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November 15, 2017 at 12:19 pm #2799
Anonymous
Hi everyone
Using placestub application, I want to place a set of stubs in target protein to use them for protein binder design. In this way, I want use 1000 scaffold (proteins to be substituted by appropriate stubs). Everything is OK with producing stubs, inverse rotamers, docking. But when I run placestub xml, it gives me this type of error in last line:
core.init: Rosetta version rosetta.binary.linux.release-154:af0fe23c4f7abb07b1e74df46596171cd53e814b 2017-09-28 07:36:11.498320 from http://www.rosettacommons.org
core.init: command: /home/highbiotech/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/highbiotech/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/database -write_failures false -boinc:max_nstruct 20000 -s 1eyh.patchdock.pdb -run:protocol jd2_scripting -jd2:dd_parser -parser:protocol Fc_2stubs_contact.xml -out:nstruct 1000 -ex1 -ex2aro -extrachi_cutoff 5 -docking:no_filters -use_input_sc -parser:patchdock -parser:patchdock_random_entry 1 500 -no_his_his_pairE -lj_hbond_hdis 1.75 -lj_hbond_OH_donor_dis 2.6 -linmem_ig 10
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-1756189348 seed_offset=0 real_seed=-1756189348
core.init.random: RandomGenerator:init: Normal mode, seed=-1756189348 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.protein_interface_design.ParserJobInputter: Instantiate ParserJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed 1eyh.patchdock.pdb nstruct indices 1 – 1000
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active …
protocols.protein_interface_design.ParserJobInputter: ParserJobInputter::pose_from_job
protocols.protein_interface_design.read_patchdock: Reading pose from disk
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 557 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.38 seconds.
core.import_pose.import_pose: File ‘1eyh.patchdock.pdb’ automatically determined to be of type PDB
core.conformation.Conformation: Found disulfide between residues 13 55
core.conformation.Conformation: current variant for 13 CYS
core.conformation.Conformation: current variant for 55 CYS
core.conformation.Conformation: current variant for 13 CYD
core.conformation.Conformation: current variant for 55 CYD
core.conformation.Conformation: Found disulfide between residues 44 89
core.conformation.Conformation: current variant for 44 CYS
core.conformation.Conformation: current variant for 89 CYS
core.conformation.Conformation: current variant for 44 CYD
core.conformation.Conformation: current variant for 89 CYD
core.conformation.Conformation: Found disulfide between residues 48 91
core.conformation.Conformation: current variant for 48 CYS
core.conformation.Conformation: current variant for 91 CYS
core.conformation.Conformation: current variant for 48 CYD
core.conformation.Conformation: current variant for 91 CYD
core.import_pose.import_pose: File ‘1eyh.patchdock.pdb’ automatically determined to be of type PDB
core.conformation.Conformation: Found disulfide between residues 13 55
core.conformation.Conformation: current variant for 13 CYS
core.conformation.Conformation: current variant for 55 CYS
core.conformation.Conformation: current variant for 13 CYD
core.conformation.Conformation: current variant for 55 CYD
core.conformation.Conformation: Found disulfide between residues 44 89
core.conformation.Conformation: current variant for 44 CYS
core.conformation.Conformation: current variant for 89 CYS
core.conformation.Conformation: current variant for 44 CYD
core.conformation.Conformation: current variant for 89 CYD
core.conformation.Conformation: Found disulfide between residues 48 91
core.conformation.Conformation: current variant for 48 CYS
core.conformation.Conformation: current variant for 91 CYS
core.conformation.Conformation: current variant for 48 CYD
core.conformation.Conformation: current variant for 91 CYD
protocols.protein_interface_design.read_patchdock: Reading from patchdock file name: 1eyh.patchdock
protocols.protein_interface_design.read_patchdock: 2541 entries in patchdock file 1eyh.patchdock
protocols.protein_interface_design.read_patchdock: sampling a number between 1 and 500
protocols.protein_interface_design.read_patchdock: Reading patchdock entry 296 from file: 1eyh.patchdock
core.conformation.Conformation: Found disulfide between residues 13 55
core.conformation.Conformation: current variant for 13 CYD
core.conformation.Conformation: current variant for 55 CYD
core.conformation.Conformation: current variant for 13 CYD
core.conformation.Conformation: current variant for 55 CYD
core.conformation.Conformation: Found disulfide between residues 44 89
core.conformation.Conformation: current variant for 44 CYD
core.conformation.Conformation: current variant for 89 CYD
core.conformation.Conformation: current variant for 44 CYD
core.conformation.Conformation: current variant for 89 CYD
core.conformation.Conformation: Found disulfide between residues 48 91
core.conformation.Conformation: current variant for 48 CYD
core.conformation.Conformation: current variant for 91 CYD
core.conformation.Conformation: current variant for 48 CYD
core.conformation.Conformation: current variant for 91 CYD
core.conformation.Conformation: Found disulfide between residues 13 55
core.conformation.Conformation: current variant for 13 CYD
core.conformation.Conformation: current variant for 55 CYD
core.conformation.Conformation: current variant for 13 CYD
core.conformation.Conformation: current variant for 55 CYD
core.conformation.Conformation: Found disulfide between residues 44 89
core.conformation.Conformation: current variant for 44 CYD
core.conformation.Conformation: current variant for 89 CYD
core.conformation.Conformation: current variant for 44 CYD
core.conformation.Conformation: current variant for 89 CYD
core.conformation.Conformation: Found disulfide between residues 48 91
core.conformation.Conformation: current variant for 48 CYD
core.conformation.Conformation: current variant for 91 CYD
core.conformation.Conformation: current variant for 48 CYD
core.conformation.Conformation: current variant for 91 CYD
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=Fc_2stubs_contact.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>
<TASKOPERATIONS>
<PreventRepacking name=”prevent_repacking_84″ resnum=”84″/>
</TASKOPERATIONS>
<SCOREFXNS>
<ScoreFunction hs_hash=”10.0″ name=”stub_docking_low” weights=”interchain_cen”/>
<ScoreFunction hs_hash=”10.0″ name=”repack_soft” weights=”ref2015_soft”/>
<ScoreFunction hs_hash=”10.0″ name=”minimize_cart” weights=”ref2015_cart”/>
<ScoreFunction hs_hash=”0.0″ name=”ddg_scorefxn” weights=”ref2015″/>
</SCOREFXNS>
<FILTERS>
<Ddg name=”ddg” repeats=”3″ scorefxn=”ddg_scorefxn” threshold=”1000000″/>
<Sasa confidence=”0.0″ name=”sasa” threshold=”800″/>
<CompoundStatement name=”ddg_sasa”>
<AND filter_name=”ddg”/>
<AND filter_name=”sasa”/>
</CompoundStatement>
<TerminusDistance distance=”3″ name=”termini”/>
<AtomicContact name=”touch_82″ residue1=”82W”/>
<AtomicContact name=”touch_87″ residue1=”87W”/>
<CompoundStatement name=”touch_RQ”>
<AND filter_name=”touch_82″/>
<AND filter_name=”touch_87″/>
</CompoundStatement>
</FILTERS>
<MOVERS>
<Docking fullatom=”0″ local_refine=”0″ name=”dock” score_low=”stub_docking_low”/>
<build_Ala_pose name=”ala_pose”/>
<SaveAndRetrieveSidechains name=”save_retrieve_sc”/>
<RepackMinimize interface_cutoff_distance=”10.0″ minimize_bb=”0″ minimize_rb=”1″ name=”des1″ scorefxn_minimize=”minimize_cart” scorefxn_repack=”repack_soft”/>
<RepackMinimize interface_cutoff_distance=”10.0″ minimize_bb=”0″ minimize_rb=”1″ name=”des2″/>
<RepackMinimize interface_cutoff_distance=”10.0″ minimize_bb=”1″ minimize_rb=”1″ name=”des3″/>
<SaveAndRetrieveSidechains name=”srsc”/>
<PlaceStub add_constraints=”true” after_placement_filter=”touch_RQ” chain_to_design=”2″ final_filter=”ddg_sasa” hurry=”false” leave_coord_csts=”1″ max_cb_dist=”4.0″ minimize_rb=”true” name=”place_phe_hr2″ score_threshold=”0.0″ stub_energy_threshold=”10″ stubfile=”all_HR2_Y102.pdb” task_operations=”prevent_repacking_84″ triage_positions=”false”>
<StubMinimize>
<Add bb_cst_weight=”10.0″ mover_name=”br”/>
</StubMinimize>
<DesignMovers>
<Add mover_name=”ala_pose”/>
<Add coord_cst_std=”1.0″ mover_name=”des1″/>
<Add coord_cst_std=”1.5″ mover_name=”des2″/>
<Add coord_cst_std=”1.5″ mover_name=”des3″/>
<Add mover_name=”srsc”/>
</DesignMovers>
</PlaceStub>
<PlaceStub hurry=”1″ leave_coord_csts=”1″ max_cb_dist=”4.0″ minimize_rb=”1″ name=”place_w_hr1″ place_scaffold=”1″ score_threshold=”10.0″ stub_energy_threshold=”3.0″ stubfile=”all_HR1_F108.pdb” task_operations=”prevent_repacking_84″>
<StubMinimize>
<Add mover_name=”br”/>
</StubMinimize>
<DesignMovers>
<Add coord_cst_std=”1.0″ mover_name=”place_phe_hr2″/>
</DesignMovers>
</PlaceStub>
</MOVERS>
<APPLY_TO_POSE>
<SetupHotspotConstraints cb_force=”0.5″ redesign_chain=”2″ stubfile=”all_HR1_F108_all_HR2_Y102.pdb”/>
<profile file_name=”1eyh.patchdock.cst” weight=”0.2″/>
</APPLY_TO_POSE>
<PROTOCOLS>
<Add filter_name=”termini” mover_name=”dock”/>
<Add mover_name=”place_w_hr1″/>
<Add filter_name=”ddg”/>
<Add filter_name=”sasa”/>
</PROTOCOLS>
</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.TaskOperationLoader: Defined TaskOperation named “prevent_repacking_84” of type PreventRepacking
protocols.jd2.parser.ScoreFunctionLoader: defined score function “stub_docking_low” with weights “interchain_cen”
protocols.jd2.parser.ScoreFunctionLoader: setting stub_docking_low backbone_stub_constraint to 10
protocols.jd2.parser.ScoreFunctionLoader: defined score function “repack_soft” with weights “ref2015_soft”
protocols.jd2.parser.ScoreFunctionLoader: setting repack_soft backbone_stub_constraint to 10
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 757 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1434 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2195 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function “minimize_cart” with weights “ref2015_cart”
protocols.jd2.parser.ScoreFunctionLoader: setting minimize_cart backbone_stub_constraint to 10
protocols.jd2.parser.ScoreFunctionLoader: defined score function “ddg_scorefxn” with weights “ref2015”
protocols.jd2.parser.ScoreFunctionLoader: setting ddg_scorefxn backbone_stub_constraint to 0
protocols.simple_filters.DdgFilter: ddg filter with threshold 1e+06 repeats=3 and scorefxn ddg_scorefxn over jump 1extreme_value_removal: 0 and repack 1
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named “ddg” of type Ddg
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named “sasa” of type Sasa
protocols.filters.Filter: CompoundStatement
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named “ddg_sasa” of type CompoundStatement
protocols.simple_filters.TerminusDistanceFilter: Distance From Terminus filter over jump number 1 with cutoff 3
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named “termini” of type TerminusDistance
protocols.filters.AtomicContactFilter: AtomicContact: residue2 was not defined. A mover/filter will have to set it during the protocol
AtomicContact filter between residues 82 and 0 with distance cutoff of 4
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named “touch_82” of type AtomicContact
protocols.filters.AtomicContactFilter: AtomicContact: residue2 was not defined. A mover/filter will have to set it during the protocol
AtomicContact filter between residues 87 and 0 with distance cutoff of 4
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named “touch_87” of type AtomicContact
protocols.filters.Filter: CompoundStatement
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named “touch_RQ” of type CompoundStatement
protocols.docking.DockingInitialPerturbation: Reading options…
protocols.protein_interface_design.movers.DockAndRetrieveSidechains: docking mover with parameters low_res_protocol_only_ 1 local_refine 0 view 0 lowres_scorefxn= stub_docking_low highres_scorefxn= commandline over rb_jumps 1, optimize fold tree=1
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named “dock” of type Docking
protocols.protein_interface_design.movers.BuildAlaPose: defined BuildAlaPose mover for partners 2 with distance cutoff 20 and convert to type ALA NOT WORK for GLY
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named “ala_pose” of type build_Ala_pose
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named “save_retrieve_sc” of type SaveAndRetrieveSidechains
protocols.protein_interface_design.movers.RepackMinimize: repack minimize mover with the following parameters:
protocols.simple_moves.DesignRepackMover: design partner1: 0
design partner2: 1
repack partner1: 1
repack partner2: 1
repack scorefxn repack_soft and minimize scorefxn minimize_cart automatic_repacking_definition set to 1 optimize fold tree=1 targeting residues
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named “des1” of type RepackMinimize
protocols.protein_interface_design.movers.RepackMinimize: repack minimize mover with the following parameters:
protocols.simple_moves.DesignRepackMover: design partner1: 0
design partner2: 1
repack partner1: 1
repack partner2: 1
repack scorefxn commandline and minimize scorefxn commandline automatic_repacking_definition set to 1 optimize fold tree=1 targeting residues
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named “des2” of type RepackMinimize
protocols.protein_interface_design.movers.RepackMinimize: repack minimize mover with the following parameters:
protocols.simple_moves.DesignRepackMover: design partner1: 0
design partner2: 1
repack partner1: 1
repack partner2: 1
repack scorefxn commandline and minimize scorefxn commandline automatic_repacking_definition set to 1 optimize fold tree=1 targeting residues
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named “des3” of type RepackMinimize
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named “srsc” of type SaveAndRetrieveSidechains
protocols.protein_interface_design.movers.PlaceStubMover: Parsing PlaceStubMover—-
protocols.RosettaScripts.util: Object place_phe_hr2 reading the following task_operations: Adding the following task operations
prevent_repacking_84
protocols.hotspot_hashing: Read 90 stubs from all_HR2_Y102.pdb
core.pack.task: Packer task: initialize from command line()
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/highbiotech/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file ‘/home/highbiotech/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin’.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.11 seconds to load from binary
core.pack.pack_rotamers: built 137 rotamers at 137 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3237276 bytes
protocols.hotspot_hashing: Associated stubs with scaffold chain 2
protocols.protein_interface_design.movers.PlaceStubMover: added design mover ala_pose to place stub with apply_coord_constraints switched to 1 with std 0.5 and hurry=0
added design mover des1 to place stub with apply_coord_constraints switched to 1 with std 1 and hurry=0
added design mover des2 to place stub with apply_coord_constraints switched to 1 with std 1.5 and hurry=0
added design mover des3 to place stub with apply_coord_constraints switched to 1 with std 1.5 and hurry=0
added design mover srsc to place stub with apply_coord_constraints switched to 1 with std 0.5 and hurry=0
No StubMinimize movers defined by user, defaulting to minimize_rb and _sc of stubs only
leaving constraints on after successful placement
max cb cb distance set to 4
place stub mover on chain 2 with score threshold of 0 minimize_rb to 1 final filter ddg_sasa and place scaffold=0
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named “place_phe_hr2” of type PlaceStub
protocols.protein_interface_design.movers.PlaceStubMover: Parsing PlaceStubMover—-
protocols.RosettaScripts.util: Object place_w_hr1 reading the following task_operations: Adding the following task operations
prevent_repacking_84
protocols.hotspot_hashing: Read 22 stubs from all_HR1_F108.pdb
core.pack.task: Packer task: initialize from command line()
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.pack.pack_rotamers: built 137 rotamers at 137 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3237276 bytes
protocols.hotspot_hashing: Associated stubs with scaffold chain 2
protocols.protein_interface_design.movers.PlaceStubMover: added design mover place_phe_hr2 to place stub with apply_coord_constraints switched to 1 with std 1 and hurry=1
No StubMinimize movers defined by user, defaulting to minimize_rb and _sc of stubs only
leaving constraints on after successful placement
max cb cb distance set to 4
place stub mover on chain 2 with score threshold of 10 minimize_rb to 1 final filter true_filter and place scaffold=1
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named “place_w_hr1” of type PlaceStub
protocols.hotspot_hashing: Read 111 stubs from all_HR1_F108_all_HR2_Y102.pdb
protocols.protein_interface_design.movers.SetupHotspotConstraintsMover: applying backbone_stub_constraint constraints to pose with cb_force weight of 0.5, apply ambiguous constraints set to 1 and colonyE set to 0
protocols.protein_interface_design.movers.SetupHotspotConstraintsMover: Setting bacbkone_stub_constraint weight in scorefxn REF2015 to 1
protocols.protein_interface_design.movers.SetupHotspotConstraintsMover: Setting bacbkone_stub_constraint weight in scorefxn commandline to 1
protocols.protein_interface_design.movers.SetupHotspotConstraintsMover: Setting bacbkone_stub_constraint weight in scorefxn ddg_scorefxn to 1
protocols.protein_interface_design.movers.SetupHotspotConstraintsMover: Skipping resetting of backbone_stub_constraint weight in minimize_cart which is already preset to 10
protocols.protein_interface_design.movers.SetupHotspotConstraintsMover: Skipping resetting of backbone_stub_constraint weight in repack_soft which is already preset to 10
protocols.protein_interface_design.movers.SetupHotspotConstraintsMover: Setting bacbkone_stub_constraint weight in scorefxn score4L to 1
protocols.protein_interface_design.movers.SetupHotspotConstraintsMover: Setting bacbkone_stub_constraint weight in scorefxn score_docking_low to 1
protocols.protein_interface_design.movers.SetupHotspotConstraintsMover: Setting bacbkone_stub_constraint weight in scorefxn soft_rep to 1
protocols.protein_interface_design.movers.SetupHotspotConstraintsMover: Skipping resetting of backbone_stub_constraint weight in stub_docking_low which is already preset to 10
protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.644651 -0.74766 -0.159468 -0.573471 0.335006 0.747598 -0.505526 0.57339 -0.644723 24.103 -13.4474 -61.566
protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.644651 -0.74766 -0.159468 -0.573471 0.335006 0.747598 -0.505526 0.57339 -0.644723 19.9843 -1.73337 -99.5899
protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.644651 -0.74766 -0.159468 -0.573471 0.335006 0.747598 -0.505526 0.57339 -0.644723 24.103 -13.4474 -61.566
protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.644651 -0.74766 -0.159468 -0.573471 0.335006 0.747598 -0.505526 0.57339 -0.644723 19.9843 -1.73337 -99.5899
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 112 rotamers at 112 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 1811514 bytes
protocols.hotspot_hashing: Associated stubs with scaffold chain 2
protocols.hotspot_hashing: Making hotspot constraints…
protocols.hotspot_hashing: Applied 98 hotspot constraints to the pose.
protocols.rosetta_scripts.RosettaScriptsParser: Defined and applied mover of type SetupHotspotConstraints
protocols.simple_moves.SequenceProfileMover: setting REF2015 res_type_constraint to 0.2
setting commandline res_type_constraint to 0.2
setting ddg_scorefxn res_type_constraint to 0.2
setting minimize_cart res_type_constraint to 0.2
setting repack_soft res_type_constraint to 0.2
setting score4L res_type_constraint to 0.2
setting score_docking_low res_type_constraint to 0.2
setting soft_rep res_type_constraint to 0.2
setting stub_docking_low res_type_constraint to 0.2
Changed all scorefxns to have profile weights of 0.2
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
core.sequence.SequenceProfile: [ WARNING ] Potentially incomplete profile row in ‘1eyh.patchdock.cst’.
protocols.simple_moves.SequenceProfileMover: Added sequence profile constraints specified in file 1eyh.patchdock.cst.
protocols.rosetta_scripts.RosettaScriptsParser: Defined and applied mover of type profile
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover “dock” with filter “termini”
protocols.rosetta_scripts.ParsedProtocol: added mover “place_w_hr1” with filter “true_filter”
protocols.rosetta_scripts.ParsedProtocol: added mover “NULL_MOVER” with filter “ddg”
protocols.rosetta_scripts.ParsedProtocol: added mover “NULL_MOVER” with filter “sasa”
protocols.protein_interface_design.ParserJobInputter: ParserJobInputter::pose_from_job
protocols.protein_interface_design.read_patchdock: Skipped reading pose from disk
protocols.protein_interface_design.read_patchdock: Reading from patchdock file name: 1eyh.patchdock
protocols.protein_interface_design.read_patchdock: 2541 entries in patchdock file 1eyh.patchdock
protocols.protein_interface_design.read_patchdock: sampling a number between 1 and 500
protocols.protein_interface_design.read_patchdock: Reading patchdock entry 9 from file: 1eyh.patchdock
core.conformation.Conformation: Found disulfide between residues 13 55
core.conformation.Conformation: current variant for 13 CYD
core.conformation.Conformation: current variant for 55 CYD
core.conformation.Conformation: current variant for 13 CYD
core.conformation.Conformation: current variant for 55 CYD
core.conformation.Conformation: Found disulfide between residues 44 89
core.conformation.Conformation: current variant for 44 CYD
core.conformation.Conformation: current variant for 89 CYD
core.conformation.Conformation: current variant for 44 CYD
core.conformation.Conformation: current variant for 89 CYD
core.conformation.Conformation: Found disulfide between residues 48 91
core.conformation.Conformation: current variant for 48 CYD
core.conformation.Conformation: current variant for 91 CYD
core.conformation.Conformation: current variant for 48 CYD
core.conformation.Conformation: current variant for 91 CYD
core.conformation.Conformation: Found disulfide between residues 13 55
core.conformation.Conformation: current variant for 13 CYD
core.conformation.Conformation: current variant for 55 CYD
core.conformation.Conformation: current variant for 13 CYD
core.conformation.Conformation: current variant for 55 CYD
core.conformation.Conformation: Found disulfide between residues 44 89
core.conformation.Conformation: current variant for 44 CYD
core.conformation.Conformation: current variant for 89 CYD
core.conformation.Conformation: current variant for 44 CYD
core.conformation.Conformation: current variant for 89 CYD
core.conformation.Conformation: Found disulfide between residues 48 91
core.conformation.Conformation: current variant for 48 CYD
core.conformation.Conformation: current variant for 91 CYD
core.conformation.Conformation: current variant for 48 CYD
core.conformation.Conformation: current variant for 91 CYD
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Docking – dock=======================
protocols.docking.DockingProtocol: Setting docking foldtree
protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 94 -1 EDGE 1 95 1 EDGE 95 238 -1
protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 41 -1 EDGE 41 94 -1 EDGE 41 161 1 EDGE 161 95 -1 EDGE 161 238 -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: off ///
protocols.docking.DockingProtocol: /// Low Resolution Filter: off ///
protocols.docking.DockingProtocol: /// High Resolution Filter: off ///
protocols.docking.DockingProtocol: ////////////////////////////////////////////////////////////////////////////////
core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 62 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.02 seconds.
protocols.docking.DockingProtocol: FOLD_TREE EDGE 1 41 -1 EDGE 41 94 -1 EDGE 41 161 1 EDGE 161 95 -1 EDGE 161 238 -1
protocols.docking.DockingInitialPerturbation: sliding into contact for centroid mode
protocols.docking.DockingInitialPerturbation: sliding into contact
protocols.docking.DockingInitialPerturbation: Moving away
protocols.docking.DockingInitialPerturbation: Moving together
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -9.21682 -9.12565 62.1384
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -9.02215 -9.0456 61.1608
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -9.02215 -9.0456 61.1608
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -8.82748 -8.96556 60.1832
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -8.82748 -8.96556 60.1832
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -8.63281 -8.88552 59.2056
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -8.63281 -8.88552 59.2056
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -8.43814 -8.80547 58.228
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -8.43814 -8.80547 58.228
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -8.24347 -8.72543 57.2504
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -8.24347 -8.72543 57.2504
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -8.0488 -8.64539 56.2728
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -8.0488 -8.64539 56.2728
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -7.85413 -8.56534 55.2952
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -7.85413 -8.56534 55.2952
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -7.65946 -8.4853 54.3176
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -7.65946 -8.4853 54.3176
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -7.46479 -8.40526 53.34
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -7.46479 -8.40526 53.34
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -7.27012 -8.32522 52.3624
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -7.27012 -8.32522 52.3624
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -7.07545 -8.24517 51.3848
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -7.07545 -8.24517 51.3848
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -6.88078 -8.16513 50.4072
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -6.88078 -8.16513 50.4072
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -6.68611 -8.08509 49.4296
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -6.68611 -8.08509 49.4296
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -6.49144 -8.00504 48.452
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -6.49144 -8.00504 48.452
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -6.29677 -7.925 47.4744
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -6.29677 -7.925 47.4744
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -6.1021 -7.84496 46.4968
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -6.1021 -7.84496 46.4968
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -5.90743 -7.76491 45.5193
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -5.90743 -7.76491 45.5193
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -5.71276 -7.68487 44.5417
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -5.71276 -7.68487 44.5417
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -5.51809 -7.60483 43.5641
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -5.51809 -7.60483 43.5641
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -5.32342 -7.52478 42.5865
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -5.32342 -7.52478 42.5865
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -5.12875 -7.44474 41.6089
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -5.12875 -7.44474 41.6089
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -4.93408 -7.3647 40.6313
protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -4.93408 -7.3647 40.6313
protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.889274 0.26245 0.374582 0.0141096 -0.834335 0.551078 0.457157 -0.484774 -0.745655 -5.12875 -7.44474 41.6089
protocols.docking.DockingProtocol: finished initial perturbation
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) (backbone_stub_constraint 10)
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: ::::::::::::::::::Centroid Rigid Body Adaptive:::::::::::::::::::
protocols.TrialMover: Acceptance rate: 0.08
protocols.TrialMover: Acceptance rate: 0.1
protocols.TrialMover: Acceptance rate: 0.22
protocols.TrialMover: Acceptance rate: 0.08
protocols.TrialMover: Acceptance rate: 0.1
protocols.TrialMover: Acceptance rate: 0.06
protocols.TrialMover: Acceptance rate: 0.14
protocols.TrialMover: Acceptance rate: 0.08
protocols.TrialMover: Acceptance rate: 0.18
protocols.TrialMover: Acceptance rate: 0.2
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER termini=======================
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.simple_filters.TerminusDistanceFilter: near terminus: 6. passing.
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER termini=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PlaceStub – place_w_hr1=======================
core.pack.task: Packer task: initialize from command line()
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.pack.pack_rotamers: built 6 rotamers at 6 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 24551 bytes
protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.889114 0.020484 -0.457227 0.0753255 -0.978826 -0.190328 -0.451445 -0.203664 0.868745 26.851 5.44041 5.98929
protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.889114 0.020484 -0.457227 0.0753255 -0.978826 -0.190328 -0.451445 -0.203664 0.868745 64.1345 18.0843 13.0654
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.protein_interface_design.movers.PlaceStubMover: removing stub constraints from pose
constraint score evaluates to 0 in this pose. Failing
switching interface to alanine
Speeding up StubMinimize…
protocols.protein_interface_design.movers.PlaceStubMover: adding 81 stub constraints to pose
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: Mover PlaceStub reports failure!
protocols.jd2.JobDistributor: [ WARNING ] 1eyh.patchdock_0174 reported failure 1 times and will no longer retry (permanent failure).
As you can see in last line, the error is related to filters (ddg, sasa). This process is one try from total 1000 try for one scaffold and take many times. I don’t have many time for try and error and due to the long time for such process on 10000, I want somebody to confirm the fidelity of process. And If there are any problem, I would be verry glade to hear that.
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