-run:protocol jd2_scripting -in::file::boinc_wu_zip HKH2024_1ACB_xak_xaq_B_input_files.zip -database database -nstruct 2 -parser:protocol relax_interface_of_chainB.xml -parser:script_vars wts=beta16_plus_lj_changes.wts relaxscript=MonomerDesign2019 -in:file:silent xaq -in:file:silent_struct_type binary -score:weights beta16_plus_lj_changes.wts -crystal_refine true -overwrite -in:file:native 1ACB_bound_native.pdb -out:file:renumber_pdb true -silent_read_through_errors -silent_gz -out:file:silent_struct_type binary -out:file:silent default.out -out:file:scorefile default.sc -mute all # -score::unmodifypot true -score::fa_Hatr true -score::hbond_new_sp3_acc true -score::elec_sigmoidal_die true -dna::specificity::lk_ball_water_fade 1.0 -dna::specificity::lk_ball_for_bb true -dna::specificity::lk_ball_bridge_angle_widthscale 2.8 -corrections::shapovalov_lib_fixes_enable true -corrections::shapovalov_lib::shap_dun10_enable false -corrections::shapovalov_lib::shap_p_aa_pp_smooth_level 1 -corrections::score::rama_pp_map scoring/score_functions/rama/fd_beta_nov2016 -corrections::score::dun10_dir rotamer/beta_nov2016 -corrections::score::bbdep_omega true -score::elec_representative_cp_flip true -score::bonded_params_dir scoring/score_functions/bondlength_bondangle -chemical::set_atom_properties fa_standard:NtrR:LK_DGFREE:-4.9280 -chemical::set_atom_properties fa_standard:aroC:LK_DGFREE:2.2228 -chemical::set_atom_properties fa_standard:CH2:LK_DGFREE:-2.5518 -chemical::set_atom_properties fa_standard:Nhis:LK_DGFREE:-9.7253 -chemical::set_atom_properties fa_standard:Ntrp:LK_DGFREE:-10.6448 -chemical::set_atom_properties fa_standard:CH3:LK_DGFREE:7.7272 -chemical::set_atom_properties fa_standard:Npro:LK_DGFREE:-1.5111 -chemical::set_atom_properties fa_standard:OOC:LK_DGFREE:-10.2082 -chemical::set_atom_properties fa_standard:CH1:LK_DGFREE:-6.4922 -chemical::set_atom_properties fa_standard:S:LK_DGFREE:-4.8980 -chemical::set_atom_properties fa_standard:Narg:LK_DGFREE:-8.6960 -chemical::set_atom_properties fa_standard:SH1:LK_DGFREE:2.0795 -chemical::set_atom_properties fa_standard:CAbb:LK_DGFREE:4.4494 -chemical::set_atom_properties fa_standard:CNH2:LK_DGFREE:3.7033 -chemical::set_atom_properties fa_standard:OH:LK_DGFREE:-5.4606 -chemical::set_atom_properties fa_standard:OW:LK_DGFREE:-5.4606 -chemical::set_atom_properties fa_standard:CObb:LK_DGFREE:3.5790 -chemical::set_atom_properties fa_standard:CH0:LK_DGFREE:1.2487 -chemical::set_atom_properties fa_standard:NH2O:LK_DGFREE:-7.6667 -chemical::set_atom_properties fa_standard:OCbb:LK_DGFREE:-9.5292 -chemical::set_atom_properties fa_standard:Nbb:LK_DGFREE:-12.8467 -chemical::set_atom_properties fa_standard:ONH2:LK_DGFREE:-5.0350 -chemical::set_atom_properties fa_standard:COO:LK_DGFREE:-2.5088 -chemical::set_atom_properties fa_standard:Nlys:LK_DGFREE:-18.7433 -chemical:set_atomic_charge fa_standard:GLU:CB:-0.16925 -chemical:set_atomic_charge fa_standard:GLU:CG:-0.25364 -chemical:set_atomic_charge fa_standard:GLU:CD:0.50590 -chemical:set_atomic_charge fa_standard:GLU:OE1:-0.65874 -chemical:set_atomic_charge fa_standard:GLU:OE2:-0.65874 -chemical:set_atomic_charge fa_standard:GLU:1HB:0.05862 -chemical:set_atomic_charge fa_standard:GLU:2HB:0.05862 -chemical:set_atomic_charge fa_standard:GLU:1HG:0.05862 -chemical:set_atomic_charge fa_standard:GLU:2HG:0.05862 -chemical:set_atomic_charge fa_standard:ALA:N:-0.77049 -chemical:set_atomic_charge fa_standard:ALA:CA:0.11475 -chemical:set_atomic_charge fa_standard:ALA:H:0.50819 -chemical:set_atomic_charge fa_standard:ALA:HA:0.14754 -chemical:set_atomic_charge fa_standard:ASN:N:-0.77049 -chemical:set_atomic_charge fa_standard:ASN:CA:0.11475 -chemical:set_atomic_charge fa_standard:ASN:H:0.50819 -chemical:set_atomic_charge fa_standard:ASN:HA:0.14754 -chemical:set_atomic_charge fa_standard:ASP:N:-0.77049 -chemical:set_atomic_charge fa_standard:ASP:CA:0.11475 -chemical:set_atomic_charge fa_standard:ASP:H:0.50819 -chemical:set_atomic_charge fa_standard:ASP:HA:0.14754 -chemical:set_atomic_charge fa_standard:ARG:N:-0.77049 -chemical:set_atomic_charge fa_standard:ARG:CA:0.11475 -chemical:set_atomic_charge fa_standard:ARG:H:0.50819 -chemical:set_atomic_charge fa_standard:ARG:HA:0.14754 -chemical:set_atomic_charge fa_standard:GLY:N:-0.77049 -chemical:set_atomic_charge fa_standard:GLY:CA:-0.03279 -chemical:set_atomic_charge fa_standard:GLY:H:0.50819 -chemical:set_atomic_charge fa_standard:GLY:1HA:0.14754 -chemical:set_atomic_charge fa_standard:GLY:2HA:0.14754 -chemical:set_atomic_charge fa_standard:CYS:N:-0.77049 -chemical:set_atomic_charge fa_standard:CYS:CA:0.11475 -chemical:set_atomic_charge fa_standard:CYS:H:0.50819 -chemical:set_atomic_charge fa_standard:CYS:HA:0.14754 -chemical:set_atomic_charge fa_standard:CYD:N:-0.77049 -chemical:set_atomic_charge fa_standard:CYD:CA:0.11475 -chemical:set_atomic_charge fa_standard:CYD:H:0.50819 -chemical:set_atomic_charge fa_standard:CYD:HA:0.14754 -chemical:set_atomic_charge fa_standard:ILE:N:-0.77049 -chemical:set_atomic_charge fa_standard:ILE:CA:0.11475 -chemical:set_atomic_charge fa_standard:ILE:H:0.50819 -chemical:set_atomic_charge fa_standard:ILE:HA:0.14754 -chemical:set_atomic_charge fa_standard:GLN:N:-0.77049 -chemical:set_atomic_charge fa_standard:GLN:CA:0.11475 -chemical:set_atomic_charge fa_standard:GLN:H:0.50819 -chemical:set_atomic_charge fa_standard:GLN:HA:0.14754 -chemical:set_atomic_charge fa_standard:GLU:N:-0.77049 -chemical:set_atomic_charge fa_standard:GLU:CA:0.11475 -chemical:set_atomic_charge fa_standard:GLU:H:0.50819 -chemical:set_atomic_charge fa_standard:GLU:HA:0.14754 -chemical:set_atomic_charge fa_standard:HIS:N:-0.77049 -chemical:set_atomic_charge fa_standard:HIS:CA:0.11475 -chemical:set_atomic_charge fa_standard:HIS:H:0.50819 -chemical:set_atomic_charge fa_standard:HIS:HA:0.14754 -chemical:set_atomic_charge fa_standard:HIS_D:N:-0.77049 -chemical:set_atomic_charge fa_standard:HIS_D:CA:0.11475 -chemical:set_atomic_charge 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fa_standard:PRO:CG:-0.29508 -chemical:set_atomic_charge fa_standard:PRO:1HD:0.14754 -chemical:set_atomic_charge fa_standard:PRO:2HD:0.14754 -chemical:set_atomic_charge fa_standard:PRO:1HG:0.14754 -chemical:set_atomic_charge fa_standard:PRO:2HG:0.14754 -chemical:set_atomic_charge fa_standard:PRO:1HB:0.14754 -chemical:set_atomic_charge fa_standard:PRO:2HB:0.14754 -chemical:set_atomic_charge fa_standard:TYR:N:-0.77049 -chemical:set_atomic_charge fa_standard:TYR:CA:0.11475 -chemical:set_atomic_charge fa_standard:TYR:H:0.50819 -chemical:set_atomic_charge fa_standard:TYR:HA:0.14754 -chemical:set_atomic_charge fa_standard:TRP:N:-0.77049 -chemical:set_atomic_charge fa_standard:TRP:CA:0.11475 -chemical:set_atomic_charge fa_standard:TRP:H:0.50819 -chemical:set_atomic_charge fa_standard:TRP:HA:0.14754 -chemical:set_atomic_charge fa_standard:VAL:N:-0.77049 -chemical:set_atomic_charge fa_standard:VAL:CA:0.11475 -chemical:set_atomic_charge fa_standard:VAL:H:0.50819 -chemical:set_atomic_charge fa_standard:VAL:HA:0.14754 -chemical:set_atomic_charge fa_standard:LYS:N:-0.77049 -chemical:set_atomic_charge fa_standard:LYS:CA:0.11475 -chemical:set_atomic_charge fa_standard:LYS:H:0.50819 -chemical:set_atomic_charge fa_standard:LYS:HA:0.14754 -chemical:set_atomic_charge fa_standard:SER:N:-0.77049 -chemical:set_atomic_charge fa_standard:SER:CA:0.11475 -chemical:set_atomic_charge fa_standard:SER:H:0.50819 -chemical:set_atomic_charge fa_standard:SER:HA:0.14754 -chemical:set_atomic_charge fa_standard:THR:N:-0.77049 -chemical:set_atomic_charge fa_standard:THR:CA:0.11475 -chemical:set_atomic_charge fa_standard:THR:H:0.50819 -chemical:set_atomic_charge fa_standard:THR:HA:0.14754 -chemical:set_atomic_charge fa_standard:ALA:C:0.76511 -chemical:set_atomic_charge fa_standard:ALA:O:-0.76511 -chemical:set_atomic_charge fa_standard:ASN:C:0.76511 -chemical:set_atomic_charge fa_standard:ASN:O:-0.76511 -chemical:set_atomic_charge fa_standard:ASP:C:0.76511 -chemical:set_atomic_charge 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-chemical:set_atomic_charge fa_standard:ILE:CG2:-0.36465 -chemical:set_atomic_charge fa_standard:ILE:CD1:-0.36465 -chemical:set_atomic_charge fa_standard:ILE:HB:0.12155 -chemical:set_atomic_charge fa_standard:ILE:1HG2:0.12155 -chemical:set_atomic_charge fa_standard:ILE:2HG2:0.12155 -chemical:set_atomic_charge fa_standard:ILE:3HG2:0.12155 -chemical:set_atomic_charge fa_standard:ILE:1HG1:0.12155 -chemical:set_atomic_charge fa_standard:ILE:2HG1:0.12155 -chemical:set_atomic_charge fa_standard:ILE:1HD1:0.12155 -chemical:set_atomic_charge fa_standard:ILE:2HD1:0.12155 -chemical:set_atomic_charge fa_standard:ILE:3HD1:0.12155 -chemical:set_atomic_charge fa_standard:LEU:CB:-0.24310 -chemical:set_atomic_charge fa_standard:LEU:CG:-0.12155 -chemical:set_atomic_charge fa_standard:LEU:CD1:-0.36465 -chemical:set_atomic_charge fa_standard:LEU:CD2:-0.36465 -chemical:set_atomic_charge fa_standard:LEU:1HB:0.12155 -chemical:set_atomic_charge fa_standard:LEU:2HB:0.12155 -chemical:set_atomic_charge 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fa_standard:HIS:NE2:-0.33825 -chemical:set_atomic_charge fa_standard:HIS:HE2:0.30067 -chemical:set_atomic_charge fa_standard:HIS:1HB:0.08456 -chemical:set_atomic_charge fa_standard:HIS:2HB:0.08456 -chemical:set_atomic_charge fa_standard:HIS:HE1:0.12215 -chemical:set_atomic_charge fa_standard:HIS:HD2:0.08456 -chemical:set_atomic_charge fa_standard:HIS_D:CB:-0.08456 -chemical:set_atomic_charge fa_standard:HIS_D:CG:-0.04698 -chemical:set_atomic_charge fa_standard:HIS_D:ND1:-0.33825 -chemical:set_atomic_charge fa_standard:HIS_D:CD2:0.20671 -chemical:set_atomic_charge fa_standard:HIS_D:CE1:0.23490 -chemical:set_atomic_charge fa_standard:HIS_D:NE2:-0.65772 -chemical:set_atomic_charge fa_standard:HIS_D:HD1:0.30067 -chemical:set_atomic_charge fa_standard:HIS_D:1HB:0.08456 -chemical:set_atomic_charge fa_standard:HIS_D:2HB:0.08456 -chemical:set_atomic_charge fa_standard:HIS_D:HE1:0.12215 -chemical:set_atomic_charge fa_standard:HIS_D:HD2:0.09396 -chemical:set_atomic_charge fa_standard:ASP:CB:-0.29888 -chemical:set_atomic_charge fa_standard:ASP:CG:0.75106 -chemical:set_atomic_charge fa_standard:ASP:OD1:-0.85885 -chemical:set_atomic_charge fa_standard:ASP:OD2:-0.85885 -chemical:set_atomic_charge fa_standard:ASP:1HB:0.13276 -chemical:set_atomic_charge fa_standard:ASP:2HB:0.13276 -chemical:set_atomic_charge fa_standard:SER:CB:0.04076 -chemical:set_atomic_charge fa_standard:SER:OG:-0.53802 -chemical:set_atomic_charge fa_standard:SER:HG:0.35053 -chemical:set_atomic_charge fa_standard:SER:1HB:0.07337 -chemical:set_atomic_charge fa_standard:SER:2HB:0.07337 -chemical:set_patch_atomic_charge fa_standard:ALA:CtermProteinFull:C:0.35448 -chemical:set_patch_atomic_charge fa_standard:ALA:CtermProteinFull:OXT:-0.67724 -chemical:set_patch_atomic_charge fa_standard:ALA:CtermProteinFull:O:-0.67724 -chemical:set_atomic_charge fa_standard:ARG:CB:-0.08557 -chemical:set_atomic_charge fa_standard:ARG:CG:-0.08557 -chemical:set_atomic_charge fa_standard:ARG:CD:0.14210 -chemical:set_atomic_charge fa_standard:ARG:NE:-0.39713 -chemical:set_atomic_charge fa_standard:ARG:CZ:0.40572 -chemical:set_atomic_charge fa_standard:ARG:NH1:-0.45704 -chemical:set_atomic_charge fa_standard:ARG:NH2:-0.45704 -chemical:set_atomic_charge fa_standard:ARG:1HH1:0.29787 -chemical:set_atomic_charge fa_standard:ARG:2HH1:0.29787 -chemical:set_atomic_charge fa_standard:ARG:1HH2:0.29787 -chemical:set_atomic_charge fa_standard:ARG:2HH2:0.29787 -chemical:set_atomic_charge fa_standard:ARG:HE:0.28589 -chemical:set_atomic_charge fa_standard:ARG:1HB:0.07619 -chemical:set_atomic_charge fa_standard:ARG:2HB:0.07619 -chemical:set_atomic_charge fa_standard:ARG:1HG:0.07619 -chemical:set_atomic_charge fa_standard:ARG:2HG:0.07619 -chemical:set_atomic_charge fa_standard:ARG:1HD:0.07619 -chemical:set_atomic_charge fa_standard:ARG:2HD:0.07619 -chemical:set_patch_atomic_charge fa_standard:ALA:NtermProteinFull:N:-0.10440 -chemical:set_patch_atomic_charge fa_standard:ALA:NtermProteinFull:CA:0.19184 -chemical:set_patch_atomic_charge fa_standard:ALA:NtermProteinFull:1H:0.26154 -chemical:set_patch_atomic_charge fa_standard:ALA:NtermProteinFull:2H:0.26154 -chemical:set_patch_atomic_charge fa_standard:ALA:NtermProteinFull:3H:0.26154 -chemical:set_patch_atomic_charge fa_standard:ALA:NtermProteinFull:HA:0.12794 -chemical:set_patch_atomic_charge fa_standard:GLY:NtermProteinFull:N:-0.11438 -chemical:set_patch_atomic_charge fa_standard:GLY:NtermProteinFull:CA:0.13539 -chemical:set_patch_atomic_charge fa_standard:GLY:NtermProteinFull:1H:0.25156 -chemical:set_patch_atomic_charge fa_standard:GLY:NtermProteinFull:2H:0.25156 -chemical:set_patch_atomic_charge fa_standard:GLY:NtermProteinFull:3H:0.25156 -chemical:set_patch_atomic_charge fa_standard:GLY:NtermProteinFull:1HA:0.11215 -chemical:set_patch_atomic_charge fa_standard:GLY:NtermProteinFull:2HA:0.11215 -chemical:set_patch_atomic_charge fa_standard:PRO:NtermProteinFull:N:-0.00127 -chemical:set_patch_atomic_charge fa_standard:PRO:NtermProteinFull:CA:0.13233 -chemical:set_patch_atomic_charge fa_standard:PRO:NtermProteinFull:1H:0.17880 -chemical:set_patch_atomic_charge fa_standard:PRO:NtermProteinFull:2H:0.17880 -chemical:set_patch_atomic_charge fa_standard:PRO:NtermProteinFull:HA:0.09167 -chemical:set_patch_atomic_charge fa_standard:PRO:NtermProteinFull:CB:-0.06516 -chemical:set_patch_atomic_charge fa_standard:PRO:NtermProteinFull:CG:-0.06516 -chemical:set_patch_atomic_charge fa_standard:PRO:NtermProteinFull:1HD:0.09167 -chemical:set_patch_atomic_charge fa_standard:PRO:NtermProteinFull:2HD:0.09167 -chemical:set_patch_atomic_charge fa_standard:PRO:NtermProteinFull:1HG:0.09167 -chemical:set_patch_atomic_charge fa_standard:PRO:NtermProteinFull:2HG:0.09167 -chemical:set_patch_atomic_charge fa_standard:PRO:NtermProteinFull:1HB:0.09167 -chemical:set_patch_atomic_charge fa_standard:PRO:NtermProteinFull:2HB:0.09167 -chemical:set_atomic_charge fa_standard:TRP:CB:-0.21662 -chemical:set_atomic_charge fa_standard:TRP:CG:-0.03610 -chemical:set_atomic_charge fa_standard:TRP:CD1:0.04212 -chemical:set_atomic_charge fa_standard:TRP:CD2:-0.02407 -chemical:set_atomic_charge fa_standard:TRP:NE1:-0.73409 -chemical:set_atomic_charge fa_standard:TRP:CE2:0.15644 -chemical:set_atomic_charge fa_standard:TRP:CE3:-0.13839 -chemical:set_atomic_charge fa_standard:TRP:CZ2:-0.13839 -chemical:set_atomic_charge fa_standard:TRP:CZ3:-0.13839 -chemical:set_atomic_charge fa_standard:TRP:CH2:-0.13839 -chemical:set_atomic_charge fa_standard:TRP:HE1:0.45730 -chemical:set_atomic_charge fa_standard:TRP:HD1:0.13839 -chemical:set_atomic_charge fa_standard:TRP:HZ2:0.13839 -chemical:set_atomic_charge fa_standard:TRP:HH2:0.13839 -chemical:set_atomic_charge fa_standard:TRP:HZ3:0.13839 -chemical:set_atomic_charge fa_standard:TRP:HE3:0.13839 -chemical:set_atomic_charge fa_standard:TRP:1HB:0.10831 -chemical:set_atomic_charge fa_standard:TRP:2HB:0.10831 -score::hb_don_strength hbdon_HXL:0.99 -score::hb_don_strength hbdon_IME:1.42 -score::hb_don_strength hbdon_GDE:1.11 -score::hb_don_strength hbdon_AHX:1.00 -score::hb_don_strength hbdon_PBA:1.45 -score::hb_don_strength hbdon_H2O:1.26 -score::hb_don_strength hbdon_AMO:1.17 -score::hb_don_strength hbdon_IND:1.15 -score::hb_don_strength hbdon_IMD:1.18 -score::hb_don_strength hbdon_CXA:1.29 -score::hb_don_strength hbdon_GDH:1.11 -score::hb_acc_strength hbacc_HXL:1.15 -score::hb_acc_strength hbacc_CXA:1.21 -score::hb_acc_strength hbacc_H2O:1.23 -score::hb_acc_strength hbacc_IMD:1.13 -score::hb_acc_strength hbacc_IME:1.17 -score::hb_acc_strength hbacc_AHX:1.15 -score::hb_acc_strength hbacc_PBA:1.19 -score::hb_acc_strength hbacc_CXL:1.10 -elec_sigmoidal_die_D 79.931 -elec_sigmoidal_die_D0 6.648 -elec_sigmoidal_die_S 0.441546 -lk_ball_waters_sp2 2.828 134.5 0.0 2.828 134.5 180.0 -lk_ball_waters_sp3 2.828 109.3 120.0 2.828 109.3 240.0 -lk_ball_waters_ring 2.828 180 0 -lk_ball_waters_donor 2.828 -set_weights lk_ball 0.92 lk_ball_iso -0.38 lk_ball_bridge -0.33 lk_ball_bridge_uncpl -0.33 -lk_ball_ramp_width_A2 3.709 -lk_ball_overlap_width_A2 2.600 -lk_ball_overlap_gap 0.500 # LJ params modified from 19A -chemical:set_atom_properties fa_standard:aroC:LJ_RADIUS:2.02 -chemical:set_atom_properties fa_standard:Haro:LJ_RADIUS:1.41 -chemical:set_atom_properties fa_standard:CH0:LJ_RADIUS:2.04 -chemical:set_atom_properties fa_standard:CH1:LJ_RADIUS:2.01 -chemical:set_atom_properties fa_standard:CH2:LJ_RADIUS:2.01 -chemical:set_atom_properties fa_standard:CH3:LJ_RADIUS:2.06 -chemical:set_atom_properties fa_standard:Hapo:LJ_RADIUS:1.45 -chemical:set_atom_properties fa_standard:Hapo:LJ_WDEPTH:0.021 -chemical:set_atom_properties fa_standard:Haro:LJ_WDEPTH:0.021 -chemical:set_atom_properties fa_standard:CH0:LJ_WDEPTH:0.075 -chemical:set_atom_properties fa_standard:CH1:LJ_WDEPTH:0.062 -chemical:set_atom_properties fa_standard:CH2:LJ_WDEPTH:0.064 -chemical:set_atom_properties fa_standard:CH3:LJ_WDEPTH:0.064 -chemical:set_atom_properties fa_standard:aroC:LJ_WDEPTH:0.070