#-database /ifs1/home/smlewis/minirosetta_database/
#-mute core.chemical core.scoring.etable core.io.database core.io.pdb.file_data core.conformation core.pack.pack_rotamers core.pack.task
#-run::version
#-options::user

-unmute protocols.loops.CcdLoopClosureMover

-s 1FNA_2DF6a_BC1_start.pdb.gz
-loops::loop_file loopsfile
-resfile resfile

#-no_frags #for speed in the integration test
#-in::file::frag3

-ex1
-ex2
-use_input_sc
-extrachi_cutoff 8
-run::min_type dfpmin_armijo

-AnchoredDesign::anchor anchor
#-AnchoredDesign::debug
#-AnchoredDesign::refine_only
#-AnchoredDesign::perturb_show
#-AnchoredDesign::perturb_temp
#-AnchoredDesign::refine_temp
-AnchoredDesign::refine_repack_cycles 50

#-AnchoredDesign::perturb_cycles 5000
#-AnchoredDesign::refine_cycles 10000
#-nstruct 50

-AnchoredDesign::perturb_cycles 250
-AnchoredDesign::refine_cycles 100
-nstruct 3

#-AnchoredDesign::vary_cutpoints

-unmute core.util.prof

-out::prefix output/