core.init: Checking for fconfig files in pwd and ./rosetta/flags 
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but -weights are also specified.  Not changing input weights file!
core.init: Rosetta version: rosetta.source.release-217 r217 2019.14+release.dfe4ffc dfe4ffc992818823029b241b83f5929be37b0392 https://www.rosettacommons.org 2019-04-07T03:12:09.988768
core.init: command: /usr/local/apps/rosetta/2019.14_gcc-9.2.0_openmpi-4.0.1_1565973369/bin_debug/rosetta_scripts -parser:protocol fold_design.xml -in:file:s 1mhx.pdb -out:nstruct 65 -in:ignore_waters -in:ignore_unrecognized_res -beta -ignore_zero_occupancy 0 -out:file:silent_struct_type binary -out:prefix 18_1mhx_ -out:file:silent 1mhx_silent_18_ -parser:script_vars frags=frag_1
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-233805961 seed_offset=0 real_seed=-233805961
core.init.random: RandomGenerator:init: Normal mode, seed=-233805961 RG_type=mt19937
core.init: found database environment variable ROSETTA3_DB: /usr/local/apps/rosetta/2019.14_gcc-9.2.0_openmpi-4.0.1_1565973369/main/database
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed 1mhx.pdb nstruct indices 1 - 65
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... 
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB 1mhx.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 979 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 40.06 seconds.
core.import_pose.import_pose: File '1mhx.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CG  on residue LYS 6
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CD  on residue LYS 6
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CE  on residue LYS 6
core.conformation.Conformation: [ WARNING ] missing heavyatom:  NZ  on residue LYS 6
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CG  on residue LYS 33
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CD  on residue LYS 33
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CE  on residue LYS 33
core.conformation.Conformation: [ WARNING ] missing heavyatom:  NZ  on residue LYS 33
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CG  on residue GLU:CtermProteinFull 58
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CD  on residue GLU:CtermProteinFull 58
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OE1 on residue GLU:CtermProteinFull 58
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OE2 on residue GLU:CtermProteinFull 58
core.pack.pack_missing_sidechains: packing residue number 6 because of missing atom number 6 atom name  CG 
core.pack.pack_missing_sidechains: packing residue number 33 because of missing atom number 6 atom name  CG 
core.pack.pack_missing_sidechains: packing residue number 58 because of missing atom number 7 atom name  CG 
core.pack.task: Packer task: initialize from command line() 
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
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_beta_nov2016/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/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/bondlength_bondangle/hydroxyl_torsion_preference.txt
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 247 torsion parameters corresponding to 852952 unique torsions.
core.scoring.GenericBondedPotential: Added total 49 improper parameters corresponding to 65 unique impropers.
core.scoring.GenericBondedEnergy: Creating new peptide-bonded energy container (58)
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: Binary rotamer library selected: /usr/local/apps/rosetta/2019.14_gcc-9.2.0_openmpi-4.0.1_1565973369/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/usr/local/apps/rosetta/2019.14_gcc-9.2.0_openmpi-4.0.1_1565973369/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 1.35 seconds to load from binary
core.pack.pack_rotamers: built 46 rotamers at 3 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: KKE, best_energy: 0.803465
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=fold_design.xml
protocols.rosetta_scripts.RosettaScriptsParser: Including RosettaScripts XML file xml_pieces/selectors.xml.
protocols.rosetta_scripts.RosettaScriptsParser: Including RosettaScripts XML file xml_pieces/movemap.xml.
protocols.rosetta_scripts.RosettaScriptsParser: Including RosettaScripts XML file xml_pieces/taskoperators.xml.
protocols.rosetta_scripts.RosettaScriptsParser: Variable substitution will occur with the following values: '%%frags%%'='frag_1';  
protocols.rosetta_scripts.RosettaScriptsParser: Substituted script:
<ROSETTASCRIPTS>

  <SCOREFXNS>
    # A weight is added to small-range hbonds to favor helix formation.
    <ScoreFunction name="beta" weights="beta">
      <Reweight scoretype="atom_pair_constraint" weight="1.6" />
    </ScoreFunction>
  </SCOREFXNS>

  <RESIDUE_SELECTORS>
    # Standard FFL ResidueSelectors.
    <ResiduePDBInfoHasLabel name="MOTIF"     property="MOTIF" />
<Not                    name="!MOTIF"    selector="MOTIF" />
<ResiduePDBInfoHasLabel name="TEMPLATE"  property="TEMPLATE" />
<Not                    name="!TEMPLATE" selector="TEMPLATE" />
<ResiduePDBInfoHasLabel name="CONTEXT"   property="CONTEXT" />
<Not                    name="!CONTEXT"  selector="CONTEXT" />
<ResiduePDBInfoHasLabel name="FLEXIBLE"  property="FLEXIBLE" />
<Not                    name="!FLEXIBLE" selector="FLEXIBLE" />
<ResiduePDBInfoHasLabel name="HOTSPOT"   property="HOTSPOT" />
<Not                    name="!HOTSPOT"  selector="HOTSPOT" />
<ResiduePDBInfoHasLabel name="COLDSPOT"  property="COLDSPOT" />
<Not                    name="!COLDSPOT" selector="COLDSPOT" />

<And name="FLEXIBLE_AND_MOTIF" selectors="FLEXIBLE,MOTIF" />
<And name="COLDSPOT_AND_MOTIF" selectors="COLDSPOT,MOTIF" />
<And name="HOTSPOT_AND_MOTIF"  selectors="HOTSPOT,MOTIF" />

<Or name="COLDSPOT_OR_TEMPLATE"                        selectors="COLDSPOT,TEMPLATE" />
<Or name="FLEXIBLE_OR_TEMPLATE"                        selectors="FLEXIBLE,TEMPLATE" />
<Or name="CONTEXT_OR_FLEXIBLE_OR_TEMPLATE"             selectors="CONTEXT,FLEXIBLE,TEMPLATE" />
<Or name="COLDSPOT_OR_FLEXIBLE_OR_TEMPLATE"            selectors="COLDSPOT,FLEXIBLE,TEMPLATE" />
<Or name="COLDSPOT_OR_CONTEXT_OR_FLEXIBLE_OR_TEMPLATE" selectors="COLDSPOT,CONTEXT,FLEXIBLE,TEMPLATE" />
<Or name="HOTSPOT_OR_CONTEXT"                          selectors="HOTSPOT,CONTEXT" />
<And name="HOTSPOT_OR_CONTEXT_AND_!FLEXIBLE"           selectors="HOTSPOT_OR_CONTEXT,!FLEXIBLE" />
<And name="FLEXIBLE_AND_!COLDSPOT"                     selectors="FLEXIBLE,!COLDSPOT" />

<ProteinResidueSelector name="PROTEIN" />
<Not name="!PROTEIN" selector="PROTEIN" />


    ## TEMPLATE (1kx8) 1mhx
    ### usable template
    <Index name="template" resnums="8A-65A" />
    <Not name="!template" selector="template" />
    ### insertion point
    <Index name="insertion" resnums="13A-26A" />

    ## MOTIF (3ixt) CR8020
    ### motif
    <Index name="motif" resnums="23B-36B" />
    <Chain name="binder" chains="H,L" />

    ### Design
    <Chain name="design" chains="B" />
  </RESIDUE_SELECTORS>

  <MOVE_MAP_FACTORIES>
    # Standard FFL MoveMap
    <MoveMapFactory name="FFLSTANDARD_MOVEMAP" bb="false" chi="false" nu="false" branches="false" jumps="false" >
  <Backbone enable="true" residue_selector="FLEXIBLE_OR_TEMPLATE" />
  <Chi      enable="true" residue_selector="COLDSPOT_OR_FLEXIBLE_OR_TEMPLATE" />
</MoveMapFactory>
<MoveMapFactory name="FFLBINDERPACK_MOVEMAP" bb="false" chi="false" nu="false" branches="false" jumps="false" >
  <Backbone enable="true" residue_selector="CONTEXT_OR_FLEXIBLE_OR_TEMPLATE" />
  <Chi      enable="true" residue_selector="COLDSPOT_OR_FLEXIBLE_OR_TEMPLATE" />
</MoveMapFactory>
<MoveMapFactory name="FFLBINDERPACKMIN_MOVEMAP" bb="false" chi="false" nu="false" branches="false" jumps="false" >
  <Backbone enable="true" residue_selector="CONTEXT_OR_FLEXIBLE_OR_TEMPLATE" />
  <Chi      enable="true" residue_selector="COLDSPOT_OR_CONTEXT_OR_FLEXIBLE_OR_TEMPLATE" />
</MoveMapFactory>

  </MOVE_MAP_FACTORIES>

  <TASKOPERATIONS>
    # Standard FFL TaskOperators
    <OperateOnResidueSubset name="FFLMOTIF_TASKOP" selector="HOTSPOT_OR_CONTEXT_AND_!FLEXIBLE" >
  <PreventRepackingRLT/>
</OperateOnResidueSubset>
<OperateOnResidueSubset name="FFLFLEX_TASKOP" selector="FLEXIBLE_AND_!COLDSPOT" >
  <RestrictToRepackingRLT/>
</OperateOnResidueSubset>
<OperateOnResidueSubset name="FFLTEMPLATE_TASKOP" selector="COLDSPOT_OR_TEMPLATE" >
  <DisallowIfNonnativeRLT disallow_aas="C" />
</OperateOnResidueSubset>
<OperateOnResidueSubset name="FFLEXTRA_TASKOP" selector="COLDSPOT_OR_TEMPLATE" >
  <ExtraRotamersGenericRLT ex1="1" ex2="1" />
</OperateOnResidueSubset>
<NoRepackDisulfides name="FFLTEMPLATE_DISULFIDES" />

  </TASKOPERATIONS>

  <FILTERS> # (confidence=0 -> to score not to filter)

    # Globals
    <RmsdFromResidueSelectorFilter name="driftRMSD" reference_name="folded_pose"
       reference_selector="design" query_selector="design" confidence="0" />
    <RmsdFromResidueSelectorFilter name="finalRMSD" reference_name="template_pose"
      reference_selector="template" query_selector="design" confidence="0" />
    <BuriedUnsatHbonds  name="BUNS" report_all_heavy_atom_unsats="true" scorefxn="beta" ignore_surface_res="false" print_out_info_to_pdb="false" atomic_depth_selection="5.5" burial_cutoff="1000" confidence="0" task_operations="FFLMOTIF_TASKOP,FFLFLEX_TASKOP,FFLTEMPLATE_TASKOP" />
    <PackStat name="packstat" repeats="5" chain="1" confidence="0" />
    <ScorePoseSegmentFromResidueSelectorFilter name="design_score" confidence="0"
      residue_selector="design" scorefxn="beta" />
  </FILTERS>

  <MOVERS>
    ## CLEAN STRUCTURE:
    <DeleteRegionMover name="delete" residue_selector="!template" />

    ## PREPROCESSING: STORING INPUT STRUCTURES
    <SavePoseMover name="saveFlded" reference_name="folded_pose" restore_pose="0" />
    <SavePoseMover name="saveTmpl"  reference_name="template_pose" restore_pose="0" />
    # ** SavePoseMover used like this does not need to be called during PROTOCOL to work.
    <SavePoseMover name="readMotif" reference_name="motif_pose" pdb_file="CR8020.pdb" />

    ## PREPROCESSING: MAKING FRAGMENTS
    <StructFragmentMover name="makeFrags" prefix="frags"
      vall_file="database/vall.jul19.2011.gz" output_frag_files="1"
      small_frag_file="frag_1.200.3mers" large_frag_file="frag_1.200.9mers"
      frag_weight_file="scores.cfg"
    />

    ## PREPROCESSING: CONSTRAINTS
    <AddConstraints name="foldingCST" >
      <AtomPairConstraintGenerator name="atompairCST1" sd="3.0" ca_only="true"
        use_harmonic="true" unweighted="true" min_seq_sep="6" max_distance="40" residue_selector="template"
      />
    </AddConstraints>

    # MAIN: NUBINITIO FOLDING
    <NubInitioMover name="FFL" fragments_id="frags" template_motif_selector="insertion"
      rmsd_threshold="5" fullatom_scorefxn="beta" >
      <Nub reference_name="motif_pose" residue_selector="motif" >
        <Segment order="1" n_term_flex="3" c_term_flex="3" />
      </Nub>
    </NubInitioMover>

    # POSTPROCESSING: CONSTRAINTS
    <AddConstraints name="designCST" >
      <AtomPairConstraintGenerator name="atompairCST2" sd="1" ca_only="true"
        use_harmonic="true" unweighted="true" min_seq_sep="6" max_distance="40" residue_selector="design"
      />
    </AddConstraints>
    <ClearConstraintsMover name="clearCST" />

    # POSTPROCESSING: SEQUENCE CONSTRAINTS
    <AddHelixSequenceConstraints name="compositionCST" />

    # POSTPROCESSING: DESING
    <FastDesign name="DesignRelax" scorefxn="beta" clear_designable_residues="true"
      task_operations="FFLMOTIF_TASKOP,FFLFLEX_TASKOP,FFLTEMPLATE_TASKOP"
      repeats="3" delete_virtual_residues_after_FastRelax="true"
      movemap_factory="FFLSTANDARD_MOVEMAP" >
    </FastDesign>

    ## VERBOSE
    <DisplayPoseLabelsMover name="showDesign" movemap_factory="FFLSTANDARD_MOVEMAP"
      task_operations="FFLMOTIF_TASKOP,FFLFLEX_TASKOP,FFLTEMPLATE_TASKOP" />

  </MOVERS>

  <PROTOCOLS>
    # PREPROCESSING:
    <Add mover="delete"     />
    <Add mover="saveTmpl"   />
    <Add mover="makeFrags"  />
    <Add mover="foldingCST" />
    # MAIN
    <Add mover="FFL"        />
    <Add mover="showDesign" />
    <Add mover="clearCST"   />
    <Add mover="saveFlded"  />
    # POSTPROCESSING
    <Add mover="designCST"      />
    <Add mover="compositionCST" />
    <Add mover="DesignRelax"    />
    <Add mover="clearCST"       />
    # EVALUATION
    <Add filter="driftRMSD"    />
    <Add filter="finalRMSD"    />
    <Add filter="BUNS"         />
    <Add filter="packstat"     />
    <Add filter="design_score" />
  </PROTOCOLS>

  <OUTPUT scorefxn="beta"/>

</ROSETTASCRIPTS>
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
	<SCOREFXNS>
		<ScoreFunction name="beta" weights="beta">
			<Reweight scoretype="atom_pair_constraint" weight="1.6"/>
		</ScoreFunction>
	</SCOREFXNS>
	<RESIDUE_SELECTORS>
		<ResiduePDBInfoHasLabel name="MOTIF" property="MOTIF"/>
		<Not name="!MOTIF" selector="MOTIF"/>
		<ResiduePDBInfoHasLabel name="TEMPLATE" property="TEMPLATE"/>
		<Not name="!TEMPLATE" selector="TEMPLATE"/>
		<ResiduePDBInfoHasLabel name="CONTEXT" property="CONTEXT"/>
		<Not name="!CONTEXT" selector="CONTEXT"/>
		<ResiduePDBInfoHasLabel name="FLEXIBLE" property="FLEXIBLE"/>
		<Not name="!FLEXIBLE" selector="FLEXIBLE"/>
		<ResiduePDBInfoHasLabel name="HOTSPOT" property="HOTSPOT"/>
		<Not name="!HOTSPOT" selector="HOTSPOT"/>
		<ResiduePDBInfoHasLabel name="COLDSPOT" property="COLDSPOT"/>
		<Not name="!COLDSPOT" selector="COLDSPOT"/>
		<And name="FLEXIBLE_AND_MOTIF" selectors="FLEXIBLE,MOTIF"/>
		<And name="COLDSPOT_AND_MOTIF" selectors="COLDSPOT,MOTIF"/>
		<And name="HOTSPOT_AND_MOTIF" selectors="HOTSPOT,MOTIF"/>
		<Or name="COLDSPOT_OR_TEMPLATE" selectors="COLDSPOT,TEMPLATE"/>
		<Or name="FLEXIBLE_OR_TEMPLATE" selectors="FLEXIBLE,TEMPLATE"/>
		<Or name="CONTEXT_OR_FLEXIBLE_OR_TEMPLATE" selectors="CONTEXT,FLEXIBLE,TEMPLATE"/>
		<Or name="COLDSPOT_OR_FLEXIBLE_OR_TEMPLATE" selectors="COLDSPOT,FLEXIBLE,TEMPLATE"/>
		<Or name="COLDSPOT_OR_CONTEXT_OR_FLEXIBLE_OR_TEMPLATE" selectors="COLDSPOT,CONTEXT,FLEXIBLE,TEMPLATE"/>
		<Or name="HOTSPOT_OR_CONTEXT" selectors="HOTSPOT,CONTEXT"/>
		<And name="HOTSPOT_OR_CONTEXT_AND_!FLEXIBLE" selectors="HOTSPOT_OR_CONTEXT,!FLEXIBLE"/>
		<And name="FLEXIBLE_AND_!COLDSPOT" selectors="FLEXIBLE,!COLDSPOT"/>
		<ProteinResidueSelector name="PROTEIN"/>
		<Not name="!PROTEIN" selector="PROTEIN"/>
		<Index name="template" resnums="8A-65A"/>
		<Not name="!template" selector="template"/>
		<Index name="insertion" resnums="13A-26A"/>
		<Index name="motif" resnums="23B-36B"/>
		<Chain chains="H,L" name="binder"/>
		<Chain chains="B" name="design"/>
	</RESIDUE_SELECTORS>
	<MOVE_MAP_FACTORIES>
		<MoveMapFactory bb="false" branches="false" chi="false" jumps="false" name="FFLSTANDARD_MOVEMAP" nu="false">
			<Backbone enable="true" residue_selector="FLEXIBLE_OR_TEMPLATE"/>
			<Chi enable="true" residue_selector="COLDSPOT_OR_FLEXIBLE_OR_TEMPLATE"/>
		</MoveMapFactory>
		<MoveMapFactory bb="false" branches="false" chi="false" jumps="false" name="FFLBINDERPACK_MOVEMAP" nu="false">
			<Backbone enable="true" residue_selector="CONTEXT_OR_FLEXIBLE_OR_TEMPLATE"/>
			<Chi enable="true" residue_selector="COLDSPOT_OR_FLEXIBLE_OR_TEMPLATE"/>
		</MoveMapFactory>
		<MoveMapFactory bb="false" branches="false" chi="false" jumps="false" name="FFLBINDERPACKMIN_MOVEMAP" nu="false">
			<Backbone enable="true" residue_selector="CONTEXT_OR_FLEXIBLE_OR_TEMPLATE"/>
			<Chi enable="true" residue_selector="COLDSPOT_OR_CONTEXT_OR_FLEXIBLE_OR_TEMPLATE"/>
		</MoveMapFactory>
	</MOVE_MAP_FACTORIES>
	<TASKOPERATIONS>
		<OperateOnResidueSubset name="FFLMOTIF_TASKOP" selector="HOTSPOT_OR_CONTEXT_AND_!FLEXIBLE">
			<PreventRepackingRLT/>
		</OperateOnResidueSubset>
		<OperateOnResidueSubset name="FFLFLEX_TASKOP" selector="FLEXIBLE_AND_!COLDSPOT">
			<RestrictToRepackingRLT/>
		</OperateOnResidueSubset>
		<OperateOnResidueSubset name="FFLTEMPLATE_TASKOP" selector="COLDSPOT_OR_TEMPLATE">
			<DisallowIfNonnativeRLT disallow_aas="C"/>
		</OperateOnResidueSubset>
		<OperateOnResidueSubset name="FFLEXTRA_TASKOP" selector="COLDSPOT_OR_TEMPLATE">
			<ExtraRotamersGenericRLT ex1="1" ex2="1"/>
		</OperateOnResidueSubset>
		<NoRepackDisulfides name="FFLTEMPLATE_DISULFIDES"/>
	</TASKOPERATIONS>
	<FILTERS>
		<RmsdFromResidueSelectorFilter confidence="0" name="driftRMSD" query_selector="design" reference_name="folded_pose" reference_selector="design"/>
		<RmsdFromResidueSelectorFilter confidence="0" name="finalRMSD" query_selector="design" reference_name="template_pose" reference_selector="template"/>
		<BuriedUnsatHbonds atomic_depth_selection="5.5" burial_cutoff="1000" confidence="0" ignore_surface_res="false" name="BUNS" print_out_info_to_pdb="false" report_all_heavy_atom_unsats="true" scorefxn="beta" task_operations="FFLMOTIF_TASKOP,FFLFLEX_TASKOP,FFLTEMPLATE_TASKOP"/>
		<PackStat chain="1" confidence="0" name="packstat" repeats="5"/>
		<ScorePoseSegmentFromResidueSelectorFilter confidence="0" name="design_score" residue_selector="design" scorefxn="beta"/>
	</FILTERS>
	<MOVERS>
		<DeleteRegionMover name="delete" residue_selector="!template"/>
		<SavePoseMover name="saveFlded" reference_name="folded_pose" restore_pose="0"/>
		<SavePoseMover name="saveTmpl" reference_name="template_pose" restore_pose="0"/>
		<SavePoseMover name="readMotif" pdb_file="CR8020.pdb" reference_name="motif_pose"/>
		<StructFragmentMover frag_weight_file="scores.cfg" large_frag_file="frag_1.200.9mers" name="makeFrags" output_frag_files="1" prefix="frags" small_frag_file="frag_1.200.3mers" vall_file="database/vall.jul19.2011.gz"/>
		<AddConstraints name="foldingCST">
			<AtomPairConstraintGenerator ca_only="true" max_distance="40" min_seq_sep="6" name="atompairCST1" residue_selector="template" sd="3.0" unweighted="true" use_harmonic="true"/>
		</AddConstraints>
		<NubInitioMover fragments_id="frags" fullatom_scorefxn="beta" name="FFL" rmsd_threshold="5" template_motif_selector="insertion">
			<Nub reference_name="motif_pose" residue_selector="motif">
				<Segment c_term_flex="3" n_term_flex="3" order="1"/>
			</Nub>
		</NubInitioMover>
		<AddConstraints name="designCST">
			<AtomPairConstraintGenerator ca_only="true" max_distance="40" min_seq_sep="6" name="atompairCST2" residue_selector="design" sd="1" unweighted="true" use_harmonic="true"/>
		</AddConstraints>
		<ClearConstraintsMover name="clearCST"/>
		<AddHelixSequenceConstraints name="compositionCST"/>
		<FastDesign clear_designable_residues="true" delete_virtual_residues_after_FastRelax="true" movemap_factory="FFLSTANDARD_MOVEMAP" name="DesignRelax" repeats="3" scorefxn="beta" task_operations="FFLMOTIF_TASKOP,FFLFLEX_TASKOP,FFLTEMPLATE_TASKOP"/>
		<DisplayPoseLabelsMover movemap_factory="FFLSTANDARD_MOVEMAP" name="showDesign" task_operations="FFLMOTIF_TASKOP,FFLFLEX_TASKOP,FFLTEMPLATE_TASKOP"/>
	</MOVERS>
	<PROTOCOLS>
		<Add mover="delete"/>
		<Add mover="saveTmpl"/>
		<Add mover="makeFrags"/>
		<Add mover="foldingCST"/>
		<Add mover="FFL"/>
		<Add mover="showDesign"/>
		<Add mover="clearCST"/>
		<Add mover="saveFlded"/>
		<Add mover="designCST"/>
		<Add mover="compositionCST"/>
		<Add mover="DesignRelax"/>
		<Add mover="clearCST"/>
		<Add filter="driftRMSD"/>
		<Add filter="finalRMSD"/>
		<Add filter="BUNS"/>
		<Add filter="packstat"/>
		<Add filter="design_score"/>
	</PROTOCOLS>
	<OUTPUT scorefxn="beta"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
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 "beta" with weights "beta"
protocols.jd2.parser.ScoreFunctionLoader:  setting beta weight atom_pair_constraint to 1.6
core.select.residue_selector.util: Found residue selector FLEXIBLE_OR_TEMPLATE
core.select.residue_selector.util: Found residue selector COLDSPOT_OR_FLEXIBLE_OR_TEMPLATE
protocols.jd2.parser.MoveMapFactoryLoader: Defined MoveMap named "FFLSTANDARD_MOVEMAP"
core.select.residue_selector.util: Found residue selector CONTEXT_OR_FLEXIBLE_OR_TEMPLATE
core.select.residue_selector.util: Found residue selector COLDSPOT_OR_FLEXIBLE_OR_TEMPLATE
protocols.jd2.parser.MoveMapFactoryLoader: Defined MoveMap named "FFLBINDERPACK_MOVEMAP"
core.select.residue_selector.util: Found residue selector CONTEXT_OR_FLEXIBLE_OR_TEMPLATE
core.select.residue_selector.util: Found residue selector COLDSPOT_OR_CONTEXT_OR_FLEXIBLE_OR_TEMPLATE
protocols.jd2.parser.MoveMapFactoryLoader: Defined MoveMap named "FFLBINDERPACKMIN_MOVEMAP"
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "FFLMOTIF_TASKOP" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "FFLFLEX_TASKOP" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "FFLTEMPLATE_TASKOP" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "FFLEXTRA_TASKOP" of type OperateOnResidueSubset
core.pack.task.operation.TaskOperation: TaskOperation::parse_tag method called with no effect for Tag with type NoRepackDisulfides. Probably due to (un/mis)implemented virtual method in derived class.
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "FFLTEMPLATE_DISULFIDES" of type NoRepackDisulfides
core.pose.ref_pose: Loading PDB: folded_pose
protocols.fold_from_loops.RmsdFromResidueSelectorFilter: Loaded reference pose: folded_pose with 0 residues
core.select.residue_selector.util: Found residue selector design
core.select.residue_selector.util: Found residue selector design
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "driftRMSD" of type RmsdFromResidueSelectorFilter
core.pose.ref_pose: Loading PDB: template_pose
protocols.fold_from_loops.RmsdFromResidueSelectorFilter: Loaded reference pose: template_pose with 0 residues
core.select.residue_selector.util: Found residue selector template
core.select.residue_selector.util: Found residue selector design
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "finalRMSD" of type RmsdFromResidueSelectorFilter
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
protocols.simple_filters.BuriedUnsatHbondFilter:  Will use task operations to tell the filter where to look for unsats. 
protocols.simple_filters.BuriedUnsatHbondFilter:  WARNING: it is now recommended to use residue_selector option instead of task_operations
core.pack.task.xml_util: Object BUNS reading the following task_operations: Adding the following task operations
FFLMOTIF_TASKOP FFLFLEX_TASKOP FFLTEMPLATE_TASKOP 
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "BUNS" of type BuriedUnsatHbonds
protocols.filters.PackStatFilter: Structures with packstat score 0.58 will be filtred.
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "packstat" of type PackStat
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.select.residue_selector.util: Found residue selector design
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "design_score" of type ScorePoseSegmentFromResidueSelectorFilter
core.select.residue_selector.util: Found residue selector !template
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "delete" of type DeleteRegionMover
core.pose.ref_pose: Loading PDB: folded_pose
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "saveFlded" of type SavePoseMover
core.pose.ref_pose: Loading PDB: template_pose
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "saveTmpl" of type SavePoseMover
core.pose.ref_pose: Loading PDB: motif_pose
core.import_pose.import_pose: File 'CR8020.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ALA:CtermProteinFull 14
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue SER:CtermProteinFull 234
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue CYS:CtermProteinFull 449
core.conformation.Conformation: Found disulfide between residues 35 109
core.conformation.Conformation: current variant for 35 CYS
core.conformation.Conformation: current variant for 109 CYS
core.conformation.Conformation: current variant for 35 CYD
core.conformation.Conformation: current variant for 109 CYD
core.conformation.Conformation: Found disulfide between residues 159 215
core.conformation.Conformation: current variant for 159 CYS
core.conformation.Conformation: current variant for 215 CYS
core.conformation.Conformation: current variant for 159 CYD
core.conformation.Conformation: current variant for 215 CYD
core.conformation.Conformation: Found disulfide between residues 257 323
core.conformation.Conformation: current variant for 257 CYS
core.conformation.Conformation: current variant for 323 CYS
core.conformation.Conformation: current variant for 257 CYD
core.conformation.Conformation: current variant for 323 CYD
core.conformation.Conformation: Found disulfide between residues 369 429
core.conformation.Conformation: current variant for 369 CYS
core.conformation.Conformation: current variant for 429 CYS
core.conformation.Conformation: current variant for 369 CYD
core.conformation.Conformation: current variant for 429 CYD
protocols.simple_moves.SavePoseMover: reading in CR8020.pdb pdb with 449 residues
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "readMotif" of type SavePoseMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "makeFrags" of type StructFragmentMover
core.select.residue_selector.util: Found residue selector template
protocols.constraint_generator.AddConstraints: Added constraint generator atompairCST1.
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "foldingCST" of type AddConstraints
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.select.residue_selector.util: Found residue selector insertion
core.pose.ref_pose: Loading PDB: motif_pose
core.select.residue_selector.util: Found residue selector motif
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "FFL" of type NubInitioMover
core.select.residue_selector.util: Found residue selector design
protocols.constraint_generator.AddConstraints: Added constraint generator atompairCST2.
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "designCST" of type AddConstraints
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "clearCST" of type ClearConstraintsMover
core.select.residue_selector.util: [ WARNING ] Selector name is empty!
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "compositionCST" of type AddHelixSequenceConstraints
protocols.relax.FastRelax: Looking for default.txt
protocols.relax.RelaxScriptManager: ================== Reading script file: /usr/local/apps/rosetta/2019.14_gcc-9.2.0_openmpi-4.0.1_1565973369/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.RelaxScriptManager: repeat %%nrepeats%%
protocols.relax.RelaxScriptManager: ramp_repack_min 0.02  0.01     1.0
protocols.relax.RelaxScriptManager: ramp_repack_min 0.250 0.01     0.5
protocols.relax.RelaxScriptManager: ramp_repack_min 0.550 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
core.pack.task.xml_util: Object DesignRelax reading the following task_operations: Adding the following task operations
FFLMOTIF_TASKOP FFLFLEX_TASKOP FFLTEMPLATE_TASKOP 
core.select.movemap.util: Found MoveMapFactory FFLSTANDARD_MOVEMAP
protocols.relax.FastRelax: Looking for default.txt
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "DesignRelax" of type FastDesign
core.select.movemap.util: Found MoveMapFactory FFLSTANDARD_MOVEMAP
core.pack.task.xml_util: Object showDesign reading the following task_operations: Adding the following task operations
FFLMOTIF_TASKOP FFLFLEX_TASKOP FFLTEMPLATE_TASKOP 
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "showDesign" of type DisplayPoseLabelsMover
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "delete" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "saveTmpl" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "makeFrags" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "foldingCST" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "FFL" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "showDesign" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "clearCST" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "saveFlded" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "designCST" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "compositionCST" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "DesignRelax" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "clearCST" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "driftRMSD"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "finalRMSD"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "BUNS"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "packstat"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "design_score"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy 1mhx.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeleteRegionMover - delete=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SavePoseMover - saveTmpl=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER StructFragmentMover - makeFrags=======================
protocols.struct_fragment.StructFragmentMover: JobStatus is 0
protocols.struct_fragment.StructFragmentMover: Small fragment file frag_1.200.3mers and large fragment file frag_1.200.9mers are provided.
protocols.struct_fragment.StructFragmentMover: Reading fragments from provided fragment files.
core.io.fragments: reading fragments from file: frag_1.200.3mers ... 
core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... 
core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file frag_1.200.3mers
core.io.fragments: reading fragments from file: frag_1.200.9mers ... 
core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... 
core.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file frag_1.200.9mers
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AddConstraints - foldingCST=======================
protocols.constraint_generator.AddConstraints: Adding 1378 constraints generated by ConstraintGenerator named atompairCST1
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER NubInitioMover - FFL=======================
protocols.DsspMover: LLEEEEEEEEELLEEEEEEEEELLHHHHHHHHHHHHHHLLLLLEEEEELLLLEEEEEL
protocols.fold_from_loops.NubInitioMover: Evaluation of input data's coherence
protocols.fold_from_loops.NubInitioMover: Is the template a single chain?
protocols.fold_from_loops.NubInitioMover:  * Yes!
protocols.fold_from_loops.NubInitioMover: Are there segments of the template that we will keep?
protocols.fold_from_loops.NubInitioMover:  * Yes!
protocols.fold_from_loops.NubInitioMover: Are there insertion regions selected for the template?
protocols.fold_from_loops.NubInitioMover:  * Yes!
protocols.fold_from_loops.NubInitioMover: Seems template a Protein Sequence
protocols.fold_from_loops.NubInitioMover: AMDTYKLFIVIGDRVVVVTTEAVDAATAEKVFKQYANDNGVDGEWTYDDAAKTFTVTE
protocols.fold_from_loops.NubInitioMover: LLEEEEEEEEELLEEEEEEEEELLHHHHHHHHHHHHHHLLLLLEEEEELLLLEEEEEL
protocols.fold_from_loops.NubInitioMover: Does the template have alpha content?
protocols.fold_from_loops.NubInitioMover:  * Yes!
protocols.fold_from_loops.NubInitioMover: Does the template have beta content?
protocols.fold_from_loops.NubInitioMover:  * Yes!
protocols.fold_from_loops.NubInitioMover: Does the template have constraints?
protocols.fold_from_loops.NubInitioMover:  * Yes!
protocols.fold_from_loops.NubInitioMover: Detecting disulfides
protocols.fold_from_loops.NubInitioMover: Processing the Template Segments to keep
protocols.fold_from_loops.NubInitioMover: *****--------------***************************************
protocols.fold_from_loops.NubInitioMover: -----**************---------------------------------------
protocols.grafting.util: Deleting 53 residues from 6 to 58
protocols.grafting.util: Deleting 19 residues from 1 to 19
protocols.fold_from_loops.NubInitioMover: Creating the Unfolded Pose.
protocols.DsspMover: LEEEEELLEEEEELLEEEELLLEEELLLLLEEEEEEEELLLHHHLEEEEEEELLLLLEEEEEEEELLLLLEEELHHHLLLEEEEEELLLLEEEEEELLLLHHHLEEEEEEEELLLLLLLLLLLEELLLEEEEELLLLLELLEEEEELLLLLLLEEEEEEEEEEEELLLLEEEEHHHLELLLEEELLLEELLLLLEEEEEEEEEELHHHLLLLLEEEEEELLLLEEEEEELLLLLLLLEEEELLEEEELLLLLEEEEEEELLLLHHHLEEEEEELLLLLLEEEEELLLEELLLLLLLEEEEEELLEEEEEELLLLLLLLEEEEEEELLLLLLEELLLEEEEELLLLELLEEEEELLLHHHHHHLEEEEEEEEEEEELLLEEEEEEELLEELLLLEEEEELLLLLLLLLEEEEEEEEEEHHHHHHLLEEEEEEEELLLLLLEEEEEELLLL
protocols.grafting.util: Deleting 435 residues from 15 to 449
core.kinematics.FoldTree: delete_jump_seqpos: deleting jump 1
core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 2 to 1
core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLY 1.  Returning BOGUS ID instead.
core.conformation.Residue: [ WARNING ] missing an atom: 1  H   that depends on a nonexistent polymer connection! 
core.conformation.Residue: [ WARNING ]  --> generating it using idealized coordinates.
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 1
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 2) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 1
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 2) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
protocols.fold_from_loops.NubInitioMover: Managing Template Constraints
protocols.fold_from_loops.NubInitioMover: Transfer Pose and Label Residues
protocols.fold_from_loops.NubInitioMover: Unfolded Pose Summary
protocols.fold_from_loops.DisplayPoseLabelsMover: SEQUENCE       AMDTYGFRHQNSEGTGQAATEAVDAATAEKVFKQYANDNGVDGEWTYDDAAKTFTVTE
protocols.fold_from_loops.DisplayPoseLabelsMover: STRUCTURE      LLEEELEEEEELLEEEEEEEELLHHHHHHHHHHHHHHLLLLLEEEEELLLLEEEEELL
protocols.fold_from_loops.DisplayPoseLabelsMover: FLEXIBLE       -----***--------***---------------------------------------
protocols.fold_from_loops.DisplayPoseLabelsMover: HOTSPOT        -----**************---------------------------------------
protocols.fold_from_loops.DisplayPoseLabelsMover: MOTIF          -----**************---------------------------------------
protocols.fold_from_loops.DisplayPoseLabelsMover: TEMPLATE       *****--------------***************************************
protocols.fold_from_loops.DisplayPoseLabelsMover: CONSTRAINTS    *****--------------***************************************
protocols.fold_from_loops.DisplayPoseLabelsMover: MVMP_BB        ********........******************************************
protocols.fold_from_loops.DisplayPoseLabelsMover: MVMP_CHI       *****..............***************************************
protocols.fold_from_loops.DisplayPoseLabelsMover: FOLDTREE       *********************************************************C
protocols.fold_from_loops.DisplayPoseLabelsMover: 
protocols.fold_from_loops.DisplayPoseLabelsMover: FOLD_TREE  EDGE 12 1 -1  EDGE 12 58 -1 
protocols.fold_from_loops.DisplayPoseLabelsMover: A[ALA:NtermProteinFull]MDTYGFRHQNSEGTGQAATEAVDAATAEKVFKQYANDNGVDGEWTYDDAAKTFTVTE[GLU:CtermProteinFull]
protocols.fold_from_loops.DisplayPoseLabelsMover: PDB file name: CR8020.pdb
protocols.fold_from_loops.DisplayPoseLabelsMover:  Pose Range  Chain    PDB Range  |   #Residues         #Atoms

protocols.fold_from_loops.DisplayPoseLabelsMover: 0001 -- 0058    B 0001  -- 0058  |   0058 residues;    00836 atoms
protocols.fold_from_loops.DisplayPoseLabelsMover:                            TOTAL |   0058 residues;    00836 atoms
protocols.fold_from_loops.NubInitioMover: Running Ab Initio protocol
core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set.  Created 62 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.64 seconds.
basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth
basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth
core.scoring: ATOM_VDW set to CENTROID_ROT_MIN
basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_params.txt
basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_env_params.txt
basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_cbeta_params.txt
basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_ang_params.txt
core.scoring.AtomVDW: Openning alternative vdw file: /usr/local/apps/rosetta/2019.14_gcc-9.2.0_openmpi-4.0.1_1565973369/main/database/chemical/atom_type_sets/centroid_rot//min.txt
core.scoring: ATOM_VDW set to CENTROID_ROT_MIN
protocols.abinitio: 
===================================================================
   Stage 1                                                         
   Folding with score0 for max of 2000
protocols.abinitio.foldconstraints: max_seq_sep: 3
protocols.abinitio.foldconstraints: setup basic minmove
protocols.abinitio.foldconstraints: minimized: ResiduePairConstraints: ... 
protocols.abinitio.foldconstraints: total violations: 0
protocols.abinitio.foldconstraints: 
protocols.abinitio.foldconstraints: ResiduePairConstraints: ... 
protocols.abinitio.foldconstraints: total violations: 0
protocols.abinitio: [ WARNING ] extended chain may still remain after 2000 cycles!
protocols.abinitio: [ WARNING ] 1 2 3 4 5 6 7 8 
protocols.abinitio.foldconstraints: ResiduePairConstraints: ... 
protocols.abinitio.foldconstraints: total violations: 0
protocols.abinitio.foldconstraints: max_seq_sep: 3
protocols.abinitio.foldconstraints: minimized: ResiduePairConstraints: ... 
protocols.abinitio.foldconstraints: total violations: 0
protocols.abinitio.foldconstraints: 
protocols.abinitio.foldconstraints: ResiduePairConstraints: ... 
protocols.abinitio.foldconstraints: total violations: 0
protocols.abinitio.foldconstraints: max_seq_sep: 5
protocols.abinitio.foldconstraints: minimized: ResiduePairConstraints: ... 
protocols.abinitio.foldconstraints: total violations: 0
protocols.abinitio.foldconstraints: 
protocols.abinitio.foldconstraints: ResiduePairConstraints: ... 
protocols.abinitio.foldconstraints: total violations: 0
protocols.abinitio.foldconstraints: max_seq_sep: 7
protocols.abinitio.foldconstraints: minimized: ResiduePairConstraints: ... 
protocols.abinitio.foldconstraints: ResiduePairConstraints ( 26 , 20 ) 
Got some signal... It is:6
Process was aborted!
protocols.abinitio.foldconstraints: AtomPairConstraint ( CA :2,20- CA :2,26) 
coords1: -25.2069 103.244 
protocols.abinitio.foldconstraints: [ WARNING ] Message(s) above was printed in the end instead of proper place because this Tracer object has some contents left in inner buffer when destructor was called. Explicitly call Tracer::flush() or end your IO with std::endl to disable this warning.

CASTOR: RUN FINISHED