RosettaScripts and commandline instructions

<ROSETTASCRIPTS>
	<TASKOPERATIONS>
		<RestrictToRepacking name="rtr"/>
		<InitializeFromCommandline name="init"/>
		<IncludeCurrent name="include_curr"/>
        <PreventResiduesFromRepacking name="fix_res" reference_pdb_id="%%pdb_reference%%" residues="%%res_to_fix%%"/> #any improtant residues
	</TASKOPERATIONS>
	<SCOREFXNS>
		<ScoreFunction name="talaris" weights="talaris2014">
			<Reweight scoretype="coordinate_constraint" weight="0.1"/>
		</ScoreFunction>
	</SCOREFXNS>	
	<FILTERS>
	</FILTERS>
	<MOVERS>
        <AtomTree name="tree" docking_ft="1"/>
        <MutateResidue name="mut0" target="41A" new_res="ALA"/>
        <MutateResidue name="mut1" target="47A" new_res="TYR"/>
        <MutateResidue name="mut2" target="53A" new_res="TYR"/>
        <MutateResidue name="mut3" target="87A" new_res="GLN"/>
        <MutateResidue name="mut4" target="92A" new_res="THR"/>
        <MutateResidue name="mut5" target="93A" new_res="PRO"/>
        <MutateResidue name="mut6" target="95A" new_res="THR"/>
        <MutateResidue name="mut7" target="98A" new_res="GLN"/>
        <MutateResidue name="mut8" target="160A" new_res="TYR"/>
        <MutateResidue name="mut9" target="196A" new_res="TYR"/>
        <MutateResidue name="mut10" target="208A" new_res="MET"/>
        <PackRotamersMover name="prm" task_operations="init,include_curr,rtr,fix_res" scorefxn="talaris"/>
        <RotamerTrialsMinMover name="rtmin" task_operations="init,include_curr,rtr,fix_res" scorefxn="talaris"/>
        <MinMover name="min" bb="1" chi="1" jump="1" scorefxn="talaris"/>
        <AddConstraintsToCurrentConformationMover name="csts"/>
	</MOVERS>
    <PROTOCOLS>
        <Add mover="tree"/>
	<Add mover="csts"/>
        <Add mover="mut0"/>
        <Add mover="mut1"/>
        <Add mover="mut2"/>
        <Add mover="mut3"/>
        <Add mover="mut4"/>
        <Add mover="mut5"/>
        <Add mover="mut6"/>
        <Add mover="mut7"/>
        <Add mover="mut8"/>
        <Add mover="mut9"/>
        <Add mover="mut10"/>
        <Add mover="prm"/>
        <Add mover="rtmin"/>
        <Add mover="rtmin"/>
        <Add mover="rtmin"/>
        <Add mover="min"/>
    </PROTOCOLS>
</ROSETTASCRIPTS>

Command line options (wrapped in “flags” file)

-use_input_sc
-extrachi_cutoff 5
-ignore_unrecognized_res
-use_occurrence_data
-chemical:exclude_patches LowerDNA  UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated  tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated  lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm
-linmem_ig 10
-ignore_zero_occupancy false
-out:path:pdb pdb/
-out:path:score score/
-mute all
-overwrite
-parser:script_vars res_to_fix=-1 # residues prevented from repacking. use with the script_vars pdb_reference
-database Rosetta/main/database/

Command line execution
rosetta_scripts.default.linuxgccrelease @flags -s <Input PDB after refinement> -parser:protocol <name of xml file e.g. 0101010101010101010101.xml>