-run:protocol threading
-run:shuffle
-database ./minirosetta_database

-in:file:alignment alignment.filt
-cm:aln_format grishin

-frag3 boinc_aaquery03_05.200_v1_3.gz
-frag9 boinc_aaquery09_05.200_v1_3.gz

-in:file:fasta query.fasta
-in:file:fullatom

-loops::frag_sizes 9 3 1
-loops::frag_files boinc_aaquery09_05.200_v1_3.gz boinc_aaquery03_05.200_v1_3.gz none



-in:file:psipred_ss2 query.psipred_ss2
-in:file:fullatom

-idealize_after_loop_close
-out:file:silent_struct_type binary

-loops::extended
-loops::build_initial
-loops::remodel quick_ccd
-loops::relax fastrelax

-silent_decoytime

-random_grow_loops_by 4
-select_best_loop_from 1

-in:detect_disulf false
-fail_on_bad_hbond false

-bGDT
-evaluation::gdtmm
-in:file:template_pdb 1bjpA.pdb 1ca7A.pdb 1cgqA.pdb 1dptA.pdb 1fimA.pdb 1gczA.pdb 1gifA.pdb 1gyjA.pdb 1hfoA.pdb 1mffA.pdb 1mfiA.pdb 1mifA.pdb 1mwwA.pdb 1otfA.pdb 1otgA.pdb 1p1gA.pdb 1s0yA.pdb 1u9dA.pdb 1uizA.pdb 2aagA.pdb 2aajA.pdb 2aalA.pdb 2fltA.pdb 2fm7A.pdb 2op8A.pdb 2ormA.pdb 2os5A.pdb 3c6vA.pdb

-nstruct 1
