-s input_docked_ligand.pdb -extra_res_fa EY1.params -resfile mutations.resfile -enzdes::cstfile EY1_finalrun3.cst -enzdes::detect_design_interface -enzdes::cut1 4.0 -enzdes::cut2 6.0 -enzdes::cut3 8.0 -enzdes::cut4 10.0 -enzdes::cst_opt -enzdes::cst_design -enzdes::cst_min -enzdes::bb_min -enzdes::chi_min -enzdes::lig_packer_weight 2 -enzdes::design_min_cycles 3 #-enzdes::favor_native_res 1 -nstruct 1000 -packing:ex1 -packing:ex2 -packing:use_input_sc -packing:soft_rep_design #-packing:linmen_ig 10 #-enzdes::final_repack_without_ligand -out::file::o scores.out -database /Applications/rosetta_src_2015.05.57576_bundle/main/database