## Keywords that are replace are listed in help_keywords.txt
-use_general_protocol

#-loop:close_loops
#-loop:short_frag_cycles .5
#-loop:scored_frag_cycles .5
#-abinitio:fastrelax
-increase_cycles 0.1

-frag3 inputs/boinc_aacs_nsp1_03_05.200_v1_3.gz
-frag9 inputs/boinc_aacs_nsp1_09_05.200_v1_3.gz
-in:file:fasta inputs/nsp1_.fasta 
-in:file:native inputs/native.pdb 
#-in:file:fullatom

-abinitio:debug
-abinitio:debug_structures


#don't have prove that this actually helps.. maybe in the refinement stage..
-increase_cycles 1
-cst_file inputs/fullatom.cst
-residues::patch_selectors CENTROID_HA
-cst_weight 0.05

-fold_cst:no_minimize
-jumps:topology_file inputs/native.top 

#-sample_ss_jumps
-ramp_chainbreaks
-sep_switch_accelerate 0.8
#-jump_residues_move
-skip_convergence_check
-overlap_chainbreak

-new_centroid_packing 
-rsd_wt_helix 0.5 
-rsd_wt_loop 0.5

-mute core.chemical
-mute core.conformation
-no_prof_info_in_silentout
-rmsd_target inputs/truncate_native.pdb
-rmsd_column noflex

-user_tag nsp1
-out:file:silent s.out 
