SubTest integration.addsan.homodimer_fnd_ref2015

Branch: rosetta:main 「revision: №62162」
Test: ubuntu.gcc.integration.addsan
SubTest: homodimer_fnd_ref2015_memb
SubTest files: 「file-system-view」
Daemon: hojo-3
State: homodimer_fnd_ref2015_memb

LogFile log ******** (C) Copyright Rosetta Commons Member Institutions. *************** * Use of Rosetta for commercial purposes may require purchase of a license. * ******** See LICENSE.md or email license@uw.edu for more details. ********** core.init: Rosetta extras: [] core.init: command: ROSETTA/source/bin/rosetta_scripts.default.linuxgccaddsan -in:path:database_cache_dir ROSETTA/.database-binaries/ubuntugccaddsan @flags -database ROSETTA/database -testing:INTEGRATION_TEST basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.import_pose.import_pose: File './input/gpa2_embed.pdb' automatically determined to be of type PDB from contents. core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'MEM' from the PDB components dictionary for residue type 'pdb_MEM' protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=./input/fnd.xml protocols.rosetta_scripts.RosettaScriptsParser: Variable substitution will occur with the following values: '%%energy_function%%'='ref'; '%%frags3mers%%'='./input/frags_pdbtm.200.3mers'; '%%frags9mers%%'='./input/frags_pdbtm.200.9mers'; '%%membrane_core%%'='10'; '%%score_func_0%%'='score0_memb'; '%%score_func_1%%'='score1_memb'; '%%score_func_2%%'='score2_memb'; '%%score_func_3%%'='score3_memb'; '%%score_func_5%%'='score5_memb'; '%%span_end_1%%'='21'; '%%span_end_2%%'='42'; '%%span_ends%%'='21,42'; '%%span_orientation_1%%'='out2in'; '%%span_orientation_2%%'='out2in'; '%%span_oris%%'='out2in,out2in'; '%%span_start_1%%'='1'; '%%span_start_2%%'='22'; '%%span_starts%%'='1,22'; '%%steepness%%'='4'; '%%symm_file%%'='./input/C2.symm'; protocols.rosetta_scripts.RosettaScriptsParser: Substituted script: <ROSETTASCRIPTS> <TASKOPERATIONS> <InitializeFromCommandline name="init"/> <RestrictToRepacking name="rtr"/> </TASKOPERATIONS> <SCOREFXNS>  <ScoreFunction name="score0" weights="score0_memb" symmetric="1"> <Reweight scoretype="mp_helicality" weight="100"/> </ScoreFunction> <ScoreFunction name="score1" weights="score1_memb" symmetric="1"> <Reweight scoretype="mp_helicality" weight="100"/> </ScoreFunction> <ScoreFunction name="score2" weights="score2_memb" symmetric="1"> <Reweight scoretype="mp_helicality" weight="100"/> </ScoreFunction> <ScoreFunction name="score3" weights="score3_memb" symmetric="1"> <Reweight scoretype="mp_helicality" weight="100"/> </ScoreFunction> <ScoreFunction name="score5" weights="score5_memb" symmetric="1"> <Reweight scoretype="mp_helicality" weight="100"/> </ScoreFunction>  <ScoreFunction name="mpframework" weights="mpframework_docking_fa_2015" symmetric="1"/> <ScoreFunction name="mpframeworkNotSymm" weights="mpframework_docking_fa_2015" symmetric="0"/> <ScoreFunction name="ref" weights="ref2015_memb" symmetric="1"> <Reweight scoretype="mp_helicality" weight="100"/> </ScoreFunction> <ScoreFunction name="refNotSymm" weights="ref2015_memb" symmetric="0"> <Reweight scoretype="mp_helicality" weight="100"/> </ScoreFunction> <ScoreFunction name="helicality" symmetric="1"> <Reweight scoretype="mp_helicality" weight="1"/> </ScoreFunction> <ScoreFunction name="helicality_notsymm" symmetric="0"> <Reweight scoretype="mp_helicality" weight="1"/> </ScoreFunction> </SCOREFXNS> <RESIDUE_SELECTORS>    <Layer name="layer" select_core="1" select_boundary="1" select_surface="1"/> </RESIDUE_SELECTORS> <MOVERS> <SetupForSymmetry name="symm" definition="./input/C2.symm"/> <SymmetricAddMembraneMover name="add_memb" membrane_core="10" steepness="4" span_starts_num="1,22" span_ends_num="21,42" span_orientations="out2in,out2in"/>     <MembranePositionFromTopologyMover name="init_pos"/> <FastRelax name="fast_relax" scorefxn="ref" task_operations="init"/> Fragment movers <SingleFragmentMover name="frag9" fragments="./input/frags_pdbtm.200.9mers" policy="uniform"> <MoveMap> <Span begin="1" end="24" chi="1" bb="1"/> </MoveMap> </SingleFragmentMover> <SingleFragmentMover name="frag3" fragments="./input/frags_pdbtm.200.3mers" policy="smooth"> <MoveMap> <Span begin="1" end="24" chi="1" bb="1"/> </MoveMap> </SingleFragmentMover> Fold-and-dock specific movers <SymFoldandDockRbTrialMover name="rbtrial" rot_mag="8.0" trans_mag="3.0" rotate_anchor_to_x="1"/> <SymFoldandDockRbTrialMover name="rbtrial_smooth" rot_mag="1.0" trans_mag="0.1" rotate_anchor_to_x="1"/> <SymFoldandDockMoveRbJumpMover name="rbjump"/> <SymFoldandDockSlideTrialMover name="slidetrial"/> Random movers <RandomMover name="early_stage_moveset" movers="frag9,rbtrial,rbjump,slidetrial" weights="1.0,0.2,1.0,0.1" repeats="1"/> <RandomMover name="final_stage_moveset" movers="frag3,rbtrial_smooth,rbjump,slidetrial" weights="1.0,0.2,1.0,0.1" repeats="1"/> Monte Carlo Movers <GenericMonteCarlo name="stage1" scorefxn_name="score0" mover_name="early_stage_moveset" temperature="2.0" trials="200" recover_low="1"/> <GenericMonteCarlo name="stage2" scorefxn_name="score1" mover_name="early_stage_moveset" temperature="2.0" trials="200" recover_low="1"/> <GenericMonteCarlo name="stage3a" scorefxn_name="score2" mover_name="early_stage_moveset" temperature="2.0" trials="20" recover_low="1"/> <GenericMonteCarlo name="stage3b" scorefxn_name="score5" mover_name="early_stage_moveset" temperature="2.0" trials="20" recover_low="1"/> <GenericMonteCarlo name="stage4" scorefxn_name="score3" mover_name="final_stage_moveset" temperature="2.0" trials="400" recover_low="1"/> Special stage 3 logic <ParsedProtocol name="stage3_cyc"> <Add mover="stage3a"/> <Add mover="stage3b"/> </ParsedProtocol> <LoopOver name="stage3" mover_name="stage3_cyc" iterations="5" drift="1"/> Converts the centroid-level pose to fullatom for scoring <SwitchResidueTypeSetMover name="fullatom" set="fa_standard"/> <ExtractAsymmetricPose name="extract_asp"/> <MinMover name="min_mover" scorefxn="refNotSymm" chi="1" bb="1" jump="1"/> <PackRotamersMover name="pack" scorefxn="refNotSymm" task_operations="init,rtr"/> <RotamerTrialsMinMover name="RTmin" scorefxn="refNotSymm" task_operations="init,rtr"/> <DumpPdb name="dump_pdb" fname="dump.pdb" scorefxn="ref"/> </MOVERS> <FILTERS> <ScoreType name="total" scorefxn="ref" score_type="total_score" confidence="0" threshold="0"/> <Sasa name="a_sasa" confidence="0" threshold="300"/> <ResidueLipophilicity name="a_res_lipo" threshold="1000" confidence="0"/> <SpanTopologyMatchPose name="a_span_topo" confidence="0"/> <Ddg name="a_ddg" scorefxn="refNotSymm" chain_num="2" repeats="5" extreme_value_removal="true" confidence="0" threshold="-5"/> <PackStat name="a_pack" confidence="0" threshold="0.3"/> <BuriedUnsatHbonds2 name="a_unsat" scorefxn="ref" confidence="0"/> <ShapeComplementarity name="a_shape" confidence="0"/> <TMsSpanMembrane name="a_tms_span" confidence="0" min_distance="25"/> <

homodimer_fnd_ref2015_memb sub-test description