refine.xml

<ROSETTASCRIPTS>

  <SCOREFXNS>
    <ScoreFunction name="ref_full" weights="ref2015">
      <Reweight scoretype="coordinate_constraint" weight="0.1"/>
      <Reweight scoretype="res_type_constraint" weight="0.1"/>
    </ScoreFunction>
    <ScoreFunction name="soft_rep_full" weights="soft_rep">
      <Reweight scoretype="coordinate_constraint" weight="0.1"/>
      <Reweight scoretype="res_type_constraint" weight="0.1"/>
    </ScoreFunction>
    <ScoreFunction name="ref_no_pssm" weights="ref2015">
      <Reweight scoretype="coordinate_constraint" weight="0.1"/>
    </ScoreFunction>
    <ScoreFunction name="ref_pure" weights="ref2015"/>
  </SCOREFXNS>

  <RESIDUE_SELECTORS>
    <Index name="ress_fix" resnums="%%res_to_fix%%"/>
  </RESIDUE_SELECTORS>

  <TASKOPERATIONS>
    <InitializeFromCommandline name="init"/>
    <RestrictToRepacking name="rtr"/>
    <OperateOnResidueSubset name="fix_res" selector="ress_fix">
      <PreventRepackingRLT/>
    </OperateOnResidueSubset>
    <OperateOnResidueSubset name="not_to_cst_sc">
      <Not selector="ress_fix"/>
      <PreventRepackingRLT/>
    </OperateOnResidueSubset>
  </TASKOPERATIONS>

  <MOVERS>
    <AtomCoordinateCstMover name="fix_res_sc_cst" coord_dev="0.5" bounded="false" sidechain="true" task_operations="not_to_cst_sc"/>
    <PackRotamersMover name="soft_repack" scorefxn="soft_rep_full" task_operations="init,rtr,fix_res"/>
    <PackRotamersMover name="hard_repack" scorefxn="ref_full" task_operations="init,rtr,fix_res"/>
    <RotamerTrialsMinMover name="RTmin" scorefxn="ref_full" task_operations="init,rtr,fix_res"/>
    <TaskAwareMinMover name="soft_min" scorefxn="soft_rep_full" chi="1" bb="1" jump="0" task_operations="init,fix_res"/>
    <TaskAwareMinMover name="hard_min" scorefxn="ref_full" chi="1" bb="1" jump="0" task_operations="init,fix_res"/>
    <ConstraintSetMover name="add_CA_cst" cst_file="%%cst_full_path%%"/>

    <ParsedProtocol name="refinement_block">
      <Add mover_name="soft_repack"/>
      <Add mover_name="soft_min"/>
      <Add mover_name="soft_repack"/>
      <Add mover_name="hard_min"/>
      <Add mover_name="hard_repack"/>
      <Add mover_name="hard_min"/>
      <Add mover_name="hard_repack"/>
      <Add mover_name="RTmin"/>
      <Add mover_name="RTmin"/>
      <Add mover_name="hard_min"/>
    </ParsedProtocol>

    <LoopOver name="iter4" mover_name="refinement_block" iterations="4"/>
  </MOVERS>

  <FILTERS>
    <ScoreType name="stability_score_full" scorefxn="ref_full" score_type="total_score" confidence="0" threshold="0"/>
    <ScoreType name="stability_without_pssm" scorefxn="ref_no_pssm" score_type="total_score" confidence="0" threshold="0"/>
    <ScoreType name="stability_pure" scorefxn="ref_pure" score_type="total_score" confidence="0" threshold="0"/>
    <Rmsd name="rmsd" confidence="0"/>
    <Time name="timer"/>
  </FILTERS>

  <PROTOCOLS>
    <Add filter_name="timer"/>
    <Add mover_name="add_CA_cst"/>
    <Add mover_name="fix_res_sc_cst"/>
    <Add mover_name="iter4"/>
    <Add filter_name="stability_score_full"/>
    <Add filter_name="stability_without_pssm"/>
    <Add filter_name="stability_pure"/>
    <Add filter_name="rmsd"/>
    <Add filter_name="timer"/>
  </PROTOCOLS>
  
  <OUTPUT scorefxn="ref_full"/>

</ROSETTASCRIPTS>