core.init: Rosetta version unknown  from unknown
core.init: command: /usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease -parser:protocol /usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -s phasermodel_in.pdb -mtzfile /home/gebauer/tmp/rosetta_6/phasermodel_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=phasermodel.symm -set_weights cart_bonded 0.5 pro_close 0 -nstruct 1 -out:suffix _1
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1830876912 seed_offset=0 real_seed=1830876912
core.init.random: RandomGenerator:init: Normal mode, seed=1830876912 RG_type=mt19937
core.init: found database environment variable ROSETTA3_DB: /usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/database
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed phasermodel_in.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 phasermodel_in.pdb
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set.  Created 4369 residue types
core.io.pdb.file_data: [ WARNING ] missing density found at residue (rosetta number) 146
core.io.pdb.file_data: [ WARNING ] missing density found at residue (rosetta number) 524
core.io.pdb.file_data: [ WARNING ] missing density found at residue (rosetta number) 902
core.io.pdb.file_data: [ WARNING ] missing density found at residue (rosetta number) 1280
core.pack.task: Packer task: initialize from command line() 
protocols.jd2.DockDesignParser: dock_design_filename=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml
protocols.jd2.DockDesignParser: Variable substitution will occur with the following values: '%%symmdef%%'='phasermodel.symm';  
protocols.jd2.DockDesignParser: Substituted script:
<ROSETTASCRIPTS>
	<TASKOPERATIONS>
		<ExtraRotamersGeneric name=extra ex1=1 ex2=1 extrachi_cutoff=0/>
		<RestrictToRepacking name=restrict/>
		<IncludeCurrent	  name=keep_curr/>
	</TASKOPERATIONS>
	<SCOREFXNS>
		<xtal weights="talaris2013" symmetric=1>
   			<Reweight scoretype=cart_bonded weight=0.5/>
   			<Reweight scoretype=pro_close weight=0.0/>
		</xtal>
		<dens_soft weights=soft_rep symmetric=1>
   			<Reweight scoretype=fa_elec weight=0.7/>
   			<Reweight scoretype=cart_bonded weight=0.5/>
   			<Reweight scoretype=pro_close weight=0.0/>
   			<Reweight scoretype=elec_dens_fast weight=20.0/>
		</dens_soft>
		<dens weights="talaris2013" symmetric=1>
   			<Reweight scoretype=cart_bonded weight=0.5/>
   			<Reweight scoretype=pro_close weight=0.0/>
			<Reweight scoretype=elec_dens_fast weight=20.0/>
		</dens>
	</SCOREFXNS>
	<MOVERS>
		<SetRefinementOptions name=setup_opts prime_and_switch=1/>

		<SetupForSymmetry name=setup_symm definition="phasermodel.symm"/>
		<ExtractAsymmetricUnit name=extract_asu/>

		<RecomputeDensityMap name=recompute_dens/>

		<FitBfactors name=fit_bs adp_strategy=individual/>

		<TagPoseWithRefinementStats name=tag_i tag=input/>
		<TagPoseWithRefinementStats name=tag_c tag=cycle/>
		<TagPoseWithRefinementStats name=tag_f tag=final/>

		<SetCrystWeight	name=set_cryst_wt_cart weight_scale=0.5 scorefxn=xtal scorefxn_ref=xtal cartesian=1 bb=1 chi=1/>
		<SetCrystWeight	name=set_cryst_wt_tors weight_scale=0.5 scorefxn=xtal scorefxn_ref=xtal bb=1 chi=1 jump=ALL bondangle=1/>

		<SymMinMover name=min_tors_xtal scorefxn=xtal type=lbfgs_armijo_rescored tolerance=0.0001 max_iter=100 bb=1 chi=1 jump=ALL bondangle=1/>
		<SymMinMover name=min_cart_xtal cartesian=1 scorefxn=xtal type=lbfgs_armijo_rescored tolerance=0.0001 max_iter=100 bb=1 chi=1/>
		<SymMinMover name=min_dens scorefxn=dens type=lbfgs_armijo tolerance=0.00001 max_iter=25 bb=1 chi=1 jump=ALL bondangle=1/>

		<SymPackRotamersMover name=screpack_soft scorefxn=dens_soft task_operations=extra,restrict,keep_curr />
		<SymPackRotamersMover name=screpack scorefxn=dens task_operations=extra,restrict,keep_curr />

		<ParsedProtocol name=stage1cycle>
			<Add mover=recompute_dens/>
			<Add mover=screpack_soft/>
			<Add mover=set_cryst_wt_tors/>
			<Add mover=min_tors_xtal/>
			<Add mover=fit_bs/>
			<Add mover=tag_c/>
		</ParsedProtocol>

		<ParsedProtocol name=stage2cycle>
			<Add mover=recompute_dens/>
			<Add mover=screpack/>
			<Add mover=min_dens/>
			<Add mover=set_cryst_wt_tors/>
			<Add mover=min_tors_xtal/>
			<Add mover=fit_bs/>
			<Add mover=tag_c/>
		</ParsedProtocol>

		<ParsedProtocol name=stage3cycle>
			<Add mover=recompute_dens/>
			<Add mover=screpack/>
			<Add mover=set_cryst_wt_cart/>
			<Add mover=min_cart_xtal/>
			<Add mover=fit_bs/>
			<Add mover=tag_c/>
		</ParsedProtocol>
	</MOVERS>

	<PROTOCOLS>
		<Add mover=setup_opts/>
		<Add mover=setup_symm/>

		<Add mover=tag_i/>
		<Add mover=stage1cycle/>
		<Add mover=stage1cycle/>
		<Add mover=stage1cycle/>
		<Add mover=stage2cycle/>
		<Add mover=stage2cycle/>
		<Add mover=stage2cycle/>
		<Add mover=stage2cycle/>
		<Add mover=stage2cycle/>
		<Add mover=stage3cycle/>
		<Add mover=stage3cycle/>
		<Add mover=tag_f/>

		<Add mover=extract_asu/>
	</PROTOCOLS>
</ROSETTASCRIPTS>
protocols.jd2.DockDesignParser: Parsed script:
<ROSETTASCRIPTS>
	<TASKOPERATIONS>
		<ExtraRotamersGeneric ex1=1 ex2=1 extrachi_cutoff=0 name=extra/>
		<RestrictToRepacking name=restrict/>
		<IncludeCurrent name=keep_curr/>
	</TASKOPERATIONS>
	<SCOREFXNS>
		<xtal symmetric=1 weights=talaris2013>
			<Reweight scoretype=cart_bonded weight=0.5/>
			<Reweight scoretype=pro_close weight=0.0/>
		</xtal>
		<dens_soft symmetric=1 weights=soft_rep>
			<Reweight scoretype=fa_elec weight=0.7/>
			<Reweight scoretype=cart_bonded weight=0.5/>
			<Reweight scoretype=pro_close weight=0.0/>
			<Reweight scoretype=elec_dens_fast weight=20.0/>
		</dens_soft>
		<dens symmetric=1 weights=talaris2013>
			<Reweight scoretype=cart_bonded weight=0.5/>
			<Reweight scoretype=pro_close weight=0.0/>
			<Reweight scoretype=elec_dens_fast weight=20.0/>
		</dens>
	</SCOREFXNS>
	<MOVERS>
		<SetRefinementOptions name=setup_opts prime_and_switch=1/>
		<SetupForSymmetry definition=phasermodel.symm name=setup_symm/>
		<ExtractAsymmetricUnit name=extract_asu/>
		<RecomputeDensityMap name=recompute_dens/>
		<FitBfactors adp_strategy=individual name=fit_bs/>
		<TagPoseWithRefinementStats name=tag_i tag=input/>
		<TagPoseWithRefinementStats name=tag_c tag=cycle/>
		<TagPoseWithRefinementStats name=tag_f tag=final/>
		<SetCrystWeight bb=1 cartesian=1 chi=1 name=set_cryst_wt_cart scorefxn=xtal scorefxn_ref=xtal weight_scale=0.5/>
		<SetCrystWeight bb=1 bondangle=1 chi=1 jump=ALL name=set_cryst_wt_tors scorefxn=xtal scorefxn_ref=xtal weight_scale=0.5/>
		<SymMinMover bb=1 bondangle=1 chi=1 jump=ALL max_iter=100 name=min_tors_xtal scorefxn=xtal tolerance=0.0001 type=lbfgs_armijo_rescored/>
		<SymMinMover bb=1 cartesian=1 chi=1 max_iter=100 name=min_cart_xtal scorefxn=xtal tolerance=0.0001 type=lbfgs_armijo_rescored/>
		<SymMinMover bb=1 bondangle=1 chi=1 jump=ALL max_iter=25 name=min_dens scorefxn=dens tolerance=0.00001 type=lbfgs_armijo/>
		<SymPackRotamersMover name=screpack_soft scorefxn=dens_soft task_operations=extra,restrict,keep_curr/>
		<SymPackRotamersMover name=screpack scorefxn=dens task_operations=extra,restrict,keep_curr/>
		<ParsedProtocol name=stage1cycle>
			<Add mover=recompute_dens/>
			<Add mover=screpack_soft/>
			<Add mover=set_cryst_wt_tors/>
			<Add mover=min_tors_xtal/>
			<Add mover=fit_bs/>
			<Add mover=tag_c/>
		</ParsedProtocol>
		<ParsedProtocol name=stage2cycle>
			<Add mover=recompute_dens/>
			<Add mover=screpack/>
			<Add mover=min_dens/>
			<Add mover=set_cryst_wt_tors/>
			<Add mover=min_tors_xtal/>
			<Add mover=fit_bs/>
			<Add mover=tag_c/>
		</ParsedProtocol>
		<ParsedProtocol name=stage3cycle>
			<Add mover=recompute_dens/>
			<Add mover=screpack/>
			<Add mover=set_cryst_wt_cart/>
			<Add mover=min_cart_xtal/>
			<Add mover=fit_bs/>
			<Add mover=tag_c/>
		</ParsedProtocol>
	</MOVERS>
	<PROTOCOLS>
		<Add mover=setup_opts/>
		<Add mover=setup_symm/>
		<Add mover=tag_i/>
		<Add mover=stage1cycle/>
		<Add mover=stage1cycle/>
		<Add mover=stage1cycle/>
		<Add mover=stage2cycle/>
		<Add mover=stage2cycle/>
		<Add mover=stage2cycle/>
		<Add mover=stage2cycle/>
		<Add mover=stage2cycle/>
		<Add mover=stage3cycle/>
		<Add mover=stage3cycle/>
		<Add mover=tag_f/>
		<Add mover=extract_asu/>
	</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/Rama09_noEH_kernel25_it08.dat
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
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 748 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1424 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 2105 bb-independent torsions.
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
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.
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
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/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
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.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "extra" of type ExtraRotamersGeneric
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict" of type RestrictToRepacking
core.pack.task.operation.TaskOperation: TaskOperation::parse_tag method called with no effect for Tag with type IncludeCurrent. Probably due to (un/mis)implemented virtual method in derived class.
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "keep_curr" of type IncludeCurrent
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: cart_bonded 0.5
core.scoring.ScoreFunctionFactory: Setting/modifying scorefxn weight from command line: pro_close 0
protocols.jd2.parser.ScoreFunctionLoader: defined score function "xtal" with weights "talaris2013"
setting xtal weight cart_bonded to 0.5
setting xtal weight pro_close to 0
symmetrizing xtal
defined score function "dens_soft" with weights "soft_rep"
setting dens_soft weight fa_elec to 0.7
setting dens_soft weight cart_bonded to 0.5
setting dens_soft weight pro_close to 0
setting dens_soft weight elec_dens_fast to 20
symmetrizing dens_soft
defined score function "dens" with weights "talaris2013"
setting dens weight cart_bonded to 0.5
setting dens weight pro_close to 0
setting dens weight elec_dens_fast to 20
symmetrizing dens
protocols.jd2.DockDesignParser: Defined mover named "setup_opts" of type SetRefinementOptions
core.conformation.symmetry.SymmData: Setting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)
core.conformation.symmetry.SymmData: Setting jump_group JUMPGROUP1: [master 1]  3:0  2:0  4:0  5:0  6:0  7:0  8:0  9:0 
core.conformation.symmetry.SymmData: Setting weight of master jump ( jump-id=10 ) to 1.0 (was undefined)
core.conformation.symmetry.SymmData: Setting jump_group JUMPGROUP2: [master 10]  14:0  12:0  16:0  18:0  20:0  22:0  24:0  26:0 
core.conformation.symmetry.SymmData: symmetry name: phasermodel_in_P_21_21_21
core.conformation.symmetry.SymmData: number of subunits: 9
core.conformation.symmetry.SymmData: number of interfaces: 1
core.conformation.symmetry.SymmData: score subunit number: VRT_0_0_0_0
core.conformation.symmetry.SymmData: anchor the subunits at residue: 1
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_0_0_0_0
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -16.4505 4.65753 -61.8953
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_0_0_0_0_base
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -17.4505 3.65753 -62.8953
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_0_1_0_0
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 72.6955 4.65753 -61.8953
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_0_1_0_0_base
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 71.6955 3.65753 -62.8953
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_0_n1_0_0
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -105.596 4.65753 -61.8953
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_0_n1_0_0_base
core.conformation.symmetry.SymmData: x: 1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -106.596 3.65753 -62.8953
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_1_n1_0_0
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: -0 -1 0
core.conformation.symmetry.SymmData: origin: -28.1225 -4.65753 21.8187
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_1_n1_0_0_base
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: -0 -1 0
core.conformation.symmetry.SymmData: origin: -27.1225 -3.65753 20.8187
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_1_n1_0_n1
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: -0 -1 0
core.conformation.symmetry.SymmData: origin: -28.1225 -4.65753 -145.609
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_1_n1_0_n1_base
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: -0 -1 0
core.conformation.symmetry.SymmData: origin: -27.1225 -3.65753 -146.609
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_3_0_0_n1
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 16.4505 85.983 -21.8187
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_3_0_0_n1_base
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 17.4505 84.983 -20.8187
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_3_0_n1_n1
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 16.4505 -76.668 -21.8187
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_3_0_n1_n1_base
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: 17.4505 -77.668 -20.8187
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_3_n1_0_n1
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -72.6955 85.983 -21.8187
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_3_n1_0_n1_base
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -71.6955 84.983 -20.8187
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_3_n1_n1_n1
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -72.6955 -76.668 -21.8187
core.conformation.symmetry.SymmData:  Virtual coordinate system VRT_3_n1_n1_n1_base
core.conformation.symmetry.SymmData: x: -1 0 0
core.conformation.symmetry.SymmData: y: 0 1 0
core.conformation.symmetry.SymmData: origin: -71.6955 -77.668 -20.8187
core.conformation.symmetry.SymmData: Dof for jump: 1
core.conformation.symmetry.SymmData: x 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: x_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z_angle 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: Dof for jump: 10
core.conformation.symmetry.SymmData: x 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z 1:0,0:0,0 n2c
core.conformation.symmetry.SymmData: x_angle 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: y_angle 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: z_angle 0:0,0:0,0 n2c
core.conformation.symmetry.SymmData: Jump JUMP_0_0_0_0_to_com VRT_0_0_0_0 VRT_0_0_0_0_base
core.conformation.symmetry.SymmData: Jump JUMP_0_0_0_0_to_subunit VRT_0_0_0_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_0_1_0_0 VRT_0_0_0_0 VRT_0_1_0_0
core.conformation.symmetry.SymmData: Jump JUMP_0_1_0_0_to_com VRT_0_1_0_0 VRT_0_1_0_0_base
core.conformation.symmetry.SymmData: Jump JUMP_0_1_0_0_to_subunit VRT_0_1_0_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_0_n1_0_0 VRT_0_0_0_0 VRT_0_n1_0_0
core.conformation.symmetry.SymmData: Jump JUMP_0_n1_0_0_to_com VRT_0_n1_0_0 VRT_0_n1_0_0_base
core.conformation.symmetry.SymmData: Jump JUMP_0_n1_0_0_to_subunit VRT_0_n1_0_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_1_n1_0_0 VRT_0_0_0_0 VRT_1_n1_0_0
core.conformation.symmetry.SymmData: Jump JUMP_1_n1_0_0_to_com VRT_1_n1_0_0 VRT_1_n1_0_0_base
core.conformation.symmetry.SymmData: Jump JUMP_1_n1_0_0_to_subunit VRT_1_n1_0_0_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_1_n1_0_n1 VRT_0_0_0_0 VRT_1_n1_0_n1
core.conformation.symmetry.SymmData: Jump JUMP_1_n1_0_n1_to_com VRT_1_n1_0_n1 VRT_1_n1_0_n1_base
core.conformation.symmetry.SymmData: Jump JUMP_1_n1_0_n1_to_subunit VRT_1_n1_0_n1_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_3_0_0_n1 VRT_0_0_0_0 VRT_3_0_0_n1
core.conformation.symmetry.SymmData: Jump JUMP_3_0_0_n1_to_com VRT_3_0_0_n1 VRT_3_0_0_n1_base
core.conformation.symmetry.SymmData: Jump JUMP_3_0_0_n1_to_subunit VRT_3_0_0_n1_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_3_0_n1_n1 VRT_0_0_0_0 VRT_3_0_n1_n1
core.conformation.symmetry.SymmData: Jump JUMP_3_0_n1_n1_to_com VRT_3_0_n1_n1 VRT_3_0_n1_n1_base
core.conformation.symmetry.SymmData: Jump JUMP_3_0_n1_n1_to_subunit VRT_3_0_n1_n1_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_3_n1_0_n1 VRT_0_0_0_0 VRT_3_n1_0_n1
core.conformation.symmetry.SymmData: Jump JUMP_3_n1_0_n1_to_com VRT_3_n1_0_n1 VRT_3_n1_0_n1_base
core.conformation.symmetry.SymmData: Jump JUMP_3_n1_0_n1_to_subunit VRT_3_n1_0_n1_base SUBUNIT
core.conformation.symmetry.SymmData: Jump JUMP_3_n1_n1_n1 VRT_0_0_0_0 VRT_3_n1_n1_n1
core.conformation.symmetry.SymmData: Jump JUMP_3_n1_n1_n1_to_com VRT_3_n1_n1_n1 VRT_3_n1_n1_n1_base
core.conformation.symmetry.SymmData: Jump JUMP_3_n1_n1_n1_to_subunit VRT_3_n1_n1_n1_base SUBUNIT
core.conformation.symmetry.SymmData: Include subunit:
core.conformation.symmetry.SymmData: Output subunit:
core.conformation.symmetry.SymmData: SlideType: RANDOM
core.conformation.symmetry.SymmData: SlideCriteriaType: CEN_DOCK_SCORE
core.conformation.symmetry.SymmData: SlideCriteriaVal: AUTOMATIC
core.conformation.symmetry.SymmData: SlideOrder: none
protocols.jd2.DockDesignParser: Defined mover named "setup_symm" of type SetupForSymmetry
protocols.jd2.DockDesignParser: Defined mover named "extract_asu" of type ExtractAsymmetricUnit
protocols.jd2.DockDesignParser: Defined mover named "recompute_dens" of type RecomputeDensityMap
protocols.jd2.DockDesignParser: Defined mover named "fit_bs" of type FitBfactors
protocols.jd2.DockDesignParser: Defined mover named "tag_i" of type TagPoseWithRefinementStats
protocols.jd2.DockDesignParser: Defined mover named "tag_c" of type TagPoseWithRefinementStats
protocols.jd2.DockDesignParser: Defined mover named "tag_f" of type TagPoseWithRefinementStats
protocols.jd2.DockDesignParser: Defined mover named "set_cryst_wt_cart" of type SetCrystWeight
protocols.jd2.DockDesignParser: Defined mover named "set_cryst_wt_tors" of type SetCrystWeight
protocols.simple_moves.MinMover: Options chi, bb: 1, 1
protocols.jd2.DockDesignParser: Defined mover named "min_tors_xtal" of type SymMinMover
protocols.simple_moves.MinMover: Options chi, bb: 1, 1
protocols.jd2.DockDesignParser: Defined mover named "min_cart_xtal" of type SymMinMover
protocols.simple_moves.MinMover: Options chi, bb: 1, 1
protocols.jd2.DockDesignParser: Defined mover named "min_dens" of type SymMinMover
protocols.RosettaScripts.util: Object screpack_soft reading the following task_operations: Adding the following task operations
extra restrict keep_curr 
protocols.jd2.DockDesignParser: Defined mover named "screpack_soft" of type SymPackRotamersMover
protocols.RosettaScripts.util: Object screpack reading the following task_operations: Adding the following task operations
extra restrict keep_curr 
protocols.jd2.DockDesignParser: Defined mover named "screpack" of type SymPackRotamersMover
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
added mover "recompute_dens" with filter "true_filter"
added mover "screpack_soft" with filter "true_filter"
added mover "set_cryst_wt_tors" with filter "true_filter"
added mover "min_tors_xtal" with filter "true_filter"
added mover "fit_bs" with filter "true_filter"
added mover "tag_c" with filter "true_filter"
protocols.jd2.DockDesignParser: Defined mover named "stage1cycle" of type ParsedProtocol
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
added mover "recompute_dens" with filter "true_filter"
added mover "screpack" with filter "true_filter"
added mover "min_dens" with filter "true_filter"
added mover "set_cryst_wt_tors" with filter "true_filter"
added mover "min_tors_xtal" with filter "true_filter"
added mover "fit_bs" with filter "true_filter"
added mover "tag_c" with filter "true_filter"
protocols.jd2.DockDesignParser: Defined mover named "stage2cycle" of type ParsedProtocol
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
added mover "recompute_dens" with filter "true_filter"
added mover "screpack" with filter "true_filter"
added mover "set_cryst_wt_cart" with filter "true_filter"
added mover "min_cart_xtal" with filter "true_filter"
added mover "fit_bs" with filter "true_filter"
added mover "tag_c" with filter "true_filter"
protocols.jd2.DockDesignParser: Defined mover named "stage3cycle" of type ParsedProtocol
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
added mover "setup_opts" with filter "true_filter"
added mover "setup_symm" with filter "true_filter"
added mover "tag_i" with filter "true_filter"
added mover "stage1cycle" with filter "true_filter"
added mover "stage1cycle" with filter "true_filter"
added mover "stage1cycle" with filter "true_filter"
added mover "stage2cycle" with filter "true_filter"
added mover "stage2cycle" with filter "true_filter"
added mover "stage2cycle" with filter "true_filter"
added mover "stage2cycle" with filter "true_filter"
added mover "stage2cycle" with filter "true_filter"
added mover "stage3cycle" with filter "true_filter"
added mover "stage3cycle" with filter "true_filter"
added mover "tag_f" with filter "true_filter"
added mover "extract_asu" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy phasermodel_in.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetRefinementOptions - setup_opts=======================
{
protocols.cryst.cryst_movers: Setting options:
protocols.cryst.cryst_movers:   prime_and_switch:1
protocols.rosetta_scripts.ParsedProtocol: 
}
=======================END MOVER SetRefinementOptions - setup_opts=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
{
protocols.rosetta_scripts.ParsedProtocol: 
}
=======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForSymmetry - setup_symm=======================
{
core.conformation.symmetry.util: =================== SYM FOLD TREE, jump notation: =symfixed= *indep* #symdof# jump[=follows] ========================
VRT_0_0_0_0(13609)
|----#j73#--->VRT_0_0_0_0_base(13610)----#j64#----->1:Sub1B(1-146)
|                                                     |146----*j1*---->147:Sub1B(147-378)
|                                                     |1------*j2*---->379:Sub1A(379-524)524----*j3*---->525:Sub1A(525-756)
|                                                     |1------*j4*---->757:Sub1C(757-902)902----*j5*---->903:Sub1C(903-1134)
|                                                     \1------*j6*---->1135:Sub1D(1135-1280)1280----*j7*---->1281:Sub1D(1281-1512)
|----=j74=--->VRT_0_1_0_0(13613)---j75=73--->VRT_0_1_0_0_base(13614)---j65=64--->3025:Sub3B(3025-3170)
|                                                                                     |3170----j15=1--->3171:Sub3B(3171-3402)
|                                                                                     |3025----j16=2--->3403:Sub3A(3403-3548)3548----j17=3--->3549:Sub3A(3549-3780)
|                                                                                     |3025----j18=4--->3781:Sub3C(3781-3926)3926----j19=5--->3927:Sub3C(3927-4158)
|                                                                                     \3025----j20=6--->4159:Sub3D(4159-4304)4304----j21=7--->4305:Sub3D(4305-4536)
|----=j76=--->VRT_0_n1_0_0(13611)---j77=73--->VRT_0_n1_0_0_base(13612)---j66=64--->1513:Sub2B(1513-1658)
|                                                                                       |1658----j8=1---->1659:Sub2B(1659-1890)
|                                                                                       |1513----j9=2---->1891:Sub2A(1891-2036)2036----j10=3--->2037:Sub2A(2037-2268)
|                                                                                       |1513----j11=4--->2269:Sub2C(2269-2414)2414----j12=5--->2415:Sub2C(2415-2646)
|                                                                                       \1513----j13=6--->2647:Sub2D(2647-2792)2792----j14=7--->2793:Sub2D(2793-3024)
|----=j78=--->VRT_1_n1_0_0(13615)---j79=73--->VRT_1_n1_0_0_base(13616)---j67=64--->4537:Sub4B(4537-4682)
|                                                                                       |4682----j22=1--->4683:Sub4B(4683-4914)
|                                                                                       |4537----j23=2--->4915:Sub4A(4915-5060)5060----j24=3--->5061:Sub4A(5061-5292)
|                                                                                       |4537----j25=4--->5293:Sub4C(5293-5438)5438----j26=5--->5439:Sub4C(5439-5670)
|                                                                                       \4537----j27=6--->5671:Sub4D(5671-5816)5816----j28=7--->5817:Sub4D(5817-6048)
|----=j80=--->VRT_1_n1_0_n1(13617)---j81=73--->VRT_1_n1_0_n1_base(13618)---j68=64--->6049:Sub5B(6049-6194)
|                                                                                         |6194----j29=1--->6195:Sub5B(6195-6426)
|                                                                                         |6049----j30=2--->6427:Sub5A(6427-6572)6572----j31=3--->6573:Sub5A(6573-6804)
|                                                                                         |6049----j32=4--->6805:Sub5C(6805-6950)6950----j33=5--->6951:Sub5C(6951-7182)
|                                                                                         \6049----j34=6--->7183:Sub5D(7183-7328)7328----j35=7--->7329:Sub5D(7329-7560)
|----=j82=--->VRT_3_0_0_n1(13619)---j83=73--->VRT_3_0_0_n1_base(13620)---j69=64--->7561:Sub6B(7561-7706)
|                                                                                       |7706----j36=1--->7707:Sub6B(7707-7938)
|                                                                                       |7561----j37=2--->7939:Sub6A(7939-8084)8084----j38=3--->8085:Sub6A(8085-8316)
|                                                                                       |7561----j39=4--->8317:Sub6C(8317-8462)8462----j40=5--->8463:Sub6C(8463-8694)
|                                                                                       \7561----j41=6--->8695:Sub6D(8695-8840)8840----j42=7--->8841:Sub6D(8841-9072)
|----=j84=--->VRT_3_0_n1_n1(13621)---j85=73--->VRT_3_0_n1_n1_base(13622)---j70=64--->9073:Sub7B(9073-9218)
|                                                                                         |9218----j43=1--->9219:Sub7B(9219-9450)
|                                                                                         |9073----j44=2--->9451:Sub7A(9451-9596)9596----j45=3--->9597:Sub7A(9597-9828)
|                                                                                         |9073----j46=4--->9829:Sub7C(9829-9974)9974----j47=5--->9975:Sub7C(9975-10206)
|                                                                                         \9073----j48=6--->10207:Sub7D(10207-10352)10352----j49=7--->10353:Sub7D(10353-10584)
|----=j86=--->VRT_3_n1_0_n1(13623)---j87=73--->VRT_3_n1_0_n1_base(13624)---j71=64--->10585:Sub8B(10585-10730)
|                                                                                          |10730----j50=1--->10731:Sub8B(10731-10962)
|                                                                                          |10585----j51=2--->10963:Sub8A(10963-11108)11108----j52=3--->11109:Sub8A(11109-11340)
|                                                                                          |10585----j53=4--->11341:Sub8C(11341-11486)11486----j54=5--->11487:Sub8C(11487-11718)
|                                                                                          \10585----j55=6--->11719:Sub8D(11719-11864)11864----j56=7--->11865:Sub8D(11865-12096)
\----=j88=--->VRT_3_n1_n1_n1(13625)---j89=73--->VRT_3_n1_n1_n1_base(13626)---j72=64--->12097:Sub9B(12097-12242)
                                                                                             |12242----j57=1--->12243:Sub9B(12243-12474)
                                                                                             |12097----j58=2--->12475:Sub9A(12475-12620)12620----j59=3--->12621:Sub9A(12621-12852)
                                                                                             |12097----j60=4--->12853:Sub9C(12853-12998)12998----j61=5--->12999:Sub9C(12999-13230)
                                                                                             \12097----j62=6--->13231:Sub9D(13231-13376)13376----j63=7--->13377:Sub9D(13377-13608)
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: Reading options...
protocols.rosetta_scripts.ParsedProtocol: 
}
=======================END MOVER SetupForSymmetry - setup_symm=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
{
protocols.rosetta_scripts.ParsedProtocol: 
}
=======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER TagPoseWithRefinementStats - tag_i=======================
{