## Keywords that are replace are listed in help_keywords.txt
-database /work/dimaio/minirosetta_database

#-in:file:fasta em_nsf.fasta 
#-abinitio:fastrelax
#-abinitio:debug
#-abinitio:debug_structures
#-abinitio:close_loops
#-abinitio:fastrelax
#-in:file:native ../inputs/native.pdb 

# we start with a relative good model... 
-skip_stages 1 2 

# otherwise the coord-cst are switched on according to their root atom :-(  
-seq_sep_stages 1 1 1

#-abinitio:close_loops
-short_frag_cycles 1
-scored_frag_cycles 1
-non_ideal_loop_closing
-alternative_closure_protocol
-fast_loops:window_accept_ratio .01
-fast_loops:nr_scored_sampling_passes 4
-fast_loops:min_breakout_good_loops 5
-fast_loops:min_breakout_fast_loops 80
-fast_loops:min_fast_loops 3
-fast_loops:min_good_loops 0
-fast_loops:nr_scored_fragments 20
-fast_loops:vdw_delta 0.5
-fast_loops:give_up 1000 

#-out::level 340
#-mute core.io.pdb 

#don't have prove that this actually helps.. maybe in the refinement stage..
-increase_cycles 1
#-cst_weight 0.01
#-fold_cst:no_minimize


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

#-mute core.chemical
#-mute core.conformation

-fail_on_bad_hbond false 
-relax::fastrelax_repeats 8

# density
-edensity::mapfile 1nsf.5A.mrc
-edensity::mapreso 5.0
-edensity::grid_spacing 2.0
-abinitio::stage3a_patch ./phase3.patch
-abinitio::stage3b_patch ./phase3.patch
-abinitio::stage4_patch  ./phase4.patch
#-mute all
