# i/o
-in:file:fasta starting.fasta
-parser:protocol rosetta_cm.xml
-database ../../rosetta/rosetta_trunk_database 

## if you would to evaluate results during modeling, turn these options on
#-in:file:native ../../../data/3j06A.pdb
#-evaluation:align_rmsd_target ../../../data/3j06A.pdb
#-evaluation:align_rmsd_column ref

-out:file:silent_struct_type binary
-out:file:silent rosetta_cm.out
-nstruct 100

-sog_upper_bound 15
-hybridize:stage1_probability 1

# relax args
-default_max_cycles 200
-relax:minimize_bond_angles
-relax:minimize_bond_lengths
-relax:min_type lbfgs_armijo_nonmonotone
-relax:jump_move true
-score:weights stage3_rlx.wts
-bonded_params 400 100 100 10
-use_bicubic_interpolation
# density map args
-edensity:mapfile starting.mrc
-edensity:mapreso 3.3
-edensity:grid_spacing 1.1
-edensity:fastdens_wt 20.0
-edensity:realign no
# 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
