-relax:minimize_bond_angles -relax:jump_move true -relax::dualspace -default_max_cycles 200 -relax:min_type lbfgs_armijo_nonmonotone -relax:jump_move true -score:weights input_t000__2_C1/ref2015_cart.wts -hybridize:stage1_probability 1.0 -hybridize:stage1_4_cycles 400 -ignore_zero_occupancy false -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 -in:file:fasta input_t000__2_C1/t000_.fasta -out:prefix t000_ -parser:protocol input_t000__2_C1/hybridize2_C1.xml -sog_upper_bound 15