core.init: Rosetta version exported  from http://www.rosettacommons.org
core.init: command: ./rosetta_scripts.linuxgccrelease -database ./database -parser::protocol enzdesTest.xml -in::file::s ChrysPoc_P3_C2_4AC0.pdb -extra_res_fa LG.params @enzdes_flags -parser::script_vars ligchain=X resfile=tetR_test.resfile -packing::unboundrot ChrysPoc_P3_C2_4AC0.pdb -out::suffix _devNull -out::file::o /dev/null/devNull.out -out::file::silent silent_devNull.out -scorefile score_devNull.sc -nstruct 1
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1928890658 seed_offset=0 real_seed=1928890658
core.init.random: RandomGenerator:init: Normal mode, seed=1928890658 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed ChrysPoc_P3_C2_4AC0.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 ChrysPoc_P3_C2_4AC0.pdb
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set.  Created 36573 residue types
core.chemical.ResidueTypeSet: Total time to initialize 1.4 seconds.
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=enzdesTest.xml
protocols.rosetta_scripts.RosettaScriptsParser: Variable substitution will occur with the following values: '%%ligchain%%'='X';  '%%resfile%%'='tetR_test.resfile';  
protocols.rosetta_scripts.RosettaScriptsParser: Substituted script:
<ROSETTASCRIPTS>
        <SCOREFXNS>
		<enzdes weights=enzdes.wts >
			<Reweight scoretype=fa_elec weight=0.25 />
			<Reweight scoretype=envsmooth weight=0 />
		</enzdes>
		<soft weights=ligand_soft_rep.wts />
        </SCOREFXNS>
        <TASKOPERATIONS>
                <ReadResfile name=shell filename="tetR_test.resfile" />
	        <OperateOnCertainResidues name=ligonly>
		  <PreventRepackingRLT/>
		  <ChainIsnt chain=X />
		</OperateOnCertainResidues>
		<RestrictToRepacking name=repack/>

	        <InitializeFromCommandline name=cmd/>
	        <ProteinLigandInterfaceUpweighter name=ligup interface_weight=2.0 />
	        <DetectProteinLigandInterface name=repackshell cut1=6.0 cut2=8.0 cut3=10.0 cut4=12.0 design=0 resfile="tetR_test.resfile" />
		<LimitAromaChi2 name=limchi2 />
        </TASKOPERATIONS>
        <FILTERS>
        </FILTERS>
        <MOVERS>
	        <PackRotamersMover name=ligpack scorefxn=enzdes task_operations=cmd,ligonly,repack,repackshell/>
	        <PredesignPerturbMover name=preturb trans_magnitude=0.025 rot_magnitude=1.25 dock_trials=16 /> sum of variances: trans 0.1, rot 5 ( ~0.25 A leverarm at 3A)
		<EnzRepackMinimize name=softdesign scorefxn_repack=soft scorefxn_minimize=enzdes cst_opt=0 repack_only=0 design=1 fix_catalytic=0 minimize_rb=1 minimize_bb=1 minimize_sc=1 minimize_lig=1 min_in_stages=1 backrub=0 cycles=2 task_operations=cmd,shell,ligup,limchi2 />
		<EnzRepackMinimize name=harddesign scorefxn_repack=enzdes scorefxn_minimize=enzdes cst_opt=0 repack_only=0 design=1 fix_catalytic=0 minimize_rb=1 minimize_bb=1 minimize_sc=1 minimize_lig=1 min_in_stages=1 backrub=0 cycles=1 task_operations=cmd,shell,ligup,limchi2 />
		<RotamerTrialsMinMover name=RTdesign scorefxn=enzdes task_operations=cmd,shell,ligup,limchi2 />
        </MOVERS>
        <APPLY_TO_POSE>
        </APPLY_TO_POSE>
        <PROTOCOLS>
	        <Add mover=preturb />
		<Add mover=ligpack />
		<Add mover=softdesign />
		<Add mover=harddesign />
		<Add mover=RTdesign />
        </PROTOCOLS>
</ROSETTASCRIPTS>
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
	<SCOREFXNS>
		<enzdes weights=enzdes.wts>
			<Reweight scoretype=fa_elec weight=0.25/>
			<Reweight scoretype=envsmooth weight=0/>
		</enzdes>
		<soft weights=ligand_soft_rep.wts/>
	</SCOREFXNS>
	<TASKOPERATIONS>
		<ReadResfile filename=tetR_test.resfile name=shell/>
		<OperateOnCertainResidues name=ligonly>
			<PreventRepackingRLT/>
			<ChainIsnt chain=X/>
		</OperateOnCertainResidues>
		<RestrictToRepacking name=repack/>
		<InitializeFromCommandline name=cmd/>
		<ProteinLigandInterfaceUpweighter interface_weight=2.0 name=ligup/>
		<DetectProteinLigandInterface cut1=6.0 cut2=8.0 cut3=10.0 cut4=12.0 design=0 name=repackshell resfile=tetR_test.resfile/>
		<LimitAromaChi2 name=limchi2/>
	</TASKOPERATIONS>
	<FILTERS/>
	<MOVERS>
		<PackRotamersMover name=ligpack scorefxn=enzdes task_operations=cmd,ligonly,repack,repackshell/>
		<PredesignPerturbMover dock_trials=16 name=preturb rot_magnitude=1.25 trans_magnitude=0.025/>
		<EnzRepackMinimize backrub=0 cst_opt=0 cycles=2 design=1 fix_catalytic=0 min_in_stages=1 minimize_bb=1 minimize_lig=1 minimize_rb=1 minimize_sc=1 name=softdesign repack_only=0 scorefxn_minimize=enzdes scorefxn_repack=soft task_operations=cmd,shell,ligup,limchi2/>
		<EnzRepackMinimize backrub=0 cst_opt=0 cycles=1 design=1 fix_catalytic=0 min_in_stages=1 minimize_bb=1 minimize_lig=1 minimize_rb=1 minimize_sc=1 name=harddesign repack_only=0 scorefxn_minimize=enzdes scorefxn_repack=enzdes task_operations=cmd,shell,ligup,limchi2/>
		<RotamerTrialsMinMover name=RTdesign scorefxn=enzdes task_operations=cmd,shell,ligup,limchi2/>
	</MOVERS>
	<APPLY_TO_POSE/>
	<PROTOCOLS>
		<Add mover=preturb/>
		<Add mover=ligpack/>
		<Add mover=softdesign/>
		<Add mover=harddesign/>
		<Add mover=RTdesign/>
	</PROTOCOLS>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013
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/sp2_elec_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv
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/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/PairEPotential/pdb_pair_stats_fine
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
basic.io.database: Database file opened: scoring/score_functions/envsmooth/envdata.txt
basic.io.database: Database file opened: scoring/score_functions/carbon_hbond/ch_o_bond_potential.dat
basic.io.database: Database file opened: scoring/score_functions/custom_pair_distance/pos_charge_repulsion
basic.io.database: Database file opened: scoring/score_functions/custom_pair_distance/neg_charge_repulsion
core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy: Added 714420 AtomPairFuncList lists
protocols.jd2.parser.ScoreFunctionLoader: defined score function "enzdes" with weights "enzdes.wts"
setting enzdes weight fa_elec to 0.25
setting enzdes weight envsmooth to 0
defined score function "soft" with weights "ligand_soft_rep.wts"
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "shell" of type ReadResfile
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "ligonly" of type OperateOnCertainResidues
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "repack" of type RestrictToRepacking
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "cmd" of type InitializeFromCommandline
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "ligup" of type ProteinLigandInterfaceUpweighter
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "repackshell" of type DetectProteinLigandInterface
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "limchi2" of type LimitAromaChi2
protocols.RosettaScripts.util: Object ligpack reading the following task_operations: Adding the following task operations
cmd ligonly repack repackshell 
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "ligpack" of type PackRotamersMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "preturb" of type PredesignPerturbMover
protocols.RosettaScripts.util: Object softdesign reading the following task_operations: Adding the following task operations
cmd shell ligup limchi2 
protocols.enzdes.EnzRepackMinimize: design=1, with repack scorefxn soft and minimize scorefxn enzdes
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "softdesign" of type EnzRepackMinimize
protocols.RosettaScripts.util: Object harddesign reading the following task_operations: Adding the following task operations
cmd shell ligup limchi2 
protocols.enzdes.EnzRepackMinimize: design=1, with repack scorefxn enzdes and minimize scorefxn enzdes
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "harddesign" of type EnzRepackMinimize
protocols.RosettaScripts.util: Object RTdesign reading the following task_operations: Adding the following task operations
cmd shell ligup limchi2 
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "RTdesign" of type RotamerTrialsMinMover
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "preturb" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "ligpack" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "softdesign" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "harddesign" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "RTdesign" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy ChrysPoc_P3_C2_4AC0.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PredesignPerturbMover - preturb=======================
core.pack.rotamer_set.UnboundRotamersOperation: Adding 'unbound' rotamers from ChrysPoc_P3_C2_4AC0.pdb
core.pack.task: Packer task: initialize from command line() 
protocols.enzdes.EnzdesTaskOperations: Final Design Shell Residues: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 
protocols.enzdes.EnzdesTaskOperations: Final Repack Shell Residues: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 
Warning: Unable to locate database file rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: cannot find binary dunbrack library under name ./database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Reading Dunbrack Libraries
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/cys.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/ile.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/lys.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/leu.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/met.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/pro.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/arg.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/ser.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/thr.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/val.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/asp.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/asp.bbdep.densities.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/asp.bbind.chi2.Definitions.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/glu.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/glu.bbdep.densities.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/glu.bbind.chi3.Definitions.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/phe.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/phe.bbdep.densities.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/phe.bbind.chi2.Definitions.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/his.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/his.bbdep.densities.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/his.bbind.chi2.Definitions.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/asn.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/asn.bbdep.densities.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/asn.bbind.chi2.Definitions.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/gln.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/gln.bbdep.densities.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/gln.bbind.chi3.Definitions.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/trp.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/trp.bbdep.densities.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/trp.bbind.chi2.Definitions.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/tyr.bbdep.rotamers.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/tyr.bbdep.densities.lib
core.pack.dunbrack.RotamerLibrary: Reading ./database/rotamer/ExtendedOpt1-5/tyr.bbind.chi2.Definitions.lib
core.pack.dunbrack.RotamerLibrary: Finished reading Dunbrack Libraries
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 42.33 seconds to load from ASCII
core.pack.dunbrack.RotamerLibrary: Memory usage: 
core.pack.dunbrack.RotamerLibrary: CYS with 188136 bytes
core.pack.dunbrack.RotamerLibrary: ILE with 655128 bytes
core.pack.dunbrack.RotamerLibrary: LYS with 6819096 bytes
core.pack.dunbrack.RotamerLibrary: LEU with 655128 bytes
core.pack.dunbrack.RotamerLibrary: MET with 2242824 bytes
core.pack.dunbrack.RotamerLibrary: PRO with 167424 bytes
core.pack.dunbrack.RotamerLibrary: ARG with 7005864 bytes
core.pack.dunbrack.RotamerLibrary: SER with 188136 bytes
core.pack.dunbrack.RotamerLibrary: THR with 188136 bytes
core.pack.dunbrack.RotamerLibrary: VAL with 188136 bytes
core.pack.dunbrack.RotamerLibrary: ASP with 10268520 bytes
core.pack.dunbrack.RotamerLibrary: GLU with 30987184 bytes
core.pack.dunbrack.RotamerLibrary: PHE with 10268520 bytes
core.pack.dunbrack.RotamerLibrary: HIS with 11201928 bytes
core.pack.dunbrack.RotamerLibrary: ASN with 11201928 bytes
core.pack.dunbrack.RotamerLibrary: GLN with 33787408 bytes
core.pack.dunbrack.RotamerLibrary: TRP with 11201928 bytes
core.pack.dunbrack.RotamerLibrary: TYR with 10268520 bytes
core.pack.dunbrack.RotamerLibrary: Total memory on Dunbrack Libraries: 147483944 bytes.
Warning: Unable to locate database file rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin
Warning: Unable to locate database file rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Random tempname will be: ./database/6dun10_binary
core.pack.dunbrack.RotamerLibrary: Opening file ./database/6dun10_binary for output.
core.pack.dunbrack.RotamerLibrary: Moving temporary file to ./database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin
protocols.enzdes.PredesignPerturbMover: starting predocking ... 
protocols.moves.TrialCounter:              unk trials=     16;  accepts= 1.0000;  energy_drop/trial=   0.00498
protocols.enzdes.PredesignPerturbMover: ... done predocking
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PackRotamersMover - ligpack=======================
core.pack.task: Packer task: initialize from command line() 
protocols.enzdes.EnzdesTaskOperations: Reading resfile input from: tetR_test.resfile
protocols.enzdes.EnzdesTaskOperations: Choosing the following residues as targets for detecting interface: 198+
protocols.enzdes.EnzdesTaskOperations: Design Interface: detected 0 design-shell residues and 51 repack-shell residues, shell sizes cut1-4 used were 0 0 10 12
protocols.enzdes.EnzdesTaskOperations: Design-shell Residues(pose-numbering): 
protocols.enzdes.EnzdesTaskOperations: Repack-shell Residues(pose-numbering): 55+56+58+59+60+63+64+65+66+67+68+77+78+81+82+84+85+86+88+89+99+100+101+102+103+104+105+107+108+109+111+112+113+114+115+116+118+119+129+130+131+132+133+134+135+136+137+138+140+141+198+
protocols.enzdes.EnzdesTaskOperations: Final Design Shell Residues: 
protocols.enzdes.EnzdesTaskOperations: Final Repack Shell Residues: 198, 
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for LG1
core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph
core.pack.pack_rotamers: built 2 rotamers at 1 positions.
core.pack.pack_rotamers: IG: 2200 bytes
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER EnzRepackMinimize - softdesign=======================
core.pack.rotamer_set.UnboundRotamersOperation: Adding 'unbound' rotamers from ChrysPoc_P3_C2_4AC0.pdb
protocols.enzdes.EnzRepackMinimize: Creating packer task based on specified task operations...
core.pack.task: Packer task: initialize from command line() 
protocols.enzdes.EnzdesTaskOperations: Packer Energies between ligand and design residues are upweighted by factor 2.
core.pack.task: Packer task: initialize from command line() 
protocols.enzdes.EnzRepackMinimize: Starting Design/Repack...
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for LG1
core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph
core.pack.pack_rotamers: built 12270 rotamers at 198 positions.
core.pack.pack_rotamers: IG: 8503367 bytes
core.pack.task: Packer task: initialize from command line() 
protocols.enzdes.EnzRepackMinimize: Starting Minimization...
core.pack.rotamer_set.UnboundRotamersOperation: Adding 'unbound' rotamers from ChrysPoc_P3_C2_4AC0.pdb
protocols.ligand_docking.ligand_functions: Torsion constraint for Rsd 198 chi 1 = 160 std dev 0.1
protocols.ligand_docking.ligand_functions: Torsion constraint for Rsd 198 chi 2 = 20 std dev 0.1
protocols.enzdes.EnzRepackMinimize: Finished non-bb dof minimization
protocols.enzdes.EnzdesBaseProtocol: Doing a pose minimization... the backbone is allowed to move at positions: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 
protocols.ligand_docking.LigandBaseProtocol: Moved ligand FOLD_TREE  EDGE 1 197 -1  EDGE 1 198 1 
protocols.ligand_docking.LigandBaseProtocol: Final loops foldtree FOLD_TREE  EDGE 1 71 -1  JEDGE 1 197 2 CA CA  END  EDGE 197 72 -1  EDGE 1 198 1 
protocols.enzdes.EnzRepackMinimize: Finished bb dof minimization
protocols.enzdes.EnzdesBaseProtocol: Doing a pose minimization... the backbone is allowed to move at positions: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 
protocols.ligand_docking.LigandBaseProtocol: Moved ligand FOLD_TREE  EDGE 1 197 -1  EDGE 1 198 1 
protocols.ligand_docking.LigandBaseProtocol: Final loops foldtree FOLD_TREE  EDGE 1 145 -1  JEDGE 1 197 2 CA CA  END  EDGE 197 146 -1  EDGE 1 198 1 
protocols.ligand_docking.ligand_functions: Torsion constraint for Rsd 198 chi 1 = 160 std dev 0.1
protocols.ligand_docking.ligand_functions: Torsion constraint for Rsd 198 chi 2 = 20 std dev 0.1
protocols.enzdes.EnzRepackMinimize: Finished Cyle#1 of EnzRepackMinimize
protocols.enzdes.EnzRepackMinimize: Creating packer task based on specified task operations...
core.pack.task: Packer task: initialize from command line() 
protocols.enzdes.EnzdesTaskOperations: Packer Energies between ligand and design residues are upweighted by factor 2.
core.pack.task: Packer task: initialize from command line() 
core.pack.task: Packer task: initialize from command line() 
protocols.enzdes.EnzRepackMinimize: Starting Design/Repack...
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for LG1
core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph
core.pack.pack_rotamers: built 12243 rotamers at 198 positions.
core.pack.pack_rotamers: IG: 8506017 bytes
core.pack.task: Packer task: initialize from command line() 
protocols.enzdes.EnzRepackMinimize: Starting Minimization...
core.pack.rotamer_set.UnboundRotamersOperation: Adding 'unbound' rotamers from ChrysPoc_P3_C2_4AC0.pdb
protocols.ligand_docking.ligand_functions: Torsion constraint for Rsd 198 chi 1 = 160 std dev 0.1
protocols.ligand_docking.ligand_functions: Torsion constraint for Rsd 198 chi 2 = 20 std dev 0.1
protocols.enzdes.EnzRepackMinimize: Finished non-bb dof minimization
protocols.enzdes.EnzdesBaseProtocol: Doing a pose minimization... the backbone is allowed to move at positions: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 
protocols.ligand_docking.LigandBaseProtocol: Moved ligand FOLD_TREE  EDGE 1 197 -1  EDGE 1 198 1 
protocols.ligand_docking.LigandBaseProtocol: Final loops foldtree FOLD_TREE  EDGE 1 179 -1  JEDGE 1 197 2 CA CA  END  EDGE 197 180 -1  EDGE 1 198 1 
protocols.enzdes.EnzRepackMinimize: Finished bb dof minimization
protocols.enzdes.EnzdesBaseProtocol: Doing a pose minimization... the backbone is allowed to move at positions: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 
protocols.ligand_docking.LigandBaseProtocol: Moved ligand FOLD_TREE  EDGE 1 197 -1  EDGE 1 198 1 
protocols.ligand_docking.LigandBaseProtocol: Final loops foldtree FOLD_TREE  EDGE 1 80 -1  JEDGE 1 197 2 CA CA  END  EDGE 197 81 -1  EDGE 1 198 1 
protocols.ligand_docking.ligand_functions: Torsion constraint for Rsd 198 chi 1 = 160 std dev 0.1
protocols.ligand_docking.ligand_functions: Torsion constraint for Rsd 198 chi 2 = 20 std dev 0.1
protocols.enzdes.EnzRepackMinimize: Finished Cyle#2 of EnzRepackMinimize
protocols.enzdes.EnzRepackMinimize: Finished EnzRepackMinimize
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER EnzRepackMinimize - harddesign=======================
core.pack.rotamer_set.UnboundRotamersOperation: Adding 'unbound' rotamers from ChrysPoc_P3_C2_4AC0.pdb
protocols.enzdes.EnzRepackMinimize: Creating packer task based on specified task operations...
core.pack.task: Packer task: initialize from command line() 
protocols.enzdes.EnzdesTaskOperations: Packer Energies between ligand and design residues are upweighted by factor 2.
core.pack.task: Packer task: initialize from command line() 
protocols.enzdes.EnzRepackMinimize: Starting Design/Repack...
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for LG1
core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph
core.pack.pack_rotamers: built 9960 rotamers at 198 positions.
core.pack.pack_rotamers: IG: 18563697 bytes
core.pack.task: Packer task: initialize from command line() 
protocols.enzdes.EnzRepackMinimize: Starting Minimization...
core.pack.rotamer_set.UnboundRotamersOperation: Adding 'unbound' rotamers from ChrysPoc_P3_C2_4AC0.pdb
protocols.ligand_docking.ligand_functions: Torsion constraint for Rsd 198 chi 1 = 180 std dev 0.1
protocols.ligand_docking.ligand_functions: Torsion constraint for Rsd 198 chi 2 = 2.3816e-11 std dev 0.1
protocols.enzdes.EnzRepackMinimize: Finished non-bb dof minimization
protocols.enzdes.EnzdesBaseProtocol: Doing a pose minimization... the backbone is allowed to move at positions: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 
protocols.ligand_docking.LigandBaseProtocol: Moved ligand FOLD_TREE  EDGE 1 197 -1  EDGE 1 198 1 
protocols.ligand_docking.LigandBaseProtocol: Final loops foldtree FOLD_TREE  EDGE 1 49 -1  JEDGE 1 197 2 CA CA  END  EDGE 197 50 -1  EDGE 1 198 1 
protocols.enzdes.EnzRepackMinimize: Finished bb dof minimization
protocols.enzdes.EnzdesBaseProtocol: Doing a pose minimization... the backbone is allowed to move at positions: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 
protocols.ligand_docking.LigandBaseProtocol: Moved ligand FOLD_TREE  EDGE 1 197 -1  EDGE 1 198 1 
protocols.ligand_docking.LigandBaseProtocol: Final loops foldtree FOLD_TREE  EDGE 1 173 -1  JEDGE 1 197 2 CA CA  END  EDGE 197 174 -1  EDGE 1 198 1 
protocols.ligand_docking.ligand_functions: Torsion constraint for Rsd 198 chi 1 = -179.972 std dev 0.1
protocols.ligand_docking.ligand_functions: Torsion constraint for Rsd 198 chi 2 = 0.0243516 std dev 0.1
protocols.enzdes.EnzRepackMinimize: Finished Cyle#1 of EnzRepackMinimize
protocols.enzdes.EnzRepackMinimize: Finished EnzRepackMinimize
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER RotamerTrialsMinMover - RTdesign=======================
core.pack.task: Packer task: initialize from command line() 
protocols.enzdes.EnzdesTaskOperations: Packer Energies between ligand and design residues are upweighted by factor 2.
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for LG1
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================
protocols.jd2.JobDistributor: ChrysPoc_P3_C2_4AC0_devNull_0001 reported success in 471 seconds
protocols.jd2.JobDistributor: no more batches to process... 
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 472 seconds
protocols.jd2.JobDistributor: WARNING: The following options have been set, but have not yet been used:
	-jd2:enzdes_out 
	-out:file:o /dev/null/devNull.out