surf_vol: not found;What is this problem and how to solve it? #270

Hylouis233 · 2024-12-10T03:38:46Z

Hylouis233
Dec 10, 2024

core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.ubuntu.release-371 r371 2024.09+release.06b3cf8ad0 06b3cf8ad0940d628690d0ed6fa2009d72ad2b44 https://www.rosettacommons.org 2024-02-29T01:16:28.135490
core.init: command: /media/lh/data3/masif_seed/rosetta.binary.ubuntu.release-371/main/source/bin/rosetta_scripts.default.linuxgccrelease -parser:protocol test.xml -s /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/1WTU_A_13_5Y10.pdb -no_nstruct_label -out:path:all ./out -overwrite -renumber_pdb -ignore_unrecognized_res -holes:dalphaball
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1696010382 seed_offset=0 real_seed=-1696010382
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1696010382 RG_type=mt19937
core.init: Resolved executable path: /media/lh/data3/masif_seed/rosetta.binary.ubuntu.release-371/main/source/build/src/release/linux/5.15/64/x86/gcc/11/default/rosetta_scripts.default.linuxgccrelease
core.init: Looking for database based on location of executable: /media/lh/data3/masif_seed/rosetta.binary.ubuntu.release-371/main/database/
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/1WTU_A_13_5Y10.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/1WTU_A_13_5Y10.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 985 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.360163 seconds.
core.import_pose.import_pose: File '/media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/1WTU_A_13_5Y10.pdb' automatically determined to be of type PDB
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'NAG' from the PDB components dictionary for residue type 'pdb_NAG'
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'MAN' from the PDB components dictionary for residue type 'pdb_MAN'
core.conformation.Conformation: Found disulfide between residues 106 129
core.conformation.Conformation: Found disulfide between residues 223 236
core.conformation.Conformation: Found disulfide between residues 260 407
core.conformation.Conformation: Found disulfide between residues 286 296
core.conformation.Conformation: Found disulfide between residues 338 385
core.conformation.Conformation: Found disulfide between residues 346 383
core.conformation.Conformation: Found disulfide between residues 354 360
core.conformation.Conformation: Found disulfide between residues 367 372
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=test.xml
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
        <SCOREFXNS>
                <ScoreFunction name="sfxn" weights="ref2015"/>
                <ScoreFunction name="sfxn_design" weights="ref2015">
                        <Reweight scoretype="approximate_buried_unsat_penalty" weight="10"/>
                        <Set approximate_buried_unsat_penalty_burial_probe_radius="2.3"/>
                        <Set approximate_buried_unsat_penalty_burial_atomic_depth="2.5"/>
                        <Set approximate_buried_unsat_penalty_hbond_energy_threshold="-0.25"/>
                        <Set approximate_buried_unsat_penalty_oversat_penalty="0"/>
                        <Reweight scoretype="hbond_sr_bb" weight="1"/>
                        <Reweight scoretype="hbond_lr_bb" weight="1"/>
                        <Reweight scoretype="hbond_bb_sc" weight="1"/>
                        <Reweight scoretype="hbond_sc" weight="1"/>
                        <Reweight scoretype="coordinate_constraint" weight="1"/>
                </ScoreFunction>
        </SCOREFXNS>
        <RESIDUE_SELECTORS>
                <Chain chains="A" name="chainA"/>
                <Chain chains="B" name="chainB"/>
                <Neighborhood distance="10.0" include_focus_in_subset="false" name="interface_chA" selector="chainB"/>
                <Neighborhood distance="10.0" include_focus_in_subset="false" name="interface_chB" selector="chainA"/>
                <InterfaceByVector cb_dist_cut="11" grp1_selector="interface_chA" grp2_selector="interface_chB" name="AB_interface" nearby_atom_cut="5.5" vector_angle_cut="75" vector_dist_cut="10"/>
                <Not name="Not_interface" selector="AB_interface"/>
        </RESIDUE_SELECTORS>
        <TASKOPERATIONS>
                <OperateOnResidueSubset name="restrict_to_interface" selector="Not_interface">
                        <PreventRepackingRLT/>
                </OperateOnResidueSubset>
                <OperateOnResidueSubset name="restrict_target2repacking" selector="chainB">
                        <RestrictToRepackingRLT/>
                </OperateOnResidueSubset>
                <DesignRestrictions name="allowed_aas">
                        <Action aas="ADEFGHIKLMNQRSTVWY" selector_logic="chainA"/>
                </DesignRestrictions>
                <IncludeCurrent name="current"/>
                <ExtraRotamersGeneric ex1="1" ex2="1" name="ex1_ex2"/>
                <ProteinProteinInterfaceUpweighter interface_weight="3" name="upweight_interface"/>
        </TASKOPERATIONS>
        <FILTERS>
                <ShapeComplementarity confidence="0" name="sc" residue_selector1="chainA" residue_selector2="chainB"/>
                <PeptideInternalHbondsFilter backbone_backbone="false" backbone_sidechain="true" exclusion_distance="100000" hbond_cutoff="0" name="hbonds" sidechain_sidechain="true"/>
                <BuriedUnsatHbonds2 jump_number="1" name="buried_unsat_hbonds"/>
                <Ddg confidence="1" jump="1" name="ddg" repack="0" repeats="1" scorefxn="sfxn" threshold="1000"/>
                <BuriedUnsatHbonds burial_cutoff_apo="0.2" confidence="0" cutoff="4" dalphaball_sasa="1" ignore_surface_res="false" name="buns_all_heavy_ball_interface" print_out_info_to_pdb="true" probe_radius="1.1" report_all_heavy_atom_unsats="true" scorefxn="sfxn" use_ddG_style="true"/>
                <Sasa confidence="1" hydrophobic="0" jump="1" name="sasa" polar="0"/>
        </FILTERS>
        <MOVERS>
                <AtomCoordinateCstMover coord_dev="0.5" name="constrainCA"/>
                <FastDesign batch="false" bondangle="false" bondlength="false" cartesian="false" min_type="dfpmin_armijo_nonmonotone" name="FastDesign" ramp_down_constraints="false" relaxscript="no_ref.rosettacon2018.beta_nov16.txt" repeats="1" scorefxn="sfxn_design" task_operations="current,ex1_ex2,restrict_to_interface,restrict_target2repacking,allowed_aas,upweight_interface">
                        <MoveMap name="MM">
                                <Chain bb="true" chi="true" number="1"/>
                                <Chain bb="false" chi="true" number="2"/>
                                <Jump number="1" setting="true"/>
                        </MoveMap>
                </FastDesign>
                <MinMover bb="0" cartesian="false" chi="0" name="chi_min" scorefxn="sfxn" tolerance="0.001" type="lbfgs_armijo_nonmonotone">
                        <MoveMap name="MM">
                                <Chain bb="false" chi="true" number="1"/>
                                <Chain bb="false" chi="true" number="2"/>
                                <Jump number="1" setting="false"/>
                        </MoveMap>
                </MinMover>
                <FilterReportAsPoseExtraScoresMover filter_name="ddg" name="report_ddg_pre" report_as="ddg_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="ddg" name="report_ddg_post" report_as="ddg_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="hbonds" name="report_hbonds_pre" report_as="hbonds_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="hbonds" name="report_hbonds_post" report_as="hbonds_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="buns_all_heavy_ball_interface" name="report_bunsh_pre" report_as="bunsh_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="buns_all_heavy_ball_interface" name="report_bunsh_post" report_as="bunsh_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="buried_unsat_hbonds" name="report_bunsh2_pre" report_as="bunsh2_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="buried_unsat_hbonds" name="report_bunsh2_post" report_as="bunsh2_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="sasa" name="report_sasa_pre" report_as="sasa_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="sasa" name="report_sasa_post" report_as="sasa_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="sc" name="report_sc_pre" report_as="sc_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="sc" name="report_sc_post" report_as="sc_post"/>
                <InterfaceAnalyzerMover jump="1" name="ia" scorefxn="sfxn"/>
        </MOVERS>
        <APPLY_TO_POSE/>
        <PROTOCOLS>
                <Add mover="report_ddg_pre"/>
                <Add mover="report_bunsh_pre"/>
                <Add mover="report_bunsh2_pre"/>
                <Add mover="report_hbonds_pre"/>
                <Add mover="report_sasa_pre"/>
                <Add mover="report_sc_pre"/>
                <Add mover="constrainCA"/>
                <Add mover="FastDesign"/>
                <Add mover="report_ddg_post"/>
                <Add mover="report_bunsh_post"/>
                <Add mover="report_bunsh2_post"/>
                <Add mover="report_hbonds_post"/>
                <Add mover="report_sasa_post"/>
                <Add mover="report_sc_post"/>
        </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 "sfxn" with weights "ref2015"
protocols.jd2.parser.ScoreFunctionLoader: defined score function "sfxn_design" with weights "ref2015"
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight approximate_buried_unsat_penalty to 10
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight hbond_sr_bb to 1
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight hbond_lr_bb to 1
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight hbond_bb_sc to 1
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight hbond_sc to 1
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight coordinate_constraint to 1
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_to_interface" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_target2repacking" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "allowed_aas" of type DesignRestrictions
core.pack.task.operation.TaskOperation: TaskOperation::parse_tag method called with no effect for Tag with type IncludeCurrent. Probably due to (un/mis)implemented virtual method in derived class.
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "current" of type IncludeCurrent
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "ex1_ex2" of type ExtraRotamersGeneric
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "upweight_interface" of type ProteinProteinInterfaceUpweighter
protocols.simple_filters.ShapeComplementarityFilter: Structures with shape complementarity < 0.5, interface area < 0 A^2, median distance > 0 will be filtered.
protocols.simple_filters.ShapeComplementarityFilter: Using Jump Selector to define surfaces.
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "sc" of type ShapeComplementarity
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "hbonds" of type PeptideInternalHbondsFilter
protocols.buns.BuriedUnsatisfiedPolarsCalculator2: Registering VarSolDist SASA Calculator
protocols.buns.BuriedUnsatisfiedPolarsCalculator2: Registering new basic buried unsat calculator.
protocols.buns.BuriedUnsatHbondFilter2: Buried Unsatisfied Hbond filter v2 over jump number 1 with cutoff 20
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_unsat_hbonds" of type BuriedUnsatHbonds2
protocols.simple_filters.DdgFilter: ddg filter with threshold 1000 and threshold_min -999999 repeats=1 and scorefxn sfxn extreme_value_removal: 0 and repack 0
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "ddg" of type Ddg
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buns_all_heavy_ball_interface" of type BuriedUnsatHbonds
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "sasa" of type Sasa
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "constrainCA" of type AtomCoordinateCstMover
protocols.relax.RelaxScriptManager: Reading relax scripts list from database.
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt
protocols.relax.RelaxScriptManager: ================== Reading script file: /media/lh/data3/masif_seed/rosetta.binary.ubuntu.release-371/main/database/sampling/relax_scripts/MonomerRelax2019.txt ==================
protocols.relax.RelaxScriptManager: repeat %%nrepeats%%
protocols.relax.RelaxScriptManager: coord_cst_weight 1.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.040
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.051
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.5
protocols.relax.RelaxScriptManager: scale:fa_rep 0.265
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.280
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.559
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.581
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 1
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: min 0.00001
protocols.relax.RelaxScriptManager: accept_to_best
protocols.relax.RelaxScriptManager: endrepeat
core.pack.task.xml_util: Object FastDesign reading the following task_operations: Adding the following task operations
current ex1_ex2 restrict_to_interface restrict_target2repacking allowed_aas upweight_interface
protocols.relax.RelaxScriptManager: ================== Reading script file: no_ref.rosettacon2018.beta_nov16.txt ==================
protocols.relax.RelaxScriptManager: repeat 1
protocols.relax.RelaxScriptManager: ramp_repack_min 0.079 0.01     1.0
protocols.relax.RelaxScriptManager: ramp_repack_min 0.295 0.01     0.5
protocols.relax.RelaxScriptManager: ramp_repack_min 0.577 0.01     0.0
protocols.relax.RelaxScriptManager: ramp_repack_min 1     0.00001  0.0
protocols.relax.RelaxScriptManager: accept_to_best
protocols.relax.RelaxScriptManager: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "FastDesign" of type FastDesign
protocols.minimization_packing.MinMover: Options chi, bb: 0, 0 omega: 1
protocols.RosettaScripts.util: [ WARNING ] Ignoring 'default' MoveMapFactory in parse_movemap_factory_legacy(), using existing MoveMapFactory MM instead
core.select.movemap.util: Found MoveMapFactory MM
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "chi_min" of type MinMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_ddg_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_ddg_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_hbonds_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_hbonds_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh2_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh2_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sasa_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sasa_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sc_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sc_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "ia" of type InterfaceAnalyzerMover
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_ddg_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_bunsh_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_bunsh2_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_hbonds_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_sasa_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_sc_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "constrainCA"

protocols.rosetta_scripts.ParsedProtocol: Added moversh: 1: surf_vol: not found

roccomoretti · 2024-12-10T04:09:57Z

roccomoretti
Dec 10, 2024
Maintainer

You need to set the -holes::dalphaball option to the path to the DalphaBall executable. This is normally found in the source/external/DAlpahBall/ directory of the Rosetta installation, but the executable needs to be compiled with make in that directory first. (And typically ends up as something like DAlphaBall.gcc in that directory -- but double check for executable files with ls after you do the compilation.)

1 reply

Hylouis233 Dec 10, 2024
Author

Thank you a lot!
ls this floder, which shows:

adjust.f  alfcx_tools.f  alf_tools_gmp.c  binding.h   DAlphaBall.c             DAlphaSurf.c  defines.h  gmpvar.h  measure_tools.f  surface_deriv_coord.f  surface_only.f       surface_tools.f  truncate_real.f  voids.f               volume_deriv_dist.f  volume_tools.f
alfcx.f   alf_gmp.c      binding.c        cavballs.f  DAlphaBall_surf_deriv.c  DAlphaVol.c   delcx.f    Makefile  sos_minor_gmp.c  surface_deriv_dist.f   surface_only_void.f  test.c           vector.f         volume_deriv_coord.f  volume_only.f        write_simplices.f ```

And the Rostta shows:

[ ERROR ]: Caught exception:


File: src/utility/options/OptionCollection.cc:1467
Option matching -holes:/media/lh/data3/masif_seed/rosetta:binary:ubuntu:release-371/main/source/external/DAlpahBall not found in command line top-level context

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

And I think this is the compiled problem, when I make in this folder.
It shows:

/media/lh/data3/masif_seed/rosetta.binary.ubuntu.release-371/main/source/external/DAlpahBall$ make
gcc -c -O3 -I/usr/local/include sos_minor_gmp.c
gcc -c -O3 -I/usr/local/include alf_tools_gmp.c
gcc -c -O3 -I/usr/local/include binding.c
binding.c: In function ‘get_cavballs’:
binding.c:349:9: warning: implicit declaration of function ‘cavballs_’; did you mean ‘cavballs__’? [-Wimplicit-function-declaration]
  349 |         cavballs_( x, y, z, r, &ncav );
      |         ^~~~~~~~~
      |         cavballs__
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore adjust.f
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore alfcx.f
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore alfcx_tools.f
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore cavballs.f
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore delcx.f
delcx.f:4288:72:

 4288 |                 pause
      |                                                                                      1
Warning: Deleted feature: PAUSE statement at (1)
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore truncate_real.f
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore measure_tools.f
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore surface_tools.f
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore surface_only.f
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore surface_deriv_coord.f
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore volume_tools.f
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore volume_only.f
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore volume_deriv_coord.f
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore vector.f
gfortran -c -O3 -x f77-cpp-input -fsecond-underscore write_simplices.f
gcc -o ./DAlphaBall.gcc -O3 DAlphaBall.o sos_minor_gmp.o alf_tools_gmp.o binding.o adjust.o alfcx.o alfcx_tools.o cavballs.o delcx.o truncate_real.o measure_tools.o surface_tools.o surface_only.o surface_deriv_coord.o volume_tools.o volume_only.o volume_deriv_coord.o vector.o write_simplices.o -L/usr/local/lib -lgmp  -lm -lgfortran
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1e85be0): multiple definition of `coord_gmp'; sos_minor_gmp.o:(.bss+0x1e85be0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xb80): multiple definition of `a_mp'; sos_minor_gmp.o:(.bss+0xb80): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xb20): multiple definition of `b_mp'; sos_minor_gmp.o:(.bss+0xb20): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xac0): multiple definition of `c_mp'; sos_minor_gmp.o:(.bss+0xac0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x13e0): multiple definition of `weight_gmp'; sos_minor_gmp.o:(.bss+0x13e0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1280): multiple definition of `temp1'; sos_minor_gmp.o:(.bss+0x1280): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1270): multiple definition of `temp2'; sos_minor_gmp.o:(.bss+0x1270): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x480): multiple definition of `Mab'; sos_minor_gmp.o:(.bss+0x480): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x340): multiple definition of `Mac'; sos_minor_gmp.o:(.bss+0x340): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x200): multiple definition of `Mbc'; sos_minor_gmp.o:(.bss+0x200): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xc0): multiple definition of `S'; sos_minor_gmp.o:(.bss+0xc0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x0): multiple definition of `T'; sos_minor_gmp.o:(.bss+0x0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xf30): multiple definition of `Dabc'; sos_minor_gmp.o:(.bss+0xf30): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x980): multiple definition of `Dab'; sos_minor_gmp.o:(.bss+0x980): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x9e0): multiple definition of `Sab'; sos_minor_gmp.o:(.bss+0x9e0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xa20): multiple definition of `Tab'; sos_minor_gmp.o:(.bss+0xa20): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xa60): multiple definition of `d_mp'; sos_minor_gmp.o:(.bss+0xa60): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xee0): multiple definition of `wa'; sos_minor_gmp.o:(.bss+0xee0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xed0): multiple definition of `wb'; sos_minor_gmp.o:(.bss+0xed0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xec0): multiple definition of `wc'; sos_minor_gmp.o:(.bss+0xec0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xeb0): multiple definition of `wd'; sos_minor_gmp.o:(.bss+0xeb0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xf437e0): multiple definition of `radius_gmp'; sos_minor_gmp.o:(.bss+0xf437e0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xea0): multiple definition of `ra_mp'; sos_minor_gmp.o:(.bss+0xea0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xe90): multiple definition of `rb_mp'; sos_minor_gmp.o:(.bss+0xe90): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xe80): multiple definition of `rc_mp'; sos_minor_gmp.o:(.bss+0xe80): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xe70): multiple definition of `rd_mp'; sos_minor_gmp.o:(.bss+0xe70): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xe60): multiple definition of `alp'; sos_minor_gmp.o:(.bss+0xe60): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x940): multiple definition of `Sac'; sos_minor_gmp.o:(.bss+0x940): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x900): multiple definition of `Sad'; sos_minor_gmp.o:(.bss+0x900): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x8c0): multiple definition of `Sbc'; sos_minor_gmp.o:(.bss+0x8c0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x880): multiple definition of `Sbd'; sos_minor_gmp.o:(.bss+0x880): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x840): multiple definition of `Scd'; sos_minor_gmp.o:(.bss+0x840): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1260): multiple definition of `temp3'; sos_minor_gmp.o:(.bss+0x1260): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x800): multiple definition of `Sa'; sos_minor_gmp.o:(.bss+0x800): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x7c0): multiple definition of `Sb'; sos_minor_gmp.o:(.bss+0x7c0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x5c0): multiple definition of `Sc'; sos_minor_gmp.o:(.bss+0x5c0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x780): multiple definition of `Sd'; sos_minor_gmp.o:(.bss+0x780): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x640): multiple definition of `Deter'; sos_minor_gmp.o:(.bss+0x640): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x740): multiple definition of `Sam1'; sos_minor_gmp.o:(.bss+0x740): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x700): multiple definition of `Sbm1'; sos_minor_gmp.o:(.bss+0x700): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x6c0): multiple definition of `Scm1'; sos_minor_gmp.o:(.bss+0x6c0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x680): multiple definition of `Sdm1'; sos_minor_gmp.o:(.bss+0x680): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xf70): multiple definition of `det1'; sos_minor_gmp.o:(.bss+0xf70): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xf60): multiple definition of `det2'; sos_minor_gmp.o:(.bss+0xf60): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xf40): multiple definition of `det4'; sos_minor_gmp.o:(.bss+0xf40): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xf50): multiple definition of `det3'; sos_minor_gmp.o:(.bss+0xf50): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xf20): multiple definition of `Dabd'; sos_minor_gmp.o:(.bss+0xf20): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xf10): multiple definition of `Dacd'; sos_minor_gmp.o:(.bss+0xf10): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xf00): multiple definition of `Dbcd'; sos_minor_gmp.o:(.bss+0xf00): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xef0): multiple definition of `Dabcd'; sos_minor_gmp.o:(.bss+0xef0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1000): multiple definition of `den'; sos_minor_gmp.o:(.bss+0x1000): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1010): multiple definition of `num'; sos_minor_gmp.o:(.bss+0x1010): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1030): multiple definition of `dist2'; sos_minor_gmp.o:(.bss+0x1030): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1040): multiple definition of `rb2'; sos_minor_gmp.o:(.bss+0x1040): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1050): multiple definition of `ra2'; sos_minor_gmp.o:(.bss+0x1050): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1020): multiple definition of `dtest'; sos_minor_gmp.o:(.bss+0x1020): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x600): multiple definition of `Tc'; sos_minor_gmp.o:(.bss+0x600): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xbe0): multiple definition of `res2_c'; sos_minor_gmp.o:(.bss+0xbe0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xd20): multiple definition of `res'; sos_minor_gmp.o:(.bss+0xd20): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xff0): multiple definition of `r_11'; sos_minor_gmp.o:(.bss+0xff0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xfe0): multiple definition of `r_22'; sos_minor_gmp.o:(.bss+0xfe0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xfd0): multiple definition of `r_33'; sos_minor_gmp.o:(.bss+0xfd0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xf90): multiple definition of `diff'; sos_minor_gmp.o:(.bss+0xf90): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xf80): multiple definition of `det0'; sos_minor_gmp.o:(.bss+0xf80): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xfc0): multiple definition of `r_14'; sos_minor_gmp.o:(.bss+0xfc0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xfb0): multiple definition of `r_313'; sos_minor_gmp.o:(.bss+0xfb0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0xfa0): multiple definition of `r_212'; sos_minor_gmp.o:(.bss+0xfa0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1060): multiple definition of `g3'; sos_minor_gmp.o:(.bss+0x1060): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1070): multiple definition of `g2'; sos_minor_gmp.o:(.bss+0x1070): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1080): multiple definition of `g1'; sos_minor_gmp.o:(.bss+0x1080): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1090): multiple definition of `f3'; sos_minor_gmp.o:(.bss+0x1090): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x10a0): multiple definition of `f2'; sos_minor_gmp.o:(.bss+0x10a0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x10b0): multiple definition of `f1'; sos_minor_gmp.o:(.bss+0x10b0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x10c0): multiple definition of `e3'; sos_minor_gmp.o:(.bss+0x10c0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x10d0): multiple definition of `e2'; sos_minor_gmp.o:(.bss+0x10d0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x10e0): multiple definition of `e1'; sos_minor_gmp.o:(.bss+0x10e0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x10f0): multiple definition of `d3'; sos_minor_gmp.o:(.bss+0x10f0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1100): multiple definition of `d2'; sos_minor_gmp.o:(.bss+0x1100): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1110): multiple definition of `d1'; sos_minor_gmp.o:(.bss+0x1110): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1120): multiple definition of `c44'; sos_minor_gmp.o:(.bss+0x1120): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1130): multiple definition of `c43'; sos_minor_gmp.o:(.bss+0x1130): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1140): multiple definition of `c42'; sos_minor_gmp.o:(.bss+0x1140): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1150): multiple definition of `c41'; sos_minor_gmp.o:(.bss+0x1150): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1160): multiple definition of `c34'; sos_minor_gmp.o:(.bss+0x1160): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1170): multiple definition of `c33'; sos_minor_gmp.o:(.bss+0x1170): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1180): multiple definition of `c32'; sos_minor_gmp.o:(.bss+0x1180): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1190): multiple definition of `c31'; sos_minor_gmp.o:(.bss+0x1190): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x11a0): multiple definition of `c24'; sos_minor_gmp.o:(.bss+0x11a0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x11b0): multiple definition of `c23'; sos_minor_gmp.o:(.bss+0x11b0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x11c0): multiple definition of `c22'; sos_minor_gmp.o:(.bss+0x11c0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x11d0): multiple definition of `c21'; sos_minor_gmp.o:(.bss+0x11d0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x11e0): multiple definition of `c14'; sos_minor_gmp.o:(.bss+0x11e0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x11f0): multiple definition of `c13'; sos_minor_gmp.o:(.bss+0x11f0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1200): multiple definition of `c12'; sos_minor_gmp.o:(.bss+0x1200): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1210): multiple definition of `c11'; sos_minor_gmp.o:(.bss+0x1210): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1220): multiple definition of `val3'; sos_minor_gmp.o:(.bss+0x1220): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1230): multiple definition of `val2'; sos_minor_gmp.o:(.bss+0x1230): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1240): multiple definition of `val1'; sos_minor_gmp.o:(.bss+0x1240): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1250): multiple definition of `temp4'; sos_minor_gmp.o:(.bss+0x1250): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1290): multiple definition of `a54_mp'; sos_minor_gmp.o:(.bss+0x1290): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x12a0): multiple definition of `a53_mp'; sos_minor_gmp.o:(.bss+0x12a0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x12b0): multiple definition of `a52_mp'; sos_minor_gmp.o:(.bss+0x12b0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x12c0): multiple definition of `a51_mp'; sos_minor_gmp.o:(.bss+0x12c0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x12d0): multiple definition of `a44_mp'; sos_minor_gmp.o:(.bss+0x12d0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x12e0): multiple definition of `a43_mp'; sos_minor_gmp.o:(.bss+0x12e0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x12f0): multiple definition of `a42_mp'; sos_minor_gmp.o:(.bss+0x12f0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1300): multiple definition of `a41_mp'; sos_minor_gmp.o:(.bss+0x1300): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1310): multiple definition of `a34_mp'; sos_minor_gmp.o:(.bss+0x1310): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1320): multiple definition of `a33_mp'; sos_minor_gmp.o:(.bss+0x1320): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1330): multiple definition of `a32_mp'; sos_minor_gmp.o:(.bss+0x1330): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1340): multiple definition of `a31_mp'; sos_minor_gmp.o:(.bss+0x1340): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1350): multiple definition of `a24_mp'; sos_minor_gmp.o:(.bss+0x1350): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1360): multiple definition of `a23_mp'; sos_minor_gmp.o:(.bss+0x1360): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1370): multiple definition of `a22_mp'; sos_minor_gmp.o:(.bss+0x1370): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1380): multiple definition of `a21_mp'; sos_minor_gmp.o:(.bss+0x1380): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x1390): multiple definition of `a14_mp'; sos_minor_gmp.o:(.bss+0x1390): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x13a0): multiple definition of `a13_mp'; sos_minor_gmp.o:(.bss+0x13a0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x13b0): multiple definition of `a12_mp'; sos_minor_gmp.o:(.bss+0x13b0): first defined here
/usr/bin/ld: alf_tools_gmp.o:(.bss+0x13c0): multiple definition of `a11_mp'; sos_minor_gmp.o:(.bss+0x13c0): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:77：DAlphaBall.gcc] error 1

How can I solve this problem, pls help me!

Thanks a lot!

roccomoretti · 2024-12-10T15:57:56Z

roccomoretti
Dec 10, 2024
Maintainer

The errors you're seeing with make are an issue that was fixed in the development Github version, but were committed after 3.14 was released. If you clone the Rosetta repository with git, you should have the updates. Failing that, you could manually apply the changes from PR #46 -- basically, download the gmpvar.c, gmpvar.h & Makefile files from https://github.com/RosettaCommons/rosetta/tree/main/source/external/DAlpahBall and replace the ones in your current directory.

Regarding the option, it would be -holes::dalphaball /media/lh/data3/masif_seed/rosetta:binary:ubuntu:release-371/main/source/external/DAlpahBall/DAlphaBall.gcc (or similar -- double check what executable files are present after a successful make)

0 replies

Hylouis233 · 2025-02-13T10:26:06Z

Hylouis233
Feb 13, 2025
Author

It still isn’t working, but thank you very much for your help!
I’ve spent about two months troubleshooting and researching the issue. I confirmed that I installed the latest Rosetta binary （rosetta.binary.ubuntu.release-371）.
To ensure everything was set up correctly, I also cloned the repository using:
git clone https://github.com/RosettaCommons/rosetta.git
Then I ran the following commands within the repository:

cp source/external/DAlpahBall /home
make

This process completed successfully with no errors.
However, when I run the rosetta scripts in the MASIF-SEED
https://github.com/LPDI-EPFL/masif_seed/blob/main/rosetta_scripts/seed_refine/interface_design.xml
It still doesn’t work. I have, of course, specified the option:
-holes:/media/lh/data3/masif_seed/rosetta_scripts/DAlpahBall/DAlphaBall.gcc
Below is the output/error message. Could you please help me resolve this issue? Thanks again!

********  (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: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.ubuntu.release-371 r371 2024.09+release.06b3cf8ad0 06b3cf8ad0940d628690d0ed6fa2009d72ad2b44 https://www.rosettacommons.org 2024-02-29T01:16:28.135490
core.init: command: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/bin/rosetta_scripts.default.linuxgccrelease -parser:protocol relax.xml -list ./tmp/tmp_list_1.txt -no_nstruct_label -out:path:all ./relax -overwrite -renumber_pdb -ignore_unrecognized_res
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=885033746 seed_offset=0 real_seed=885033746
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=885033746 RG_type=mt19937
core.init: Resolved executable path: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/build/src/release/linux/5.15/64/x86/gcc/11/default/rosetta_scripts.default.linuxgccrelease
core.init: Looking for database based on location of executable: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed ./input/1WTU_A_13.pdb ./input/5Y10.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB ./input/1WTU_A_13.pdb ./input/5Y10.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 985 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.319035 seconds.
core.import_pose.import_pose: File './input/1WTU_A_13.pdb ./input/5Y10.pdb' automatically determined to be of type PDB
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'NAG' from the PDB components dictionary for residue type 'pdb_NAG'
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'MAN' from the PDB components dictionary for residue type 'pdb_MAN'
core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 100
core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 101
core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_MAN 102
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ASN:CtermProteinFull 420
core.conformation.Conformation: Found disulfide between residues 106 129
core.conformation.Conformation: Found disulfide between residues 223 236
core.conformation.Conformation: Found disulfide between residues 260 407
core.conformation.Conformation: Found disulfide between residues 286 296
core.conformation.Conformation: Found disulfide between residues 338 385
core.conformation.Conformation: Found disulfide between residues 346 383
core.conformation.Conformation: Found disulfide between residues 354 360
core.conformation.Conformation: Found disulfide between residues 367 372
core.pack.pack_missing_sidechains: packing residue number 100 because of missing atom number 10 atom name O1
core.pack.pack_missing_sidechains: packing residue number 101 because of missing atom number 10 atom name O1
core.pack.pack_missing_sidechains: packing residue number 102 because of missing atom number 7 atom name O1
core.pack.task: Packer task: initialize from command line()
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
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: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.06575 seconds to load from binary
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 49 rotamers at 3 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=relax.xml
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
        <SCOREFXNS>
                <ScoreFunction name="sfxn" weights="ref2015">
                        <Reweight scoretype="coordinate_constraint" weight="1.0"/>
                </ScoreFunction>
        </SCOREFXNS>
        <RESIDUE_SELECTORS/>
        <SIMPLE_METRICS/>
        <TASKOPERATIONS>
                <IncludeCurrent name="current"/>
                <LimitAromaChi2 chi2max="135" chi2min="45" include_trp="true" name="limitchi2"/>
        </TASKOPERATIONS>
        <FILTERS/>
        <MOVERS>
                <VirtualRoot name="root" removable="false" remove="false"/>
                <AtomCoordinateCstMover coord_dev="5" name="cst" sidechain="false"/>
                <FastRelax name="fast-relax" repeats="10" scorefxn="sfxn" task_operations="current,limitchi2"/>
        </MOVERS>
        <APPLY_TO_POSE/>
        <PROTOCOLS>
                <Add mover_name="root"/>
                <Add mover_name="cst"/>
                <Add mover_name="fast-relax"/>
        </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/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 "sfxn" with weights "ref2015"
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn weight coordinate_constraint to 1
core.pack.task.operation.TaskOperation: TaskOperation::parse_tag method called with no effect for Tag with type IncludeCurrent. Probably due to (un/mis)implemented virtual method in derived class.
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "current" of type IncludeCurrent
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "limitchi2" of type LimitAromaChi2
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "root" of type VirtualRoot
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "cst" of type AtomCoordinateCstMover
protocols.relax.RelaxScriptManager: Reading relax scripts list from database.
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt
protocols.relax.RelaxScriptManager: ================== Reading script file: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/sampling/relax_scripts/MonomerRelax2019.txt ==================
protocols.relax.RelaxScriptManager: repeat %%nrepeats%%
protocols.relax.RelaxScriptManager: coord_cst_weight 1.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.040
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.051
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.5
protocols.relax.RelaxScriptManager: scale:fa_rep 0.265
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.280
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.559
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.581
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 1
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: min 0.00001
protocols.relax.RelaxScriptManager: accept_to_best
protocols.relax.RelaxScriptManager: endrepeat
core.pack.task.xml_util: Object fast-relax reading the following task_operations: Adding the following task operations
current limitchi2
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "fast-relax" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings
protocols.rosetta_scripts.ParsedProtocol: Added mover "root"
protocols.rosetta_scripts.ParsedProtocol: Added mover "cst"
protocols.rosetta_scripts.ParsedProtocol: Added mover "fast-relax"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy ./input/1WTU_A_13.pdb ./input/5Y10.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER VirtualRoot - root=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AtomCoordinateCstMover - cst=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - fast-relax=======================
protocols.relax.FastRelax: CMD: repeat  7216.22  0  0  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  7216.22  0  0  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  1193.42  0  0  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6413 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -435.185  0  0  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -385.644  0  0  0.02805
protocols.relax.FastRelax: CMD: min  -1361.32  0.716453  0.716453  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1361.32  0.716453  0.716453  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -769.503  0.716453  0.716453  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5833 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -779.975  0.716453  0.716453  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -740.777  0.716453  0.716453  0.154
protocols.relax.FastRelax: CMD: min  -1128.9  0.63549  0.63549  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1128.9  0.63549  0.63549  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -931.923  0.63549  0.63549  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5696 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -910.577  0.63549  0.63549  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -894.243  0.63549  0.63549  0.31955
protocols.relax.FastRelax: CMD: min  -997.828  0.679887  0.679887  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -997.828  0.679887  0.679887  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -826.45  0.679887  0.679887  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5697 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -744.89  0.679887  0.679887  0.55
protocols.relax.FastRelax: CMD: min  -893.846  0.732506  0.732506  0.55
protocols.relax.FastRelax: MRP: 0  -893.846  -893.846  0.732506  0.732506
protocols.relax.FastRelax: CMD: accept_to_best  -893.846  0.732506  0.732506  0.55
protocols.relax.FastRelax: CMD: endrepeat  -893.846  0.732506  0.732506  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -893.846  0.732506  0.732506  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1159.09  0.732506  0.732506  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6294 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1195  0.732506  0.732506  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1185.56  0.732506  0.732506  0.02805
protocols.relax.FastRelax: CMD: min  -1484.45  0.799  0.799  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1484.45  0.799  0.799  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -926.551  0.799  0.799  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5805 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -945.187  0.799  0.799  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -908.556  0.799  0.799  0.154
protocols.relax.FastRelax: CMD: min  -1222.12  0.713432  0.713432  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1222.12  0.713432  0.713432  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1027.87  0.713432  0.713432  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5702 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -995.58  0.713432  0.713432  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -978.991  0.713432  0.713432  0.31955
protocols.relax.FastRelax: CMD: min  -1056.9  0.727301  0.727301  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1056.9  0.727301  0.727301  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -872.279  0.727301  0.727301  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5620 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -873.639  0.727301  0.727301  0.55
protocols.relax.FastRelax: CMD: min  -940.165  0.757852  0.757852  0.55
protocols.relax.FastRelax: MRP: 1  -940.165  -940.165  0.757852  0.757852
protocols.relax.FastRelax: CMD: accept_to_best  -940.165  0.757852  0.757852  0.55
protocols.relax.FastRelax: CMD: endrepeat  -940.165  0.757852  0.757852  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -940.165  0.757852  0.757852  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1210.2  0.757852  0.757852  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6279 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1233.08  0.757852  0.757852  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1225.01  0.757852  0.757852  0.02805
protocols.relax.FastRelax: CMD: min  -1493.88  0.798309  0.798309  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1493.88  0.798309  0.798309  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -950.21  0.798309  0.798309  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5809 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -923.807  0.798309  0.798309  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -885.746  0.798309  0.798309  0.154
protocols.relax.FastRelax: CMD: min  -1235.8  0.718362  0.718362  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1235.8  0.718362  0.718362  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1048.64  0.718362  0.718362  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5736 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -993.442  0.718362  0.718362  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -976.794  0.718362  0.718362  0.31955
protocols.relax.FastRelax: CMD: min  -1079.57  0.730841  0.730841  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1079.57  0.730841  0.730841  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -909.79  0.730841  0.730841  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5695 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -846.969  0.730841  0.730841  0.55
protocols.relax.FastRelax: CMD: min  -947.248  0.767656  0.767656  0.55
protocols.relax.FastRelax: MRP: 2  -947.248  -947.248  0.767656  0.767656
protocols.relax.FastRelax: CMD: accept_to_best  -947.248  0.767656  0.767656  0.55
protocols.relax.FastRelax: CMD: endrepeat  -947.248  0.767656  0.767656  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -947.248  0.767656  0.767656  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1217.34  0.767656  0.767656  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6291 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1240.63  0.767656  0.767656  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1231.78  0.767656  0.767656  0.02805
protocols.relax.FastRelax: CMD: min  -1502.74  0.804094  0.804094  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1502.74  0.804094  0.804094  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -967.921  0.804094  0.804094  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5838 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -985.008  0.804094  0.804094  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -949.911  0.804094  0.804094  0.154
protocols.relax.FastRelax: CMD: min  -1247.08  0.735334  0.735334  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1247.08  0.735334  0.735334  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1056.52  0.735334  0.735334  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5695 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1033.39  0.735334  0.735334  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1017.55  0.735334  0.735334  0.31955
protocols.relax.FastRelax: CMD: min  -1092.41  0.747899  0.747899  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1092.41  0.747899  0.747899  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -915.323  0.747899  0.747899  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5648 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -913.613  0.747899  0.747899  0.55
protocols.relax.FastRelax: CMD: min  -955.711  0.784465  0.784465  0.55
protocols.relax.FastRelax: MRP: 3  -955.711  -955.711  0.784465  0.784465
protocols.relax.FastRelax: CMD: accept_to_best  -955.711  0.784465  0.784465  0.55
protocols.relax.FastRelax: CMD: endrepeat  -955.711  0.784465  0.784465  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -955.711  0.784465  0.784465  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1234.72  0.784465  0.784465  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6278 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1254.89  0.784465  0.784465  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1246.04  0.784465  0.784465  0.02805
protocols.relax.FastRelax: CMD: min  -1515.56  0.804195  0.804195  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1515.56  0.804195  0.804195  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -977.596  0.804195  0.804195  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5862 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -992.473  0.804195  0.804195  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -957.813  0.804195  0.804195  0.154
protocols.relax.FastRelax: CMD: min  -1252.2  0.739444  0.739444  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1252.2  0.739444  0.739444  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1062.2  0.739444  0.739444  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5744 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1060.31  0.739444  0.739444  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1045.37  0.739444  0.739444  0.31955
protocols.relax.FastRelax: CMD: min  -1089.69  0.751933  0.751933  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1089.69  0.751933  0.751933  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -901.847  0.751933  0.751933  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5675 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -901.923  0.751933  0.751933  0.55
protocols.relax.FastRelax: CMD: min  -956.489  0.781201  0.781201  0.55
protocols.relax.FastRelax: MRP: 4  -956.489  -956.489  0.781201  0.781201
protocols.relax.FastRelax: CMD: accept_to_best  -956.489  0.781201  0.781201  0.55
protocols.relax.FastRelax: CMD: endrepeat  -956.489  0.781201  0.781201  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -956.489  0.781201  0.781201  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1234.91  0.781201  0.781201  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6316 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1259.34  0.781201  0.781201  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1250.73  0.781201  0.781201  0.02805
protocols.relax.FastRelax: CMD: min  -1515.68  0.807848  0.807848  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1515.68  0.807848  0.807848  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -988.356  0.807848  0.807848  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5865 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1006.61  0.807848  0.807848  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -972.061  0.807848  0.807848  0.154
protocols.relax.FastRelax: CMD: min  -1258.96  0.741202  0.741202  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1258.96  0.741202  0.741202  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1067.51  0.741202  0.741202  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5711 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1066.18  0.741202  0.741202  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1051.16  0.741202  0.741202  0.31955
protocols.relax.FastRelax: CMD: min  -1097.61  0.755389  0.755389  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1097.61  0.755389  0.755389  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -915.784  0.755389  0.755389  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5648 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -915.917  0.755389  0.755389  0.55
protocols.relax.FastRelax: CMD: min  -960.249  0.788437  0.788437  0.55
protocols.relax.FastRelax: MRP: 5  -960.249  -960.249  0.788437  0.788437
protocols.relax.FastRelax: CMD: accept_to_best  -960.249  0.788437  0.788437  0.55
protocols.relax.FastRelax: CMD: endrepeat  -960.249  0.788437  0.788437  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -960.249  0.788437  0.788437  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1240.86  0.788437  0.788437  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6303 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1260.89  0.788437  0.788437  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1252.62  0.788437  0.788437  0.02805
protocols.relax.FastRelax: CMD: min  -1521.82  0.807067  0.807067  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1521.82  0.807067  0.807067  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -991.11  0.807067  0.807067  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5882 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1005.04  0.807067  0.807067  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -970.06  0.807067  0.807067  0.154
protocols.relax.FastRelax: CMD: min  -1260.59  0.745187  0.745187  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1260.59  0.745187  0.745187  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1066.05  0.745187  0.745187  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5730 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1064.76  0.745187  0.745187  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1049.4  0.745187  0.745187  0.31955
protocols.relax.FastRelax: CMD: min  -1098.1  0.757539  0.757539  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1098.1  0.757539  0.757539  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -914.8  0.757539  0.757539  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5670 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -916.855  0.757539  0.757539  0.55
protocols.relax.FastRelax: CMD: min  -962.34  0.789004  0.789004  0.55
protocols.relax.FastRelax: MRP: 6  -962.34  -962.34  0.789004  0.789004
protocols.relax.FastRelax: CMD: accept_to_best  -962.34  0.789004  0.789004  0.55
protocols.relax.FastRelax: CMD: endrepeat  -962.34  0.789004  0.789004  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -962.34  0.789004  0.789004  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1242.53  0.789004  0.789004  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6312 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1261.95  0.789004  0.789004  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1253.62  0.789004  0.789004  0.02805
protocols.relax.FastRelax: CMD: min  -1522.5  0.810719  0.810719  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1522.5  0.810719  0.810719  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -987.462  0.810719  0.810719  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5881 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1001.54  0.810719  0.810719  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -967.006  0.810719  0.810719  0.154
protocols.relax.FastRelax: CMD: min  -1257.84  0.742147  0.742147  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1257.84  0.742147  0.742147  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1066.68  0.742147  0.742147  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5767 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1062.05  0.742147  0.742147  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1046.98  0.742147  0.742147  0.31955
protocols.relax.FastRelax: CMD: min  -1098.99  0.747445  0.747445  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1098.99  0.747445  0.747445  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -922.613  0.747445  0.747445  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5663 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -921.688  0.747445  0.747445  0.55
protocols.relax.FastRelax: CMD: min  -959.48  0.780967  0.780967  0.55
protocols.relax.FastRelax: MRP: 7  -959.48  -962.34  0.789004  0.789004
protocols.relax.FastRelax: CMD: accept_to_best  -959.48  0.780967  0.780967  0.55
protocols.relax.FastRelax: CMD: endrepeat  -959.48  0.780967  0.780967  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -959.48  0.780967  0.780967  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1237.44  0.780967  0.780967  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6289 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1260.59  0.780967  0.780967  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1253.48  0.780967  0.780967  0.02805
protocols.relax.FastRelax: CMD: min  -1520.29  0.815875  0.815875  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1520.29  0.815875  0.815875  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -995.139  0.815875  0.815875  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5876 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1009.32  0.815875  0.815875  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -974.436  0.815875  0.815875  0.154
protocols.relax.FastRelax: CMD: min  -1260.84  0.742343  0.742343  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1260.84  0.742343  0.742343  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1067.98  0.742343  0.742343  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5681 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1066.72  0.742343  0.742343  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1051.48  0.742343  0.742343  0.31955
protocols.relax.FastRelax: CMD: min  -1100.45  0.752385  0.752385  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1100.45  0.752385  0.752385  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -919.679  0.752385  0.752385  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5645 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -920.514  0.752385  0.752385  0.55
protocols.relax.FastRelax: CMD: min  -961.448  0.787749  0.787749  0.55
protocols.relax.FastRelax: MRP: 8  -961.448  -962.34  0.789004  0.789004
protocols.relax.FastRelax: CMD: accept_to_best  -961.448  0.787749  0.787749  0.55
protocols.relax.FastRelax: CMD: endrepeat  -961.448  0.787749  0.787749  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -961.448  0.787749  0.787749  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1242.04  0.787749  0.787749  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6296 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1261.29  0.787749  0.787749  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1253.74  0.787749  0.787749  0.02805
protocols.relax.FastRelax: CMD: min  -1519.57  0.815425  0.815425  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1519.57  0.815425  0.815425  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -991.123  0.815425  0.815425  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5865 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1005.65  0.815425  0.815425  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -970.765  0.815425  0.815425  0.154
protocols.relax.FastRelax: CMD: min  -1259.95  0.742269  0.742269  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1259.95  0.742269  0.742269  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1067.27  0.742269  0.742269  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5716 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1066.15  0.742269  0.742269  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1050.92  0.742269  0.742269  0.31955
protocols.relax.FastRelax: CMD: min  -1097.37  0.75625  0.75625  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1097.37  0.75625  0.75625  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -910.701  0.75625  0.75625  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5649 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -910.583  0.75625  0.75625  0.55
protocols.relax.FastRelax: CMD: min  -961.692  0.793999  0.793999  0.55
protocols.relax.FastRelax: MRP: 9  -961.692  -962.34  0.789004  0.789004
protocols.relax.FastRelax: CMD: accept_to_best  -961.692  0.793999  0.793999  0.55
protocols.relax.FastRelax: CMD: endrepeat  -961.692  0.793999  0.793999  0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: 1WTU_A_13_5Y10 reported success in 497 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 497 seconds
basic.citation_manager.CitationManager:
The following Rosetta modules were used during this run of Rosetta, and should be cited:

rosetta_scripts Application's citation(s):
Fleishman SJ, Leaver-Fay A, Corn JE, Strauch E-M, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, and Baker D.  (2011).  RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite.  PLoS ONE 6(6):e20161.  doi: 10.1371/journal.pone.0020161.

FastRelax Mover's citation(s):
*Tyka MD, *Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, and Baker D.  (2011).  Alternate states of proteins revealed by detailed energy landscape mapping.  J Mol Biol 405(2):607-18.  doi: 10.1016/j.jmb.2010.11.008.  (*Co-primary authors.)

Khatib F, Cooper S, Tyka MD, Xu K, Makedon I, Popovic Z, Baker D, and Players F.  (2011).  Algorithm discovery by protein folding game players.  Proc Natl Acad Sci USA 108(47):18949-53.  doi: 10.1073/pnas.1115898108.

Maguire JB, Haddox HK, Strickland D, Halabiya SF, Coventry B, Griffin JR, Pulavarti SVSRK, Cummins M, Thieker DF, Klavins E, Szyperski T, DiMaio F, Baker D, and Kuhlman B.  (2021).  Perturbing the energy landscape for improved packing during computational protein design.  Proteins 89(4):436-449.  doi: 10.1002/prot.26030.



[ ERROR ]: Caught exception:


File: src/utility/options/OptionCollection.cc:1467
Option matching -holes:/media/lh/data3/masif_seed/rosetta_scripts/DAlpahBall/DAlphaBall:gcc not found in command line top-level context
Did you mean:
         -PCS
         -canonical_sampling:probabilities:sc
         -cm
         -cp
         -dc
         -dump_trajectory:gz
         -evaluation:I_sc
         -evaluation:rdc
         -gpu
         -in:file:dc
         -in:file:pca
         -in:file:rdc
         -in:path:bcl
         -loops:ccd
         -mc
         -mp:geo
         -ms:checkpoint:gz
         -nmr:pcs
         -nmr:rdc
         -rdc
         -testing:HCF



AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

5 replies

roccomoretti Feb 13, 2025
Maintainer

This is a formatting issue -- you need -holes:dalphaball <path>, where -holes:dalphaball is the literal string "-holes:dalphaball" followed by a space, followed by your path.

You used -holes:<path>:gcc -- the colons separate the various hierarchical levels of options (Rosetta has enough option we need to split them up into namespaces) -- the actual value of the parameter is separated from the option name with a space.

Hylouis233 Feb 14, 2025
Author

Thank you again for your kind and friendly reply.
However, after modifying the code as per your suggestion, it still doesn't work.
I received the following error:
protocols.rosetta_sh: 1: /media/lh/data3/masif_seed/rosetta_scripts/DAlpahBall: Permission denied
Of course, I ran the code with sudo privileges.
Could you please help me figure out what the issue is? Thanks a lot again!

root@bibilab:/media/lh/data3/masif_seed/rosetta_scripts/seed_refine# ./1_submitter_test.sh
********  (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: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.ubuntu.release-371 r371 2024.09+release.06b3cf8ad0 06b3cf8ad0940d628690d0ed6fa2009d72ad2b44 https://www.rosettacommons.org 2024-02-29T01:16:28.135490
core.init: command: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/bin/rosetta_scripts.default.linuxgccrelease -parser:protocol relax.xml -list ./tmp/tmp_list_1.txt -no_nstruct_label -out:path:all ./relax -overwrite -renumber_pdb -ignore_unrecognized_res
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-633847856 seed_offset=0 real_seed=-633847856
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-633847856 RG_type=mt19937
core.init: Resolved executable path: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/build/src/release/linux/5.15/64/x86/gcc/11/default/rosetta_scripts.default.linuxgccrelease
core.init: Looking for database based on location of executable: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed ./input/1WTU_A_13.pdb ./input/5Y10.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB ./input/1WTU_A_13.pdb ./input/5Y10.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 985 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.322261 seconds.
core.import_pose.import_pose: File './input/1WTU_A_13.pdb ./input/5Y10.pdb' automatically determined to be of type PDB
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'NAG' from the PDB components dictionary for residue type 'pdb_NAG'
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'MAN' from the PDB components dictionary for residue type 'pdb_MAN'
core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 100
core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 101
core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_MAN 102
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ASN:CtermProteinFull 420
core.conformation.Conformation: Found disulfide between residues 106 129
core.conformation.Conformation: Found disulfide between residues 223 236
core.conformation.Conformation: Found disulfide between residues 260 407
core.conformation.Conformation: Found disulfide between residues 286 296
core.conformation.Conformation: Found disulfide between residues 338 385
core.conformation.Conformation: Found disulfide between residues 346 383
core.conformation.Conformation: Found disulfide between residues 354 360
core.conformation.Conformation: Found disulfide between residues 367 372
core.pack.pack_missing_sidechains: packing residue number 100 because of missing atom number 10 atom name O1
core.pack.pack_missing_sidechains: packing residue number 101 because of missing atom number 10 atom name O1
core.pack.pack_missing_sidechains: packing residue number 102 because of missing atom number 7 atom name O1
core.pack.task: Packer task: initialize from command line()
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
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: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.06171 seconds to load from binary
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 49 rotamers at 3 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=relax.xml
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
        <SCOREFXNS>
                <ScoreFunction name="sfxn" weights="ref2015">
                        <Reweight scoretype="coordinate_constraint" weight="1.0"/>
                </ScoreFunction>
        </SCOREFXNS>
        <RESIDUE_SELECTORS/>
        <SIMPLE_METRICS/>
        <TASKOPERATIONS>
                <IncludeCurrent name="current"/>
                <LimitAromaChi2 chi2max="135" chi2min="45" include_trp="true" name="limitchi2"/>
        </TASKOPERATIONS>
        <FILTERS/>
        <MOVERS>
                <VirtualRoot name="root" removable="false" remove="false"/>
                <AtomCoordinateCstMover coord_dev="5" name="cst" sidechain="false"/>
                <FastRelax name="fast-relax" repeats="10" scorefxn="sfxn" task_operations="current,limitchi2"/>
        </MOVERS>
        <APPLY_TO_POSE/>
        <PROTOCOLS>
                <Add mover_name="root"/>
                <Add mover_name="cst"/>
                <Add mover_name="fast-relax"/>
        </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/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 "sfxn" with weights "ref2015"
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn weight coordinate_constraint to 1
core.pack.task.operation.TaskOperation: TaskOperation::parse_tag method called with no effect for Tag with type IncludeCurrent. Probably due to (un/mis)implemented virtual method in derived class.
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "current" of type IncludeCurrent
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "limitchi2" of type LimitAromaChi2
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "root" of type VirtualRoot
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "cst" of type AtomCoordinateCstMover
protocols.relax.RelaxScriptManager: Reading relax scripts list from database.
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt
protocols.relax.RelaxScriptManager: ================== Reading script file: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/sampling/relax_scripts/MonomerRelax2019.txt ==================
protocols.relax.RelaxScriptManager: repeat %%nrepeats%%
protocols.relax.RelaxScriptManager: coord_cst_weight 1.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.040
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.051
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.5
protocols.relax.RelaxScriptManager: scale:fa_rep 0.265
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.280
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.559
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.581
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 1
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: min 0.00001
protocols.relax.RelaxScriptManager: accept_to_best
protocols.relax.RelaxScriptManager: endrepeat
core.pack.task.xml_util: Object fast-relax reading the following task_operations: Adding the following task operations
current limitchi2
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "fast-relax" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings
protocols.rosetta_scripts.ParsedProtocol: Added mover "root"
protocols.rosetta_scripts.ParsedProtocol: Added mover "cst"
protocols.rosetta_scripts.ParsedProtocol: Added mover "fast-relax"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy ./input/1WTU_A_13.pdb ./input/5Y10.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER VirtualRoot - root=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AtomCoordinateCstMover - cst=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - fast-relax=======================
protocols.relax.FastRelax: CMD: repeat  7216.22  0  0  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  7216.22  0  0  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  1193.42  0  0  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6413 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -441.202  0  0  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -391.147  0  0  0.02805
protocols.relax.FastRelax: CMD: min  -1363.92  0.743127  0.743127  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1363.92  0.743127  0.743127  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -746.72  0.743127  0.743127  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5894 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -772.993  0.743127  0.743127  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -732.049  0.743127  0.743127  0.154
protocols.relax.FastRelax: CMD: min  -1167.3  0.686986  0.686986  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1167.3  0.686986  0.686986  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -970.856  0.686986  0.686986  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5694 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -937.942  0.686986  0.686986  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -921.342  0.686986  0.686986  0.31955
protocols.relax.FastRelax: CMD: min  -1038.37  0.729542  0.729542  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1038.37  0.729542  0.729542  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -869.417  0.729542  0.729542  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5615 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -830.161  0.729542  0.729542  0.55
protocols.relax.FastRelax: CMD: min  -912.208  0.762833  0.762833  0.55
protocols.relax.FastRelax: MRP: 0  -912.208  -912.208  0.762833  0.762833
protocols.relax.FastRelax: CMD: accept_to_best  -912.208  0.762833  0.762833  0.55
protocols.relax.FastRelax: CMD: endrepeat  -912.208  0.762833  0.762833  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -912.208  0.762833  0.762833  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1177.21  0.762833  0.762833  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6328 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1202.82  0.762833  0.762833  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1194.19  0.762833  0.762833  0.02805
protocols.relax.FastRelax: CMD: min  -1480.52  0.838951  0.838951  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1480.52  0.838951  0.838951  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -950.266  0.838951  0.838951  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5859 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -969.754  0.838951  0.838951  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -934.869  0.838951  0.838951  0.154
protocols.relax.FastRelax: CMD: min  -1225.65  0.731525  0.731525  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1225.65  0.731525  0.731525  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1035.14  0.731525  0.731525  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5730 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1003.13  0.731525  0.731525  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -986.946  0.731525  0.731525  0.31955
protocols.relax.FastRelax: CMD: min  -1073.64  0.734806  0.734806  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1073.64  0.734806  0.734806  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -902.144  0.734806  0.734806  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5626 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -901.061  0.734806  0.734806  0.55
protocols.relax.FastRelax: CMD: min  -946.254  0.760381  0.760381  0.55
protocols.relax.FastRelax: MRP: 1  -946.254  -946.254  0.760381  0.760381
protocols.relax.FastRelax: CMD: accept_to_best  -946.254  0.760381  0.760381  0.55
protocols.relax.FastRelax: CMD: endrepeat  -946.254  0.760381  0.760381  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -946.254  0.760381  0.760381  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1211.6  0.760381  0.760381  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6276 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1234.72  0.760381  0.760381  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1227.33  0.760381  0.760381  0.02805
protocols.relax.FastRelax: CMD: min  -1487.36  0.859973  0.859973  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1487.36  0.859973  0.859973  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -966.649  0.859973  0.859973  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5803 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -985.531  0.859973  0.859973  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -951.973  0.859973  0.859973  0.154
protocols.relax.FastRelax: CMD: min  -1232.34  0.741871  0.741871  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1232.34  0.741871  0.741871  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1046.48  0.741871  0.741871  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5688 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1035.96  0.741871  0.741871  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1020.93  0.741871  0.741871  0.31955
protocols.relax.FastRelax: CMD: min  -1077.48  0.738275  0.738275  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1077.48  0.738275  0.738275  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -905.451  0.738275  0.738275  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5621 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -905.664  0.738275  0.738275  0.55
protocols.relax.FastRelax: CMD: min  -952.335  0.756357  0.756357  0.55
protocols.relax.FastRelax: MRP: 2  -952.335  -952.335  0.756357  0.756357
protocols.relax.FastRelax: CMD: accept_to_best  -952.335  0.756357  0.756357  0.55
protocols.relax.FastRelax: CMD: endrepeat  -952.335  0.756357  0.756357  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -952.335  0.756357  0.756357  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1215.88  0.756357  0.756357  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6269 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1238.72  0.756357  0.756357  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1232.13  0.756357  0.756357  0.02805
protocols.relax.FastRelax: CMD: min  -1492.69  0.850208  0.850208  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1492.69  0.850208  0.850208  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -982.847  0.850208  0.850208  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5817 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -998.694  0.850208  0.850208  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -965.42  0.850208  0.850208  0.154
protocols.relax.FastRelax: CMD: min  -1236.73  0.740304  0.740304  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1236.73  0.740304  0.740304  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1050.67  0.740304  0.740304  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5679 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1051.62  0.740304  0.740304  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1037.05  0.740304  0.740304  0.31955
protocols.relax.FastRelax: CMD: min  -1083.65  0.738269  0.738269  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1083.65  0.738269  0.738269  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -910.215  0.738269  0.738269  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5616 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -903.761  0.738269  0.738269  0.55
protocols.relax.FastRelax: CMD: min  -952.733  0.762551  0.762551  0.55
protocols.relax.FastRelax: MRP: 3  -952.733  -952.733  0.762551  0.762551
protocols.relax.FastRelax: CMD: accept_to_best  -952.733  0.762551  0.762551  0.55
protocols.relax.FastRelax: CMD: endrepeat  -952.733  0.762551  0.762551  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -952.733  0.762551  0.762551  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1218.61  0.762551  0.762551  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6259 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1244.76  0.762551  0.762551  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1238.02  0.762551  0.762551  0.02805
protocols.relax.FastRelax: CMD: min  -1499.33  0.848577  0.848577  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1499.33  0.848577  0.848577  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -986.964  0.848577  0.848577  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5853 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1000.2  0.848577  0.848577  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -966.564  0.848577  0.848577  0.154
protocols.relax.FastRelax: CMD: min  -1241.89  0.738001  0.738001  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1241.89  0.738001  0.738001  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1055.38  0.738001  0.738001  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5704 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1055.83  0.738001  0.738001  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1041.2  0.738001  0.738001  0.31955
protocols.relax.FastRelax: CMD: min  -1085.02  0.737684  0.737684  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1085.02  0.737684  0.737684  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -907.431  0.737684  0.737684  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5637 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -907.519  0.737684  0.737684  0.55
protocols.relax.FastRelax: CMD: min  -953.341  0.758692  0.758692  0.55
protocols.relax.FastRelax: MRP: 4  -953.341  -953.341  0.758692  0.758692
protocols.relax.FastRelax: CMD: accept_to_best  -953.341  0.758692  0.758692  0.55
protocols.relax.FastRelax: CMD: endrepeat  -953.341  0.758692  0.758692  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -953.341  0.758692  0.758692  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1224.13  0.758692  0.758692  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6258 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1250.47  0.758692  0.758692  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1244.25  0.758692  0.758692  0.02805
protocols.relax.FastRelax: CMD: min  -1503.83  0.846396  0.846396  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1503.83  0.846396  0.846396  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -989.051  0.846396  0.846396  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5861 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1003.09  0.846396  0.846396  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -969.062  0.846396  0.846396  0.154
protocols.relax.FastRelax: CMD: min  -1246.43  0.740105  0.740105  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1246.43  0.740105  0.740105  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1058.6  0.740105  0.740105  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5705 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1057.77  0.740105  0.740105  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1042.98  0.740105  0.740105  0.31955
protocols.relax.FastRelax: CMD: min  -1089.28  0.735893  0.735893  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1089.28  0.735893  0.735893  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -911.946  0.735893  0.735893  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5619 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -912.006  0.735893  0.735893  0.55
protocols.relax.FastRelax: CMD: min  -957.792  0.76284  0.76284  0.55
protocols.relax.FastRelax: MRP: 5  -957.792  -957.792  0.76284  0.76284
protocols.relax.FastRelax: CMD: accept_to_best  -957.792  0.76284  0.76284  0.55
protocols.relax.FastRelax: CMD: endrepeat  -957.792  0.76284  0.76284  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -957.792  0.76284  0.76284  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1230.17  0.76284  0.76284  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6263 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1252.76  0.76284  0.76284  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1247  0.76284  0.76284  0.02805
protocols.relax.FastRelax: CMD: min  -1505.11  0.843931  0.843931  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1505.11  0.843931  0.843931  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -991.836  0.843931  0.843931  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5840 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1003.04  0.843931  0.843931  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -969.031  0.843931  0.843931  0.154
protocols.relax.FastRelax: CMD: min  -1247.03  0.736704  0.736704  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1247.03  0.736704  0.736704  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1059.66  0.736704  0.736704  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5708 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1058.3  0.736704  0.736704  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1043.55  0.736704  0.736704  0.31955
protocols.relax.FastRelax: CMD: min  -1092.35  0.741117  0.741117  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1092.35  0.741117  0.741117  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -919.788  0.741117  0.741117  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5638 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -913.326  0.741117  0.741117  0.55
protocols.relax.FastRelax: CMD: min  -958.591  0.76411  0.76411  0.55
protocols.relax.FastRelax: MRP: 6  -958.591  -958.591  0.76411  0.76411
protocols.relax.FastRelax: CMD: accept_to_best  -958.591  0.76411  0.76411  0.55
protocols.relax.FastRelax: CMD: endrepeat  -958.591  0.76411  0.76411  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -958.591  0.76411  0.76411  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1230.56  0.76411  0.76411  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6263 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1254.45  0.76411  0.76411  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1248.58  0.76411  0.76411  0.02805
protocols.relax.FastRelax: CMD: min  -1506.97  0.847735  0.847735  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1506.97  0.847735  0.847735  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -989.364  0.847735  0.847735  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5841 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1000.55  0.847735  0.847735  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -966.111  0.847735  0.847735  0.154
protocols.relax.FastRelax: CMD: min  -1249.2  0.740707  0.740707  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1249.2  0.740707  0.740707  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1062.77  0.740707  0.740707  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5713 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1062.71  0.740707  0.740707  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1048.06  0.740707  0.740707  0.31955
protocols.relax.FastRelax: CMD: min  -1092.18  0.739255  0.739255  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1092.18  0.739255  0.739255  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -913.596  0.739255  0.739255  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5623 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -905.601  0.739255  0.739255  0.55
protocols.relax.FastRelax: CMD: min  -959.278  0.762038  0.762038  0.55
protocols.relax.FastRelax: MRP: 7  -959.278  -959.278  0.762038  0.762038
protocols.relax.FastRelax: CMD: accept_to_best  -959.278  0.762038  0.762038  0.55
protocols.relax.FastRelax: CMD: endrepeat  -959.278  0.762038  0.762038  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -959.278  0.762038  0.762038  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1230.66  0.762038  0.762038  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6266 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1253.87  0.762038  0.762038  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1248.04  0.762038  0.762038  0.02805
protocols.relax.FastRelax: CMD: min  -1507.52  0.853085  0.853085  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1507.52  0.853085  0.853085  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -987.158  0.853085  0.853085  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5836 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -999.882  0.853085  0.853085  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -965.425  0.853085  0.853085  0.154
protocols.relax.FastRelax: CMD: min  -1248.83  0.745387  0.745387  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1248.83  0.745387  0.745387  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1061.05  0.745387  0.745387  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5702 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1061.02  0.745387  0.745387  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1046.27  0.745387  0.745387  0.31955
protocols.relax.FastRelax: CMD: min  -1091.21  0.744575  0.744575  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1091.21  0.744575  0.744575  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -912.148  0.744575  0.744575  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5610 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -912.488  0.744575  0.744575  0.55
protocols.relax.FastRelax: CMD: min  -959.033  0.764482  0.764482  0.55
protocols.relax.FastRelax: MRP: 8  -959.033  -959.278  0.762038  0.762038
protocols.relax.FastRelax: CMD: accept_to_best  -959.033  0.764482  0.764482  0.55
protocols.relax.FastRelax: CMD: endrepeat  -959.033  0.764482  0.764482  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -959.033  0.764482  0.764482  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -1231.36  0.764482  0.764482  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 6264 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1255.94  0.764482  0.764482  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1250  0.764482  0.764482  0.02805
protocols.relax.FastRelax: CMD: min  -1507.29  0.849614  0.849614  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -1507.29  0.849614  0.849614  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -985.805  0.849614  0.849614  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5841 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -998.137  0.849614  0.849614  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -963.52  0.849614  0.849614  0.154
protocols.relax.FastRelax: CMD: min  -1248.62  0.7399  0.7399  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -1248.62  0.7399  0.7399  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1060.49  0.7399  0.7399  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5697 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1059.41  0.7399  0.7399  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1044.58  0.7399  0.7399  0.31955
protocols.relax.FastRelax: CMD: min  -1094.01  0.741908  0.741908  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1094.01  0.741908  0.741908  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -920.35  0.741908  0.741908  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 5662 rotamers at 421 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -912.691  0.741908  0.741908  0.55
protocols.relax.FastRelax: CMD: min  -958.895  0.766004  0.766004  0.55
protocols.relax.FastRelax: MRP: 9  -958.895  -959.278  0.762038  0.762038
protocols.relax.FastRelax: CMD: accept_to_best  -958.895  0.766004  0.766004  0.55
protocols.relax.FastRelax: CMD: endrepeat  -958.895  0.766004  0.766004  0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: 1WTU_A_13_5Y10 reported success in 512 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 512 seconds
basic.citation_manager.CitationManager:
The following Rosetta modules were used during this run of Rosetta, and should be cited:

rosetta_scripts Application's citation(s):
Fleishman SJ, Leaver-Fay A, Corn JE, Strauch E-M, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, and Baker D.  (2011).  RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite.  PLoS ONE 6(6):e20161.  doi: 10.1371/journal.pone.0020161.

FastRelax Mover's citation(s):
*Tyka MD, *Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, and Baker D.  (2011).  Alternate states of proteins revealed by detailed energy landscape mapping.  J Mol Biol 405(2):607-18.  doi: 10.1016/j.jmb.2010.11.008.  (*Co-primary authors.)

Khatib F, Cooper S, Tyka MD, Xu K, Makedon I, Popovic Z, Baker D, and Players F.  (2011).  Algorithm discovery by protein folding game players.  Proc Natl Acad Sci USA 108(47):18949-53.  doi: 10.1073/pnas.1115898108.

Maguire JB, Haddox HK, Strickland D, Halabiya SF, Coventry B, Griffin JR, Pulavarti SVSRK, Cummins M, Thieker DF, Klavins E, Szyperski T, DiMaio F, Baker D, and Kuhlman B.  (2021).  Perturbing the energy landscape for improved packing during computational protein design.  Proteins 89(4):436-449.  doi: 10.1002/prot.26030.


********  (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: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.ubuntu.release-371 r371 2024.09+release.06b3cf8ad0 06b3cf8ad0940d628690d0ed6fa2009d72ad2b44 https://www.rosettacommons.org 2024-02-29T01:16:28.135490
core.init: command: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/bin/rosetta_scripts.default.linuxgccrelease -parser:protocol test.xml -s /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/1WTU_A_13_5Y10.pdb -no_nstruct_label -out:path:all ./out -overwrite -renumber_pdb -ignore_unrecognized_res -holes:dalphaball /media/lh/data3/masif_seed/rosetta_scripts/DAlpahBall
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-113475243 seed_offset=0 real_seed=-113475243
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-113475243 RG_type=mt19937
core.init: Resolved executable path: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/build/src/release/linux/5.15/64/x86/gcc/11/default/rosetta_scripts.default.linuxgccrelease
core.init: Looking for database based on location of executable: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/1WTU_A_13_5Y10.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/1WTU_A_13_5Y10.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 985 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.318021 seconds.
core.import_pose.import_pose: File '/media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/1WTU_A_13_5Y10.pdb' automatically determined to be of type PDB
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'NAG' from the PDB components dictionary for residue type 'pdb_NAG'
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'MAN' from the PDB components dictionary for residue type 'pdb_MAN'
core.conformation.Conformation: Found disulfide between residues 106 129
core.conformation.Conformation: Found disulfide between residues 223 236
core.conformation.Conformation: Found disulfide between residues 260 407
core.conformation.Conformation: Found disulfide between residues 286 296
core.conformation.Conformation: Found disulfide between residues 338 385
core.conformation.Conformation: Found disulfide between residues 346 383
core.conformation.Conformation: Found disulfide between residues 354 360
core.conformation.Conformation: Found disulfide between residues 367 372
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=test.xml
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
        <SCOREFXNS>
                <ScoreFunction name="sfxn" weights="ref2015"/>
                <ScoreFunction name="sfxn_design" weights="ref2015">
                        <Reweight scoretype="approximate_buried_unsat_penalty" weight="10"/>
                        <Set approximate_buried_unsat_penalty_burial_probe_radius="2.3"/>
                        <Set approximate_buried_unsat_penalty_burial_atomic_depth="2.5"/>
                        <Set approximate_buried_unsat_penalty_hbond_energy_threshold="-0.25"/>
                        <Set approximate_buried_unsat_penalty_oversat_penalty="0"/>
                        <Reweight scoretype="hbond_sr_bb" weight="1"/>
                        <Reweight scoretype="hbond_lr_bb" weight="1"/>
                        <Reweight scoretype="hbond_bb_sc" weight="1"/>
                        <Reweight scoretype="hbond_sc" weight="1"/>
                        <Reweight scoretype="coordinate_constraint" weight="1"/>
                </ScoreFunction>
        </SCOREFXNS>
        <RESIDUE_SELECTORS>
                <Chain chains="A" name="chainA"/>
                <Chain chains="B" name="chainB"/>
                <Neighborhood distance="10.0" include_focus_in_subset="false" name="interface_chA" selector="chainB"/>
                <Neighborhood distance="10.0" include_focus_in_subset="false" name="interface_chB" selector="chainA"/>
                <InterfaceByVector cb_dist_cut="11" grp1_selector="interface_chA" grp2_selector="interface_chB" name="AB_interface" nearby_atom_cut="5.5" vector_angle_cut="75" vector_dist_cut="10"/>
                <Not name="Not_interface" selector="AB_interface"/>
        </RESIDUE_SELECTORS>
        <TASKOPERATIONS>
                <OperateOnResidueSubset name="restrict_to_interface" selector="Not_interface">
                        <PreventRepackingRLT/>
                </OperateOnResidueSubset>
                <OperateOnResidueSubset name="restrict_target2repacking" selector="chainB">
                        <RestrictToRepackingRLT/>
                </OperateOnResidueSubset>
                <DesignRestrictions name="allowed_aas">
                        <Action aas="ADEFGHIKLMNQRSTVWY" selector_logic="chainA"/>
                </DesignRestrictions>
                <IncludeCurrent name="current"/>
                <ExtraRotamersGeneric ex1="1" ex2="1" name="ex1_ex2"/>
                <ProteinProteinInterfaceUpweighter interface_weight="3" name="upweight_interface"/>
        </TASKOPERATIONS>
        <FILTERS>
                <ShapeComplementarity confidence="0" name="sc" residue_selector1="chainA" residue_selector2="chainB"/>
                <PeptideInternalHbondsFilter backbone_backbone="false" backbone_sidechain="true" exclusion_distance="100000" hbond_cutoff="0" name="hbonds" sidechain_sidechain="true"/>
                <BuriedUnsatHbonds2 jump_number="1" name="buried_unsat_hbonds"/>
                <Ddg confidence="1" jump="1" name="ddg" repack="0" repeats="1" scorefxn="sfxn" threshold="1000"/>
                <BuriedUnsatHbonds burial_cutoff_apo="0.2" confidence="0" cutoff="4" dalphaball_sasa="1" ignore_surface_res="false" name="buns_all_heavy_ball_interface" print_out_info_to_pdb="true" probe_radius="1.1" report_all_heavy_atom_unsats="true" scorefxn="sfxn" use_ddG_style="true"/>
                <Sasa confidence="1" hydrophobic="0" jump="1" name="sasa" polar="0"/>
        </FILTERS>
        <MOVERS>
                <AtomCoordinateCstMover coord_dev="0.5" name="constrainCA"/>
                <FastDesign batch="false" bondangle="false" bondlength="false" cartesian="false" min_type="dfpmin_armijo_nonmonotone" name="FastDesign" ramp_down_constraints="false" relaxscript="no_ref.rosettacon2018.beta_nov16.txt" repeats="1" scorefxn="sfxn_design" task_operations="current,ex1_ex2,restrict_to_interface,restrict_target2repacking,allowed_aas,upweight_interface">
                        <MoveMap name="MM">
                                <Chain bb="true" chi="true" number="1"/>
                                <Chain bb="false" chi="true" number="2"/>
                                <Jump number="1" setting="true"/>
                        </MoveMap>
                </FastDesign>
                <MinMover bb="0" cartesian="false" chi="0" name="chi_min" scorefxn="sfxn" tolerance="0.001" type="lbfgs_armijo_nonmonotone">
                        <MoveMap name="MM">
                                <Chain bb="false" chi="true" number="1"/>
                                <Chain bb="false" chi="true" number="2"/>
                                <Jump number="1" setting="false"/>
                        </MoveMap>
                </MinMover>
                <FilterReportAsPoseExtraScoresMover filter_name="ddg" name="report_ddg_pre" report_as="ddg_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="ddg" name="report_ddg_post" report_as="ddg_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="hbonds" name="report_hbonds_pre" report_as="hbonds_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="hbonds" name="report_hbonds_post" report_as="hbonds_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="buns_all_heavy_ball_interface" name="report_bunsh_pre" report_as="bunsh_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="buns_all_heavy_ball_interface" name="report_bunsh_post" report_as="bunsh_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="buried_unsat_hbonds" name="report_bunsh2_pre" report_as="bunsh2_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="buried_unsat_hbonds" name="report_bunsh2_post" report_as="bunsh2_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="sasa" name="report_sasa_pre" report_as="sasa_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="sasa" name="report_sasa_post" report_as="sasa_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="sc" name="report_sc_pre" report_as="sc_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="sc" name="report_sc_post" report_as="sc_post"/>
                <InterfaceAnalyzerMover jump="1" name="ia" scorefxn="sfxn"/>
        </MOVERS>
        <APPLY_TO_POSE/>
        <PROTOCOLS>
                <Add mover="report_ddg_pre"/>
                <Add mover="report_bunsh_pre"/>
                <Add mover="report_bunsh2_pre"/>
                <Add mover="report_hbonds_pre"/>
                <Add mover="report_sasa_pre"/>
                <Add mover="report_sc_pre"/>
                <Add mover="constrainCA"/>
                <Add mover="FastDesign"/>
                <Add mover="report_ddg_post"/>
                <Add mover="report_bunsh_post"/>
                <Add mover="report_bunsh2_post"/>
                <Add mover="report_hbonds_post"/>
                <Add mover="report_sasa_post"/>
                <Add mover="report_sc_post"/>
        </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 "sfxn" with weights "ref2015"
protocols.jd2.parser.ScoreFunctionLoader: defined score function "sfxn_design" with weights "ref2015"
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight approximate_buried_unsat_penalty to 10
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight hbond_sr_bb to 1
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight hbond_lr_bb to 1
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight hbond_bb_sc to 1
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight hbond_sc to 1
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight coordinate_constraint to 1
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_to_interface" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_target2repacking" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "allowed_aas" of type DesignRestrictions
core.pack.task.operation.TaskOperation: TaskOperation::parse_tag method called with no effect for Tag with type IncludeCurrent. Probably due to (un/mis)implemented virtual method in derived class.
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "current" of type IncludeCurrent
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "ex1_ex2" of type ExtraRotamersGeneric
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "upweight_interface" of type ProteinProteinInterfaceUpweighter
protocols.simple_filters.ShapeComplementarityFilter: Structures with shape complementarity < 0.5, interface area < 0 A^2, median distance > 0 will be filtered.
protocols.simple_filters.ShapeComplementarityFilter: Using Jump Selector to define surfaces.
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "sc" of type ShapeComplementarity
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "hbonds" of type PeptideInternalHbondsFilter
protocols.buns.BuriedUnsatisfiedPolarsCalculator2: Registering VarSolDist SASA Calculator
protocols.buns.BuriedUnsatisfiedPolarsCalculator2: Registering new basic buried unsat calculator.
protocols.buns.BuriedUnsatHbondFilter2: Buried Unsatisfied Hbond filter v2 over jump number 1 with cutoff 20
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_unsat_hbonds" of type BuriedUnsatHbonds2
protocols.simple_filters.DdgFilter: ddg filter with threshold 1000 and threshold_min -999999 repeats=1 and scorefxn sfxn extreme_value_removal: 0 and repack 0
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "ddg" of type Ddg
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buns_all_heavy_ball_interface" of type BuriedUnsatHbonds
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "sasa" of type Sasa
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "constrainCA" of type AtomCoordinateCstMover
protocols.relax.RelaxScriptManager: Reading relax scripts list from database.
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt
protocols.relax.RelaxScriptManager: ================== Reading script file: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/sampling/relax_scripts/MonomerRelax2019.txt ==================
protocols.relax.RelaxScriptManager: repeat %%nrepeats%%
protocols.relax.RelaxScriptManager: coord_cst_weight 1.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.040
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.051
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.5
protocols.relax.RelaxScriptManager: scale:fa_rep 0.265
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.280
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.559
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.581
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 1
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: min 0.00001
protocols.relax.RelaxScriptManager: accept_to_best
protocols.relax.RelaxScriptManager: endrepeat
core.pack.task.xml_util: Object FastDesign reading the following task_operations: Adding the following task operations
current ex1_ex2 restrict_to_interface restrict_target2repacking allowed_aas upweight_interface
protocols.relax.RelaxScriptManager: ================== Reading script file: no_ref.rosettacon2018.beta_nov16.txt ==================
protocols.relax.RelaxScriptManager: repeat 1
protocols.relax.RelaxScriptManager: ramp_repack_min 0.079 0.01     1.0
protocols.relax.RelaxScriptManager: ramp_repack_min 0.295 0.01     0.5
protocols.relax.RelaxScriptManager: ramp_repack_min 0.577 0.01     0.0
protocols.relax.RelaxScriptManager: ramp_repack_min 1     0.00001  0.0
protocols.relax.RelaxScriptManager: accept_to_best
protocols.relax.RelaxScriptManager: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "FastDesign" of type FastDesign
protocols.minimization_packing.MinMover: Options chi, bb: 0, 0 omega: 1
protocols.RosettaScripts.util: [ WARNING ] Ignoring 'default' MoveMapFactory in parse_movemap_factory_legacy(), using existing MoveMapFactory MM instead
core.select.movemap.util: Found MoveMapFactory MM
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "chi_min" of type MinMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_ddg_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_ddg_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_hbonds_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_hbonds_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh2_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh2_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sasa_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sasa_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sc_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sc_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "ia" of type InterfaceAnalyzerMover
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_ddg_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_bunsh_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_bunsh2_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_hbonds_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_sasa_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_sc_pre"
protocols.rosetta_sh: 1: /media/lh/data3/masif_seed/rosetta_scripts/DAlpahBall: Permission denied

roccomoretti Feb 14, 2025
Maintainer

From the core.init: command: line in your log, it doesn't look like the DAlphaBall path is being passed to Rosetta. Additionally, the error message doesn't seem to be coming from Rosetta itself.

If I had to guess, you have a line break or some other formatting issue in your shell script, which puts the DAlphaBall line as its own separate command. Rosetta runs but only prints out part of its output, and then the shell tries to run the DAlphaBall path as a command, is not able to (as it's a directory, rather than a command,) and prints "sh: 1: /media/lh/data3/masif_seed/rosetta_scripts/DAlpahBall: Permission denied" on top of the partial Rosetta output.

I'll also note that what you should pass to -holes:dalphaball would be the full name of the compiled file, not just the path. So it would be something like -holes::dalphaball /media/lh/data3/masif_seed/rosetta_scripts/DAlpahBall/DAlphaBall.gcc

Hylouis233 Feb 15, 2025
Author

I sincerely thank you for your reply. According to your suggestion, I will modify it and no longer report this error.
However, the program has encountered a new problem, could you please see what the cause is?
Thanks a lot again!

********  (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: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.ubuntu.release-371 r371 2024.09+release.06b3cf8ad0 06b3cf8ad0940d628690d0ed6fa2009d72ad2b44 https://www.rosettacommons.org 2024-02-29T01:16:28.135490
core.init: command: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/bin/rosetta_scripts.default.linuxgccrelease -parser:protocol relax.xml -list ./tmp/tmp_list_261.txt -no_nstruct_label -out:path:all ./relax -overwrite -renumber_pdb -ignore_unrecognized_res
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-541396616 seed_offset=0 real_seed=-541396616
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-541396616 RG_type=mt19937
core.init: Resolved executable path: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/build/src/release/linux/5.15/64/x86/gcc/11/default/rosetta_scripts.default.linuxgccrelease
core.init: Looking for database based on location of executable: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed ./input/3O3P_B_17.pdb ./input/5Y10.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB ./input/3O3P_B_17.pdb ./input/5Y10.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 985 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.592073 seconds.
core.import_pose.import_pose: File './input/3O3P_B_17.pdb ./input/5Y10.pdb' automatically determined to be of type PDB
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom  CB  in residue 177 B.  Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom  CG  in residue 177 B.  Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom  CD  in residue 177 B.  Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom  OE1 in residue 177 B.  Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom  OE2 in residue 177 B.  Pass flag -ignore_zero_occupancy false to change this behavior
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'NAG' from the PDB components dictionary for residue type 'pdb_NAG'
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'MAN' from the PDB components dictionary for residue type 'pdb_MAN'
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CB  on residue GLU 161
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CG  on residue GLU 161
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CD  on residue GLU 161
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OE1 on residue GLU 161
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OE2 on residue GLU 161
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ARG:CtermProteinFull 317
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ASN:CtermProteinFull 635
core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 636
core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_NAG 637
core.conformation.Conformation: [ WARNING ] missing heavyatom: O1 on residue pdb_MAN 638
core.conformation.Conformation: Found disulfide between residues 321 344
core.conformation.Conformation: Found disulfide between residues 438 451
core.conformation.Conformation: Found disulfide between residues 475 622
core.conformation.Conformation: Found disulfide between residues 501 511
core.conformation.Conformation: Found disulfide between residues 553 600
core.conformation.Conformation: Found disulfide between residues 561 598
core.conformation.Conformation: Found disulfide between residues 569 575
core.conformation.Conformation: Found disulfide between residues 582 587
core.pack.pack_missing_sidechains: packing residue number 161 because of missing atom number 5 atom name  CB
core.pack.pack_missing_sidechains: packing residue number 636 because of missing atom number 10 atom name O1
core.pack.pack_missing_sidechains: packing residue number 637 because of missing atom number 10 atom name O1
core.pack.pack_missing_sidechains: packing residue number 638 because of missing atom number 7 atom name O1
core.pack.task: Packer task: initialize from command line()
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
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: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.130425 seconds to load from binary
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 64 rotamers at 4 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=relax.xml
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
        <SCOREFXNS>
                <ScoreFunction name="sfxn" weights="ref2015">
                        <Reweight scoretype="coordinate_constraint" weight="1.0"/>
                </ScoreFunction>
        </SCOREFXNS>
        <RESIDUE_SELECTORS/>
        <SIMPLE_METRICS/>
        <TASKOPERATIONS>
                <IncludeCurrent name="current"/>
                <LimitAromaChi2 chi2max="135" chi2min="45" include_trp="true" name="limitchi2"/>
        </TASKOPERATIONS>
        <FILTERS/>
        <MOVERS>
                <VirtualRoot name="root" removable="false" remove="false"/>
                <AtomCoordinateCstMover coord_dev="5" name="cst" sidechain="false"/>
                <FastRelax name="fast-relax" repeats="10" scorefxn="sfxn" task_operations="current,limitchi2"/>
        </MOVERS>
        <APPLY_TO_POSE/>
        <PROTOCOLS>
                <Add mover_name="root"/>
                <Add mover_name="cst"/>
                <Add mover_name="fast-relax"/>
        </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/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 "sfxn" with weights "ref2015"
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn weight coordinate_constraint to 1
core.pack.task.operation.TaskOperation: TaskOperation::parse_tag method called with no effect for Tag with type IncludeCurrent. Probably due to (un/mis)implemented virtual method in derived class.
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "current" of type IncludeCurrent
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "limitchi2" of type LimitAromaChi2
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "root" of type VirtualRoot
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "cst" of type AtomCoordinateCstMover
protocols.relax.RelaxScriptManager: Reading relax scripts list from database.
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt
protocols.relax.RelaxScriptManager: ================== Reading script file: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/sampling/relax_scripts/MonomerRelax2019.txt ==================
protocols.relax.RelaxScriptManager: repeat %%nrepeats%%
protocols.relax.RelaxScriptManager: coord_cst_weight 1.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.040
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.051
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.5
protocols.relax.RelaxScriptManager: scale:fa_rep 0.265
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.280
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.559
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.581
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 1
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: min 0.00001
protocols.relax.RelaxScriptManager: accept_to_best
protocols.relax.RelaxScriptManager: endrepeat
core.pack.task.xml_util: Object fast-relax reading the following task_operations: Adding the following task operations
current limitchi2
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "fast-relax" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings
protocols.rosetta_scripts.ParsedProtocol: Added mover "root"
protocols.rosetta_scripts.ParsedProtocol: Added mover "cst"
protocols.rosetta_scripts.ParsedProtocol: Added mover "fast-relax"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy ./input/3O3P_B_17.pdb ./input/5Y10.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER VirtualRoot - root=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AtomCoordinateCstMover - cst=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - fast-relax=======================
protocols.relax.FastRelax: CMD: repeat  6291.49  0  0  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  6291.49  0  0  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  209.191  0  0  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8938 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1471.29  0  0  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -1414.05  0  0  0.02805
protocols.relax.FastRelax: CMD: min  -2568.85  0.770356  0.770356  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -2568.85  0.770356  0.770356  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -1638.15  0.770356  0.770356  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7850 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1663.79  0.770356  0.770356  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -1601.95  0.770356  0.770356  0.154
protocols.relax.FastRelax: CMD: min  -2194.12  0.571879  0.571879  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -2194.12  0.571879  0.571879  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1892.05  0.571879  0.571879  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7766 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1849.92  0.571879  0.571879  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1824.43  0.571879  0.571879  0.31955
protocols.relax.FastRelax: CMD: min  -1958.18  0.531052  0.531052  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1958.18  0.531052  0.531052  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -1684.3  0.531052  0.531052  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7643 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1635.24  0.531052  0.531052  0.55
protocols.relax.FastRelax: CMD: min  -1752.98  0.544111  0.544111  0.55
protocols.relax.FastRelax: MRP: 0  -1752.98  -1752.98  0.544111  0.544111
protocols.relax.FastRelax: CMD: accept_to_best  -1752.98  0.544111  0.544111  0.55
protocols.relax.FastRelax: CMD: endrepeat  -1752.98  0.544111  0.544111  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -1752.98  0.544111  0.544111  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -2182.69  0.544111  0.544111  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8699 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -2213.05  0.544111  0.544111  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -2200.42  0.544111  0.544111  0.02805
protocols.relax.FastRelax: CMD: min  -2647.12  0.816157  0.816157  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -2647.12  0.816157  0.816157  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -1780.14  0.816157  0.816157  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7947 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1796.69  0.816157  0.816157  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -1740.25  0.816157  0.816157  0.154
protocols.relax.FastRelax: CMD: min  -2221.44  0.610118  0.610118  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -2221.44  0.610118  0.610118  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1917.97  0.610118  0.610118  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7754 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1866.35  0.610118  0.610118  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1840.98  0.610118  0.610118  0.31955
protocols.relax.FastRelax: CMD: min  -1978.45  0.551444  0.551444  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1978.45  0.551444  0.551444  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -1709.65  0.551444  0.551444  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7602 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1667.36  0.551444  0.551444  0.55
protocols.relax.FastRelax: CMD: min  -1766.44  0.563459  0.563459  0.55
protocols.relax.FastRelax: MRP: 1  -1766.44  -1766.44  0.563459  0.563459
protocols.relax.FastRelax: CMD: accept_to_best  -1766.44  0.563459  0.563459  0.55
protocols.relax.FastRelax: CMD: endrepeat  -1766.44  0.563459  0.563459  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -1766.44  0.563459  0.563459  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -2196.94  0.563459  0.563459  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8726 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -2232.89  0.563459  0.563459  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -2222.55  0.563459  0.563459  0.02805
protocols.relax.FastRelax: CMD: min  -2651.27  0.825956  0.825956  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -2651.27  0.825956  0.825956  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -1797.06  0.825956  0.825956  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7861 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1810.14  0.825956  0.825956  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -1753.92  0.825956  0.825956  0.154
protocols.relax.FastRelax: CMD: min  -2224.46  0.604729  0.604729  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -2224.46  0.604729  0.604729  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1919.45  0.604729  0.604729  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7691 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1896.97  0.604729  0.604729  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1872.12  0.604729  0.604729  0.31955
protocols.relax.FastRelax: CMD: min  -1986.3  0.556653  0.556653  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1986.3  0.556653  0.556653  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -1713.23  0.556653  0.556653  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7584 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1697.37  0.556653  0.556653  0.55
protocols.relax.FastRelax: CMD: min  -1771.02  0.564642  0.564642  0.55
protocols.relax.FastRelax: MRP: 2  -1771.02  -1771.02  0.564642  0.564642
protocols.relax.FastRelax: CMD: accept_to_best  -1771.02  0.564642  0.564642  0.55
protocols.relax.FastRelax: CMD: endrepeat  -1771.02  0.564642  0.564642  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -1771.02  0.564642  0.564642  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -2205.45  0.564642  0.564642  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8709 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -2243.07  0.564642  0.564642  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -2232.35  0.564642  0.564642  0.02805
protocols.relax.FastRelax: CMD: min  -2652.76  0.822974  0.822974  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -2652.76  0.822974  0.822974  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -1806.45  0.822974  0.822974  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7890 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1828.28  0.822974  0.822974  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -1772.45  0.822974  0.822974  0.154
protocols.relax.FastRelax: CMD: min  -2235.62  0.615896  0.615896  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -2235.62  0.615896  0.615896  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1934.58  0.615896  0.615896  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7696 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1922.14  0.615896  0.615896  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1898.23  0.615896  0.615896  0.31955
protocols.relax.FastRelax: CMD: min  -1986.35  0.564516  0.564516  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1986.35  0.564516  0.564516  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -1708.03  0.564516  0.564516  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7609 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1690.25  0.564516  0.564516  0.55
protocols.relax.FastRelax: CMD: min  -1775.84  0.572479  0.572479  0.55
protocols.relax.FastRelax: MRP: 3  -1775.84  -1775.84  0.572479  0.572479
protocols.relax.FastRelax: CMD: accept_to_best  -1775.84  0.572479  0.572479  0.55
protocols.relax.FastRelax: CMD: endrepeat  -1775.84  0.572479  0.572479  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -1775.84  0.572479  0.572479  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -2209.58  0.572479  0.572479  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8692 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -2248.93  0.572479  0.572479  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -2238.64  0.572479  0.572479  0.02805
protocols.relax.FastRelax: CMD: min  -2666.03  0.836856  0.836856  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -2666.03  0.836856  0.836856  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -1807.8  0.836856  0.836856  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7856 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1829.79  0.836856  0.836856  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -1773.07  0.836856  0.836856  0.154
protocols.relax.FastRelax: CMD: min  -2247.05  0.620456  0.620456  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -2247.05  0.620456  0.620456  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1945.86  0.620456  0.620456  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7735 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1935.32  0.620456  0.620456  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1911.18  0.620456  0.620456  0.31955
protocols.relax.FastRelax: CMD: min  -2002.75  0.569491  0.569491  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -2002.75  0.569491  0.569491  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -1730.65  0.569491  0.569491  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7625 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1708.58  0.569491  0.569491  0.55
protocols.relax.FastRelax: CMD: min  -1787.85  0.577568  0.577568  0.55
protocols.relax.FastRelax: MRP: 4  -1787.85  -1787.85  0.577568  0.577568
protocols.relax.FastRelax: CMD: accept_to_best  -1787.85  0.577568  0.577568  0.55
protocols.relax.FastRelax: CMD: endrepeat  -1787.85  0.577568  0.577568  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -1787.85  0.577568  0.577568  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -2223.09  0.577568  0.577568  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8719 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -2252.99  0.577568  0.577568  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -2243.25  0.577568  0.577568  0.02805
protocols.relax.FastRelax: CMD: min  -2671.94  0.840359  0.840359  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -2671.94  0.840359  0.840359  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -1806.62  0.840359  0.840359  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7862 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1826.23  0.840359  0.840359  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -1768.39  0.840359  0.840359  0.154
protocols.relax.FastRelax: CMD: min  -2251.09  0.623128  0.623128  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -2251.09  0.623128  0.623128  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1947.19  0.623128  0.623128  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7715 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1935.91  0.623128  0.623128  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1911.53  0.623128  0.623128  0.31955
protocols.relax.FastRelax: CMD: min  -2009.27  0.576565  0.576565  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -2009.27  0.576565  0.576565  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -1739.17  0.576565  0.576565  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7634 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1710.52  0.576565  0.576565  0.55
protocols.relax.FastRelax: CMD: min  -1790.19  0.578418  0.578418  0.55
protocols.relax.FastRelax: MRP: 5  -1790.19  -1790.19  0.578418  0.578418
protocols.relax.FastRelax: CMD: accept_to_best  -1790.19  0.578418  0.578418  0.55
protocols.relax.FastRelax: CMD: endrepeat  -1790.19  0.578418  0.578418  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -1790.19  0.578418  0.578418  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -2224.11  0.578418  0.578418  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8746 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -2254.55  0.578418  0.578418  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -2244.85  0.578418  0.578418  0.02805
protocols.relax.FastRelax: CMD: min  -2662.61  0.833988  0.833988  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -2662.61  0.833988  0.833988  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -1821.14  0.833988  0.833988  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7888 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1841.95  0.833988  0.833988  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -1785.78  0.833988  0.833988  0.154
protocols.relax.FastRelax: CMD: min  -2251.78  0.620633  0.620633  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -2251.78  0.620633  0.620633  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1949.91  0.620633  0.620633  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7751 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1940.23  0.620633  0.620633  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1916.08  0.620633  0.620633  0.31955
protocols.relax.FastRelax: CMD: min  -2010.81  0.571941  0.571941  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -2010.81  0.571941  0.571941  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -1741.4  0.571941  0.571941  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7622 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1720.31  0.571941  0.571941  0.55
protocols.relax.FastRelax: CMD: min  -1790.87  0.583307  0.583307  0.55
protocols.relax.FastRelax: MRP: 6  -1790.87  -1790.87  0.583307  0.583307
protocols.relax.FastRelax: CMD: accept_to_best  -1790.87  0.583307  0.583307  0.55
protocols.relax.FastRelax: CMD: endrepeat  -1790.87  0.583307  0.583307  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -1790.87  0.583307  0.583307  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -2228.08  0.583307  0.583307  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8724 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -2256.25  0.583307  0.583307  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -2245.96  0.583307  0.583307  0.02805
protocols.relax.FastRelax: CMD: min  -2665.39  0.838525  0.838525  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -2665.39  0.838525  0.838525  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -1809.79  0.838525  0.838525  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7892 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1833.11  0.838525  0.838525  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -1776.14  0.838525  0.838525  0.154
protocols.relax.FastRelax: CMD: min  -2247.72  0.617993  0.617993  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -2247.72  0.617993  0.617993  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1945.11  0.617993  0.617993  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7743 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1945.65  0.617993  0.617993  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1921.85  0.617993  0.617993  0.31955
protocols.relax.FastRelax: CMD: min  -2010.37  0.573592  0.573592  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -2010.37  0.573592  0.573592  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -1740.9  0.573592  0.573592  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7630 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1712.44  0.573592  0.573592  0.55
protocols.relax.FastRelax: CMD: min  -1790.87  0.580936  0.580936  0.55
protocols.relax.FastRelax: MRP: 7  -1790.87  -1790.87  0.580936  0.580936
protocols.relax.FastRelax: CMD: accept_to_best  -1790.87  0.580936  0.580936  0.55
protocols.relax.FastRelax: CMD: endrepeat  -1790.87  0.580936  0.580936  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -1790.87  0.580936  0.580936  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -2225.5  0.580936  0.580936  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8716 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -2245.21  0.580936  0.580936  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -2234.62  0.580936  0.580936  0.02805
protocols.relax.FastRelax: CMD: min  -2666.18  0.845681  0.845681  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -2666.18  0.845681  0.845681  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -1781.54  0.845681  0.845681  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7903 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1797.12  0.845681  0.845681  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -1738.84  0.845681  0.845681  0.154
protocols.relax.FastRelax: CMD: min  -2241.84  0.611895  0.611895  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -2241.84  0.611895  0.611895  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1941.57  0.611895  0.611895  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7685 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1941.46  0.611895  0.611895  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1917.82  0.611895  0.611895  0.31955
protocols.relax.FastRelax: CMD: min  -2005.37  0.569744  0.569744  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -2005.37  0.569744  0.569744  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -1737.4  0.569744  0.569744  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7637 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1704.27  0.569744  0.569744  0.55
protocols.relax.FastRelax: CMD: min  -1788.69  0.577947  0.577947  0.55
protocols.relax.FastRelax: MRP: 8  -1788.69  -1790.87  0.580936  0.580936
protocols.relax.FastRelax: CMD: accept_to_best  -1788.69  0.577947  0.577947  0.55
protocols.relax.FastRelax: CMD: endrepeat  -1788.69  0.577947  0.577947  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -1788.69  0.577947  0.577947  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -2219.15  0.577947  0.577947  0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8731 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -2250.2  0.577947  0.577947  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -2237.01  0.577947  0.577947  0.02805
protocols.relax.FastRelax: CMD: min  -2667.86  0.837579  0.837579  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -2667.86  0.837579  0.837579  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -1793.36  0.837579  0.837579  0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7872 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1813.04  0.837579  0.837579  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -1755.29  0.837579  0.837579  0.154
protocols.relax.FastRelax: CMD: min  -2241.12  0.615365  0.615365  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -2241.12  0.615365  0.615365  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -1939.93  0.615365  0.615365  0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7721 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1938.72  0.615365  0.615365  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -1914.98  0.615365  0.615365  0.31955
protocols.relax.FastRelax: CMD: min  -1999.81  0.574178  0.574178  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -1999.81  0.574178  0.574178  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -1727.94  0.574178  0.574178  0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7613 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -1694.4  0.574178  0.574178  0.55
protocols.relax.FastRelax: CMD: min  -1784.8  0.582392  0.582392  0.55
protocols.relax.FastRelax: MRP: 9  -1784.8  -1790.87  0.580936  0.580936
protocols.relax.FastRelax: CMD: accept_to_best  -1784.8  0.582392  0.582392  0.55
protocols.relax.FastRelax: CMD: endrepeat  -1784.8  0.582392  0.582392  0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: 3O3P_B_17_5Y10 reported success in 5194 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 5194 seconds
basic.citation_manager.CitationManager:
The following Rosetta modules were used during this run of Rosetta, and should be cited:

rosetta_scripts Application's citation(s):
Fleishman SJ, Leaver-Fay A, Corn JE, Strauch E-M, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, and Baker D.  (2011).  RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite.  PLoS ONE 6(6):e20161.  doi: 10.1371/journal.pone.0020161.

FastRelax Mover's citation(s):
*Tyka MD, *Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, and Baker D.  (2011).  Alternate states of proteins revealed by detailed energy landscape mapping.  J Mol Biol 405(2):607-18.  doi: 10.1016/j.jmb.2010.11.008.  (*Co-primary authors.)

Khatib F, Cooper S, Tyka MD, Xu K, Makedon I, Popovic Z, Baker D, and Players F.  (2011).  Algorithm discovery by protein folding game players.  Proc Natl Acad Sci USA 108(47):18949-53.  doi: 10.1073/pnas.1115898108.

Maguire JB, Haddox HK, Strickland D, Halabiya SF, Coventry B, Griffin JR, Pulavarti SVSRK, Cummins M, Thieker DF, Klavins E, Szyperski T, DiMaio F, Baker D, and Kuhlman B.  (2021).  Perturbing the energy landscape for improved packing during computational protein design.  Proteins 89(4):436-449.  doi: 10.1002/prot.26030.


********  (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: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.ubuntu.release-371 r371 2024.09+release.06b3cf8ad0 06b3cf8ad0940d628690d0ed6fa2009d72ad2b44 https://www.rosettacommons.org 2024-02-29T01:16:28.135490
core.init: command: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/bin/rosetta_scripts.default.linuxgccrelease -parser:protocol interface_design.xml -s /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/3O3P_B_17_5Y10.pdb -no_nstruct_label -out:path:all ./out -overwrite -renumber_pdb -ignore_unrecognized_res -holes:dalphaball /media/lh/data3/masif_seed/rosetta_scripts/DAlpahBall/DAlphaBall.gcc
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1293585145 seed_offset=0 real_seed=1293585145
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1293585145 RG_type=mt19937
core.init: Resolved executable path: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/build/src/release/linux/5.15/64/x86/gcc/11/default/rosetta_scripts.default.linuxgccrelease
core.init: Looking for database based on location of executable: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/3O3P_B_17_5Y10.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/3O3P_B_17_5Y10.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 985 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.593078 seconds.
core.import_pose.import_pose: File '/media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/3O3P_B_17_5Y10.pdb' automatically determined to be of type PDB
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'NAG' from the PDB components dictionary for residue type 'pdb_NAG'
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'MAN' from the PDB components dictionary for residue type 'pdb_MAN'
core.conformation.Conformation: Found disulfide between residues 321 344
core.conformation.Conformation: Found disulfide between residues 438 451
core.conformation.Conformation: Found disulfide between residues 475 622
core.conformation.Conformation: Found disulfide between residues 501 511
core.conformation.Conformation: Found disulfide between residues 553 600
core.conformation.Conformation: Found disulfide between residues 561 598
core.conformation.Conformation: Found disulfide between residues 569 575
core.conformation.Conformation: Found disulfide between residues 582 587
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=interface_design.xml
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
        <SCOREFXNS>
                <ScoreFunction name="sfxn" weights="ref2015"/>
                <ScoreFunction name="sfxn_design" weights="ref2015">
                        <Reweight scoretype="approximate_buried_unsat_penalty" weight="10"/>
                        <Set approximate_buried_unsat_penalty_burial_probe_radius="2.3"/>
                        <Set approximate_buried_unsat_penalty_burial_atomic_depth="2.5"/>
                        <Set approximate_buried_unsat_penalty_hbond_energy_threshold="-0.25"/>
                        <Set approximate_buried_unsat_penalty_oversat_penalty="0"/>
                        <Reweight scoretype="hbond_sr_bb" weight="1"/>
                        <Reweight scoretype="hbond_lr_bb" weight="1"/>
                        <Reweight scoretype="hbond_bb_sc" weight="1"/>
                        <Reweight scoretype="hbond_sc" weight="1"/>
                        <Reweight scoretype="coordinate_constraint" weight="1"/>
                </ScoreFunction>
        </SCOREFXNS>
        <RESIDUE_SELECTORS>
                <Chain chains="A" name="chainA"/>
                <Chain chains="B" name="chainB"/>
                <Neighborhood distance="10.0" include_focus_in_subset="false" name="interface_chA" selector="chainB"/>
                <Neighborhood distance="10.0" include_focus_in_subset="false" name="interface_chB" selector="chainA"/>
                <InterfaceByVector cb_dist_cut="11" grp1_selector="interface_chA" grp2_selector="interface_chB" name="AB_interface" nearby_atom_cut="5.5" vector_angle_cut="75" vector_dist_cut="10"/>
                <Not name="Not_interface" selector="AB_interface"/>
        </RESIDUE_SELECTORS>
        <TASKOPERATIONS>
                <OperateOnResidueSubset name="restrict_to_interface" selector="Not_interface">
                        <PreventRepackingRLT/>
                </OperateOnResidueSubset>
                <OperateOnResidueSubset name="restrict_target2repacking" selector="chainB">
                        <RestrictToRepackingRLT/>
                </OperateOnResidueSubset>
                <DesignRestrictions name="allowed_aas">
                        <Action aas="ADEFGHIKLMNQRSTVWY" selector_logic="chainA"/>
                </DesignRestrictions>
                <IncludeCurrent name="current"/>
                <ExtraRotamersGeneric ex1="1" ex2="1" name="ex1_ex2"/>
                <ProteinProteinInterfaceUpweighter interface_weight="3" name="upweight_interface"/>
        </TASKOPERATIONS>
        <FILTERS>
                <ShapeComplementarity confidence="0" name="sc" residue_selector1="chainA" residue_selector2="chainB"/>
                <PeptideInternalHbondsFilter backbone_backbone="false" backbone_sidechain="true" exclusion_distance="100000" hbond_cutoff="0" name="hbonds" sidechain_sidechain="true"/>
                <BuriedUnsatHbonds2 jump_number="1" name="buried_unsat_hbonds"/>
                <Ddg confidence="1" jump="1" name="ddg" repack="0" repeats="1" scorefxn="sfxn" threshold="1000"/>
                <BuriedUnsatHbonds burial_cutoff_apo="0.2" confidence="0" cutoff="4" dalphaball_sasa="1" ignore_surface_res="false" name="buns_all_heavy_ball_interface" print_out_info_to_pdb="true" probe_radius="1.1" report_all_heavy_atom_unsats="true" scorefxn="sfxn" use_ddG_style="true"/>
                <Sasa confidence="1" hydrophobic="0" jump="1" name="sasa" polar="0"/>
        </FILTERS>
        <MOVERS>
                <AtomCoordinateCstMover coord_dev="0.5" name="constrainCA"/>
                <FastDesign batch="false" bondangle="false" bondlength="false" cartesian="false" min_type="dfpmin_armijo_nonmonotone" name="FastDesign" ramp_down_constraints="false" relaxscript="no_ref.rosettacon2018.beta_nov16.txt" repeats="1" scorefxn="sfxn_design" task_operations="current,ex1_ex2,restrict_to_interface,restrict_target2repacking,allowed_aas,upweight_interface">
                        <MoveMap name="MM">
                                <Chain bb="true" chi="true" number="1"/>
                                <Chain bb="false" chi="true" number="2"/>
                                <Jump number="1" setting="true"/>
                        </MoveMap>
                </FastDesign>
                <MinMover bb="0" cartesian="false" chi="0" name="chi_min" scorefxn="sfxn" tolerance="0.001" type="lbfgs_armijo_nonmonotone">
                        <MoveMap name="MM">
                                <Chain bb="false" chi="true" number="1"/>
                                <Chain bb="false" chi="true" number="2"/>
                                <Jump number="1" setting="false"/>
                        </MoveMap>
                </MinMover>
                <FilterReportAsPoseExtraScoresMover filter_name="ddg" name="report_ddg_pre" report_as="ddg_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="ddg" name="report_ddg_post" report_as="ddg_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="hbonds" name="report_hbonds_pre" report_as="hbonds_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="hbonds" name="report_hbonds_post" report_as="hbonds_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="buns_all_heavy_ball_interface" name="report_bunsh_pre" report_as="bunsh_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="buns_all_heavy_ball_interface" name="report_bunsh_post" report_as="bunsh_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="buried_unsat_hbonds" name="report_bunsh2_pre" report_as="bunsh2_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="buried_unsat_hbonds" name="report_bunsh2_post" report_as="bunsh2_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="sasa" name="report_sasa_pre" report_as="sasa_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="sasa" name="report_sasa_post" report_as="sasa_post"/>
                <FilterReportAsPoseExtraScoresMover filter_name="sc" name="report_sc_pre" report_as="sc_pre"/>
                <FilterReportAsPoseExtraScoresMover filter_name="sc" name="report_sc_post" report_as="sc_post"/>
                <InterfaceAnalyzerMover jump="1" name="ia" scorefxn="sfxn"/>
        </MOVERS>
        <APPLY_TO_POSE/>
        <PROTOCOLS>
                <Add mover="report_ddg_pre"/>
                <Add mover="report_bunsh_pre"/>
                <Add mover="report_bunsh2_pre"/>
                <Add mover="report_hbonds_pre"/>
                <Add mover="report_sasa_pre"/>
                <Add mover="report_sc_pre"/>
                <Add mover="constrainCA"/>
                <Add mover="FastDesign"/>
                <Add mover="report_ddg_post"/>
                <Add mover="report_bunsh_post"/>
                <Add mover="report_bunsh2_post"/>
                <Add mover="report_hbonds_post"/>
                <Add mover="report_sasa_post"/>
                <Add mover="report_sc_post"/>
        </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 "sfxn" with weights "ref2015"
protocols.jd2.parser.ScoreFunctionLoader: defined score function "sfxn_design" with weights "ref2015"
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight approximate_buried_unsat_penalty to 10
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight hbond_sr_bb to 1
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight hbond_lr_bb to 1
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight hbond_bb_sc to 1
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight hbond_sc to 1
protocols.jd2.parser.ScoreFunctionLoader:  setting sfxn_design weight coordinate_constraint to 1
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_to_interface" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_target2repacking" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "allowed_aas" of type DesignRestrictions
core.pack.task.operation.TaskOperation: TaskOperation::parse_tag method called with no effect for Tag with type IncludeCurrent. Probably due to (un/mis)implemented virtual method in derived class.
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "current" of type IncludeCurrent
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "ex1_ex2" of type ExtraRotamersGeneric
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "upweight_interface" of type ProteinProteinInterfaceUpweighter
protocols.simple_filters.ShapeComplementarityFilter: Structures with shape complementarity < 0.5, interface area < 0 A^2, median distance > 0 will be filtered.
protocols.simple_filters.ShapeComplementarityFilter: Using Jump Selector to define surfaces.
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "sc" of type ShapeComplementarity
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "hbonds" of type PeptideInternalHbondsFilter
protocols.buns.BuriedUnsatisfiedPolarsCalculator2: Registering VarSolDist SASA Calculator
protocols.buns.BuriedUnsatisfiedPolarsCalculator2: Registering new basic buried unsat calculator.
protocols.buns.BuriedUnsatHbondFilter2: Buried Unsatisfied Hbond filter v2 over jump number 1 with cutoff 20
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_unsat_hbonds" of type BuriedUnsatHbonds2
protocols.simple_filters.DdgFilter: ddg filter with threshold 1000 and threshold_min -999999 repeats=1 and scorefxn sfxn extreme_value_removal: 0 and repack 0
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "ddg" of type Ddg
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buns_all_heavy_ball_interface" of type BuriedUnsatHbonds
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "sasa" of type Sasa
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "constrainCA" of type AtomCoordinateCstMover
protocols.relax.RelaxScriptManager: Reading relax scripts list from database.
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt
protocols.relax.RelaxScriptManager: ================== Reading script file: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/sampling/relax_scripts/MonomerRelax2019.txt ==================
protocols.relax.RelaxScriptManager: repeat %%nrepeats%%
protocols.relax.RelaxScriptManager: coord_cst_weight 1.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.040
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.051
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.5
protocols.relax.RelaxScriptManager: scale:fa_rep 0.265
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.280
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.559
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.581
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 1
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: min 0.00001
protocols.relax.RelaxScriptManager: accept_to_best
protocols.relax.RelaxScriptManager: endrepeat
core.pack.task.xml_util: Object FastDesign reading the following task_operations: Adding the following task operations
current ex1_ex2 restrict_to_interface restrict_target2repacking allowed_aas upweight_interface
protocols.relax.RelaxScriptManager: ================== Reading script file: no_ref.rosettacon2018.beta_nov16.txt ==================
protocols.relax.RelaxScriptManager: repeat 1
protocols.relax.RelaxScriptManager: ramp_repack_min 0.079 0.01     1.0
protocols.relax.RelaxScriptManager: ramp_repack_min 0.295 0.01     0.5
protocols.relax.RelaxScriptManager: ramp_repack_min 0.577 0.01     0.0
protocols.relax.RelaxScriptManager: ramp_repack_min 1     0.00001  0.0
protocols.relax.RelaxScriptManager: accept_to_best
protocols.relax.RelaxScriptManager: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "FastDesign" of type FastDesign
protocols.minimization_packing.MinMover: Options chi, bb: 0, 0 omega: 1
protocols.RosettaScripts.util: [ WARNING ] Ignoring 'default' MoveMapFactory in parse_movemap_factory_legacy(), using existing MoveMapFactory MM instead
core.select.movemap.util: Found MoveMapFactory MM
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "chi_min" of type MinMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_ddg_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_ddg_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_hbonds_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_hbonds_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh2_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh2_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sasa_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sasa_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sc_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sc_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "ia" of type InterfaceAnalyzerMover
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_ddg_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_bunsh_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_bunsh2_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_hbonds_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_sasa_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_sc_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "constrainCA"
protocols.rosetta_scripts.ParsedProtocol: Added mover "FastDesign"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_ddg_post"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_bunsh_post"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_bunsh2_post"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_hbonds_post"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_sasa_post"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_sc_post"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/3O3P_B_17_5Y10.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FilterReportAsPoseExtraScoresMover - report_ddg_pre=======================
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: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.129239 seconds to load from binary
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FilterReportAsPoseExtraScoresMover - report_bunsh_pre=======================
protocols.simple_filters.BuriedUnsatHbondFilter: /////////////////////////////////////////////////////////////////////////////////////////
protocols.simple_filters.BuriedUnsatHbondFilter:
protocols.simple_filters.BuriedUnsatHbondFilter:     USING DEFAULT BEHAVIOR: filter will report total number of heavy-atom donor/acceptor buried unsats
protocols.simple_filters.BuriedUnsatHbondFilter:
protocols.simple_filters.BuriedUnsatHbondFilter: /////////////////////////////////////////////////////////////////////////////////////////
protocols.simple_filters.BuriedUnsatHbondFilter:
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv
protocols.simple_filters.BuriedUnsatHbondFilter:   buried unsats in input pose:
protocols.simple_filters.BuriedUnsatHbondFilter:   all_heavy_atom_unsats = 83
protocols.simple_filters.BuriedUnsatHbondFilter:   bb_heavy_atom_unsats = 69
protocols.simple_filters.BuriedUnsatHbondFilter:   sc_heavy_atom_unsats = 14
protocols.simple_filters.BuriedUnsatHbondFilter:   countable_nonheavy_unsats = 48
protocols.simple_filters.BuriedUnsatHbondFilter:  use_ddG_style=true: Using ddG style calculation ( will substract unsats in unbound state from those in bound state ):
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing protocol:

File: src/protocols/simple_filters/BuriedUnsatHbondFilter.cc:530
[ ERROR ] UtilityExitException
ERROR: Assertion `symmetric || pose.num_chains() < 4` failed. MSG:ERROR: use_ddG_style not compatible with symmetry or poses with > 3 chains


protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job 3O3P_B_17_5Y10
protocols.jd2.JobDistributor: [ WARNING ] 3O3P_B_17_5Y10 reported failure and will NOT retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 8 seconds

ERROR: Assertion `symmetric || pose.num_chains() < 4` failed. MSG:ERROR: use_ddG_style not compatible with symmetry or poses with > 3 chains
ERROR:: Exit from: src/protocols/simple_filters/BuriedUnsatHbondFilter.cc line: 530

[ ERROR ]: Caught exception:


File: src/protocols/simple_filters/BuriedUnsatHbondFilter.cc:530
[ ERROR ] UtilityExitException
ERROR: Assertion `symmetric || pose.num_chains() < 4` failed. MSG:ERROR: use_ddG_style not compatible with symmetry or poses with > 3 chains




AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.



---------------------------------------------------------------
[ ERROR ]: Error(s) were encountered when running jobs.
1 jobs failed;
Check the output further up for additional error messages.
---------------------------------------------------------------

Hylouis233 Feb 15, 2025
Author

This Rosetta script is from masif_seed (https://github.com/LPDI-EPFL/masif_seed/blob/main/rosetta_scripts/seed_refine/submitter.slurm)
I rewrote it as a.sh file：

JOBS=32

# Path to Rosetta binary files
export ROSETTA_BIN=/media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/bin/rosetta_scripts.default.linuxgccrelease
ROSETTA_BIN=/media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/bin/rosetta_scripts.default.linuxgccrelease
# Function to process a single task
run_task() {
    LINE=$1
    MYID=$2
    SEED_PATH=$(echo "$LINE" | awk '{print $1;}')
    SEED_NAME=$(basename "$SEED_PATH" | cut -d "." -f1)
    IN_FILE=/media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/${SEED_NAME}_5Y10.pdb

    # Create a temporary list for this task
    echo "$LINE" > ./tmp/tmp_list_${MYID}.txt


    $ROSETTA_BIN -parser:protocol relax.xml \
        -list ./tmp/tmp_list_${MYID}.txt \
        -no_nstruct_label \
        -out:path:all ./relax \
        -overwrite \
        -renumber_pdb \
        -ignore_unrecognized_res

    $ROSETTA_BIN -parser:protocol interface_design.xml \
        -s "$IN_FILE" \
        -no_nstruct_label \
        -out:path:all ./out \
        -overwrite \
        -renumber_pdb \
        -ignore_unrecognized_res \
        -holes:dalphaball /media/lh/data3/masif_seed/rosetta_scripts/DAlpahBall/DAlphaBall.gcc


    # Clean up temporary file
    rm ./tmp/tmp_list_${MYID}.txt

}

export -f run_task  # Export the function so Parallel can use it

# Ensure necessary directories exist
mkdir -p ./tmp ./relax ./out ./exelogs/out ./exelogs/err

# Use Parallel to run tasks
cat output.txt | nl | parallel -j $JOBS --colsep '\t' run_task {2} {1}

I did not modify the interface_design.xml file. Sincerely invite you to answer my doubts, thank you very much!

surf_vol: not found;What is this problem and how to solve it? #270

Uh oh!

Uh oh!

Hylouis233 Dec 10, 2024

Replies: 3 comments · 6 replies

Uh oh!

roccomoretti Dec 10, 2024 Maintainer

Uh oh!

Uh oh!

Hylouis233 Dec 10, 2024 Author

Uh oh!

roccomoretti Dec 10, 2024 Maintainer

Uh oh!

Hylouis233 Feb 13, 2025 Author

Uh oh!

roccomoretti Feb 13, 2025 Maintainer

Uh oh!

Hylouis233 Feb 14, 2025 Author

Uh oh!

roccomoretti Feb 14, 2025 Maintainer

Uh oh!

Hylouis233 Feb 15, 2025 Author

Uh oh!

Hylouis233 Feb 15, 2025 Author

Hylouis233
Dec 10, 2024

Replies: 3 comments 6 replies

roccomoretti
Dec 10, 2024
Maintainer

Hylouis233 Dec 10, 2024
Author

roccomoretti
Dec 10, 2024
Maintainer

Hylouis233
Feb 13, 2025
Author

roccomoretti Feb 13, 2025
Maintainer

Hylouis233 Feb 14, 2025
Author

roccomoretti Feb 14, 2025
Maintainer

Hylouis233 Feb 15, 2025
Author

Hylouis233 Feb 15, 2025
Author