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P1.xml
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<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="r15_for_cart" weights="ref2015_cart">
</ScoreFunction>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Layer name="core_layer" select_core="true" use_sidechain_neighbors="true" core_cutoff="3.9" surface_cutoff="1.6" />
#select entire pose
<True name="full_pose" />
# get all network residues as output by HBNet
<ResiduePDBInfoHasLabel name="hbnet_residues" property="HBNet" />
# select everything within 5A around the network residues
<Neighborhood name="around_hbnet" selector="hbnet_residues" distance="5.0" />
# select only the buried residues within this set
<Layer name="hbnet_core" select_core="true" core_cutoff="3.9" /> # select core us
ing sidechain neighbors (don’t use SASA because of potential voids!)
<And name="core_around_hbnet" selectors="hbnet_core,around_hbnet"/>
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<InitializeFromCommandline name="ex_flags" />
<LimitAromaChi2 name="limit_aroma_chi"/>
<OperateOnResidueSubset name="no_cys" selector="full_pose" >
<RestrictAbsentCanonicalAASRLT aas="AFDEGHIKLMNPQRSTVWY" />
</OperateOnResidueSubset>
</TASKOPERATIONS>
<FILTERS>
<BuriedUnsatHbonds name="Unsatisfied_hbonds_core" residue_selector="core_layer" report_bb_heavy_atom_unsats="true" scorefxn="r15_for_cart" ignore_surface_res="true" print_out_info_to_pdb="true" confidence="0.0"/>
<BuriedUnsatHbonds name="buns_bb_heavy" residue_selector="core_layer" report_bb_heavy_atom_unsats="true" scorefxn="r15_for_cart" cutoff="4" ignore_surface_res="true" print_out_info_to_pdb="true" />
<BuriedUnsatHbonds name="buns_sc_heavy" residue_selector="core_layer" report_sc_heavy_atom_unsats="true" scorefxn="r15_for_cart" cutoff="0" ignore_surface_res="true" print_out_info_to_pdb="true" />
<SequenceRecovery name="recovery_of_og_seq" rate_threshold="0.0" task_operations="limit_aroma_chi,ex_flags" report_mutations="0" scorefxn="r15_for_cart" confidence="0.0"/>
<Rmsd name="rmsd_to_input" chains="%%chain%%" threshold="15" superimpose="1" confidence="0.0">
<span begin_res_num="1" end_res_num="104" />
</Rmsd>
<PackStat chain="0" confidence="0" name="pack_stat" repeats="2" threshold="0.65"/>
<Rmsd name="rmsd_filter" chains="%%chain%%" threshold="1.5" superimpose="1" confidence="1">
<span begin_res_num="1" end_res_num="104" />
</Rmsd>
<ExposedHydrophobics name="exposed_hydrophobics" threshold="-1" confidence="0.0" />
<Holes name="full_holes" threshold="1.8" confidence="0"/>
# holes score only around h-bond networks
<Holes name="network_holes" threshold="1.8" residue_selector="core_around_hbnet" normalize_per_atom="true" exclude_bb_atoms="true" confidence="0"/>
</FILTERS>
<MOVERS>
<FastDesign name="fastdes_all" scorefxn="r15_for_cart" task_operations="limit_aroma_chi,ex_flags,no_cys" repeats="2" ramp_down_constraints="0" />
<ParsedProtocol name="try_this">
<Add mover_name="fastdes_all" />
<Add filter="buns_bb_heavy" />
<Add filter="rmsd_filter" />
</ParsedProtocol>
<LoopOver name="feeling_loopy" mover_name="fastdes_all" filter_name="buns_sc_heavy" iterations="40" drift="false" ms_whenfail="FAIL_DO_NOT_RETRY" />
</MOVERS>
<APPLY_TO_POSE>
</APPLY_TO_POSE>
<PROTOCOLS>
<Add mover_name="feeling_loopy" />
<Add filter="pack_stat" />
<Add filter="Unsatisfied_hbonds_core"/>
<Add filter="exposed_hydrophobics" />
<Add filter="full_holes" />
<Add filter="network_holes" />
<Add filter="recovery_of_og_seq"/>
</PROTOCOLS>
<OUTPUT scorefxn="r15_for_cart" />
</ROSETTASCRIPTS>