core.init: (0) Checking for fconfig files in pwd and ./rosetta/flags 
core.init: (0) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184
core.init: (0) command: /opt/software/rosetta_src_2021.16.61629_bundle/main/source/bin/rosetta_scripts.mpi.linuxgccrelease -parser:protocol /home/dengxj/RIFdock/supplemental_files/cao_2021_protocol/paper_interface_design.xml -beta_nov16 -in:file:silent /home/dengxj/RIFdock/binder/site1/pilot_splits/xaa.silent -keep_input_scores False -silent_read_through_errors -out:file:silent out.silent -out:file:silent_struct_type binary -mute protocols.rosetta_scripts.ParsedProtocol.REPORT -parser:script_vars CAO_2021_PROTOCOL=/home/dengxj/RIFdock/supplemental_files/cao_2021_protocol @/home/dengxj/RIFdock/binder/site1/design.flags
basic.random.init_random_generator: (0) 'RNG device' seed mode, using '/dev/urandom', seed=-665725873 seed_offset=0 real_seed=-665725873
basic.random.init_random_generator: (0) RandomGenerator:init: Normal mode, seed=-665725873 RG_type=mt19937
core.init: (0) found database environment variable ROSETTA3_DB: /opt/software/rosetta_src_2021.16.61629_bundle/main/database
core.io.silent.SilentFileData: (0) Reading all structures from /home/dengxj/RIFdock/binder/site1/pilot_splits/xaa.silent
core.io.silent.SilentFileData: (0) Finished reading 20 structures from /home/dengxj/RIFdock/binder/site1/pilot_splits/xaa.silent
protocols.evaluation.ChiWellRmsdEvaluatorCreator: (0) Evaluation Creator active ... 
core.chemical.GlobalResidueTypeSet: (0) Finished initializing fa_standard residue type set.  Created 984 residue types
core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 1.14 seconds.
core.conformation.Conformation: (0) Found disulfide between residues 72 83
core.conformation.Conformation: (0) current variant for 72 CYS
core.conformation.Conformation: (0) current variant for 83 CYS
core.conformation.Conformation: (0) current variant for 72 CYD
core.conformation.Conformation: (0) current variant for 83 CYD
core.conformation.Conformation: (0) Found disulfide between residues 113 124
core.conformation.Conformation: (0) current variant for 113 CYS
core.conformation.Conformation: (0) current variant for 124 CYS
core.conformation.Conformation: (0) current variant for 113 CYD
core.conformation.Conformation: (0) current variant for 124 CYD
protocols.rosetta_scripts.RosettaScriptsParser: (0) dock_design_filename=/home/dengxj/RIFdock/supplemental_files/cao_2021_protocol/paper_interface_design.xml
protocols.rosetta_scripts.RosettaScriptsParser: (0) Variable substitution will occur with the following values: '%%CAO_2021_PROTOCOL%%'='/home/dengxj/RIFdock/supplemental_files/cao_2021_protocol';  '%%patchdock_res%%'='131,132,181';  '%%runpsipred_single%%'='/home/dengxj/software/psipred/runpsipred_single';  
protocols.rosetta_scripts.RosettaScriptsParser: (0) Substituted script:


<ROSETTASCRIPTS>

# Brian Coventry and Longxing Cao 2020
# Derived (20 versions later) from protocol by Franziska Seeger, TaYi Yu, and Danny Sahtoe


# This file contains a lot of arbitrary decisions that may or may not actually improve binding
# To this end, BC went through and labeled lines with # X / 3 where X refers to how important this is
# # 0 / 3 -- truly arbitrary
# # 1 / 3 -- might help
# # 2 / 3 -- definitely helps
# # 3 / 3 -- protocol relies on this

# It's hard to experimentally test all parts of xmls, but hopefully these numbers will give you a guideline
#  as to what is arbitary and what is important



    <SCOREFXNS>
        <ScoreFunction name="sfxn" weights="beta_nov16" /> # 0 / 3 -- beta_nov16 vs ref2015. Beta16 was touted as the best, unclear if it is.

        # Should sfxn_relax be a vanilla ScoreFunction? Open question
        <ScoreFunction name="sfxn_relax" weights="beta_nov16" >
            <Reweight scoretype="arg_cation_pi" weight="3" /> 
            <Reweight scoretype="approximate_buried_unsat_penalty" weight="5" />
            <Set approximate_buried_unsat_penalty_burial_atomic_depth="3.5" />
            <Set approximate_buried_unsat_penalty_hbond_energy_threshold="-0.5" />
        </ScoreFunction>
        <ScoreFunction name="sfxn_design" weights="beta_nov16" >
            <Reweight scoretype="res_type_constraint" weight="1.5" /> -- required for StructProfileMover
            <Reweight scoretype="aa_composition" weight="1.0" />
            <Reweight scoretype="arg_cation_pi" weight="3" /> # 1 / 3 -- Early we thought these were key, unclear now
            <Reweight scoretype="approximate_buried_unsat_penalty" weight="5" /> # 2 / 3 -- approx works on the computer, however unclear
            <Set approximate_buried_unsat_penalty_burial_atomic_depth="3.5" />   #             how much buns matter in real life
            <Set approximate_buried_unsat_penalty_hbond_energy_threshold="-0.5" />
            <Set approximate_buried_unsat_penalty_hbond_bonus_cross_chain="-1" /> # 1 / 3 -- seemed like a good idea at the time
        </ScoreFunction>
    </SCOREFXNS>
    <TASKOPERATIONS>
        <SelectBySASA name="PR_monomer_core_sel" mode="sc" state="unbound" probe_radius="2.2" core_asa="15" surface_asa="15" core="0" boundary="1" surface="1" verbose="0" />
    </TASKOPERATIONS>
    <RESIDUE_SELECTORS>
        <Chain name="chainA" chains="A"/>
        <Chain name="chainB" chains="B"/>
        <Neighborhood name="interface_chA" selector="chainB" distance="10.0" /> # 1 / 3 -- interface size. 8 - 12 seems reasonable
        <Neighborhood name="interface_chB" selector="chainA" distance="10.0" /> #          at 8, you have trouble with ARG and LYS though
        <And name="AB_interface" selectors="interface_chA,interface_chB" />
        <Not name="Not_interface" selector="AB_interface" />
        <And name="actual_interface_chA" selectors="AB_interface,chainA" />
        <And name="actual_interface_chB" selectors="AB_interface,chainB" />
        <And name="chainB_not_interface" selectors="Not_interface,chainB" />

        <ResidueName name="pro_and_gly_positions" residue_name3="PRO,GLY" />

        <InterfaceByVector name="interface_by_vector" cb_dist_cut="11" nearby_atom_cut="5.5" vector_angle_cut="75" vector_dist_cut="9" grp1_selector="actual_interface_chA" grp2_selector="actual_interface_chB"/>

        <Task name="all_cores" fixed="true" task_operations="PR_monomer_core_sel" packable="false" designable="false"/>

        <And name="for_hydrophobic" selectors="actual_interface_chA,interface_by_vector">
            <Not selector="all_cores" />
        </And>
        <ResiduePDBInfoHasLabel name="HOTSPOT_res" property="HOTSPOT" />

        <Index name="res1" resnums="1" />
        <Slice name="patchdock_res" indices="131,132,181" selector="chainB" />

        <ResidueName name="apolar" residue_name3="ALA,CYS,PHE,ILE,LEU,MET,THR,PRO,VAL,TRP,TYR" />

        <And name="apolar_A" selectors="apolar,actual_interface_chA" />
        <And name="apolar_B" selectors="apolar,actual_interface_chB" />

        
        <True name="true_sel" />


    </RESIDUE_SELECTORS>


    <RESIDUE_SELECTORS>
        # These are the default paramters to the old TaskOperation LayerDesign
        <Layer name="surface" select_core="false" select_boundary="false" select_surface="true" use_sidechain_neighbors="true"/>
        <Layer name="boundary" select_core="false" select_boundary="true" select_surface="false" use_sidechain_neighbors="true"/>
        <Layer name="core" select_core="true" select_boundary="false" select_surface="false" use_sidechain_neighbors="true"/>
        <SecondaryStructure name="sheet" overlap="0" minH="3" minE="2" include_terminal_loops="false" use_dssp="true" ss="E"/>
        <SecondaryStructure name="entire_loop" overlap="0" minH="3" minE="2" include_terminal_loops="true" use_dssp="true" ss="L"/>
        <SecondaryStructure name="entire_helix" overlap="0" minH="3" minE="2" include_terminal_loops="false" use_dssp="true" ss="H"/>
        <And name="helix_cap" selectors="entire_loop">
            <PrimarySequenceNeighborhood lower="1" upper="0" selector="entire_helix"/>
        </And>
        <And name="helix_start" selectors="entire_helix">
            <PrimarySequenceNeighborhood lower="0" upper="1" selector="helix_cap"/>
        </And>
        <And name="helix" selectors="entire_helix">
            <Not selector="helix_start"/>
        </And>
        <And name="loop" selectors="entire_loop">
            <Not selector="helix_cap"/>
        </And>

    </RESIDUE_SELECTORS>

    <TASKOPERATIONS>
        <DesignRestrictions name="layer_design_F_boundary_M"> # 2 / 3 -- This is 3 / 3 if you don't have approx, StructProfile, and sap
                                                                         Rosetta will put hydrophobics on your surface and polars in your core
                                                                         We do need core polars for interfaces though
            <Action selector_logic="surface AND helix_start"  aas="DEHKPQR"/>
            <Action selector_logic="surface AND helix"        aas="EHKQR"/>
            <Action selector_logic="surface AND sheet"        aas="EHKNQRST"/>
            <Action selector_logic="surface AND loop"         aas="DEGHKNPQRST"/>
            <Action selector_logic="boundary AND helix_start" aas="ADEFHIKLMNPQRSTVWY"/>
            <Action selector_logic="boundary AND helix"       aas="ADEFHIKLMNQRSTVWY"/>
            <Action selector_logic="boundary AND sheet"       aas="DEFHIKLMNQRSTVWY"/>
            <Action selector_logic="boundary AND loop"        aas="ADEFGHIKLNPQRSTVWY"/>
            <Action selector_logic="core AND helix_start"     aas="AFILMPVWY"/>
            <Action selector_logic="core AND helix"           aas="AFILMVWYDENQSTH"/>
            <Action selector_logic="core AND sheet"           aas="FILMVWYDENQSTH"/>
            <Action selector_logic="core AND loop"            aas="AFGILPVWYDENQSTH"/>
            <Action selector_logic="helix_cap"                aas="DNST"/>
        </DesignRestrictions>
    </TASKOPERATIONS>
    <MOVERS>
        <AddCompositionConstraintMover name="3trp" > # 2 / 3 -- penalize TRP by 3. This leads to a reasonable number of TRP given everything else
            <Comp entry="PENALTY_DEFINITION;TYPE TRP;ABSOLUTE 0;PENALTIES 0 3;DELTA_START 0;DELTA_END 1;BEFORE_FUNCTION CONSTANT;AFTER_FUNCTION LINEAR;END_PENALTY_DEFINITION;" />
        </AddCompositionConstraintMover>
        <AddCompositionConstraintMover name="2met" > # 2 / 3 -- Rosetta loves MET, but the Bakerlab doesn't.
            <Comp entry="PENALTY_DEFINITION;TYPE MET;ABSOLUTE 0;PENALTIES 0 2;DELTA_START 0;DELTA_END 1;BEFORE_FUNCTION CONSTANT;AFTER_FUNCTION LINEAR;END_PENALTY_DEFINITION;" />
        </AddCompositionConstraintMover>
        <AddCompositionConstraintMover name="30_percent_polar" selector="for_hydrophobic"> # 2 / 3 -- Bad way to prevent totally hydrophobic interfaces. The SapConstraint is a much better method here, but we didn't develop it until after we finished these designs. See adjust_total_netcharge.xml for ideas on how to use it.
            <Comp entry="PENALTY_DEFINITION;TYPE ASP GLU HIS LYS ASN GLN ARG SER THR TYR;FRACT_DELTA_START -0.01;FRACT_DELTA_END 0.0;PENALTIES 0.1 0 ;FRACTION 0.30;BEFORE_FUNCTION QUADRATIC;AFTER_FUNCTION CONSTANT;END_PENALTY_DEFINITION" />
        </AddCompositionConstraintMover>
    </MOVERS>
    <TASKOPERATIONS>

        <PruneBuriedUnsats name="prune_buried_unsats" allow_even_trades="false" atomic_depth_cutoff="3.5" minimum_hbond_energy="-0.5" /> # 2 / 3 -- see approx comments above. With both enabled, this mostly serves to speed up packing

        <ProteinProteinInterfaceUpweighter name="upweight_interface" interface_weight="3" /> # 3 / 3 -- Massive improvement. Without this, Rosetta leaves your interface full of holes where obvious things can go. Upweighting by 2 is also reasonable here.

        <ProteinInterfaceDesign name="pack_long" design_chain1="0" design_chain2="0" jump="1" interface_distance_cutoff="15"/> # 0 / 3 -- distance cutoff

        <IncludeCurrent name="current" /> # 1 / 3 -- With this, you get to reuse minimized rotamers. This hasn't been tested

        <LimitAromaChi2 name="limitchi2" chi2max="110" chi2min="70" include_trp="True" /> # 1 / 3 -- Bakerlab folklore. Some people don't like this.

        <ExtraRotamersGeneric name="ex1_ex2" ex1="1" ex2aro="1" ex2="0" /> # 2 / 3 -- This has been extensively tested. ex2 wastes time without improving results. ex2aro is hardly a slowdown and improves results. ex1 is a slowdown, but also improves results. Improved results are on the computer, not biochemically.


        <OperateOnResidueSubset name="restrict_target_not_interface" selector="chainB_not_interface">
            <PreventRepackingRLT/>
        </OperateOnResidueSubset>
        <OperateOnResidueSubset name="restrict_to_interface" selector="Not_interface">
            <PreventRepackingRLT/>
        </OperateOnResidueSubset>
        <OperateOnResidueSubset name="restrict_target2repacking" selector="chainB">
            <RestrictToRepackingRLT/>
        </OperateOnResidueSubset>
        <OperateOnResidueSubset name="restrict_hotspots2repacking" selector="HOTSPOT_res"> # 1 / 3 -- For rifdock, we found it's better to allow the rifres to redesign. For motif graft, we haven't tested it as much, but with the complicated process that goes into picking the motif residues, we think it's probably better to keep them. (Motif picking is on fully relaxed structures whereas rifdock is very low res)
            <RestrictToRepackingRLT/>
        </OperateOnResidueSubset>

        <DisallowIfNonnative name="disallow_GLY" resnum="0" disallow_aas="G" /> # 1 / 3 -- Bakerlab folklore
        <DisallowIfNonnative name="disallow_PRO" resnum="0" disallow_aas="P" /> # 1 / 3 -- Bakerlab folklore

    	<OperateOnResidueSubset name="restrict_PRO_GLY" selector="pro_and_gly_positions"> # 2 / 3 -- This makes sense, don't drop PRO and GLY
    		<PreventRepackingRLT/>
    	</OperateOnResidueSubset>

        <SelectBySASA name="PR_monomer_core" mode="sc" state="unbound" probe_radius="2.2" core_asa="10" surface_asa="10" core="0" boundary="1" surface="1" verbose="0" /> # 0 / 3 -- Honestly, this might even hurt, but it gives a massive 2-3x speedup

    </TASKOPERATIONS>
    <MOVERS>

        <SwitchChainOrder name="chain1only" chain_order="1" />

        <TaskAwareMinMover name="min" scorefxn="sfxn" bb="0" chi="1" task_operations="pack_long" /> # 1 / 3 -- bb min? We haven't tested it

        <StructProfileMover name="genProfile" add_csts_to_pose="1" consider_topN_frags="100" eliminate_background="0" ignore_terminal_residue="1" only_loops="0" burialWt="0" RMSthreshold="0.6" residue_selector="chainA" /> # 2 / 3 -- You can get by without this, but it gives a massive increase to your success in experimental folding (and mismatch_probability)

        <ClearConstraintsMover name="clear_constraints" />

    </MOVERS>
    <FILTERS>

        <Sasa name="interface_buried_sasa" confidence="0" />

        <Ddg name="ddg"  threshold="-10" jump="1" repeats="5" repack="1" relax_mover="min" confidence="0" scorefxn="sfxn" extreme_value_removal="1" />

        <ShapeComplementarity name="interface_sc" verbose="0" min_sc="0.55" write_int_area="1" write_median_dist="1" jump="1" confidence="0"/>

        <ScoreType name="total_score_MBF" scorefxn="sfxn" score_type="total_score" threshold="0" confidence="0" />
        <MoveBeforeFilter name="total_score_monomer" mover="chain1only" filter="total_score_MBF" confidence="0" />
        <ResidueCount name="res_count_MBF" max_residue_count="9999" confidence="0"/>
        <MoveBeforeFilter name="res_count_monomer" mover="chain1only" filter="res_count_MBF" confidence="0" />

        <CalculatorFilter name="score_per_res" equation="total_score_monomer / res" threshold="-3.5" confidence="0">
            <Var name="total_score_monomer" filter="total_score_monomer"/>
            <Var name="res" filter="res_count_monomer"/>
        </CalculatorFilter>


        <BuriedUnsatHbonds name="buns_heavy_ball_1.1D" use_reporter_behavior="true" report_all_heavy_atom_unsats="true" scorefxn="sfxn" residue_selector="AB_interface" ignore_surface_res="false" print_out_info_to_pdb="true" confidence="0" use_ddG_style="true" burial_cutoff="0.01" dalphaball_sasa="true" probe_radius="1.1" max_hbond_energy="1.5" burial_cutoff_apo="0.2" />

        <ContactMolecularSurface name="contact_molecular_surface" distance_weight="0.5" target_selector="chainA" binder_selector="chainB" confidence="0" />
        <ContactMolecularSurface name="contact_patch" distance_weight="0.5" target_selector="patchdock_res" binder_selector="chainA" confidence="0" />
        <ContactMolecularSurface name="contact_patch_apolar" distance_weight="0.5" target_selector="patchdock_res" binder_selector="chainA" apolar_target="true" confidence="0" />
        <ContactMolecularSurface name="contact_patch_apolar_sq5" distance_weight="0.5" target_selector="patchdock_res" binder_selector="chainA" apolar_target="true" near_squared_size="5" confidence="0" />


        <SSPrediction name="pre_mismatch_probability" confidence="0" cmd="/home/dengxj/software/psipred/runpsipred_single" use_probability="1" mismatch_probability="1" use_svm="0" />
        <MoveBeforeFilter name="mismatch_probability" mover="chain1only" filter="pre_mismatch_probability" confidence="0" />


        <SSShapeComplementarity name="ss_sc_pre" verbose="0" confidence="0" />
        <MoveBeforeFilter name="ss_sc" mover="chain1only" filter="ss_sc_pre" confidence="0"/>

        <ContactMolecularSurface name="contact_molecular_surface_ap_target" distance_weight="0.5" target_selector="apolar_B" binder_selector="chainA" confidence="0" />
        <ContactMolecularSurface name="contact_molec_sq5_ap_target" distance_weight="0.5" target_selector="apolar_B" binder_selector="chainA" confidence="0" near_squared_size="5" />

        <ContactMolecularSurface name="contact_molecular_surface_apap_target" distance_weight="0.5" target_selector="apolar_B" binder_selector="chainA" confidence="0" apolar_target="true" />
        <ContactMolecularSurface name="contact_molec_sq5_apap_target" distance_weight="0.5" target_selector="apolar_B" binder_selector="chainA" confidence="0" near_squared_size="5" apolar_target="true" />



        <ContactMolecularSurface name="contact_molecular_surface_ap_binder" distance_weight="0.5" target_selector="apolar_A" binder_selector="chainB" confidence="0" />
        <ContactMolecularSurface name="contact_molec_sq5_ap_binder" distance_weight="0.5" target_selector="apolar_A" binder_selector="chainB" confidence="0" near_squared_size="5" />

        <ContactMolecularSurface name="contact_molecular_surface_apap_binder" distance_weight="0.5" target_selector="apolar_A" binder_selector="chainB" confidence="0" apolar_target="true" />
        <ContactMolecularSurface name="contact_molec_sq5_apap_binder" distance_weight="0.5" target_selector="apolar_A" binder_selector="chainB" confidence="0" near_squared_size="5" apolar_target="true" />




        <Time name="timed"/>
    </FILTERS>
    <SIMPLE_METRICS>

        <SapScoreMetric name="sap_score" score_selector="chainA" />
        <SapScoreMetric name="sap_score_target" score_selector="chainB" />
        <SapScoreMetric name="binder_blocked_sap" score_selector="chainA" sap_calculate_selector="chainA" sasa_selector="true_sel" />
        <SapScoreMetric name="target_blocked_sap" score_selector="chainB" sap_calculate_selector="chainB" sasa_selector="true_sel" />

        <CalculatorMetric name="binder_delta_sap" equation="binder_sap_score - binder_blocked_sap" >
            <VAR name="binder_sap_score" metric="sap_score"/>
            <VAR name="binder_blocked_sap" metric="binder_blocked_sap"/>
        </CalculatorMetric>

        <CalculatorMetric name="target_delta_sap" equation="target_sap_score - target_blocked_sap" >
            <VAR name="target_sap_score" metric="sap_score_target"/>
            <VAR name="target_blocked_sap" metric="target_blocked_sap"/>
        </CalculatorMetric>

    </SIMPLE_METRICS>
    <MOVERS>


        <FastDesign name="FastDesign" scorefxn="sfxn_design" repeats="1" task_operations="current,limitchi2,ex1_ex2,restrict_to_interface,restrict_target2repacking,restrict_hotspots2repacking,disallow_GLY,disallow_PRO,PR_monomer_core,upweight_interface,restrict_PRO_GLY,prune_buried_unsats,layer_design_F_boundary_M" batch="false" ramp_down_constraints="false" cartesian="false" bondangle="false" bondlength="false" min_type="dfpmin_armijo_nonmonotone" relaxscript="/home/dengxj/RIFdock/supplemental_files/cao_2021_protocol/old_beta_16_ref.rosettacon2018.txt" >
            # 3 / 3 -- relax script. The rosettacon2018 relax script gives much better performance than the original FastRelax-based one. Newer ones likely work too.
            # 1 / 3 -- cartesian. Through much testing, cartesian artifically gives better numbers. However, controlled experiments will show that the sequences it produce do not have intrinsically better metrics. It's also way slower.
            # 0 / 3 -- min_type. We haven't tested this very much.
            # 1 / 3 -- old ref weights. It's just what we've always used. Our aa_comps are trained based on these.
            <MoveMap name="MM" >
                    <Chain number="1" chi="true" bb="true" /> # 2 / 3 -- flexible binder backbone. We haven't explicitly tested this, but we feel it's important
                    <Chain number="2" chi="true" bb="false" /> # 1 / 3 -- fixed target backbone. Cuts down on metric noise and prevents rosetta from doing bad things
                    <Jump number="1" setting="true" /> # 3 / 3 -- You absolutely must let the two proteins move relative to one another
            </MoveMap>
        </FastDesign>

        <FastRelax name="FastRelax" scorefxn="sfxn_design" repeats="1" batch="false" ramp_down_constraints="false" cartesian="false" bondangle="false" bondlength="false" min_type="dfpmin_armijo_nonmonotone" task_operations="restrict_target_not_interface,ex1_ex2,limitchi2,prune_buried_unsats" >
            # 1 / 3 -- Do you even need to run FastRelax? We've never actually tested it.
            <MoveMap name="MM" >
                <Chain number="1" chi="true" bb="true" />
                <Chain number="2" chi="true" bb="false" />
                <Jump number="1" setting="true" />
            </MoveMap>
        </FastRelax>


    </MOVERS>
    <APPLY_TO_POSE>
    </APPLY_TO_POSE>
    <PROTOCOLS>
        <Add filter="timed" />

        # apply sequence constraints
        <Add mover="3trp" />
        <Add mover="2met" />
        <Add mover="30_percent_polar" />
        <Add mover="genProfile" />

        # perform sequence optimization
        <Add mover="FastDesign" />
        <Add mover="FastDesign" />
        <Add mover="clear_constraints" />
        <Add mover="FastRelax" />

        # calculate interface metrics
        <Add filter_name="interface_buried_sasa" />
        <Add filter_name="ddg" />
        <Add filter_name="interface_sc" />
        <Add filter_name="score_per_res" />
        <Add filter="buns_heavy_ball_1.1D" />
        <Add filter="mismatch_probability" />
        <Add filter="contact_molecular_surface" />
        <Add filter="contact_patch" />
        <Add filter="contact_patch_apolar" />
        <Add filter="contact_patch_apolar_sq5" />
        <Add filter="ss_sc" />

        <Add filter="contact_molecular_surface_ap_target" />
        <Add filter="contact_molec_sq5_ap_target" />
        <Add filter="contact_molecular_surface_apap_target" />
        <Add filter="contact_molec_sq5_apap_target" />
        

        <Add metrics="sap_score" />
        <Add metrics="sap_score_target" />
        <Add metrics="binder_delta_sap" />
        <Add metrics="target_delta_sap" />

        <Add filter="timed" />
    </PROTOCOLS>
</ROSETTASCRIPTS>
protocols.rosetta_scripts.RosettaScriptsParser: (0) Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: (0) ...done
protocols.rosetta_scripts.RosettaScriptsParser: (0) Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: (0) ...done
protocols.rosetta_scripts.RosettaScriptsParser: (0) Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: (0) ...done
protocols.rosetta_scripts.RosettaScriptsParser: (0) Parsed script:
<ROSETTASCRIPTS>
	<SCOREFXNS>
		<ScoreFunction name="sfxn" weights="beta_nov16"/>
		<ScoreFunction name="sfxn_relax" weights="beta_nov16">
			<Reweight scoretype="arg_cation_pi" weight="3"/>
			<Reweight scoretype="approximate_buried_unsat_penalty" weight="5"/>
			<Set approximate_buried_unsat_penalty_burial_atomic_depth="3.5"/>
			<Set approximate_buried_unsat_penalty_hbond_energy_threshold="-0.5"/>
		</ScoreFunction>
		<ScoreFunction name="sfxn_design" weights="beta_nov16">
			<Reweight scoretype="res_type_constraint" weight="1.5"/>
			<Reweight scoretype="aa_composition" weight="1.0"/>
			<Reweight scoretype="arg_cation_pi" weight="3"/>
			<Reweight scoretype="approximate_buried_unsat_penalty" weight="5"/>
			<Set approximate_buried_unsat_penalty_burial_atomic_depth="3.5"/>
			<Set approximate_buried_unsat_penalty_hbond_energy_threshold="-0.5"/>
			<Set approximate_buried_unsat_penalty_hbond_bonus_cross_chain="-1"/>
		</ScoreFunction>
	</SCOREFXNS>
	<TASKOPERATIONS>
		<SelectBySASA boundary="1" core="0" core_asa="15" mode="sc" name="PR_monomer_core_sel" probe_radius="2.2" state="unbound" surface="1" surface_asa="15" verbose="0"/>
	</TASKOPERATIONS>
	<RESIDUE_SELECTORS>
		<Chain chains="A" name="chainA"/>
		<Chain chains="B" name="chainB"/>
		<Neighborhood distance="10.0" name="interface_chA" selector="chainB"/>
		<Neighborhood distance="10.0" name="interface_chB" selector="chainA"/>
		<And name="AB_interface" selectors="interface_chA,interface_chB"/>
		<Not name="Not_interface" selector="AB_interface"/>
		<And name="actual_interface_chA" selectors="AB_interface,chainA"/>
		<And name="actual_interface_chB" selectors="AB_interface,chainB"/>
		<And name="chainB_not_interface" selectors="Not_interface,chainB"/>
		<ResidueName name="pro_and_gly_positions" residue_name3="PRO,GLY"/>
		<InterfaceByVector cb_dist_cut="11" grp1_selector="actual_interface_chA" grp2_selector="actual_interface_chB" name="interface_by_vector" nearby_atom_cut="5.5" vector_angle_cut="75" vector_dist_cut="9"/>
		<Task designable="false" fixed="true" name="all_cores" packable="false" task_operations="PR_monomer_core_sel"/>
		<And name="for_hydrophobic" selectors="actual_interface_chA,interface_by_vector">
			<Not selector="all_cores"/>
		</And>
		<ResiduePDBInfoHasLabel name="HOTSPOT_res" property="HOTSPOT"/>
		<Index name="res1" resnums="1"/>
		<Slice indices="131,132,181" name="patchdock_res" selector="chainB"/>
		<ResidueName name="apolar" residue_name3="ALA,CYS,PHE,ILE,LEU,MET,THR,PRO,VAL,TRP,TYR"/>
		<And name="apolar_A" selectors="apolar,actual_interface_chA"/>
		<And name="apolar_B" selectors="apolar,actual_interface_chB"/>
		<True name="true_sel"/>
	</RESIDUE_SELECTORS>
	<RESIDUE_SELECTORS>
		<Layer name="surface" select_boundary="false" select_core="false" select_surface="true" use_sidechain_neighbors="true"/>
		<Layer name="boundary" select_boundary="true" select_core="false" select_surface="false" use_sidechain_neighbors="true"/>
		<Layer name="core" select_boundary="false" select_core="true" select_surface="false" use_sidechain_neighbors="true"/>
		<SecondaryStructure include_terminal_loops="false" minE="2" minH="3" name="sheet" overlap="0" ss="E" use_dssp="true"/>
		<SecondaryStructure include_terminal_loops="true" minE="2" minH="3" name="entire_loop" overlap="0" ss="L" use_dssp="true"/>
		<SecondaryStructure include_terminal_loops="false" minE="2" minH="3" name="entire_helix" overlap="0" ss="H" use_dssp="true"/>
		<And name="helix_cap" selectors="entire_loop">
			<PrimarySequenceNeighborhood lower="1" selector="entire_helix" upper="0"/>
		</And>
		<And name="helix_start" selectors="entire_helix">
			<PrimarySequenceNeighborhood lower="0" selector="helix_cap" upper="1"/>
		</And>
		<And name="helix" selectors="entire_helix">
			<Not selector="helix_start"/>
		</And>
		<And name="loop" selectors="entire_loop">
			<Not selector="helix_cap"/>
		</And>
	</RESIDUE_SELECTORS>
	<TASKOPERATIONS>
		<DesignRestrictions name="layer_design_F_boundary_M">
			<Action aas="DEHKPQR" selector_logic="surface AND helix_start"/>
			<Action aas="EHKQR" selector_logic="surface AND helix"/>
			<Action aas="EHKNQRST" selector_logic="surface AND sheet"/>
			<Action aas="DEGHKNPQRST" selector_logic="surface AND loop"/>
			<Action aas="ADEFHIKLMNPQRSTVWY" selector_logic="boundary AND helix_start"/>
			<Action aas="ADEFHIKLMNQRSTVWY" selector_logic="boundary AND helix"/>
			<Action aas="DEFHIKLMNQRSTVWY" selector_logic="boundary AND sheet"/>
			<Action aas="ADEFGHIKLNPQRSTVWY" selector_logic="boundary AND loop"/>
			<Action aas="AFILMPVWY" selector_logic="core AND helix_start"/>
			<Action aas="AFILMVWYDENQSTH" selector_logic="core AND helix"/>
			<Action aas="FILMVWYDENQSTH" selector_logic="core AND sheet"/>
			<Action aas="AFGILPVWYDENQSTH" selector_logic="core AND loop"/>
			<Action aas="DNST" selector_logic="helix_cap"/>
		</DesignRestrictions>
	</TASKOPERATIONS>
	<MOVERS>
		<AddCompositionConstraintMover name="3trp">
			<Comp entry="PENALTY_DEFINITION;TYPE TRP;ABSOLUTE 0;PENALTIES 0 3;DELTA_START 0;DELTA_END 1;BEFORE_FUNCTION CONSTANT;AFTER_FUNCTION LINEAR;END_PENALTY_DEFINITION;"/>
		</AddCompositionConstraintMover>
		<AddCompositionConstraintMover name="2met">
			<Comp entry="PENALTY_DEFINITION;TYPE MET;ABSOLUTE 0;PENALTIES 0 2;DELTA_START 0;DELTA_END 1;BEFORE_FUNCTION CONSTANT;AFTER_FUNCTION LINEAR;END_PENALTY_DEFINITION;"/>
		</AddCompositionConstraintMover>
		<AddCompositionConstraintMover name="30_percent_polar" selector="for_hydrophobic">
			<Comp entry="PENALTY_DEFINITION;TYPE ASP GLU HIS LYS ASN GLN ARG SER THR TYR;FRACT_DELTA_START -0.01;FRACT_DELTA_END 0.0;PENALTIES 0.1 0 ;FRACTION 0.30;BEFORE_FUNCTION QUADRATIC;AFTER_FUNCTION CONSTANT;END_PENALTY_DEFINITION"/>
		</AddCompositionConstraintMover>
	</MOVERS>
	<TASKOPERATIONS>
		<PruneBuriedUnsats allow_even_trades="false" atomic_depth_cutoff="3.5" minimum_hbond_energy="-0.5" name="prune_buried_unsats"/>
		<ProteinProteinInterfaceUpweighter interface_weight="3" name="upweight_interface"/>
		<ProteinInterfaceDesign design_chain1="0" design_chain2="0" interface_distance_cutoff="15" jump="1" name="pack_long"/>
		<IncludeCurrent name="current"/>
		<LimitAromaChi2 chi2max="110" chi2min="70" include_trp="True" name="limitchi2"/>
		<ExtraRotamersGeneric ex1="1" ex2="0" ex2aro="1" name="ex1_ex2"/>
		<OperateOnResidueSubset name="restrict_target_not_interface" selector="chainB_not_interface">
			<PreventRepackingRLT/>
		</OperateOnResidueSubset>
		<OperateOnResidueSubset name="restrict_to_interface" selector="Not_interface">
			<PreventRepackingRLT/>
		</OperateOnResidueSubset>
		<OperateOnResidueSubset name="restrict_target2repacking" selector="chainB">
			<RestrictToRepackingRLT/>
		</OperateOnResidueSubset>
		<OperateOnResidueSubset name="restrict_hotspots2repacking" selector="HOTSPOT_res">
			<RestrictToRepackingRLT/>
		</OperateOnResidueSubset>
		<DisallowIfNonnative disallow_aas="G" name="disallow_GLY" resnum="0"/>
		<DisallowIfNonnative disallow_aas="P" name="disallow_PRO" resnum="0"/>
		<OperateOnResidueSubset name="restrict_PRO_GLY" selector="pro_and_gly_positions">
			<PreventRepackingRLT/>
		</OperateOnResidueSubset>
		<SelectBySASA boundary="1" core="0" core_asa="10" mode="sc" name="PR_monomer_core" probe_radius="2.2" state="unbound" surface="1" surface_asa="10" verbose="0"/>
	</TASKOPERATIONS>
	<MOVERS>
		<SwitchChainOrder chain_order="1" name="chain1only"/>
		<TaskAwareMinMover bb="0" chi="1" name="min" scorefxn="sfxn" task_operations="pack_long"/>
		<StructProfileMover RMSthreshold="0.6" add_csts_to_pose="1" burialWt="0" consider_topN_frags="100" eliminate_background="0" ignore_terminal_residue="1" name="genProfile" only_loops="0" residue_selector="chainA"/>
		<ClearConstraintsMover name="clear_constraints"/>
	</MOVERS>
	<FILTERS>
		<Sasa confidence="0" name="interface_buried_sasa"/>
		<Ddg confidence="0" extreme_value_removal="1" jump="1" name="ddg" relax_mover="min" repack="1" repeats="5" scorefxn="sfxn" threshold="-10"/>
		<ShapeComplementarity confidence="0" jump="1" min_sc="0.55" name="interface_sc" verbose="0" write_int_area="1" write_median_dist="1"/>
		<ScoreType confidence="0" name="total_score_MBF" score_type="total_score" scorefxn="sfxn" threshold="0"/>
		<MoveBeforeFilter confidence="0" filter="total_score_MBF" mover="chain1only" name="total_score_monomer"/>
		<ResidueCount confidence="0" max_residue_count="9999" name="res_count_MBF"/>
		<MoveBeforeFilter confidence="0" filter="res_count_MBF" mover="chain1only" name="res_count_monomer"/>
		<CalculatorFilter confidence="0" equation="total_score_monomer / res" name="score_per_res" threshold="-3.5">
			<Var filter="total_score_monomer" name="total_score_monomer"/>
			<Var filter="res_count_monomer" name="res"/>
		</CalculatorFilter>
		<BuriedUnsatHbonds burial_cutoff="0.01" burial_cutoff_apo="0.2" confidence="0" dalphaball_sasa="true" ignore_surface_res="false" max_hbond_energy="1.5" name="buns_heavy_ball_1.1D" print_out_info_to_pdb="true" probe_radius="1.1" report_all_heavy_atom_unsats="true" residue_selector="AB_interface" scorefxn="sfxn" use_ddG_style="true" use_reporter_behavior="true"/>
		<ContactMolecularSurface binder_selector="chainB" confidence="0" distance_weight="0.5" name="contact_molecular_surface" target_selector="chainA"/>
		<ContactMolecularSurface binder_selector="chainA" confidence="0" distance_weight="0.5" name="contact_patch" target_selector="patchdock_res"/>
		<ContactMolecularSurface apolar_target="true" binder_selector="chainA" confidence="0" distance_weight="0.5" name="contact_patch_apolar" target_selector="patchdock_res"/>
		<ContactMolecularSurface apolar_target="true" binder_selector="chainA" confidence="0" distance_weight="0.5" name="contact_patch_apolar_sq5" near_squared_size="5" target_selector="patchdock_res"/>
		<SSPrediction cmd="/home/dengxj/software/psipred/runpsipred_single" confidence="0" mismatch_probability="1" name="pre_mismatch_probability" use_probability="1" use_svm="0"/>
		<MoveBeforeFilter confidence="0" filter="pre_mismatch_probability" mover="chain1only" name="mismatch_probability"/>
		<SSShapeComplementarity confidence="0" name="ss_sc_pre" verbose="0"/>
		<MoveBeforeFilter confidence="0" filter="ss_sc_pre" mover="chain1only" name="ss_sc"/>
		<ContactMolecularSurface binder_selector="chainA" confidence="0" distance_weight="0.5" name="contact_molecular_surface_ap_target" target_selector="apolar_B"/>
		<ContactMolecularSurface binder_selector="chainA" confidence="0" distance_weight="0.5" name="contact_molec_sq5_ap_target" near_squared_size="5" target_selector="apolar_B"/>
		<ContactMolecularSurface apolar_target="true" binder_selector="chainA" confidence="0" distance_weight="0.5" name="contact_molecular_surface_apap_target" target_selector="apolar_B"/>
		<ContactMolecularSurface apolar_target="true" binder_selector="chainA" confidence="0" distance_weight="0.5" name="contact_molec_sq5_apap_target" near_squared_size="5" target_selector="apolar_B"/>
		<ContactMolecularSurface binder_selector="chainB" confidence="0" distance_weight="0.5" name="contact_molecular_surface_ap_binder" target_selector="apolar_A"/>
		<ContactMolecularSurface binder_selector="chainB" confidence="0" distance_weight="0.5" name="contact_molec_sq5_ap_binder" near_squared_size="5" target_selector="apolar_A"/>
		<ContactMolecularSurface apolar_target="true" binder_selector="chainB" confidence="0" distance_weight="0.5" name="contact_molecular_surface_apap_binder" target_selector="apolar_A"/>
		<ContactMolecularSurface apolar_target="true" binder_selector="chainB" confidence="0" distance_weight="0.5" name="contact_molec_sq5_apap_binder" near_squared_size="5" target_selector="apolar_A"/>
		<Time name="timed"/>
	</FILTERS>
	<SIMPLE_METRICS>
		<SapScoreMetric name="sap_score" score_selector="chainA"/>
		<SapScoreMetric name="sap_score_target" score_selector="chainB"/>
		<SapScoreMetric name="binder_blocked_sap" sap_calculate_selector="chainA" sasa_selector="true_sel" score_selector="chainA"/>
		<SapScoreMetric name="target_blocked_sap" sap_calculate_selector="chainB" sasa_selector="true_sel" score_selector="chainB"/>
		<CalculatorMetric equation="binder_sap_score - binder_blocked_sap" name="binder_delta_sap">
			<VAR metric="sap_score" name="binder_sap_score"/>
			<VAR metric="binder_blocked_sap" name="binder_blocked_sap"/>
		</CalculatorMetric>
		<CalculatorMetric equation="target_sap_score - target_blocked_sap" name="target_delta_sap">
			<VAR metric="sap_score_target" name="target_sap_score"/>
			<VAR metric="target_blocked_sap" name="target_blocked_sap"/>
		</CalculatorMetric>
	</SIMPLE_METRICS>
	<MOVERS>
		<FastDesign batch="false" bondangle="false" bondlength="false" cartesian="false" min_type="dfpmin_armijo_nonmonotone" name="FastDesign" ramp_down_constraints="false" relaxscript="/home/dengxj/RIFdock/supplemental_files/cao_2021_protocol/old_beta_16_ref.rosettacon2018.txt" repeats="1" scorefxn="sfxn_design" task_operations="current,limitchi2,ex1_ex2,restrict_to_interface,restrict_target2repacking,restrict_hotspots2repacking,disallow_GLY,disallow_PRO,PR_monomer_core,upweight_interface,restrict_PRO_GLY,prune_buried_unsats,layer_design_F_boundary_M">
			<MoveMap name="MM">
				<Chain bb="true" chi="true" number="1"/>
				<Chain bb="false" chi="true" number="2"/>
				<Jump number="1" setting="true"/>
			</MoveMap>
		</FastDesign>
		<FastRelax batch="false" bondangle="false" bondlength="false" cartesian="false" min_type="dfpmin_armijo_nonmonotone" name="FastRelax" ramp_down_constraints="false" repeats="1" scorefxn="sfxn_design" task_operations="restrict_target_not_interface,ex1_ex2,limitchi2,prune_buried_unsats">
			<MoveMap name="MM">
				<Chain bb="true" chi="true" number="1"/>
				<Chain bb="false" chi="true" number="2"/>
				<Jump number="1" setting="true"/>
			</MoveMap>
		</FastRelax>
	</MOVERS>
	<APPLY_TO_POSE/>
	<PROTOCOLS>
		<Add filter="timed"/>
		<Add mover="3trp"/>
		<Add mover="2met"/>
		<Add mover="30_percent_polar"/>
		<Add mover="genProfile"/>
		<Add mover="FastDesign"/>
		<Add mover="FastDesign"/>
		<Add mover="clear_constraints"/>
		<Add mover="FastRelax"/>
		<Add filter_name="interface_buried_sasa"/>
		<Add filter_name="ddg"/>
		<Add filter_name="interface_sc"/>
		<Add filter_name="score_per_res"/>
		<Add filter="buns_heavy_ball_1.1D"/>
		<Add filter="mismatch_probability"/>
		<Add filter="contact_molecular_surface"/>
		<Add filter="contact_patch"/>
		<Add filter="contact_patch_apolar"/>
		<Add filter="contact_patch_apolar_sq5"/>
		<Add filter="ss_sc"/>
		<Add filter="contact_molecular_surface_ap_target"/>
		<Add filter="contact_molec_sq5_ap_target"/>
		<Add filter="contact_molecular_surface_apap_target"/>
		<Add filter="contact_molec_sq5_apap_target"/>
		<Add metrics="sap_score"/>
		<Add metrics="sap_score_target"/>
		<Add metrics="binder_delta_sap"/>
		<Add metrics="target_delta_sap"/>
		<Add filter="timed"/>
	</PROTOCOLS>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: beta_nov16.wts
core.scoring.etable: (0) Starting energy table calculation
core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: (0) Finished calculating energy tables.
basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb
basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb
basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: (0) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: (0) Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
core.scoring.etable: (0) Starting energy table calculation
core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: (0) Finished calculating energy tables.
basic.io.database: (0) Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: (0) Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: (0) Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: (0) shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: (0) Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
protocols.jd2.parser.ScoreFunctionLoader: (0) defined score function "sfxn" with weights "beta_nov16"
protocols.jd2.parser.ScoreFunctionLoader: (0) defined score function "sfxn_relax" with weights "beta_nov16"
protocols.jd2.parser.ScoreFunctionLoader: (0)  setting sfxn_relax weight arg_cation_pi to 3
protocols.jd2.parser.ScoreFunctionLoader: (0)  setting sfxn_relax weight approximate_buried_unsat_penalty to 5
protocols.jd2.parser.ScoreFunctionLoader: (0) defined score function "sfxn_design" with weights "beta_nov16"
protocols.jd2.parser.ScoreFunctionLoader: (0)  setting sfxn_design weight res_type_constraint to 1.5
protocols.jd2.parser.ScoreFunctionLoader: (0)  setting sfxn_design weight aa_composition to 1
protocols.jd2.parser.ScoreFunctionLoader: (0)  setting sfxn_design weight arg_cation_pi to 3
protocols.jd2.parser.ScoreFunctionLoader: (0)  setting sfxn_design weight approximate_buried_unsat_penalty to 5
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "PR_monomer_core_sel" of type SelectBySASA
protocols.residue_selectors.TaskSelector: (0) Adding task operation PR_monomer_core_sel
core.select.residue_selector.LayerSelector: (0) Setting LayerSelector to use sidechain neighbors to determine burial.
core.select.residue_selector.LayerSelector: (0) Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.
core.select.residue_selector.LayerSelector: (0) Setting core=false boundary=false surface=true in LayerSelector.
core.select.residue_selector.LayerSelector: (0) Setting LayerSelector to use sidechain neighbors to determine burial.
core.select.residue_selector.LayerSelector: (0) Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.
core.select.residue_selector.LayerSelector: (0) Setting LayerSelector to use sidechain neighbors to determine burial.
core.select.residue_selector.LayerSelector: (0) Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.
core.select.residue_selector.LayerSelector: (0) Setting core=false boundary=true surface=false in LayerSelector.
core.select.residue_selector.LayerSelector: (0) Setting LayerSelector to use sidechain neighbors to determine burial.
core.select.residue_selector.LayerSelector: (0) Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.
core.select.residue_selector.LayerSelector: (0) Setting LayerSelector to use sidechain neighbors to determine burial.
core.select.residue_selector.LayerSelector: (0) Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.
core.select.residue_selector.LayerSelector: (0) Setting core=true boundary=false surface=false in LayerSelector.
core.select.residue_selector.LayerSelector: (0) Setting LayerSelector to use sidechain neighbors to determine burial.
core.select.residue_selector.LayerSelector: (0) Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector.
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: (0) Using residue selector entire_helix
core.select.residue_selector.PrimarySequenceNeighborhoodSelector: (0) Using residue selector helix_cap
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "layer_design_F_boundary_M" of type DesignRestrictions
protocols.aa_composition.AddCompositionConstraintMover: (0) Read composition contraint from tags.Initialized AACompositionConstraint object from file contents:
PENALTY_DEFINITION
TYPE TRP
ABSOLUTE 0
PENALTIES 0 3
DELTA_START 0
DELTA_END 1
BEFORE_FUNCTION CONSTANT
AFTER_FUNCTION LINEAR
END_PENALTY_DEFINITION

protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named "3trp" of type AddCompositionConstraintMover
protocols.aa_composition.AddCompositionConstraintMover: (0) Read composition contraint from tags.Initialized AACompositionConstraint object from file contents:
PENALTY_DEFINITION
TYPE MET
ABSOLUTE 0
PENALTIES 0 2
DELTA_START 0
DELTA_END 1
BEFORE_FUNCTION CONSTANT
AFTER_FUNCTION LINEAR
END_PENALTY_DEFINITION

protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named "2met" of type AddCompositionConstraintMover
protocols.aa_composition.AddCompositionConstraintMover: (0) Read composition contraint from tags.Initialized AACompositionConstraint object from file contents:
PENALTY_DEFINITION
TYPE ASP GLU HIS LYS ASN GLN ARG SER THR TYR
FRACT_DELTA_START -0.01
FRACT_DELTA_END 0.0
PENALTIES 0.1 0 
FRACTION 0.30
BEFORE_FUNCTION QUADRATIC
AFTER_FUNCTION CONSTANT
END_PENALTY_DEFINITION

protocols.aa_composition.AddCompositionConstraintMover: (0) Set selector name to for_hydrophobic.
protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named "30_percent_polar" of type AddCompositionConstraintMover
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "prune_buried_unsats" of type PruneBuriedUnsats
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "upweight_interface" of type ProteinProteinInterfaceUpweighter
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "pack_long" of type ProteinInterfaceDesign
core.pack.task.operation.TaskOperation: (0) 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: (0) Defined TaskOperation named "current" of type IncludeCurrent
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "limitchi2" of type LimitAromaChi2
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "ex1_ex2" of type ExtraRotamersGeneric
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "restrict_target_not_interface" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "restrict_to_interface" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "restrict_target2repacking" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "restrict_hotspots2repacking" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "disallow_GLY" of type DisallowIfNonnative
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "disallow_PRO" of type DisallowIfNonnative
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "restrict_PRO_GLY" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: (0) Defined TaskOperation named "PR_monomer_core" of type SelectBySASA
core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: beta_nov16.wts
protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named "chain1only" of type SwitchChainOrder
core.pack.task.xml_util: (0) Object min reading the following task_operations: Adding the following task operations
pack_long 
protocols.rosetta_scripts.RosettaScriptsParser: (0) Defined mover named "min" of type TaskAwareMinMover
basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_SS_cen6/P_AA_SS_cen6.txt
core.indexed_structure_store.BinaryFragmentStoreBackend: (0) Loading backend: /opt/software/ss_grouped_vall_all


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


terminate called after throwing an instance of 'utility::json_spirit::Error_position'
Got some signal... It is:6
Signal 6 (SIGABRT) means that the process was aborted.  This usually means an internal Rosetta error caused by (often) bad inputs, (sometimes) developer error, or (rarely) hardware problems.