-run:protocol threading
-in:file:alignment /home/ucbechz/Scratch/20150123_minirosetta_disulfide/input/C226S.4KMT.aln 
-cm:aln_format general 
-frag3 /home/ucbechz/Scratch/20150123_minirosetta_disulfide/input/aaC226S_03_05.200_v1_3 
-frag9 /home/ucbechz/Scratch/20150123_minirosetta_disulfide/input/aaC226S_09_05.200_v1_3 
-in:file:fasta /home/ucbechz/Scratch/20150123_minirosetta_disulfide/input/C226S.fasta 
-in:file:fullatom 
-loops:frag_sizes 9 3 1 
-loops:frag_files /home/ucbechz/Scratch/20150123_minirosetta_disulfide/input/aaC226S_09_05.200_v1_3 /home/ucbechz/Scratch/20150123_minirosetta_disulfide/input/aaC226S_03_05.200_v1_3 none	
-in:file:psipred_ss2 /home/ucbechz/Scratch/20150123_minirosetta_disulfide/input/C226S.psipass2 
-in:file:fullatom 
-out:nstruct 10000
-in:file:template_pdb /home/ucbechz/Scratch/20150123_minirosetta_disulfide/input/4KMT_FullAtom_missing_residue_in_HC.pdb 
-loops:extended 
-loops:build_initial 
-loops:remodel quick_ccd 
-loops:refine refine_ccd 
-silent_decoytime 
-random_grow_loops_by 4 
-select_best_loop_from 1 
-out:file:fullatom 
-out:output 
-out:pdb
-out:file:scorefile threaded_model.fasc 
-overwrite 
-loops:relax fastrelax  
-relax:default_repeats 8