jd2.JobDistributor: Parser is present.  Input mover will be overwritten with whatever the parser creates.
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB 3PBL_A.pdb
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set.  Created 75 residue types
core.chemical.ResidueTypeSet: Total time to initialize 0.12 seconds.
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CG  on residue GLN 113
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CD  on residue GLN 113
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OE1 on residue GLN 113
core.conformation.Conformation: [ WARNING ] missing heavyatom:  NE2 on residue GLN 113
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OG  on residue SER 114
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CG  on residue GLU 297
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CD  on residue GLU 297
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OE1 on residue GLU 297
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OE2 on residue GLU 297
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OG1 on residue THR 389
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CG2 on residue THR 389
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue CYS:CtermProteinFull 432
core.conformation.Conformation: Found disulfide between residues 72 150
core.conformation.Conformation: current variant for 72 CYS
core.conformation.Conformation: current variant for 150 CYS
core.conformation.Conformation: current variant for 72 CYD
core.conformation.Conformation: current variant for 150 CYD
core.conformation.Conformation: Found disulfide between residues 387 390
core.conformation.Conformation: current variant for 387 CYS
core.conformation.Conformation: current variant for 390 CYS
core.conformation.Conformation: current variant for 387 CYD
core.conformation.Conformation: current variant for 390 CYD
core.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name  CG 
core.pack.pack_missing_sidechains: packing residue number 114 because of missing atom number 6 atom name  OG 
core.pack.pack_missing_sidechains: packing residue number 297 because of missing atom number 6 atom name  CG 
core.pack.pack_missing_sidechains: packing residue number 389 because of missing atom number 6 atom name  OG1
core.pack.task: Packer task: initialize from command line() 
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
basic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/ssabban/.rosetta/database/rotamer/bbdep02.May.sortlib.Dunbrack02.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack library took 0.05 seconds to load from binary
core.pack.pack_rotamers: built 87 rotamers at 4 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 2624 bytes
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: pre_talaris_2013_standard.wts
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 1029 rotamers at 432 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 1308696 bytes
core.io.pdb.file_data: [ OPT-H WARNING ] heavyatom chi angle change: chidev=   180.000 chino=  2 position:   16 ASN ASN
core.io.pdb.file_data: [ OPT-H WARNING ] heavyatom chi angle change: chidev=   180.000 chino=  2 position:   66 ASN ASN
core.io.pdb.file_data: [ OPT-H WARNING ] heavyatom chi angle change: chidev=   180.000 chino=  3 position:  108 GLN GLN
core.io.pdb.file_data: [ OPT-H WARNING ] heavyatom chi angle change: chidev=   180.000 chino=  2 position:  329 ASN ASN
core.io.pdb.file_data: [ OPT-H WARNING ] heavyatom chi angle change: chidev=   180.000 chino=  2 position:  386 HIS HIS
core.io.pdb.file_data: [ OPT-H WARNING ] heavyatom chi angle change: chidev=   180.000 chino=  3 position:  388 GLN GLN
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=dock.xml
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
	<SCOREFXNS>
		<ScoreFunction name=ligand_soft_rep weights=ligand_soft_rep/>
		<ScoreFunction name=hard_rep weights=ligand/>
	</SCOREFXNS>
	<LIGAND_AREAS>
		<LigandArea add_nbr_radius=true all_atom_mode=false chain=X cutoff=6.0 name=inhibitor_dock_sc/>
		<LigandArea add_nbr_radius=true all_atom_mode=false chain=X cutoff=6.0 name=inhibitor_final_sc/>
		<LigandArea Calpha_restraints=0.3 add_nbr_radius=false all_atom_mode=true chain=X cutoff=7.0 name=inhibitor_final_bb/>
	</LIGAND_AREAS>
	<INTERFACE_BUILDERS>
		<InterfaceBuilder ligand_areas=inhibitor_dock_sc name=side_chain_for_docking/>
		<InterfaceBuilder ligand_areas=inhibitor_final_sc name=side_chain_for_final/>
		<InterfaceBuilder extension_window=3 ligand_areas=inhibitor_final_bb name=backbone/>
	</INTERFACE_BUILDERS>
	<MOVEMAP_BUILDERS>
		<MoveMapBuilder minimize_water=false name=docking sc_interface=side_chain_for_docking/>
		<MoveMapBuilder bb_interface=backbone minimize_water=false name=final sc_interface=side_chain_for_final/>
	</MOVEMAP_BUILDERS>
	<SCORINGGRIDS ligand_chain=X width=15>
		<ClassicGrid grid_name=classic weight=1.0/>
	</SCORINGGRIDS>
	<MOVERS>
		<Transform angle=20 box_size=7.0 chain=X cycles=500 move_distance=0.2 name=transform repeats=1 temperature=5/>
		<HighResDocker cycles=6 movemap_builder=docking name=high_res_docker repack_every_Nth=3 scorefxn=ligand_soft_rep/>
		<FinalMinimizer movemap_builder=final name=final scorefxn=hard_rep/>
		<InterfaceScoreCalculator chains=X name=add_scores native=crystal_complex.pdb scorefxn=hard_rep/>
	</MOVERS>
	<PROTOCOLS>
		<Add mover_name=transform/>
		<Add mover_name=high_res_docker/>
		<Add mover_name=final/>
		<Add mover_name=add_scores/>
	</PROTOCOLS>
</ROSETTASCRIPTS>
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"
defined score function "hard_rep" with weights "ligand"
protocols.ligand_docking.LigandDockingLoaders: WARNING WARNING ligand_area of name "LigandArea) already exists. Skipping
<LigandArea add_nbr_radius=true all_atom_mode=false chain=X cutoff=6.0 name=inhibitor_final_sc/>

protocols.ligand_docking.LigandDockingLoaders: WARNING WARNING ligand_area of name "LigandArea) already exists. Skipping
<LigandArea Calpha_restraints=0.3 add_nbr_radius=false all_atom_mode=true chain=X cutoff=7.0 name=inhibitor_final_bb/>

Error: ERROR: Exception caught by JobDistributor while trying to get pose from job '3PBL_A_0001'
Error: ERROR: Could not find ligand_areas and name inhibitor_dock_sc in Datamap

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: 3PBL_A_0001
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB ETQ.pdb
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: pre_talaris_2013_standard.wts
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
core.pack.rotamers.SingleLigandRotamerLibrary: Read in 58 rotamers from ETQ_conformers.pdb !
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 6 rotamers at 1 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 804 bytes
core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev=    93.717 chino=  1 position:    1 ETQ ETQ
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=dock.xml
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
	<SCOREFXNS>
		<ScoreFunction name=ligand_soft_rep weights=ligand_soft_rep/>
		<ScoreFunction name=hard_rep weights=ligand/>
	</SCOREFXNS>
	<LIGAND_AREAS>
		<LigandArea add_nbr_radius=true all_atom_mode=false chain=X cutoff=6.0 name=inhibitor_dock_sc/>
		<LigandArea add_nbr_radius=true all_atom_mode=false chain=X cutoff=6.0 name=inhibitor_final_sc/>
		<LigandArea Calpha_restraints=0.3 add_nbr_radius=false all_atom_mode=true chain=X cutoff=7.0 name=inhibitor_final_bb/>
	</LIGAND_AREAS>
	<INTERFACE_BUILDERS>
		<InterfaceBuilder ligand_areas=inhibitor_dock_sc name=side_chain_for_docking/>
		<InterfaceBuilder ligand_areas=inhibitor_final_sc name=side_chain_for_final/>
		<InterfaceBuilder extension_window=3 ligand_areas=inhibitor_final_bb name=backbone/>
	</INTERFACE_BUILDERS>
	<MOVEMAP_BUILDERS>
		<MoveMapBuilder minimize_water=false name=docking sc_interface=side_chain_for_docking/>
		<MoveMapBuilder bb_interface=backbone minimize_water=false name=final sc_interface=side_chain_for_final/>
	</MOVEMAP_BUILDERS>
	<SCORINGGRIDS ligand_chain=X width=15>
		<ClassicGrid grid_name=classic weight=1.0/>
	</SCORINGGRIDS>
	<MOVERS>
		<Transform angle=20 box_size=7.0 chain=X cycles=500 move_distance=0.2 name=transform repeats=1 temperature=5/>
		<HighResDocker cycles=6 movemap_builder=docking name=high_res_docker repack_every_Nth=3 scorefxn=ligand_soft_rep/>
		<FinalMinimizer movemap_builder=final name=final scorefxn=hard_rep/>
		<InterfaceScoreCalculator chains=X name=add_scores native=crystal_complex.pdb scorefxn=hard_rep/>
	</MOVERS>
	<PROTOCOLS>
		<Add mover_name=transform/>
		<Add mover_name=high_res_docker/>
		<Add mover_name=final/>
		<Add mover_name=add_scores/>
	</PROTOCOLS>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: pre_talaris_2013_standard.wts
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
protocols.jd2.parser.ScoreFunctionLoader: defined score function "ligand_soft_rep" with weights "ligand_soft_rep"
defined score function "hard_rep" with weights "ligand"
protocols.ligand_docking.LigandDockingLoaders: WARNING WARNING ligand_area of name "LigandArea) already exists. Skipping
<LigandArea add_nbr_radius=true all_atom_mode=false chain=X cutoff=6.0 name=inhibitor_final_sc/>

protocols.ligand_docking.LigandDockingLoaders: WARNING WARNING ligand_area of name "LigandArea) already exists. Skipping
<LigandArea Calpha_restraints=0.3 add_nbr_radius=false all_atom_mode=true chain=X cutoff=7.0 name=inhibitor_final_bb/>

Error: ERROR: Exception caught by JobDistributor while trying to get pose from job 'ETQ_0001'
Error: ERROR: Could not find ligand_areas and name inhibitor_dock_sc in Datamap

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: ETQ_0001
protocols.jd2.JobDistributor: no more batches to process... 
protocols.jd2.JobDistributor: 2 jobs considered, 2 jobs attempted in 98 seconds
Error: ERROR: Exception caught by rosetta_scripts application:2 jobs failed; check output for error messages
Error: