core.init: (0) Rosetta version: rosetta.source.release-171 r171 2018.09+release.333d9969977 333d99699777cd6a50d1c1736bacd689f8f1d1df https://www.rosettacommons.org 2018-02-27T20:08:15.525183
core.init: (0) command: /home/swillard/Rosetta_3.9_60072/main/source/bin/calibur.mpi.linuxgccrelease -pdb_list pdblist.txt
core.init: (0) 'RNG device' seed mode, using '/dev/urandom', seed=-1375975393 seed_offset=0 real_seed=-1375975393
core.init.random: (0) RandomGenerator:init: Normal mode, seed=-1375975393 RG_type=mt19937
core.init: (0) Resolved executable path: /home/swillard/Rosetta_3.9_60072/main/source/build/src/release/linux/4.8/64/x86/gcc/5.4/mpi/calibur.mpi.linuxgccrelease
core.init: (0) Looking for database based on location of executable: /home/swillard/Rosetta_3.9_60072/main/database/
Using C-alphas #1-end
Filtering on
Signature mode off
Using chains 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z', 'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm', 'n', 'o', 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z', '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', ' ' in PDB files
Before names_ assignment
Read 9983 decoy names
Estimating threshold range... complete
Estimated threshold range = [9.66641, 137.85963]
Most frequent distance = 21.30353
0.00000 percent distances below 10.67416
Finding threshold to keep 0.00000% edges
Threshold = 10.67416
Reading decoys with signature mode off and filter mode on
Read 9910 decoys. Filtered 73 outlier decoys.
Decoys read in 0.32263 s
Initialized 9910 decoys.
Use of SCUD's bound on
Realigning decoys... completed in 0.07946 s
Using MATRIX mode
Auxiliary clustering... 100.0%
AuxiliaryClustering... completed in 112.99304 s
Finding decoys' neighbors... completed 100.0%
Finding all neighbors completed in 311.58400 s
Finding and removing largest clusters...Removing 1-th (313) in 20's LIST
 swap with 9 with id 9581
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Removing 0-th (4793) in 4483's LIST
 swap with 0 with id 4793
Removing 0-th (4555) in 4555's LIST
 swap with 1 with id 5576
Removing 0-th (5576) in 4555's LIST
 swap with 0 with id 5576
 completed in 0.22621 s


Largest 2 cluster centers: S_0445_4.pdb(35), S_0001_2.pdb(28). Margin = 20.00000%

cluster = 0; center = S_0445_4.pdb; n_decoy_members = 35; members = 


cluster = 1; center = S_0001_2.pdb; n_decoy_members = 28; members =