# i/o
-in:file:fasta ../hsgf29.fasta
-nstruct 200
-parser:protocol rosetta_cm.xml
-out:file:silent_struct_type binary

# relax options
-relax:minimize_bond_angles
-relax:minimize_bond_lengths
-relax:jump_move true
-default_max_cycles 200
-relax:min_type lbfgs_armijo_nonmonotone
-relax:jump_move true
-score:weights stage3_rlx.wts
-use_bicubic_interpolation
-hybridize:stage1_probability 1.0
-sog_upper_bound 15
-constraints:cst_fa_file hsgf29.cst
-constraints:cst_file hsgf29.cst

# reduce memory footprint
-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