-database /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database   #/path/to/database

#IO
-in::file::s /mnt/hgfs/Mutagenesis_Rosetta/4KMT/4.0_loop_modeling/4KMT_HC_native_442residue_FullAtom.pdb
#-out::prefix looped #I prefer suffix, but "-suffix" seems not exist

#packing to taste
-ex1
-ex2
-ndruns 10

#necessary for some stupid reason
-in::file::fullatom
-out::file::fullatom

#tell loops what to do
-loops::loop_file 4KMT_HC.loops
-loops::build_initial
-loops::remodel perturb_kic
-loops::intermedrelax no
-loops::refine refine_kic
-loops::relax no
-loops::frag_sizes 9 3
-loops::frag_files  /mnt/hgfs/Mutagenesis_Rosetta/4KMT/4.0_loop_modeling/aa4KMT_HC09_05.200_v1_3  /mnt/hgfs/Mutagenesis_Rosetta/4KMT/4.0_loop_modeling/aa4KMT_HC03_05.200_v1_3