core.init: Rosetta version rosetta.source.release-156:b1dc16ff17da7a38b52c000abb74f85e4f0333c8 2017-10-27 12:03:34.443146 from http://www.rosettacommons.org
core.init: command: rosetta_scripts.macosclangrelease -s complex.prepack.pdb -parser:protocol test1.xml -nstruct 1 @flags.dockdesign
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=183283900 seed_offset=0 real_seed=183283900
core.init.random: RandomGenerator:init: Normal mode, seed=183283900 RG_type=mt19937
core.init: Resolved executable path: /Users/danilo/Programs/rosetta-3.7/main/source/bin/rosetta_scripts.macosclangrelease
core.init: Looking for database based on location of executable: /Users/danilo/Programs/rosetta-3.7/main/database/
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed complex.prepack.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... 
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB complex.prepack.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 569 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.486107 seconds.
core.import_pose.import_pose: File 'complex.prepack.pdb' automatically determined to be of type PDB
core.conformation.Conformation: Found disulfide between residues 131 206
core.conformation.Conformation: current variant for 131 CYS
core.conformation.Conformation: current variant for 206 CYS
core.conformation.Conformation: current variant for 131 CYD
core.conformation.Conformation: current variant for 206 CYD
core.conformation.Conformation: Found disulfide between residues 23 88
core.conformation.Conformation: current variant for 23 CYS
core.conformation.Conformation: current variant for 88 CYS
core.conformation.Conformation: current variant for 23 CYD
core.conformation.Conformation: current variant for 88 CYD
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=test1.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:
<ROSETTASCRIPTS>
	<SCOREFXNS>
		<ScoreFunction name="ref2015" weights="ref2015.wts"/>
		<ScoreFunction name="interchain_cen" weights="interchain_cen.wts"/>
	</SCOREFXNS>
	<RESIDUE_SELECTORS/>
	<TASKOPERATIONS>
		<InitializeFromCommandline name="ifcl"/>
		<ExtraRotamersGeneric ex1="1" ex2="1" ex2aro="1" name="extra"/>
	</TASKOPERATIONS>
	<FILTERS>
		<ShapeComplementarity confidence="0" jump="2" min_sc="2.0" name="Sc" write_int_area="1"/>
		<Ddg confidence="0" jump="2" name="ddg" repack="1" repack_bound="0" repeats="5" scorefxn="ref2015" threshold="0"/>
		<BuriedUnsatHbonds confidence="0" name="unsat"/>
	</FILTERS>
	<MOVERS>
		<DockingProtocol dock_min="0" docking_local_refine="0" docking_score_high="ref2015" docking_score_low="interchain_cen" ignore_default_docking_task="0" low_res_protocol_only="0" name="docking" partners="LH_A" task_operations="ifcl,extra"/>
		<MinMover bb="1" chi="1" jump="2" max_iter="1000" name="minimization" scorefxn="ref2015" tolerance="0.001"/>
	</MOVERS>
	<APPLY_TO_POSE/>
	<PROTOCOLS>
		<Add mover="docking"/>
		<Add mover="minimization"/>
		<Add filter="Sc"/>
		<Add filter="ddg"/>
		<Add filter="unsat"/>
	</PROTOCOLS>
	<OUTPUT/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
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.ScoreFunctionLoader: defined score function "ref2015" with weights "ref2015.wts"
protocols.jd2.parser.ScoreFunctionLoader: defined score function "interchain_cen" with weights "interchain_cen.wts"
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "ifcl" of type InitializeFromCommandline
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "extra" of type ExtraRotamersGeneric
protocols.simple_filters.ShapeComplementarityFilter: Structures with shape complementarity < 2, interface area < 0 A^2 will be filtered.
protocols.simple_filters.ShapeComplementarityFilter: Ignoring residue range selection since residues2 is empty.
protocols.simple_filters.ShapeComplementarityFilter: Using Jump ID 2 to define surfaces.
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "Sc" of type ShapeComplementarity
protocols.simple_filters.DdgFilter: ddg filter with threshold 0 repeats=5 and scorefxn ref2015 over jump 2extreme_value_removal: 0 and repack 1
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "ddg" of type Ddg
protocols.simple_filters.BuriedUnsatHbondFilter: Buried Unsatisfied Hbond filter over jump number 1 with cutoff 20
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "unsat" of type BuriedUnsatHbonds
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.docking.DockingInitialPerturbation: Reading options...
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.RosettaScripts.util: Object docking reading the following task_operations: Adding the following task operations
ifcl extra 
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "docking" of type DockingProtocol
protocols.simple_moves.MinMover: Setting min on jump 2
protocols.simple_moves.MinMover: Options chi, bb: 1, 1 omega: 1
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "minimization" of type MinMover
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "docking" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "minimization" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "Sc"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "ddg"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "unsat"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy complex.prepack.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DockingProtocol - docking=======================
protocols.docking.DockingProtocol: Danger Will Robinson! Native is an impostor!
protocols.docking.DockingProtocol: Setting docking foldtree
protocols.docking.DockingProtocol: old fold tree: FOLD_TREE  EDGE 1 109 -1  EDGE 1 110 1  EDGE 110 240 -1  EDGE 1 241 2  EDGE 241 337 -1 
protocols.docking.DockingProtocol: new fold tree: FOLD_TREE  EDGE 1 109 -1  EDGE 109 110 2  EDGE 110 228 -1  EDGE 228 240 -1  EDGE 228 293 1  EDGE 293 241 -1  EDGE 293 337 -1 
protocols.docking.DockingProtocol: ////////////////////////////////////////////////////////////////////////////////
protocols.docking.DockingProtocol: ///                     Rosetta 3 Docking Protocol                           ///
protocols.docking.DockingProtocol: ///                                                                          ///
protocols.docking.DockingProtocol: /// Dockable Jumps: 1                                                        ///
protocols.docking.DockingProtocol: /// Low Resolution Docking Protocol:   on                                    ///
protocols.docking.DockingProtocol: /// High Resolution Docking Protocol:  on                                    ///
protocols.docking.DockingProtocol: /// Low Resolution Filter:   on                                              ///
protocols.docking.DockingProtocol: /// High Resolution Filter:  on                                              ///
protocols.docking.DockingProtocol: ////////////////////////////////////////////////////////////////////////////////
core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set.  Created 62 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.021084 seconds.
protocols.docking.DockingProtocol: FOLD_TREE  EDGE 1 109 -1  EDGE 109 110 2  EDGE 110 228 -1  EDGE 228 240 -1  EDGE 228 293 1  EDGE 293 241 -1  EDGE 293 337 -1 
protocols.docking.DockingLowRes: in DockingLowRes.apply
protocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////
protocols.docking.DockingLowRes: ///                       Docking Low Res Protocol                           ///
protocols.docking.DockingLowRes: ///                                                                          ///
protocols.docking.DockingLowRes: /// Centroid Inner Cycles: 50                                                ///
protocols.docking.DockingLowRes: /// Centroid Outer Cycles: 10                                                ///
protocols.docking.DockingLowRes: /// Scorefunction:                                                           ///
protocols.docking.DockingLowRes: ScoreFunction::show():
weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2)
energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: 
protocols.docking.DockingLowRes: EnergyMethodOptions::show: aspartimide_penalty_value: 25
protocols.docking.DockingLowRes: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT
analytic_etable_evaluation: 1
EnergyMethodOptions::show: method_weights: free_res
EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12
protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM
protocols.docking.DockingLowRes: EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ
protocols.docking.DockingLowRes: EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid
protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false
protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_monomer_fa_elec: false
protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_max_dis: 5.5
protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_min_dis: 1.6
protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_die: 10
protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_no_dis_dep_die: false
protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_die: true
protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D: 80
protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_D0: 6
protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_sigmoidal_S: 0.4
protocols.docking.DockingLowRes: EnergyMethodOptions::show: smooth_fa_elec: true
protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_type: false
protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param1: 1
protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_param2: 1
protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_fade_hbond: 0
protocols.docking.DockingLowRes: EnergyMethodOptions::show: grp_cpfxn: 1
protocols.docking.DockingLowRes: EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat
protocols.docking.DockingLowRes: EnergyMethodOptions::show: grpelec_context_dependent: 0
protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_polarization: true
protocols.docking.DockingLowRes: EnergyMethodOptions::show: use_gen_kirkwood: true
protocols.docking.DockingLowRes: EnergyMethodOptions::show: protein_dielectric: 1
protocols.docking.DockingLowRes: EnergyMethodOptions::show: water_dielectric: 78.3
protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_DNA_DNA: true
protocols.docking.DockingLowRes: EnergyMethodOptions::show: exclude_intra_res_protein: true
protocols.docking.DockingLowRes: EnergyMethodOptions::show: put_intra_into_total: false
protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false
protocols.docking.DockingLowRes: EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true
protocols.docking.DockingLowRes: EnergyMethodOptions::show: eval_intrares_elec_ST_only: false
protocols.docking.DockingLowRes: EnergyMethodOptions::show: envsmooth_zero_negatives: false
protocols.docking.DockingLowRes: EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615
protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_bound_tag: bound
protocols.docking.DockingLowRes: EnergyMethodOptions::show: pb_unbound_tag: unbound
protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_central_atoms_to_score:
protocols.docking.DockingLowRes: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none
protocols.docking.DockingLowRes: HBondOptions::show: exclude_DNA_DNA: true
protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_protein_: true
protocols.docking.DockingLowRes: HBondOptions::show: exclude_intra_res_RNA_: false
protocols.docking.DockingLowRes: HBondOptions::show: put_intra_into_total_: false
protocols.docking.DockingLowRes: HBondOptions::show: exclude_self_hbonds: true
protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep: true
protocols.docking.DockingLowRes: HBondOptions::show: use_hb_env_dep_DNA: true
protocols.docking.DockingLowRes: HBondOptions::show: smooth_hb_env_dep: true
protocols.docking.DockingLowRes: HBondOptions::show: bb_donor_acceptor_check: true
protocols.docking.DockingLowRes: HBondOptions::show: decompose_bb_hb_into_pair_energies: false
protocols.docking.DockingLowRes: HBondOptions::show: params_database_tag_: ref2015_params
protocols.docking.DockingLowRes: HBondOptions::show: use_sp2_chi_penalty_: true
protocols.docking.DockingLowRes: HBondOptions::show: sp2_BAH180_rise_: 0.75
protocols.docking.DockingLowRes: HBondOptions::show: sp2_outer_width_: 0.357
protocols.docking.DockingLowRes: HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true
protocols.docking.DockingLowRes: HBondOptions::show: fade_energy_: 1
protocols.docking.DockingLowRes: HBondOptions::show: exclude_ether_oxygens_: 0
protocols.docking.DockingLowRes: HBondOptions::show: Mbhbond: false 
protocols.docking.DockingLowRes: HbondOptions::show: mphbond: false
protocols.docking.DockingLowRes: HBondOptions::show: hbond_energy_shift: 0
protocols.docking.DockingLowRes: HBondOptions::show: water_hybrid_sf: false
protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0
protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011
protocols.docking.DockingLowRes: RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson
protocols.docking.DockingLowRes: FreeDOF_Options::show: free_suite_bonus: -1
protocols.docking.DockingLowRes: FreeDOF_Options::show: free_2HOprime_bonus: -0.5
protocols.docking.DockingLowRes: FreeDOF_Options::show: free_sugar_bonus: -1
protocols.docking.DockingLowRes: FreeDOF_Options::show: pack_phosphate_penalty: 0.25
protocols.docking.DockingLowRes: FreeDOF_Options::show: free_side_chain_bonus: -0.5
protocols.docking.DockingLowRes: 
protocols.docking.DockingLowRes: 
protocols.docking.DockingLowRes: ////////////////////////////////////////////////////////////////////////////////
protocols.docking.DockingLowRes: /// Ensemble 1: off                                                            ///
protocols.docking.DockingLowRes: /// Ensemble 2: off                                                            ///
protocols.docking.DockingLowRes: ::::::::::::::::::Centroid Rigid Body Adaptive:::::::::::::::::::
Segmentation fault: 11