# i/o
-in:file:fasta t000_.fasta
#-in:file:native native.pdb
#-in:file:native_exclude_res 2 133

-nstruct 2000
#-out:file:silent_struct_type binary

#-in:detect_disulf true
#-fix_disulf ss_bond.cst

-cst_fa_file noe.cst
-cst_file noe.cst
-constraints:cst_fa_weight 1.0
-constraints:cst_weight 1.0

# relax options
-relax:minimize_bond_angles
-relax:minimize_bond_lengths
-relax:jump_move true
-default_max_cycles 2000
-relax:min_type lbfgs_armijo_nonmonotone
-score::weights stage3_rlx.wts
-use_bicubic_interpolation

-rsd_wt_helix 0.5
-rsd_wt_loop 0.5
-rg_reweight 0.5
-correct
-increase_cycles 2

-hybridize:frag_weight_aligned 0.5
-hybridize:relax 1

-hybridize:stage1_probability 1.0
-sog_upper_bound 15

#flexible residues according talos prediction
#please check those residues listed below, better to exclude only those from tails
-in:replonly_residues 1 2 3 87
-chemical:patch_selectors replonly

-evaluation:chemical_shifts in.tab cs
-out:file:fullatom # output in fullatom mode
-out:output

# 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