# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0327/ # command:# Making conformation for sequence T0327 numbered 1 through 102 Created new target T0327 from T0327.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0327/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0327//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0327/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0327//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0327/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0327/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0327/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z7uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z7uA expands to /projects/compbio/data/pdb/1z7u.pdb.gz 1z7uA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 60, because occupancy 0.5 <= existing 0.500 in 1z7uA Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 1z7uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 263, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 297, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 299, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 301, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 303, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 305, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 307, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 309, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 311, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 313, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 315, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 317, because occupancy 0.400 <= existing 0.600 in 1z7uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 911, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 921, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 923, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 927, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 929, because occupancy 0.500 <= existing 0.500 in 1z7uA # T0327 read from 1z7uA/merged-good-all-a2m # 1z7uA read from 1z7uA/merged-good-all-a2m # adding 1z7uA to template set # found chain 1z7uA in template set T0327 3 :KDKLRYAILKEIFEGNTP 1z7uA 17 :NGKWKLSLMDELFQGTKR # choosing archetypes in rotamer library T0327 21 :LS 1z7uA 42 :LD T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1z7uA 44 :GITQRVLTDRLREMEKDGLVHRESFNELPPRVE T0327 64 :ELTEKGENYLKENGTWSKAYKTIKEIKD 1z7uA 78 :TLTPEGYALYDALSSLCHWGETFAQKKA Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 Number of alignments=1 # 1z7uA read from 1z7uA/merged-good-all-a2m # found chain 1z7uA in template set T0327 4 :DKLRYAILKEIFEGNTP 1z7uA 18 :GKWKLSLMDELFQGTKR T0327 21 :LS 1z7uA 42 :LD T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1z7uA 44 :GITQRVLTDRLREMEKDGLVHRESFNELPPRVE T0327 64 :ELTEKGENYLKENGTWSKAYKTIKEIKD 1z7uA 78 :TLTPEGYALYDALSSLCHWGETFAQKKA Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 Number of alignments=2 # 1z7uA read from 1z7uA/merged-good-all-a2m # found chain 1z7uA in template set T0327 3 :KDKLRYAIL 1z7uA 35 :NGELMRALD T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1z7uA 44 :GITQRVLTDRLREMEKDGLVHRESFNELPPRVE T0327 63 :PELTEKGENYLKENGTWSKAYKTIKEIKD 1z7uA 77 :YTLTPEGYALYDALSSLCHWGETFAQKKA Number of specific fragments extracted= 3 number of extra gaps= 0 total=11 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fswA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fswA expands to /projects/compbio/data/pdb/2fsw.pdb.gz 2fswA:Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 326, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 330, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 397, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 399, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 401, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 403, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 405, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 407, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 409, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 411, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 413, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 415, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 417, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 524, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 526, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 694, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 696, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 698, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 894, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 896, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 898, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 900, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 902, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 904, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 906, because occupancy 0.300 <= existing 0.340 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 908, because occupancy 0.400 <= existing 0.600 in 2fswA # T0327 read from 2fswA/merged-good-all-a2m # 2fswA read from 2fswA/merged-good-all-a2m # adding 2fswA to template set # found chain 2fswA in template set T0327 5 :KLRYAI 2fswA 26 :LIIFQI T0327 11 :LKEIFEG 2fswA 41 :LKRAIPG T0327 28 :VTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 2fswA 48 :ISEKMLIDELKFLCGKGLIKKKQYPEVPPRVE T0327 60 :KLGP 2fswA 81 :SLTP T0327 66 :TEKGENYLKENGTWS 2fswA 86 :GEKVLPIIDEIAKFG Number of specific fragments extracted= 5 number of extra gaps= 0 total=16 Number of alignments=4 # 2fswA read from 2fswA/merged-good-all-a2m # found chain 2fswA in template set T0327 6 :LRYAI 2fswA 27 :IIFQI T0327 11 :LKEIF 2fswA 41 :LKRAI T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 2fswA 46 :PGISEKMLIDELKFLCGKGLIKKKQYPEVPPRVE T0327 60 :KLGP 2fswA 81 :SLTP T0327 66 :TEKGENYLKENGTWS 2fswA 86 :GEKVLPIIDEIAKFG Number of specific fragments extracted= 5 number of extra gaps= 0 total=21 Number of alignments=5 # 2fswA read from 2fswA/merged-good-all-a2m # found chain 2fswA in template set T0327 5 :KLRYAI 2fswA 40 :ELKRAI T0327 16 :E 2fswA 46 :P T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYK 2fswA 47 :GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEY T0327 64 :ELTEKGENYLKE 2fswA 81 :SLTPLGEKVLPI T0327 79 :WSKAYKT 2fswA 93 :IDEIAKF Number of specific fragments extracted= 5 number of extra gaps= 0 total=26 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yyvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yyvA expands to /projects/compbio/data/pdb/1yyv.pdb.gz 1yyvA:Skipped atom 310, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 312, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 314, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 316, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 318, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 320, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 322, because occupancy 0.490 <= existing 0.510 in 1yyvA Bad short name: CH1 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: CH1 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 637, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 639, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 641, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 643, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 645, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 647, because occupancy 0.460 <= existing 0.540 in 1yyvA Bad short name: CH1 for alphabet: pdb_atoms # T0327 read from 1yyvA/merged-good-all-a2m # 1yyvA read from 1yyvA/merged-good-all-a2m # adding 1yyvA to template set # found chain 1yyvA in template set Warning: unaligning (T0327)E30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0327)Q32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0327)I46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yyvA)N77 Warning: unaligning (T0327)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0327)K74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0327)N76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 T0327 4 :DKLRYAILKEIFEGNTP 1yyvA 31 :SRWGVLILVALRDGTHR T0327 27 :GVT 1yyvA 57 :GVS T0327 33 :FDDAVNFLKREGY 1yyvA 63 :LAQSLQALEQDGF T0327 48 :GVHYSDDRPHLY 1yyvA 78 :RVSYPVVPPHVE T0327 60 :K 1yyvA 91 :S T0327 65 :LTEKGENYL 1yyvA 92 :LTPLGEQVS T0327 77 :GTWSKAYKTI 1yyvA 104 :AALADWIELN Number of specific fragments extracted= 7 number of extra gaps= 1 total=33 Number of alignments=7 # 1yyvA read from 1yyvA/merged-good-all-a2m # found chain 1yyvA in template set Warning: unaligning (T0327)D25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0327)E30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0327)Q32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0327)I46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yyvA)N77 Warning: unaligning (T0327)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0327)K74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0327)N76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 T0327 4 :DKLRYAILKEIFEGN 1yyvA 31 :SRWGVLILVALRDGT T0327 26 :IGVT 1yyvA 56 :GGVS T0327 33 :FDDAVNFLKREGY 1yyvA 63 :LAQSLQALEQDGF T0327 48 :GVHYSDDRPHLY 1yyvA 78 :RVSYPVVPPHVE T0327 64 :ELTEKGENYL 1yyvA 91 :SLTPLGEQVS T0327 77 :GTWSKAYKTI 1yyvA 104 :AALADWIELN Number of specific fragments extracted= 6 number of extra gaps= 1 total=39 Number of alignments=8 # 1yyvA read from 1yyvA/merged-good-all-a2m # found chain 1yyvA in template set Warning: unaligning (T0327)E30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0327)Q32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0327)I46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yyvA)N77 Warning: unaligning (T0327)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0327)K74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0327)N76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 T0327 27 :GVT 1yyvA 57 :GVS T0327 33 :FDDAVNFLKREGY 1yyvA 63 :LAQSLQALEQDGF T0327 48 :GVHYSDDRPHLY 1yyvA 78 :RVSYPVVPPHVE T0327 63 :PELTEKGENYL 1yyvA 90 :YSLTPLGEQVS T0327 77 :GTWSKAYKTI 1yyvA 104 :AALADWIELN Number of specific fragments extracted= 5 number of extra gaps= 1 total=44 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tbxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tbxA expands to /projects/compbio/data/pdb/1tbx.pdb.gz 1tbxA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0327 read from 1tbxA/merged-good-all-a2m # 1tbxA read from 1tbxA/merged-good-all-a2m # adding 1tbxA to template set # found chain 1tbxA in template set T0327 7 :RYAILKEIFEGN 1tbxA 10 :EAIVLAYLYDNE T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIG 1tbxA 34 :AEFPMSTATFYDAKKFLIQEGFVKE T0327 50 :HYSDDRPHLY 1tbxA 59 :RQERGEKRLY T0327 65 :LTEKGENYLKENGTWSKAYKTIKEIK 1tbxA 69 :LTEKGKLFAISLKTAIETYKQIKKRH Number of specific fragments extracted= 4 number of extra gaps= 0 total=48 Number of alignments=10 # 1tbxA read from 1tbxA/merged-good-all-a2m # found chain 1tbxA in template set T0327 9 :AILKEIFEGN 1tbxA 12 :IVLAYLYDNE T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIG 1tbxA 33 :NAEFPMSTATFYDAKKFLIQEGFVKE T0327 50 :HYSDDRPHLY 1tbxA 59 :RQERGEKRLY T0327 65 :LTEKGENYLKENGTWSKAYKTIKEI 1tbxA 69 :LTEKGKLFAISLKTAIETYKQIKKR Number of specific fragments extracted= 4 number of extra gaps= 0 total=52 Number of alignments=11 # 1tbxA read from 1tbxA/merged-good-all-a2m # found chain 1tbxA in template set T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHY 1tbxA 34 :AEFPMSTATFYDAKKFLIQEGFVKERQE T0327 53 :DDRPHL 1tbxA 62 :RGEKRL T0327 64 :ELTEKGENYLKENGTWSKAYKTIKEI 1tbxA 68 :YLTEKGKLFAISLKTAIETYKQIKKR Number of specific fragments extracted= 3 number of extra gaps= 0 total=55 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p4xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1p4xA expands to /projects/compbio/data/pdb/1p4x.pdb.gz 1p4xA:# T0327 read from 1p4xA/merged-good-all-a2m # 1p4xA read from 1p4xA/merged-good-all-a2m # adding 1p4xA to template set # found chain 1p4xA in template set T0327 5 :KLRYAILKEIFEGN 1p4xA 158 :FVEFTILAIITSQN T0327 19 :TP 1p4xA 173 :NI T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1p4xA 184 :IHHKYPQTVRALNNLKKQGYLIKERSTEDERKIL T0327 60 :KLGP 1p4xA 219 :HMDD T0327 77 :GTWSKAYKTIKEIKDWIKLEHHHH 1p4xA 223 :AQQDHAEQLLAQVNQLLADKDHLH Number of specific fragments extracted= 5 number of extra gaps= 0 total=60 Number of alignments=13 # 1p4xA read from 1p4xA/merged-good-all-a2m # found chain 1p4xA in template set T0327 5 :KLRYAILKEIFEGNTP 1p4xA 158 :FVEFTILAIITSQNKN T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHYSD 1p4xA 182 :ETIHHKYPQTVRALNNLKKQGYLIKERSTE T0327 54 :DRPHLYKLGP 1p4xA 213 :ERKILIHMDD T0327 77 :GTWSKAYKTIKEIKDWIKLEHHHH 1p4xA 223 :AQQDHAEQLLAQVNQLLADKDHLH Number of specific fragments extracted= 4 number of extra gaps= 0 total=64 Number of alignments=14 # 1p4xA read from 1p4xA/merged-good-all-a2m # found chain 1p4xA in template set T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYKL 1p4xA 184 :IHHKYPQTVRALNNLKKQGYLIKERSTEDERKILIH T0327 65 :LTEKGEN 1p4xA 220 :MDDAQQD T0327 81 :KAYKTIKEIKDW 1p4xA 227 :HAEQLLAQVNQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=67 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e2xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1e2xA expands to /projects/compbio/data/pdb/1e2x.pdb.gz 1e2xA:Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 1732, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 1734, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 1736, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 1738, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 1740, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 1742, because occupancy 0.500 <= existing 0.500 in 1e2xA # T0327 read from 1e2xA/merged-good-all-a2m # 1e2xA read from 1e2xA/merged-good-all-a2m # adding 1e2xA to template set # found chain 1e2xA in template set T0327 4 :DKLRYAILKEIFEGNTP 1e2xA 10 :GFAEEYIIESIWNNRFP T0327 21 :LSEN 1e2xA 31 :LPAE T0327 26 :IGVTEDQFDDAVNFLKREGYIIG 1e2xA 41 :IGVTRTTLREVLQRLARDGWLTI T0327 52 :SDDRP 1e2xA 64 :QHGKP T0327 59 :YKLGP 1e2xA 69 :TKVNN T0327 69 :GENYLK 1e2xA 79 :GLNILE T0327 75 :ENGTWSKAYKTIKEI 1e2xA 91 :HESVPQLIDNLLSVR Number of specific fragments extracted= 7 number of extra gaps= 0 total=74 Number of alignments=16 # 1e2xA read from 1e2xA/merged-good-all-a2m # found chain 1e2xA in template set T0327 4 :DKLRYAILKEIFEGNTP 1e2xA 10 :GFAEEYIIESIWNNRFP T0327 21 :LSEND 1e2xA 31 :LPAER T0327 26 :IGVTEDQFDDAVNFLKREGYIIG 1e2xA 41 :IGVTRTTLREVLQRLARDGWLTI T0327 52 :SDD 1e2xA 64 :QHG T0327 56 :PH 1e2xA 67 :KP T0327 59 :YKLGP 1e2xA 69 :TKVNN T0327 69 :GENYLK 1e2xA 79 :GLNILE T0327 75 :ENGTWSKAYKTIKE 1e2xA 91 :HESVPQLIDNLLSV Number of specific fragments extracted= 8 number of extra gaps= 0 total=82 Number of alignments=17 # 1e2xA read from 1e2xA/merged-good-all-a2m # found chain 1e2xA in template set T0327 3 :KDKLRYAILKEIFEGNTPLSEND 1e2xA 13 :EEYIIESIWNNRFPPGTILPAER T0327 26 :IGVTEDQFDDAVNFLKREGYIIGV 1e2xA 41 :IGVTRTTLREVLQRLARDGWLTIQ T0327 53 :DDRP 1e2xA 65 :HGKP T0327 58 :LYKLG 1e2xA 69 :TKVNN T0327 69 :GENYLK 1e2xA 79 :GLNILE Number of specific fragments extracted= 5 number of extra gaps= 0 total=87 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 8rucI/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 8rucI expands to /projects/compbio/data/pdb/8ruc.pdb.gz 8rucI:# T0327 read from 8rucI/merged-good-all-a2m # 8rucI read from 8rucI/merged-good-all-a2m # adding 8rucI to template set # found chain 8rucI in template set T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 8rucI 17 :YLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVY T0327 60 :KLGPELTEK 8rucI 56 :HNSPGYYDG T0327 73 :LKENGTWSKAYKTIKEIKDWI 8rucI 74 :MFGCTDPAQVLNELEECKKEY Number of specific fragments extracted= 3 number of extra gaps= 0 total=90 Number of alignments=19 # 8rucI read from 8rucI/merged-good-all-a2m # found chain 8rucI in template set T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYKLG 8rucI 16 :SYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREH T0327 63 :PELTEK 8rucI 59 :PGYYDG T0327 73 :LKENGTWSKAYKTIKEIKDW 8rucI 74 :MFGCTDPAQVLNELEECKKE Number of specific fragments extracted= 3 number of extra gaps= 0 total=93 Number of alignments=20 # 8rucI read from 8rucI/merged-good-all-a2m # found chain 8rucI in template set T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYKLG 8rucI 16 :SYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREH T0327 63 :PELTEKGENYLKENG 8rucI 77 :CTDPAQVLNELEECK Number of specific fragments extracted= 2 number of extra gaps= 0 total=95 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ub9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ub9A expands to /projects/compbio/data/pdb/1ub9.pdb.gz 1ub9A:# T0327 read from 1ub9A/merged-good-all-a2m # 1ub9A read from 1ub9A/merged-good-all-a2m # adding 1ub9A to template set # found chain 1ub9A in template set T0327 3 :KDKLRYAILKEIF 1ub9A 14 :GNPVRLGIMIFLL T0327 17 :GN 1ub9A 28 :RR T0327 19 :TP 1ub9A 31 :AP T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1ub9A 40 :LDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTV T0327 64 :ELTEKGENYLKENGTWSKAYKT 1ub9A 75 :EITDFGMEEAKRFLSSLKAVID Number of specific fragments extracted= 5 number of extra gaps= 0 total=100 Number of alignments=22 # 1ub9A read from 1ub9A/merged-good-all-a2m # found chain 1ub9A in template set T0327 3 :KDKLRYAILKEIFEGN 1ub9A 14 :GNPVRLGIMIFLLPRR T0327 25 :DIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1ub9A 39 :VLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTV T0327 64 :ELTEKGENYLKENGTWSKAYKT 1ub9A 75 :EITDFGMEEAKRFLSSLKAVID Number of specific fragments extracted= 3 number of extra gaps= 0 total=103 Number of alignments=23 # 1ub9A read from 1ub9A/merged-good-all-a2m # found chain 1ub9A in template set T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1ub9A 40 :LDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTV T0327 63 :PELTEKGENYLKENGTWSKAYK 1ub9A 74 :VEITDFGMEEAKRFLSSLKAVI Number of specific fragments extracted= 2 number of extra gaps= 0 total=105 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jgsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jgsA expands to /projects/compbio/data/pdb/1jgs.pdb.gz 1jgsA:# T0327 read from 1jgsA/merged-good-all-a2m # 1jgsA read from 1jgsA/merged-good-all-a2m # adding 1jgsA to template set # found chain 1jgsA in template set T0327 4 :DKLRYAILKEIF 1jgsA 39 :TAAQFKVLCSIR T0327 18 :N 1jgsA 53 :A T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSD 1jgsA 64 :LSVDLGALTRMLDRLVCKGWVERLPNPN T0327 54 :DRPHLYK 1jgsA 93 :KRGVLVK T0327 65 :LTEKGENYLKENGTWSKAYKTIKEIK 1jgsA 100 :LTTGGAAICEQCHQLVGQDLHQELTK Number of specific fragments extracted= 5 number of extra gaps= 0 total=110 Number of alignments=25 # 1jgsA read from 1jgsA/merged-good-all-a2m # found chain 1jgsA in template set T0327 5 :KLRYAILKEIFEGN 1jgsA 40 :AAQFKVLCSIRCAA T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHYSD 1jgsA 62 :KVLSVDLGALTRMLDRLVCKGWVERLPNPN T0327 54 :DRPHLYK 1jgsA 93 :KRGVLVK T0327 65 :LTEKGENYLKENGTWSKAYKTIKEIK 1jgsA 100 :LTTGGAAICEQCHQLVGQDLHQELTK Number of specific fragments extracted= 4 number of extra gaps= 0 total=114 Number of alignments=26 # 1jgsA read from 1jgsA/merged-good-all-a2m # found chain 1jgsA in template set T0327 4 :DKLRYAI 1jgsA 58 :VELKKVL T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1jgsA 65 :SVDLGALTRMLDRLVCKGWVERLPNPNDKRGVL T0327 63 :PELTEKGENYLKENGTWSKA 1jgsA 98 :VKLTTGGAAICEQCHQLVGQ T0327 84 :KTIKEIK 1jgsA 118 :DLHQELT Number of specific fragments extracted= 4 number of extra gaps= 0 total=118 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0327 read from 1hw1A/merged-good-all-a2m # 1hw1A read from 1hw1A/merged-good-all-a2m # found chain 1hw1A in training set T0327 4 :DKLRYAILKEIFEGNTP 1hw1A 10 :GFAEEYIIESIWNNRFP T0327 21 :LSEN 1hw1A 31 :LPAE T0327 26 :IGVTEDQFDDAVNFLKREGYII 1hw1A 41 :IGVTRTTLREVLQRLARDGWLT T0327 51 :YSDDRPH 1hw1A 63 :IQHGKPT T0327 60 :KLG 1hw1A 70 :KVN Number of specific fragments extracted= 5 number of extra gaps= 0 total=123 Number of alignments=28 # 1hw1A read from 1hw1A/merged-good-all-a2m # found chain 1hw1A in training set T0327 4 :DKLRYAILKEIFEGNTP 1hw1A 10 :GFAEEYIIESIWNNRFP T0327 21 :LSEND 1hw1A 31 :LPAER T0327 26 :IGVTEDQFDDAVNFLKREGYIIG 1hw1A 41 :IGVTRTTLREVLQRLARDGWLTI T0327 52 :SDDRP 1hw1A 64 :QHGKP T0327 59 :YKLG 1hw1A 69 :TKVN Number of specific fragments extracted= 5 number of extra gaps= 0 total=128 Number of alignments=29 # 1hw1A read from 1hw1A/merged-good-all-a2m # found chain 1hw1A in training set T0327 3 :KDKLRYAILKEIFEGNTPLSEND 1hw1A 13 :EEYIIESIWNNRFPPGTILPAER T0327 26 :IGVTEDQFDDAVNFLKREGYIIG 1hw1A 41 :IGVTRTTLREVLQRLARDGWLTI T0327 52 :SDDRPH 1hw1A 64 :QHGKPT Number of specific fragments extracted= 3 number of extra gaps= 0 total=131 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g7uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2g7uA expands to /projects/compbio/data/pdb/2g7u.pdb.gz 2g7uA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0327 read from 2g7uA/merged-good-all-a2m # 2g7uA read from 2g7uA/merged-good-all-a2m # adding 2g7uA to template set # found chain 2g7uA in template set T0327 5 :KLRYAIL 2g7uA 13 :ERGFAVL T0327 13 :EIFEGNTP 2g7uA 20 :LAFDAQRP T0327 26 :IGVTEDQFDDAVNFLKREGYIIG 2g7uA 38 :AGLSRPAVRRILLTLQKLGYVAG T0327 59 :YKLGPELTEKGENYLKENGTWSKAYKTIKEIKDWIK 2g7uA 65 :WSLTPRVLSIGQHYSESHALIEAAMPRLLEVAEKTQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=135 Number of alignments=31 # 2g7uA read from 2g7uA/merged-good-all-a2m # found chain 2g7uA in template set T0327 6 :LRYAIL 2g7uA 14 :RGFAVL T0327 13 :EIFEGNTP 2g7uA 20 :LAFDAQRP T0327 21 :LSEND 2g7uA 29 :PTLAE T0327 26 :IGVTEDQFDDAVNFLKREGYIIG 2g7uA 38 :AGLSRPAVRRILLTLQKLGYVAG T0327 59 :YKLGPELTEKGENYLKENGTWSKAYKTIKEIKDWIK 2g7uA 65 :WSLTPRVLSIGQHYSESHALIEAAMPRLLEVAEKTQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=140 Number of alignments=32 # 2g7uA read from 2g7uA/merged-good-all-a2m # found chain 2g7uA in template set T0327 3 :KDKLRYA 2g7uA 31 :LAELATE T0327 26 :IGVTEDQFDDAVNFLKREGYIIGV 2g7uA 38 :AGLSRPAVRRILLTLQKLGYVAGS T0327 53 :DDRPHL 2g7uA 62 :GGRWSL T0327 62 :GPELTEKGENYLKENGTWSKAYKTIKEIKDW 2g7uA 68 :TPRVLSIGQHYSESHALIEAAMPRLLEVAEK Number of specific fragments extracted= 4 number of extra gaps= 0 total=144 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mkmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mkmA expands to /projects/compbio/data/pdb/1mkm.pdb.gz 1mkmA:# T0327 read from 1mkmA/merged-good-all-a2m # 1mkmA read from 1mkmA/merged-good-all-a2m # adding 1mkmA to template set # found chain 1mkmA in template set T0327 1 :MNKDKLRYAILKEIFEGNTPLSEN 1mkmA 1 :MNTLKKAFEILDFIVKNPGDVSVS T0327 25 :DIGVTEDQFDDAVNFLKREGYI 1mkmA 29 :KFNMSVSNAYKYMVVLEEKGFV T0327 50 :HYSDDRPHL 1mkmA 51 :LRKKDKRYV T0327 61 :LGPELTEKGENYLKENGTWSKAYKTIKEIKDW 1mkmA 60 :PGYKLIEYGSFVLRRFNIRDIAHDHLVDIMKR Number of specific fragments extracted= 4 number of extra gaps= 0 total=148 Number of alignments=34 # 1mkmA read from 1mkmA/merged-good-all-a2m # found chain 1mkmA in template set T0327 1 :MNKDKLRYAILKEIFEGNTPLSEN 1mkmA 1 :MNTLKKAFEILDFIVKNPGDVSVS T0327 25 :DIGVTEDQFDDAVNFLKREGYI 1mkmA 29 :KFNMSVSNAYKYMVVLEEKGFV T0327 50 :HYSDDRPHLY 1mkmA 51 :LRKKDKRYVP T0327 62 :GPELTEKGENYLKENGTWSKAYKTIKEIKD 1mkmA 61 :GYKLIEYGSFVLRRFNIRDIAHDHLVDIMK Number of specific fragments extracted= 4 number of extra gaps= 0 total=152 Number of alignments=35 # 1mkmA read from 1mkmA/merged-good-all-a2m # found chain 1mkmA in template set T0327 10 :ILKEIFEGNTPLSEN 1mkmA 10 :ILDFIVKNPGDVSVS T0327 25 :DIGVTEDQFDDAVNFLKREGYIIG 1mkmA 29 :KFNMSVSNAYKYMVVLEEKGFVLR T0327 52 :SDDRP 1mkmA 53 :KKDKR T0327 59 :YKLGPELTEKGENYLKENGTWSKAYKTIKEIKD 1mkmA 58 :YVPGYKLIEYGSFVLRRFNIRDIAHDHLVDIMK Number of specific fragments extracted= 4 number of extra gaps= 0 total=156 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xmaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xmaA expands to /projects/compbio/data/pdb/1xma.pdb.gz 1xmaA:Skipped atom 237, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 239, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 241, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 243, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 245, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 436, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 438, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 440, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 722, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 724, because occupancy 0.350 <= existing 0.650 in 1xmaA # T0327 read from 1xmaA/merged-good-all-a2m # 1xmaA read from 1xmaA/merged-good-all-a2m # adding 1xmaA to template set # found chain 1xmaA in template set Warning: unaligning (T0327)D53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmaA)K72 Warning: unaligning (T0327)P56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmaA)K72 T0327 5 :KLRYAILKEIFEGN 1xmaA 10 :YVDTIILSLLIEGD T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHY 1xmaA 38 :DELYVIKETTLYSAFARLEKNGYIKSYYG T0327 52 :S 1xmaA 68 :E T0327 57 :HLYKL 1xmaA 73 :RRTYY T0327 64 :ELTEKGENYLKENGT 1xmaA 78 :RITPEGIKYYKQKCE T0327 82 :AYKTIKEIKD 1xmaA 93 :EWELTKKVIN Number of specific fragments extracted= 6 number of extra gaps= 0 total=162 Number of alignments=37 # 1xmaA read from 1xmaA/merged-good-all-a2m # found chain 1xmaA in template set Warning: unaligning (T0327)D53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmaA)K72 Warning: unaligning (T0327)P56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmaA)K72 T0327 4 :DKLRYAILKEIFEGN 1xmaA 9 :GYVDTIILSLLIEGD T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHY 1xmaA 38 :DELYVIKETTLYSAFARLEKNGYIKSYYG T0327 52 :S 1xmaA 68 :E T0327 57 :HLYKL 1xmaA 73 :RRTYY T0327 64 :ELTEKGENYLKENGT 1xmaA 78 :RITPEGIKYYKQKCE T0327 82 :AYKTIKEIKD 1xmaA 93 :EWELTKKVIN Number of specific fragments extracted= 6 number of extra gaps= 0 total=168 Number of alignments=38 # 1xmaA read from 1xmaA/merged-good-all-a2m # found chain 1xmaA in template set Warning: unaligning (T0327)S52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmaA)K72 Warning: unaligning (T0327)R55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmaA)K72 T0327 5 :KLRYAILKEI 1xmaA 28 :EISKNIRIKT T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHY 1xmaA 38 :DELYVIKETTLYSAFARLEKNGYIKSYYG T0327 56 :PHLY 1xmaA 73 :RRTY T0327 63 :PELTEKGENYLKENGT 1xmaA 77 :YRITPEGIKYYKQKCE T0327 82 :AYKTIKEIK 1xmaA 93 :EWELTKKVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=173 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r7jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0327 read from 1r7jA/merged-good-all-a2m # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set T0327 2 :NKDKLRYAILKEIFEGN 1r7jA 5 :SKLEIIQAILEACKSGS T0327 20 :P 1r7jA 22 :P T0327 26 :IGVTEDQFDDAVNFLKREGYII 1r7jA 30 :ANLSYALTGRYIKMLMDLEIIR T0327 51 :YSDD 1r7jA 52 :QEGK T0327 57 :HL 1r7jA 56 :QY T0327 64 :ELTEKGENYLKENGTWSKAYKTIKEIKD 1r7jA 58 :MLTKKGEELLEDIRKFNEMRKNMDQLKE Number of specific fragments extracted= 6 number of extra gaps= 0 total=179 Number of alignments=40 # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set T0327 2 :NKDKLRYAILKEIF 1r7jA 5 :SKLEIIQAILEACK T0327 17 :GNTP 1r7jA 19 :SGSP T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIG 1r7jA 28 :YGANLSYALTGRYIKMLMDLEIIRQ T0327 52 :SDD 1r7jA 53 :EGK T0327 57 :HL 1r7jA 56 :QY T0327 64 :ELTEKGENYLKENGTWSKAYKTIKEIKD 1r7jA 58 :MLTKKGEELLEDIRKFNEMRKNMDQLKE Number of specific fragments extracted= 6 number of extra gaps= 0 total=185 Number of alignments=41 # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set T0327 3 :KDKLRYA 1r7jA 23 :KTRIMYG T0327 26 :IGVTEDQFDDAVNFLKREGYIIGV 1r7jA 30 :ANLSYALTGRYIKMLMDLEIIRQE T0327 53 :DDR 1r7jA 54 :GKQ T0327 63 :PELTEKGENYLKENGTWSKAYKTIKEIKD 1r7jA 57 :YMLTKKGEELLEDIRKFNEMRKNMDQLKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=189 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1an7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1an7A expands to /projects/compbio/data/pdb/1an7.pdb.gz 1an7A:# T0327 read from 1an7A/merged-good-all-a2m # 1an7A read from 1an7A/merged-good-all-a2m # adding 1an7A to template set # found chain 1an7A in template set T0327 5 :KLRYAILKEIFEGNT 1an7A 8 :DMLTRIRNATRVYKE T0327 27 :G 1an7A 27 :P T0327 29 :TEDQFDDAVNFLKREGYIIGVHYSD 1an7A 28 :ASRFKEEILRILAREGFIKGYERVD T0327 54 :DRPH 1an7A 54 :DGKP Number of specific fragments extracted= 4 number of extra gaps= 0 total=193 Number of alignments=43 # 1an7A read from 1an7A/merged-good-all-a2m # found chain 1an7A in template set T0327 5 :KLRYAI 1an7A 5 :PIADML T0327 11 :LKEIFEGNTP 1an7A 13 :IRNATRVYKE T0327 29 :TEDQFDDAVNFLKREGYIIGVHYSD 1an7A 28 :ASRFKEEILRILAREGFIKGYERVD T0327 54 :DRPH 1an7A 54 :DGKP Number of specific fragments extracted= 4 number of extra gaps= 0 total=197 Number of alignments=44 # 1an7A read from 1an7A/merged-good-all-a2m # found chain 1an7A in template set T0327 4 :DKLRYAILKEIFEGNTP 1an7A 11 :TRIRNATRVYKESTDVP T0327 29 :TEDQFDDAVNFLKREGYIIGVHY 1an7A 28 :ASRFKEEILRILAREGFIKGYER T0327 52 :SDDRPHLY 1an7A 53 :VDGKPYLR Number of specific fragments extracted= 3 number of extra gaps= 0 total=200 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fbhA expands to /projects/compbio/data/pdb/2fbh.pdb.gz 2fbhA:Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 286, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 484, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 486, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 488, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 847, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 849, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1004, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1006, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1008, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 2fbhA # T0327 read from 2fbhA/merged-good-all-a2m # 2fbhA read from 2fbhA/merged-good-all-a2m # adding 2fbhA to template set # found chain 2fbhA in template set Warning: unaligning (T0327)L6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbhA)R37 Warning: unaligning (T0327)R7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbhA)R37 Warning: unaligning (T0327)I26 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0327)G27 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0327 5 :K 2fbhA 35 :Q T0327 8 :YAILKEIFEGNTPLSEND 2fbhA 38 :WLVLLHLARHRDSPTQRE T0327 28 :VTEDQFDDAVNFLKREGYIIGVHYSDD 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLAVAED T0327 55 :RPHLY 2fbhA 91 :AKHIV T0327 65 :LTEKGENYLKENGTWSKAYKT 2fbhA 96 :LTPKADVLIADIEAIAASVRN Number of specific fragments extracted= 5 number of extra gaps= 2 total=205 Number of alignments=46 # 2fbhA read from 2fbhA/merged-good-all-a2m # found chain 2fbhA in template set Warning: unaligning (T0327)L6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbhA)R37 Warning: unaligning (T0327)R7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbhA)R37 Warning: unaligning (T0327)I26 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0327)G27 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0327 4 :DK 2fbhA 34 :SQ T0327 8 :YAILKEIFEGNTPLSEND 2fbhA 38 :WLVLLHLARHRDSPTQRE T0327 28 :VTEDQFDDAVNFLKREGYIIGVHYSDDR 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLAVAEDR T0327 56 :PHLY 2fbhA 92 :KHIV T0327 65 :LTEKGENYLKENGTWSKAYKT 2fbhA 96 :LTPKADVLIADIEAIAASVRN Number of specific fragments extracted= 5 number of extra gaps= 2 total=210 Number of alignments=47 # 2fbhA read from 2fbhA/merged-good-all-a2m # found chain 2fbhA in template set Warning: unaligning (T0327)I26 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0327)G27 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0327 28 :VTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLAVAEDRRAKH T0327 63 :PELTEKGENYLKENGTWSKAYKT 2fbhA 94 :IVLTPKADVLIADIEAIAASVRN Number of specific fragments extracted= 2 number of extra gaps= 1 total=212 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a61A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a61A expands to /projects/compbio/data/pdb/2a61.pdb.gz 2a61A:Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2a61A # T0327 read from 2a61A/merged-good-all-a2m # 2a61A read from 2a61A/merged-good-all-a2m # adding 2a61A to template set # found chain 2a61A in template set T0327 4 :DKLRYAILKEIF 2a61A 33 :TPAQFDILQKIY T0327 16 :EGNTP 2a61A 46 :EGPKR T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 2a61A 58 :LGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYF T0327 64 :ELTEKGENYLKENGTWSKAY 2a61A 93 :VITRKGEEVIEKVIERRENF T0327 86 :IKEIKD 2a61A 113 :IEKITS Number of specific fragments extracted= 5 number of extra gaps= 0 total=217 Number of alignments=49 # 2a61A read from 2a61A/merged-good-all-a2m # found chain 2a61A in template set T0327 4 :DKLRYAILKEIFEGNTP 2a61A 33 :TPAQFDILQKIYFEGPK T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 2a61A 58 :LGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYF T0327 64 :ELTEKGENYLKENGTWSKAY 2a61A 93 :VITRKGEEVIEKVIERRENF T0327 86 :IKEIKD 2a61A 113 :IEKITS Number of specific fragments extracted= 4 number of extra gaps= 0 total=221 Number of alignments=50 # 2a61A read from 2a61A/merged-good-all-a2m # found chain 2a61A in template set T0327 2 :NKDKLRYAI 2a61A 50 :RPGELSVLL T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 2a61A 59 :GVAKSTVTGLVKRLEADGYLTRTPDPADRRAYF T0327 63 :PELTEKGENYLKENGTWSKAYK 2a61A 92 :LVITRKGEEVIEKVIERRENFI T0327 87 :KEIK 2a61A 114 :EKIT Number of specific fragments extracted= 4 number of extra gaps= 0 total=225 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fbiA expands to /projects/compbio/data/pdb/2fbi.pdb.gz 2fbiA:Skipped atom 2, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 443, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 445, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 447, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 831, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 833, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 835, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 837, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 839, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 895, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1099, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1101, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 2fbiA # T0327 read from 2fbiA/merged-good-all-a2m # 2fbiA read from 2fbiA/merged-good-all-a2m # adding 2fbiA to template set # found chain 2fbiA in template set Warning: unaligning (T0327)D53 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0327)D54 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0327 5 :KLRYAILKEIF 2fbiA 34 :EQQWRVIRILR T0327 16 :EGN 2fbiA 46 :QGE T0327 25 :DIGVTEDQFDDAVNFLKREGYIIGVHYS 2fbiA 57 :QACILRPSMTGVLARLERDGIVRRWKAP T0327 55 :RPHLY 2fbiA 87 :QRRVY T0327 60 :K 2fbiA 93 :N T0327 65 :LTEKGENYLKENGT 2fbiA 94 :LTEKGQQCFVSMSG T0327 79 :WSKAYKTIKEI 2fbiA 109 :MEKNYQRIQER Number of specific fragments extracted= 7 number of extra gaps= 1 total=232 Number of alignments=52 # 2fbiA read from 2fbiA/merged-good-all-a2m # found chain 2fbiA in template set Warning: unaligning (T0327)D53 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0327)D54 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0327 5 :KLRYAILKEIFEGN 2fbiA 34 :EQQWRVIRILRQQG T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHYS 2fbiA 56 :NQACILRPSMTGVLARLERDGIVRRWKAP T0327 55 :RPHLY 2fbiA 87 :QRRVY T0327 60 :K 2fbiA 93 :N T0327 65 :LTEKGENYLKENGT 2fbiA 94 :LTEKGQQCFVSMSG T0327 79 :WSKAYKTIKEI 2fbiA 109 :MEKNYQRIQER Number of specific fragments extracted= 6 number of extra gaps= 1 total=238 Number of alignments=53 # 2fbiA read from 2fbiA/merged-good-all-a2m # found chain 2fbiA in template set Warning: unaligning (T0327)D53 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0327)D54 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYS 2fbiA 58 :ACILRPSMTGVLARLERDGIVRRWKAP T0327 55 :RPHLY 2fbiA 87 :QRRVY T0327 63 :PELTEKGENYLKENGT 2fbiA 92 :VNLTEKGQQCFVSMSG T0327 79 :WSKAYKTIKEI 2fbiA 109 :MEKNYQRIQER Number of specific fragments extracted= 4 number of extra gaps= 1 total=242 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f2eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f2eA expands to /projects/compbio/data/pdb/2f2e.pdb.gz 2f2eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 2f2eA # T0327 read from 2f2eA/merged-good-all-a2m # 2f2eA read from 2f2eA/merged-good-all-a2m # adding 2f2eA to template set # found chain 2f2eA in template set T0327 5 :KLRYAILKEIFEGNTP 2f2eA 24 :GWSMLIVRDAFEGLTR T0327 25 :DIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYKL 2f2eA 46 :SLGLAKNILAARLRNLVEHGVMVAVPAESGSHQEYRL T0327 66 :TEKG 2f2eA 83 :TDKG T0327 74 :KENGTWSKAYKTIKE 2f2eA 87 :RALFPLLVAIRQWGE Number of specific fragments extracted= 4 number of extra gaps= 0 total=246 Number of alignments=55 # 2f2eA read from 2f2eA/merged-good-all-a2m # found chain 2f2eA in template set T0327 4 :DKLRYAILKEIFEGNTP 2f2eA 23 :DGWSMLIVRDAFEGLTR T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYKL 2f2eA 44 :QKSLGLAKNILAARLRNLVEHGVMVAVPAESGSHQEYRL T0327 66 :TEKG 2f2eA 83 :TDKG T0327 74 :KENGTWSKAYKTIKE 2f2eA 87 :RALFPLLVAIRQWGE Number of specific fragments extracted= 4 number of extra gaps= 0 total=250 Number of alignments=56 # 2f2eA read from 2f2eA/merged-good-all-a2m # found chain 2f2eA in template set T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPH 2f2eA 47 :LGLAKNILAARLRNLVEHGVMVAVPAESGSHQ T0327 62 :GPELTEKGENY 2f2eA 79 :EYRLTDKGRAL T0327 77 :GTWSKAYKTIKE 2f2eA 90 :FPLLVAIRQWGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=253 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3rubS/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3rubS expands to /projects/compbio/data/pdb/3rub.pdb.gz 3rubS:# T0327 read from 3rubS/merged-good-all-a2m # 3rubS read from 3rubS/merged-good-all-a2m # adding 3rubS to template set # found chain 3rubS in template set T0327 20 :PLSENDI 3rubS 6 :PINKKKY T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 3rubS 20 :DLSQEQLLSEVEYLLKNGWVPCLEFETEHGFVY T0327 60 :KLGPELTEK 3rubS 56 :NKSPGYYDG T0327 73 :LKENGTWSKAYKTIKEIKDW 3rubS 74 :MFGCTDATQVLAEVEEAKKA Number of specific fragments extracted= 4 number of extra gaps= 0 total=257 Number of alignments=58 # 3rubS read from 3rubS/merged-good-all-a2m # found chain 3rubS in template set T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHY 3rubS 16 :SYLPDLSQEQLLSEVEYLLKNGWVPCLEF T0327 52 :SD 3rubS 58 :SP T0327 54 :DRPHLYKLGPEL 3rubS 63 :DGRYWTMWKLPM T0327 75 :ENGTWSKAYKTIKEIKDW 3rubS 76 :GCTDATQVLAEVEEAKKA Number of specific fragments extracted= 4 number of extra gaps= 0 total=261 Number of alignments=59 # 3rubS read from 3rubS/merged-good-all-a2m # found chain 3rubS in template set T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYKLG 3rubS 17 :YLPDLSQEQLLSEVEYLLKNGWVPCLEFETEHGFVYREN T0327 66 :TEKGENYLKENGTWSKA 3rubS 77 :CTDATQVLAEVEEAKKA Number of specific fragments extracted= 2 number of extra gaps= 0 total=263 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cg4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cg4A expands to /projects/compbio/data/pdb/2cg4.pdb.gz 2cg4A:# T0327 read from 2cg4A/merged-good-all-a2m # 2cg4A read from 2cg4A/merged-good-all-a2m # adding 2cg4A to template set # found chain 2cg4A in template set Warning: unaligning (T0327)K3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)I6 T0327 4 :DKLRYAILKEIF 2cg4A 7 :DNLDRGILEALM T0327 16 :EGNTP 2cg4A 20 :NARTA T0327 25 :DIGVTEDQFDDAVNFLKREGYIIGVHY 2cg4A 31 :QFGVSPETIHVRVEKMKQAGIITGARI T0327 52 :SD 2cg4A 60 :SP T0327 54 :DRPHLY 2cg4A 65 :GYDVGC T0327 60 :KLG 2cg4A 75 :ILK T0327 63 :PELTEKGENYLKENG 2cg4A 79 :AKDYPSALAKLESLD Number of specific fragments extracted= 7 number of extra gaps= 1 total=270 Number of alignments=61 # 2cg4A read from 2cg4A/merged-good-all-a2m # found chain 2cg4A in template set Warning: unaligning (T0327)K3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)I6 T0327 4 :DKLRYAILKEIFEGNTP 2cg4A 7 :DNLDRGILEALMGNART T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHY 2cg4A 30 :KQFGVSPETIHVRVEKMKQAGIITGARI T0327 52 :SD 2cg4A 60 :SP T0327 54 :DRPHLY 2cg4A 65 :GYDVGC T0327 60 :KL 2cg4A 75 :IL T0327 62 :GPELTEKGENYLKENG 2cg4A 78 :SAKDYPSALAKLESLD Number of specific fragments extracted= 6 number of extra gaps= 1 total=276 Number of alignments=62 # 2cg4A read from 2cg4A/merged-good-all-a2m # found chain 2cg4A in template set T0327 4 :DKLRYAILKEIFEGNTP 2cg4A 8 :NLDRGILEALMGNARTA T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHY 2cg4A 30 :KQFGVSPETIHVRVEKMKQAGIITGARI T0327 52 :SDDRPH 2cg4A 63 :QLGYDV T0327 58 :LYKLGPELTEKGENYLKE 2cg4A 74 :IILKSAKDYPSALAKLES Number of specific fragments extracted= 4 number of extra gaps= 0 total=280 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b0lA expands to /projects/compbio/data/pdb/2b0l.pdb.gz 2b0lA:Skipped atom 32, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 34, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 36, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 38, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 40, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 42, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 44, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 46, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 48, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 50, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 123, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 125, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 127, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 129, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 131, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 133, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 135, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 137, because occupancy 0.200 <= existing 0.800 in 2b0lA # T0327 read from 2b0lA/merged-good-all-a2m # 2b0lA read from 2b0lA/merged-good-all-a2m # adding 2b0lA to template set # found chain 2b0lA in template set Warning: unaligning (T0327)E16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0327)G17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0327)D35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0327)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0327)I46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0327)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0327)V49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0327)H50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0327)Y51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0327)S52 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 Warning: unaligning (T0327)D53 because of BadResidue code BAD_PEPTIDE at template residue (2b0lA)M237 T0327 5 :KLRYAILKEIF 2b0lA 181 :YSELEAIEHIF T0327 18 :NTP 2b0lA 194 :LDG T0327 26 :IGVTEDQFD 2b0lA 210 :VGITRSVIV T0327 37 :VNFLKREGY 2b0lA 221 :LRKLESAGV T0327 48 :G 2b0lA 232 :S T0327 54 :DR 2b0lA 238 :KG T0327 57 :HLYKLG 2b0lA 240 :TYIKVL T0327 66 :TE 2b0lA 246 :NN T0327 84 :KTIKEIK 2b0lA 248 :KFLIELE Number of specific fragments extracted= 9 number of extra gaps= 4 total=289 Number of alignments=64 # 2b0lA read from 2b0lA/merged-good-all-a2m # found chain 2b0lA in template set Warning: unaligning (T0327)E16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0327)G17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0327)D35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0327)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0327)I46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0327)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0327)V49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0327)H50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0327)Y51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0327)S52 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 Warning: unaligning (T0327)D53 because of BadResidue code BAD_PEPTIDE at template residue (2b0lA)M237 T0327 6 :LRYAILKEIF 2b0lA 182 :SELEAIEHIF T0327 18 :NTP 2b0lA 194 :LDG T0327 24 :NDIGVTEDQFD 2b0lA 208 :DRVGITRSVIV T0327 37 :VNFLKREGY 2b0lA 221 :LRKLESAGV T0327 48 :G 2b0lA 232 :S T0327 54 :DRPHLYKL 2b0lA 238 :KGTYIKVL T0327 66 :TE 2b0lA 246 :NN T0327 84 :KTIKEIK 2b0lA 248 :KFLIELE Number of specific fragments extracted= 8 number of extra gaps= 4 total=297 Number of alignments=65 # 2b0lA read from 2b0lA/merged-good-all-a2m # found chain 2b0lA in template set Warning: unaligning (T0327)D35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0327)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0327)I46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0327)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0327)V49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0327)H50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0327)Y51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0327)S52 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 Warning: unaligning (T0327)D53 because of BadResidue code BAD_PEPTIDE at template residue (2b0lA)M237 T0327 26 :IGVTEDQFD 2b0lA 210 :VGITRSVIV T0327 37 :VNFLKREGY 2b0lA 221 :LRKLESAGV T0327 48 :G 2b0lA 232 :S T0327 54 :DRPHLYKLG 2b0lA 238 :KGTYIKVLN T0327 67 :E 2b0lA 247 :N T0327 84 :KTIKEIK 2b0lA 248 :KFLIELE Number of specific fragments extracted= 6 number of extra gaps= 3 total=303 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ir21/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ir21 expands to /projects/compbio/data/pdb/1ir2.pdb.gz 1ir21:# T0327 read from 1ir21/merged-good-all-a2m # 1ir21 read from 1ir21/merged-good-all-a2m # adding 1ir21 to template set # found chain 1ir21 in template set T0327 16 :EGNT 1ir21 16 :SYLP T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYK 1ir21 20 :PLSDEQIAAQVDYIVANGWIPCLEFAESDKAYVS Number of specific fragments extracted= 2 number of extra gaps= 0 total=305 Number of alignments=67 # 1ir21 read from 1ir21/merged-good-all-a2m # found chain 1ir21 in template set T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHL 1ir21 17 :YLPPLSDEQIAAQVDYIVANGWIPCLEFAESDKAY Number of specific fragments extracted= 1 number of extra gaps= 0 total=306 Number of alignments=68 # 1ir21 read from 1ir21/merged-good-all-a2m # found chain 1ir21 in template set T0327 16 :EGNTPLSE 1ir21 7 :VNNKMFET T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHY 1ir21 17 :YLPPLSDEQIAAQVDYIVANGWIPCLEF T0327 52 :SDDRPHLYKLGPELTEKGENYLKENGTWSK 1ir21 69 :DNRYWTMWKLPMFGCRDPMQVLREIVACTK Number of specific fragments extracted= 3 number of extra gaps= 0 total=309 Number of alignments=69 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0327//projects/compbio/experiments/protein-predict/casp7/T0327/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0327//projects/compbio/experiments/protein-predict/casp7/T0327/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0327/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0327/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0327)V37.CB, (T0327)I46.CB) [> 3.8872 = 6.4786 < 8.4222] w=1.0000 to align # Constraint # added constraint: constraint((T0327)G48.CA, (T0327)Y59.CB) [> 3.5982 = 5.9969 < 7.7960] w=0.8145 to align # Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)L65.CB) [> 3.9784 = 6.6307 < 8.6199] w=0.7396 to align # Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)T66.CB) [> 3.4226 = 5.7043 < 7.4156] w=0.7206 to align # Constraint # added constraint: constraint((T0327)G44.CA, (T0327)T66.CB) [> 3.4424 = 5.7373 < 7.4585] w=0.7206 to align # Constraint # added constraint: constraint((T0327)G48.CA, (T0327)L58.CB) [> 3.6531 = 6.0884 < 7.9150] w=0.7150 to align # Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)G69.CA) [> 2.5601 = 4.2668 < 5.5468] w=0.7018 to align # Constraint # added constraint: constraint((T0327)L6.CB, (T0327)A36.CB) [> 3.4400 = 5.7334 < 7.4534] w=0.6974 to align # Constraint # added constraint: constraint((T0327)L11.CB, (T0327)L40.CB) [> 4.2632 = 7.1053 < 9.2368] w=0.6868 to align # Constraint # added constraint: constraint((T0327)I10.CB, (T0327)L40.CB) [> 4.0639 = 6.7732 < 8.8051] w=0.6862 to align # Constraint # added constraint: constraint((T0327)I10.CB, (T0327)A36.CB) [> 3.4983 = 5.8305 < 7.5797] w=0.6681 to align # Constraint # added constraint: constraint((T0327)L11.CB, (T0327)Y45.CB) [> 3.9489 = 6.5815 < 8.5560] w=0.6491 to align # Constraint # added constraint: constraint((T0327)I10.CB, (T0327)V37.CB) [> 4.2253 = 7.0422 < 9.1548] w=0.6491 to align # Constraint # added constraint: constraint((T0327)I46.CB, (T0327)T66.CB) [> 3.8748 = 6.4579 < 8.3953] w=0.6468 to align # Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)K68.CB) [> 3.5817 = 5.9695 < 7.7603] w=0.6450 to align # Constraint # added constraint: constraint((T0327)I47.CB, (T0327)T66.CB) [> 3.4537 = 5.7561 < 7.4830] w=0.6277 to align # Constraint # added constraint: constraint((T0327)A9.CB, (T0327)I26.CB) [> 3.5770 = 5.9616 < 7.7502] w=0.6110 to align # Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)Y72.CB) [> 3.6592 = 6.0987 < 7.9283] w=0.6070 to align # Constraint # added constraint: constraint((T0327)L6.CB, (T0327)V28.CB) [> 3.7689 = 6.2815 < 8.1660] w=0.5921 to align # Constraint # added constraint: constraint((T0327)I46.CB, (T0327)L65.CB) [> 3.7231 = 6.2052 < 8.0668] w=0.5879 to align # Constraint # added constraint: constraint((T0327)I10.CB, (T0327)F33.CB) [> 4.2740 = 7.1233 < 9.2603] w=0.5872 to align # Constraint # added constraint: constraint((T0327)V49.CB, (T0327)Y59.CB) [> 3.3641 = 5.6069 < 7.2889] w=0.5819 to align # Constraint # added constraint: constraint((T0327)R7.CB, (T0327)A36.CB) [> 3.3425 = 5.5708 < 7.2421] w=0.5734 to align # Constraint # added constraint: constraint((T0327)V49.CB, (T0327)L58.CB) [> 4.0462 = 6.7437 < 8.7668] w=0.5629 to align # Constraint # added constraint: constraint((T0327)I46.CB, (T0327)G69.CA) [> 4.2771 = 7.1285 < 9.2671] w=0.5502 to align # Constraint # added constraint: constraint((T0327)R7.CB, (T0327)F39.CB) [> 4.1803 = 6.9672 < 9.0573] w=0.5354 to align # Constraint # added constraint: constraint((T0327)I10.CB, (T0327)I26.CB) [> 3.8582 = 6.4303 < 8.3594] w=0.5161 to align # Constraint # added constraint: constraint((T0327)I14.CB, (T0327)I46.CB) [> 4.0780 = 6.7966 < 8.8356] w=0.5116 to align # Constraint # added constraint: constraint((T0327)L6.CB, (T0327)F33.CB) [> 4.0638 = 6.7730 < 8.8049] w=0.4584 to align # Constraint # added constraint: constraint((T0327)G48.CA, (T0327)E64.CB) [> 3.8730 = 6.4550 < 8.3915] w=0.4362 to align # Constraint # added constraint: constraint((T0327)F15.CB, (T0327)L65.CB) [> 3.8191 = 6.3652 < 8.2747] w=0.4362 to align # Constraint # added constraint: constraint((T0327)G48.CA, (T0327)K60.CB) [> 4.0418 = 6.7363 < 8.7571] w=0.4215 to align # Constraint # added constraint: constraint((T0327)L6.CB, (T0327)Q32.CB) [> 3.9348 = 6.5579 < 8.5253] w=0.4207 to align # Constraint # added constraint: constraint((T0327)I46.CB, (T0327)E64.CB) [> 4.0008 = 6.6680 < 8.6684] w=0.4192 to align # Constraint # added constraint: constraint((T0327)I47.CB, (T0327)E64.CB) [> 3.0732 = 5.1220 < 6.6586] w=0.4173 to align # Constraint # added constraint: constraint((T0327)V37.CB, (T0327)G48.CA) [> 4.4075 = 7.3458 < 9.5496] w=0.4121 to align # Constraint # added constraint: constraint((T0327)H50.CB, (T0327)Y59.CB) [> 4.2613 = 7.1022 < 9.2329] w=0.3992 to align # Constraint # added constraint: constraint((T0327)I47.CB, (T0327)L65.CB) [> 4.3936 = 7.3226 < 9.5194] w=0.3983 to align # Constraint # added constraint: constraint((T0327)L6.CB, (T0327)I26.CB) [> 3.7564 = 6.2606 < 8.1388] w=0.3957 to align # Constraint # added constraint: constraint((T0327)F15.CB, (T0327)L73.CB) [> 3.2169 = 5.3615 < 6.9699] w=0.3794 to align # Constraint # added constraint: constraint((T0327)I14.CB, (T0327)L65.CB) [> 2.9604 = 4.9340 < 6.4142] w=0.3794 to align # Constraint # added constraint: constraint((T0327)L11.CB, (T0327)L73.CB) [> 3.0195 = 5.0326 < 6.5423] w=0.3794 to align # Constraint # added constraint: constraint((T0327)E13.CB, (T0327)I26.CB) [> 4.0565 = 6.7609 < 8.7891] w=0.3789 to align # Constraint # added constraint: constraint((T0327)I47.CB, (T0327)Y59.CB) [> 3.9767 = 6.6279 < 8.6162] w=0.3767 to align # Constraint # added constraint: constraint((T0327)V49.CB, (T0327)E64.CB) [> 4.0732 = 6.7887 < 8.8253] w=0.3605 to align # Constraint # added constraint: constraint((T0327)Y8.CB, (T0327)N76.CB) [> 3.9233 = 6.5388 < 8.5004] w=0.3604 to align # Constraint # added constraint: constraint((T0327)I46.CB, (T0327)K60.CB) [> 4.0562 = 6.7604 < 8.7885] w=0.3578 to align # Constraint # added constraint: constraint((T0327)K12.CB, (T0327)L73.CB) [> 4.0309 = 6.7181 < 8.7336] w=0.3414 to align # Constraint # added constraint: constraint((T0327)I10.CB, (T0327)I46.CB) [> 4.5237 = 7.5396 < 9.8014] w=0.3406 to align # Constraint # added constraint: constraint((T0327)G48.CA, (T0327)H57.CB) [> 3.6551 = 6.0918 < 7.9193] w=0.3219 to align # Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)L61.CB) [> 4.2079 = 7.0132 < 9.1172] w=0.3195 to align # Constraint # added constraint: constraint((T0327)I46.CB, (T0327)Y59.CB) [> 3.6059 = 6.0098 < 7.8127] w=0.3009 to align # Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)L73.CB) [> 4.5197 = 7.5328 < 9.7927] w=0.2846 to align # Constraint # added constraint: constraint((T0327)L11.CB, (T0327)N76.CB) [> 4.0917 = 6.8196 < 8.8654] w=0.2655 to align # Constraint # added constraint: constraint((T0327)A9.CB, (T0327)V28.CB) [> 4.4409 = 7.4015 < 9.6220] w=0.2652 to align # Constraint # added constraint: constraint((T0327)E13.CB, (T0327)D25.CB) [> 3.8469 = 6.4115 < 8.3350] w=0.2650 to align # Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)G62.CA) [> 3.8920 = 6.4867 < 8.4328] w=0.2628 to align # Constraint # added constraint: constraint((T0327)I10.CB, (T0327)V28.CB) [> 3.6957 = 6.1595 < 8.0074] w=0.2462 to align # Constraint # added constraint: constraint((T0327)I47.CB, (T0327)G62.CA) [> 3.5793 = 5.9655 < 7.7551] w=0.2151 to align # Constraint # added constraint: constraint((T0327)V37.CB, (T0327)Y59.CB) [> 3.8275 = 6.3791 < 8.2928] w=0.2132 to align # Constraint # added constraint: constraint((T0327)I14.CB, (T0327)L61.CB) [> 3.5082 = 5.8470 < 7.6010] w=0.2131 to align # Constraint # added constraint: constraint((T0327)G48.CA, (T0327)P63.CB) [> 3.3202 = 5.5336 < 7.1937] w=0.2104 to align # Constraint # added constraint: constraint((T0327)I14.CB, (T0327)E64.CB) [> 4.0215 = 6.7025 < 8.7133] w=0.2087 to align # Constraint # added constraint: constraint((T0327)D4.CB, (T0327)A36.CB) [> 4.3307 = 7.2179 < 9.3832] w=0.2084 to align # Constraint # added constraint: constraint((T0327)I46.CB, (T0327)L58.CB) [> 3.6285 = 6.0475 < 7.8618] w=0.2014 to align # Constraint # added constraint: constraint((T0327)I47.CB, (T0327)L61.CB) [> 4.1236 = 6.8726 < 8.9344] w=0.2013 to align # Constraint # added constraint: constraint((T0327)N18.CB, (T0327)E64.CB) [> 3.3413 = 5.5688 < 7.2394] w=0.1898 to align # Constraint # added constraint: constraint((T0327)Y8.CB, (T0327)L73.CB) [> 3.9756 = 6.6259 < 8.6137] w=0.1897 to align # Constraint # added constraint: constraint((T0327)I14.CB, (T0327)Y59.CB) [> 3.9631 = 6.6052 < 8.5868] w=0.1893 to align # Constraint # added constraint: constraint((T0327)I47.CB, (T0327)L58.CB) [> 4.4225 = 7.3708 < 9.5821] w=0.1825 to align # Constraint # added constraint: constraint((T0327)Y8.CB, (T0327)S80.CB) [> 4.2370 = 7.0616 < 9.1801] w=0.1707 to align # Constraint # added constraint: constraint((T0327)I14.CB, (T0327)L58.CB) [> 3.7420 = 6.2366 < 8.1076] w=0.1704 to align # Constraint # added constraint: constraint((T0327)F15.CB, (T0327)L61.CB) [> 3.7852 = 6.3086 < 8.2011] w=0.1703 to align # Constraint # added constraint: constraint((T0327)G17.CA, (T0327)E64.CB) [> 4.1665 = 6.9442 < 9.0274] w=0.1518 to align # Constraint # added constraint: constraint((T0327)E43.CB, (T0327)G69.CA) [> 4.7341 = 7.8901 < 10.2572] w=0.1494 to align # Constraint # added constraint: constraint((T0327)L21.CB, (T0327)P56.CB) [> 4.1034 = 6.8390 < 8.8907] w=0.1374 to align # Constraint # added constraint: constraint((T0327)R7.CB, (T0327)V28.CB) [> 3.6926 = 6.1544 < 8.0007] w=0.1328 to align # Constraint # added constraint: constraint((T0327)L6.CB, (T0327)V37.CB) [> 4.3915 = 7.3192 < 9.5150] w=0.1257 to align # Constraint # added constraint: constraint((T0327)L21.CB, (T0327)H57.CB) [> 3.2942 = 5.4903 < 7.1374] w=0.1255 to align # Constraint # added constraint: constraint((T0327)V37.CB, (T0327)I47.CB) [> 3.9926 = 6.6543 < 8.6506] w=0.1187 to align # Constraint # added constraint: constraint((T0327)L40.CB, (T0327)G69.CA) [> 4.6539 = 7.7565 < 10.0834] w=0.1158 to align # Constraint # added constraint: constraint((T0327)I14.CB, (T0327)L73.CB) [> 4.0573 = 6.7622 < 8.7909] w=0.1137 to align # Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)E64.CB) [> 3.1115 = 5.1858 < 6.7415] w=0.1137 to align # Constraint # added constraint: constraint((T0327)G44.CA, (T0327)E64.CB) [> 2.8163 = 4.6939 < 6.1021] w=0.1137 to align # Constraint # added constraint: constraint((T0327)K5.CB, (T0327)I26.CB) [> 3.9036 = 6.5060 < 8.4578] w=0.1113 to align # Constraint # added constraint: constraint((T0327)K41.CB, (T0327)Y59.CB) [> 4.6355 = 7.7258 < 10.0436] w=0.0996 to align # Constraint # added constraint: constraint((T0327)L6.CB, (T0327)L40.CB) [> 3.8646 = 6.4411 < 8.3734] w=0.0876 to align # Constraint # added constraint: constraint((T0327)L73.CB, (T0327)T85.CB) [> 4.3315 = 7.2191 < 9.3848] w=0.0803 to align # Constraint # added constraint: constraint((T0327)F15.CB, (T0327)K74.CB) [> 4.1585 = 6.9309 < 9.0102] w=0.0759 to align # Constraint # added constraint: constraint((T0327)Y8.CB, (T0327)Y83.CB) [> 4.1152 = 6.8586 < 8.9162] w=0.0759 to align # Constraint # added constraint: constraint((T0327)G48.CA, (T0327)L61.CB) [> 3.6432 = 6.0721 < 7.8937] w=0.0757 to align # Constraint # added constraint: constraint((T0327)R7.CB, (T0327)Q32.CB) [> 3.9313 = 6.5521 < 8.5178] w=0.0756 to align # Constraint # added constraint: constraint((T0327)F15.CB, (T0327)I86.CB) [> 3.7935 = 6.3225 < 8.2193] w=0.0754 to align # Constraint # added constraint: constraint((T0327)K41.CB, (T0327)W79.CB) [> 3.4420 = 5.7367 < 7.4577] w=0.0753 to align # Constraint # added constraint: constraint((T0327)N38.CB, (T0327)W79.CB) [> 2.9360 = 4.8934 < 6.3614] w=0.0753 to align # Constraint # added constraint: constraint((T0327)D34.CB, (T0327)Y83.CB) [> 3.8516 = 6.4194 < 8.3452] w=0.0753 to align # Constraint # added constraint: constraint((T0327)F33.CB, (T0327)Y83.CB) [> 4.1879 = 6.9798 < 9.0737] w=0.0753 to align # Constraint # added constraint: constraint((T0327)I47.CB, (T0327)N76.CB) [> 3.5997 = 5.9995 < 7.7994] w=0.0753 to align # Constraint # added constraint: constraint((T0327)I47.CB, (T0327)A82.CB) [> 2.8876 = 4.8126 < 6.2564] w=0.0753 to align # Constraint # added constraint: constraint((T0327)G48.CA, (T0327)A82.CB) [> 4.5496 = 7.5826 < 9.8574] w=0.0753 to align # Constraint # added constraint: constraint((T0327)G48.CA, (T0327)T85.CB) [> 4.7749 = 7.9581 < 10.3456] w=0.0753 to align # Constraint # added constraint: constraint((T0327)V49.CB, (T0327)T85.CB) [> 3.3639 = 5.6065 < 7.2884] w=0.0753 to align # Constraint # added constraint: constraint((T0327)V49.CB, (T0327)I86.CB) [> 3.9456 = 6.5761 < 8.5489] w=0.0753 to align # Constraint # added constraint: constraint((T0327)V49.CB, (T0327)I89.CB) [> 3.3654 = 5.6090 < 7.2918] w=0.0753 to align # Constraint # added constraint: constraint((T0327)Y51.CB, (T0327)I89.CB) [> 3.5026 = 5.8377 < 7.5890] w=0.0753 to align # Constraint # added constraint: constraint((T0327)A9.CB, (T0327)A36.CB) [> 4.2423 = 7.0704 < 9.1916] w=0.0750 to align # Constraint # added constraint: constraint((T0327)D25.CB, (T0327)K84.CB) [> 4.5117 = 7.5194 < 9.7753] w=0.0570 to align # Constraint # added constraint: constraint((T0327)T19.CB, (T0327)E64.CB) [> 4.1795 = 6.9659 < 9.0556] w=0.0569 to align # Constraint # added constraint: constraint((T0327)D4.CB, (T0327)F39.CB) [> 4.0865 = 6.8108 < 8.8541] w=0.0569 to align # Constraint # added constraint: constraint((T0327)H50.CB, (T0327)G62.CA) [> 3.2985 = 5.4976 < 7.1469] w=0.0568 to align # Constraint # added constraint: constraint((T0327)V49.CB, (T0327)L61.CB) [> 3.7579 = 6.2632 < 8.1422] w=0.0568 to align # Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)A82.CB) [> 3.9166 = 6.5277 < 8.4860] w=0.0566 to align # Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)K81.CB) [> 4.4023 = 7.3371 < 9.5383] w=0.0566 to align # Constraint # added constraint: constraint((T0327)Y45.CB, (T0327)T85.CB) [> 3.1576 = 5.2626 < 6.8414] w=0.0565 to align # Constraint # added constraint: constraint((T0327)N18.CB, (T0327)H57.CB) [> 3.0773 = 5.1289 < 6.6676] w=0.0562 to align # Constraint # added constraint: constraint((T0327)T29.CB, (T0327)Y51.CB) [> 3.8889 = 6.4815 < 8.4260] w=0.0546 to align # Constraint # added constraint: constraint((T0327)T29.CB, (T0327)H57.CB) [> 2.6235 = 4.3726 < 5.6843] w=0.0546 to align # Constraint # added constraint: constraint((T0327)D34.CB, (T0327)V49.CB) [> 4.3083 = 7.1805 < 9.3347] w=0.0546 to align # Constraint # added constraint: constraint((T0327)L21.CB, (T0327)L58.CB) [> 3.0302 = 5.0504 < 6.5655] w=0.0497 to align # Constraint # added constraint: constraint((T0327)G48.CA, (T0327)Y72.CB) [> 4.6521 = 7.7535 < 10.0796] w=0.0396 to align # Constraint # added constraint: constraint((T0327)K12.CB, (T0327)K81.CB) [> 4.7553 = 7.9255 < 10.3032] w=0.0380 to align # Constraint # added constraint: constraint((T0327)L40.CB, (T0327)Y59.CB) [> 4.7957 = 7.9927 < 10.3906] w=0.0380 to align # Constraint # added constraint: constraint((T0327)L21.CB, (T0327)F33.CB) [> 4.3785 = 7.2975 < 9.4868] w=0.0380 to align # Constraint # added constraint: constraint((T0327)F15.CB, (T0327)F33.CB) [> 4.4530 = 7.4217 < 9.6482] w=0.0379 to align # Constraint # added constraint: constraint((T0327)E16.CB, (T0327)V28.CB) [> 4.4473 = 7.4121 < 9.6358] w=0.0379 to align # Constraint # added constraint: constraint((T0327)E13.CB, (T0327)L58.CB) [> 4.6018 = 7.6697 < 9.9706] w=0.0379 to align # Constraint # added constraint: constraint((T0327)S52.CB, (T0327)E64.CB) [> 3.2245 = 5.3741 < 6.9864] w=0.0379 to align # Constraint # added constraint: constraint((T0327)Y51.CB, (T0327)E64.CB) [> 4.3824 = 7.3039 < 9.4951] w=0.0379 to align # Constraint # added constraint: constraint((T0327)H50.CB, (T0327)L61.CB) [> 4.0050 = 6.6750 < 8.6775] w=0.0378 to align # Constraint # added constraint: constraint((T0327)Y8.CB, (T0327)I89.CB) [> 4.5925 = 7.6542 < 9.9504] w=0.0378 to align # Constraint # added constraint: constraint((T0327)L11.CB, (T0327)A82.CB) [> 3.5828 = 5.9714 < 7.7628] w=0.0378 to align # Constraint # added constraint: constraint((T0327)L11.CB, (T0327)I86.CB) [> 4.7522 = 7.9203 < 10.2964] w=0.0378 to align # Constraint # added constraint: constraint((T0327)F33.CB, (T0327)I86.CB) [> 4.5855 = 7.6425 < 9.9353] w=0.0377 to align # Constraint # added constraint: constraint((T0327)E30.CB, (T0327)Y83.CB) [> 4.2667 = 7.1112 < 9.2446] w=0.0377 to align # Constraint # added constraint: constraint((T0327)V49.CB, (T0327)Y72.CB) [> 4.0922 = 6.8203 < 8.8664] w=0.0377 to align # Constraint # added constraint: constraint((T0327)L40.CB, (T0327)A82.CB) [> 4.7908 = 7.9847 < 10.3801] w=0.0377 to align # Constraint # added constraint: constraint((T0327)L61.CB, (T0327)T85.CB) [> 3.7026 = 6.1710 < 8.0223] w=0.0377 to align # Constraint # added constraint: constraint((T0327)K12.CB, (T0327)I89.CB) [> 3.8503 = 6.4172 < 8.3423] w=0.0377 to align # Constraint # added constraint: constraint((T0327)L11.CB, (T0327)I89.CB) [> 4.0439 = 6.7398 < 8.7618] w=0.0377 to align # Constraint # added constraint: constraint((T0327)I47.CB, (T0327)Y72.CB) [> 2.8945 = 4.8242 < 6.2715] w=0.0207 to align # Constraint # added constraint: constraint((T0327)Y51.CB, (T0327)W79.CB) [> 3.4451 = 5.7419 < 7.4644] w=0.0207 to align # Constraint # added constraint: constraint((T0327)R55.CB, (T0327)E64.CB) [> 3.8315 = 6.3858 < 8.3016] w=0.0190 to align # Constraint # added constraint: constraint((T0327)E70.CB, (T0327)A82.CB) [> 3.4822 = 5.8037 < 7.5448] w=0.0189 to align # Constraint # added constraint: constraint((T0327)E70.CB, (T0327)Y83.CB) [> 3.6903 = 6.1505 < 7.9956] w=0.0189 to align # Constraint # added constraint: constraint((T0327)L61.CB, (T0327)I89.CB) [> 3.2324 = 5.3873 < 7.0034] w=0.0188 to align # Constraint # added constraint: constraint((T0327)Y51.CB, (T0327)I93.CB) [> 3.3778 = 5.6297 < 7.3186] w=0.0188 to align # Constraint # added constraint: constraint((T0327)D53.CB, (T0327)I93.CB) [> 3.8463 = 6.4105 < 8.3336] w=0.0188 to align # Constraint # added constraint: constraint((T0327)T29.CB, (T0327)L58.CB) [> 2.6487 = 4.4144 < 5.7388] w=0.0182 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0327/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0327/decoys/ # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-1ub9A-dimer11.pdb.gz looking for chain 'A' model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-1ub9A-dimer11 # ReadConformPDB reading from PDB file ../dimer/decoys/dimer1-1tbxA-dimer6.pdb.gz looking for chain 'A' model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation dimer//dimer1-1tbxA-dimer6 # ReadConformPDB reading from PDB file ../dimer/decoys/dimer2-1tbxA-dimer6.pdb.gz looking for chain 'A' model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation dimer//dimer2-1tbxA-dimer6 # ReadConformPDB reading from PDB file ../dimer/decoys/dimer3-1tbxA-dimer6.pdb.gz looking for chain 'A' model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation dimer//dimer3-1tbxA-dimer6 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 34 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 34 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 Skipped atom 265, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 Skipped atom 265, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 Skipped atom 323, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 325, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 327, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 329, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 331, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 Error: Reading chain '' from PDB file servers/MIG_FROST_AL1.pdb.gz failed---no such chain. # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 10 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 24 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 10 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 19 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 75 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 Skipped atom 50, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 52, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 70, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 72, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 74, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 75 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 21 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0327)N76.CA and (T0327)K87.CA only 0.000 apart, marking (T0327)K87.CA as missing WARNING: atoms too close: (T0327)G77.CA and (T0327)E88.CA only 0.000 apart, marking (T0327)E88.CA as missing # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 170, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 172, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 174, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 222, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 224, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 226, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 228, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 5 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 19 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0327 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 0.2177 model score 0.2250 model score 0.2250 model score 0.2250 model score 0.0070 model score 0.2365 model score 0.1308 model score 0.1032 model score 1.1716 model score 0.2480 model score -0.0401 model score -0.0010 model score 0.2739 model score 0.0088 model score 1.2009 model score 1.0168 model score 0.6183 model score 1.8545 model score 0.2660 model score -0.0149 model score 1.2093 model score 0.9078 model score 1.5949 model score 0.8878 model score 0.8878 model score 0.7710 model score 0.5165 model score 0.9189 model score 0.5985 model score -0.0351 model score 1.6746 model score 1.4623 model score -0.0126 model score -0.0117 model score -0.0117 model score -0.1155 model score -0.0946 model score -0.2592 model score -0.0654 model score 0.1986 model score -0.0545 model score -0.1209 model score 0.1986 model score -0.0293 model score 1.5758 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.0101 model score 0.1986 model score -0.1458 model score 0.0203 model score -0.0761 model score -0.0683 model score -0.1155 model score -0.0946 model score -0.2592 model score -0.1458 model score -0.0717 model score -0.2529 model score 1.2152 model score 2.0199 model score -0.0527 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.0091 model score 2.0925 model score 2.0313 model score 2.0649 model score 1.7033 model score 2.3320 model score 1.7267 model score 0.1129 model score 1.9217 model score 1.6760 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.1260 model score 0.7195 model score -0.0656 model score 0.0311 model score 0.1265 model score 0.0696 model score 0.0074 model score -0.1736 model score 1.3273 model score 0.1335 model score -0.0432 model score -0.0351 model score -0.0351 model score 0.0553 model score 0.7707 model score 1.2084 model score 0.9861 model score 1.0440 model score -0.0708 model score 0.0984 model score -0.0233 model score 1.7313 model score 2.4199 model score -0.0184 model score -0.0754 model score 2.0109 model score 1.5176 model score 2.2464 model score 0.0066 model score 0.2795 model score 2.0109 model score 1.5014 model score 2.2464 model score -0.0896 model score 0.0469 model score -0.0398 model score -0.0361 model score -0.0505 model score -0.1140 model score 1.4268 model score 0.4898 model score 1.1104 model score 0.8184 model score 1.2637 model score -0.1086 model score -0.1348 model score -0.1306 model score -0.1199 model score -0.1495 model score -0.0550 model score -0.1247 model score -0.1330 model score -0.0792 model score -0.0914 model score 0.0154 model score -0.2712 model score -0.0242 model score 1.3422 model score -0.0432 model score 0.9310 model score 0.0409 model score 0.1285 model score 0.0529 model score 0.0409 model score 0.1682 model score -0.1850 model score -0.0700 model score 0.0161 model score -0.2289 model score 0.0803 model score -0.1659 model score 0.0283 model score -0.1140 model score -0.1401 model score -0.1766 model score -0.0915 model score 0.0576 model score 0.2884 model score -0.0248 model score -0.0012 model score -0.1356 model score 0.0448 model score 0.2646 model score -0.1559 model score -0.0352 model score 0.0161 model score 0.1988 model score 0.1151 model score 0.0803 model score -0.0700 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.7311 model score 0.5050 model score 0.7318 model score -0.2324 model score 0.8198 model score -0.1140 model score 0.3338 model score -0.0475 model score 0.2002 model score -0.1659 model score 0.0454 model score 0.0028 model score 0.0461 model score 1.5412 model score 1.7425 model score -0.1140 model score 0.0136 model score -0.0054 model score 0.3076 model score 1.9754 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.5047 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.1034 model score -0.2473 model score -0.0685 model score -0.0047 model score -0.2256 model score -0.0977 model score -0.1944 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.0066 model score -0.1659 model score 0.0961 model score 0.0336 model score 0.1539 model score 1.9117 model score 1.8922 model score 2.1149 model score 2.0236 model score 1.7840 model score -0.0025 model score -0.2344 model score 0.3843 model score 0.2915 model score 0.2116 model score -0.1832 model score -0.0848 model score -0.0370 model score 0.0165 model score 0.0223 model score 0.3466 model score 0.2766 model score 0.0111 model score 0.0102 model score -0.2317 model score 0.5369 model score 1.9117 model score -0.1351 USE_META, weight: 0.8365 cost: 0.2177 min: -0.2712 max: 2.4199 USE_META, weight: 0.8341 cost: 0.2250 min: -0.2712 max: 2.4199 USE_META, weight: 0.8340 cost: 0.2250 min: -0.2712 max: 2.4199 USE_META, weight: 0.8340 cost: 0.2250 min: -0.2712 max: 2.4199 USE_META, weight: 0.9070 cost: 0.0070 min: -0.2712 max: 2.4199 USE_META, weight: 0.8302 cost: 0.2365 min: -0.2712 max: 2.4199 USE_META, weight: 0.8656 cost: 0.1308 min: -0.2712 max: 2.4199 USE_META, weight: 0.8748 cost: 0.1032 min: -0.2712 max: 2.4199 USE_META, weight: 0.5175 cost: 1.1716 min: -0.2712 max: 2.4199 USE_META, weight: 0.8264 cost: 0.2480 min: -0.2712 max: 2.4199 USE_META, weight: 0.9227 cost: -0.0401 min: -0.2712 max: 2.4199 USE_META, weight: 0.9096 cost: -0.0010 min: -0.2712 max: 2.4199 USE_META, weight: 0.8177 cost: 0.2739 min: -0.2712 max: 2.4199 USE_META, weight: 0.9064 cost: 0.0088 min: -0.2712 max: 2.4199 USE_META, weight: 0.5077 cost: 1.2009 min: -0.2712 max: 2.4199 USE_META, weight: 0.5692 cost: 1.0168 min: -0.2712 max: 2.4199 USE_META, weight: 0.7025 cost: 0.6183 min: -0.2712 max: 2.4199 USE_META, weight: 0.2891 cost: 1.8545 min: -0.2712 max: 2.4199 USE_META, weight: 0.8203 cost: 0.2660 min: -0.2712 max: 2.4199 USE_META, weight: 0.9143 cost: -0.0149 min: -0.2712 max: 2.4199 USE_META, weight: 0.5049 cost: 1.2093 min: -0.2712 max: 2.4199 USE_META, weight: 0.6057 cost: 0.9078 min: -0.2712 max: 2.4199 USE_META, weight: 0.3759 cost: 1.5949 min: -0.2712 max: 2.4199 USE_META, weight: 0.6124 cost: 0.8878 min: -0.2712 max: 2.4199 USE_META, weight: 0.6124 cost: 0.8878 min: -0.2712 max: 2.4199 USE_META, weight: 0.6514 cost: 0.7710 min: -0.2712 max: 2.4199 USE_META, weight: 0.7366 cost: 0.5165 min: -0.2712 max: 2.4199 USE_META, weight: 0.6020 cost: 0.9189 min: -0.2712 max: 2.4199 USE_META, weight: 0.7091 cost: 0.5985 min: -0.2712 max: 2.4199 USE_META, weight: 0.9210 cost: -0.0351 min: -0.2712 max: 2.4199 USE_META, weight: 0.3492 cost: 1.6746 min: -0.2712 max: 2.4199 USE_META, weight: 0.4203 cost: 1.4623 min: -0.2712 max: 2.4199 USE_META, weight: 0.9135 cost: -0.0126 min: -0.2712 max: 2.4199 USE_META, weight: 0.9132 cost: -0.0117 min: -0.2712 max: 2.4199 USE_META, weight: 0.9132 cost: -0.0117 min: -0.2712 max: 2.4199 USE_META, weight: 0.9479 cost: -0.1155 min: -0.2712 max: 2.4199 USE_META, weight: 0.9409 cost: -0.0946 min: -0.2712 max: 2.4199 USE_META, weight: 0.9960 cost: -0.2592 min: -0.2712 max: 2.4199 USE_META, weight: 0.9312 cost: -0.0654 min: -0.2712 max: 2.4199 USE_META, weight: 0.8429 cost: 0.1986 min: -0.2712 max: 2.4199 USE_META, weight: 0.9275 cost: -0.0545 min: -0.2712 max: 2.4199 USE_META, weight: 0.9497 cost: -0.1209 min: -0.2712 max: 2.4199 USE_META, weight: 0.8429 cost: 0.1986 min: -0.2712 max: 2.4199 USE_META, weight: 0.9191 cost: -0.0293 min: -0.2712 max: 2.4199 USE_META, weight: 0.3823 cost: 1.5758 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.9059 cost: 0.0101 min: -0.2712 max: 2.4199 USE_META, weight: 0.8429 cost: 0.1986 min: -0.2712 max: 2.4199 USE_META, weight: 0.9581 cost: -0.1458 min: -0.2712 max: 2.4199 USE_META, weight: 0.9025 cost: 0.0203 min: -0.2712 max: 2.4199 USE_META, weight: 0.9348 cost: -0.0761 min: -0.2712 max: 2.4199 USE_META, weight: 0.9321 cost: -0.0683 min: -0.2712 max: 2.4199 USE_META, weight: 0.9479 cost: -0.1155 min: -0.2712 max: 2.4199 USE_META, weight: 0.9409 cost: -0.0946 min: -0.2712 max: 2.4199 USE_META, weight: 0.9960 cost: -0.2592 min: -0.2712 max: 2.4199 USE_META, weight: 0.9581 cost: -0.1458 min: -0.2712 max: 2.4199 USE_META, weight: 0.9333 cost: -0.0717 min: -0.2712 max: 2.4199 USE_META, weight: 0.9939 cost: -0.2529 min: -0.2712 max: 2.4199 USE_META, weight: 0.5029 cost: 1.2152 min: -0.2712 max: 2.4199 USE_META, weight: 0.2338 cost: 2.0199 min: -0.2712 max: 2.4199 USE_META, weight: 0.9269 cost: -0.0527 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.2374 cost: 2.0091 min: -0.2712 max: 2.4199 USE_META, weight: 0.2095 cost: 2.0925 min: -0.2712 max: 2.4199 USE_META, weight: 0.2300 cost: 2.0313 min: -0.2712 max: 2.4199 USE_META, weight: 0.2187 cost: 2.0649 min: -0.2712 max: 2.4199 USE_META, weight: 0.3396 cost: 1.7033 min: -0.2712 max: 2.4199 USE_META, weight: 0.1294 cost: 2.3320 min: -0.2712 max: 2.4199 USE_META, weight: 0.3318 cost: 1.7267 min: -0.2712 max: 2.4199 USE_META, weight: 0.8716 cost: 0.1129 min: -0.2712 max: 2.4199 USE_META, weight: 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cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.6648 cost: 0.7311 min: -0.2712 max: 2.4199 USE_META, weight: 0.7404 cost: 0.5050 min: -0.2712 max: 2.4199 USE_META, weight: 0.6646 cost: 0.7318 min: -0.2712 max: 2.4199 USE_META, weight: 0.9870 cost: -0.2324 min: -0.2712 max: 2.4199 USE_META, weight: 0.6351 cost: 0.8198 min: -0.2712 max: 2.4199 USE_META, weight: 0.9474 cost: -0.1140 min: -0.2712 max: 2.4199 USE_META, weight: 0.7977 cost: 0.3338 min: -0.2712 max: 2.4199 USE_META, weight: 0.9252 cost: -0.0475 min: -0.2712 max: 2.4199 USE_META, weight: 0.8424 cost: 0.2002 min: -0.2712 max: 2.4199 USE_META, weight: 0.9648 cost: -0.1659 min: -0.2712 max: 2.4199 USE_META, weight: 0.8941 cost: 0.0454 min: -0.2712 max: 2.4199 USE_META, weight: 0.9084 cost: 0.0028 min: -0.2712 max: 2.4199 USE_META, weight: 0.8939 cost: 0.0461 min: -0.2712 max: 2.4199 USE_META, weight: 0.3939 cost: 1.5412 min: -0.2712 max: 2.4199 USE_META, 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USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.9439 cost: -0.1034 min: -0.2712 max: 2.4199 USE_META, weight: 0.9920 cost: -0.2473 min: -0.2712 max: 2.4199 USE_META, weight: 0.9322 cost: -0.0685 min: -0.2712 max: 2.4199 USE_META, weight: 0.9109 cost: -0.0047 min: -0.2712 max: 2.4199 USE_META, weight: 0.9847 cost: -0.2256 min: -0.2712 max: 2.4199 USE_META, weight: 0.9420 cost: -0.0977 min: -0.2712 max: 2.4199 USE_META, weight: 0.9743 cost: -0.1944 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.4822 cost: 1.2771 min: -0.2712 max: 2.4199 USE_META, weight: 0.9115 cost: -0.0066 min: 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weight: 0.9995 eval: 0.0283 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9995 eval: 0.0283 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9986 eval: 0.0809 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9986 eval: 0.0809 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9986 eval: 0.0809 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 1.0000 eval: 0.0009 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 1.0000 eval: 0.0009 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 1.0000 eval: 0.0009 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9943 eval: 0.3192 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9943 eval: 0.3192 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9943 eval: 0.3192 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.6255 eval: 21.1000 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.6255 eval: 21.1000 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.6255 eval: 21.1000 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9921 eval: 0.4456 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9921 eval: 0.4456 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9921 eval: 0.4456 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9999 eval: 0.0050 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9999 eval: 0.0050 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9999 eval: 0.0050 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9991 eval: 0.0490 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9991 eval: 0.0490 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9991 eval: 0.0490 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9983 eval: 0.0973 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9983 eval: 0.0973 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9983 eval: 0.0973 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9997 eval: 0.0197 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9997 eval: 0.0197 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9997 eval: 0.0197 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9967 eval: 0.1870 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9967 eval: 0.1870 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9967 eval: 0.1870 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9992 eval: 0.0436 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9992 eval: 0.0436 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9992 eval: 0.0436 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9995 eval: 0.0284 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9995 eval: 0.0284 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9995 eval: 0.0284 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9592 eval: 2.3000 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9592 eval: 2.3000 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9592 eval: 2.3000 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9965 eval: 0.1957 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9965 eval: 0.1957 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9965 eval: 0.1957 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9999 eval: 0.0070 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9999 eval: 0.0070 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9999 eval: 0.0070 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9998 eval: 0.0104 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9998 eval: 0.0104 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9998 eval: 0.0104 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9998 eval: 0.0138 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9998 eval: 0.0138 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9998 eval: 0.0138 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9922 eval: 0.4413 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9922 eval: 0.4413 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9922 eval: 0.4413 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9920 eval: 0.4502 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9920 eval: 0.4502 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9920 eval: 0.4502 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9919 eval: 0.4589 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9919 eval: 0.4589 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.9919 eval: 0.4589 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.1000 eval: 50.7000 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.1000 eval: 50.7000 min: 0.0009 max: 50.7000 USE_EVALUE, weight: 0.1000 eval: 50.7000 min: 0.0009 max: 50.7000 Number of contacts in models: 268 Number of contacts in alignments: 69 NUMB_ALIGNS: 69 Adding 2918 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -170.8101, CN propb: -170.8101 weights: 0.2732 constraints: 161 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 161 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 161 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 2757 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 2757 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 2918 # command: