<ROSETTASCRIPTS>

<SCOREFXNS>

<ligand_soft_rep weights=ligand_soft_rep/>

<hard rep weights=ligandprime/>

</SCOREFXNS>

<TASKOPERATIONS>

<DetectProteinLigandInterface name=design_

interface cut1=6.0 cut2=8.0 cut3=10.0 cut4=12.0

design=1 resfi le=“PDB.resfile”/> # see Note 19

</TASKOPERATIONS>

<LIGAND_AREAS>

<docking_sidechain chain=X cutoff=6.0 add_

nbr_radius=true all_atom_mode=true minimize_

ligand=10/>

<final_sidechain chain=X cutoff=6.0 add_nbr

radius=true all_atom_mode=true/>

<final_backbone chain=X cutoff=7.0 add_

nbr_radius=false all_atom_mode=true Calpha_

restraints=0.3/>

</LIGAND_AREAS>

<INTERFACE_BUILDERS>

<side_chain_for_docking ligand_areas=docking_

sidechain/>

<side_chain_for_final ligand_areas=final_

sidechain/>

<backbone ligand_areas=final_backbone extension_

window=3/>

</INTERFACE_BUILDERS>

<MOVEMAP_BUILDERS>

<docking sc_interface=side_chain_for_docking

minimize_water=true/>

<final sc_interface=side_chain_for_final bb_

interface=backbone minimize_water=true/>

</MOVEMAP_BUILDERS>

<SCORINGGRIDS ligand_chain=X width=15> # see Note 20

<vdw grid_type=ClassicGrid weight=1.0/>

</SCORINGGRIDS>

<MOVERS>

<FavorNativeResidue name=favor_native bonus=

1.00/> # see Notes 21 and 22

<Transform name=transform chain=X box_size=

5.0 move_distance=0.1 angle=5 cycles=500

repeats=1 temperature=5 rmsd=4.0/> # see

Note 23

<HighResDocker name=high_res_docker cycles=6

repack_every_Nth=3 scorefxn=ligand_soft_rep

movemap_builder=docking/>

<PackRotamersMover name=designinterface score-

fxn=hard_rep task_operations=design_inter-

face/>

<FinalMinimizer name=final scorefxn=hard_rep

movemap_builder=final/>

<InterfaceScoreCalculator name=add_scores

chains=X scorefxn=hard_rep/>

<ParsedProtocol name=low_res_dock>

<Add mover_name=transform/>

</ParsedProtocol>

<ParsedProtocol name=high_res_dock>

<Add mover_name=high_res_docker/>

<Add mover_name=final/>

</ParsedProtocol>

</MOVERS>

<PROTOCOLS>

<Add mover_name=favor_native/>

<Add mover_name=low_res_dock/>

< Add mover_name=design_interface/> # see

Note 24

<Add mover_name=high_res_dock/>

<Add mover_name=add_scores/>

</PROTOCOLS>

</ROSETTASCRIPTS>