# 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/T0360/ # command:# Making conformation for sequence T0360 numbered 1 through 141 Created new target T0360 from T0360.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0360/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0360//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0360/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0360//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0360/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0360/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0360/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iscA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1iscA expands to /projects/compbio/data/pdb/1isc.pdb.gz 1iscA:# T0360 read from 1iscA/merged-good-all-a2m # 1iscA read from 1iscA/merged-good-all-a2m # adding 1iscA to template set # found chain 1iscA in template set T0360 19 :SKKKQTEMIADHIYGKYDVFKR 1iscA 30 :HHQTYVTNLNNLIKGTAFEGKS # choosing archetypes in rotamer library T0360 49 :DQDLIAAL 1iscA 52 :LEEIIRSS T0360 60 :DAALIARVLANHC 1iscA 60 :EGGVFNNAAQVWN T0360 74 :RPRYLKALARGG 1iscA 73 :HTFYWNCLAPNA T0360 95 :KGEVTPEEQAIAQNHPFVQ 1iscA 85 :GGEPTGKVAEAIAASFGSF Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 Number of alignments=1 # 1iscA read from 1iscA/merged-good-all-a2m # found chain 1iscA in template set T0360 18 :MSKKKQTEMIADHIYGKYDVFKR 1iscA 29 :KHHQTYVTNLNNLIKGTAFEGKS T0360 49 :DQDLIAALP 1iscA 52 :LEEIIRSSE T0360 61 :AALIARVLANHC 1iscA 61 :GGVFNNAAQVWN T0360 74 :RPRYLKALARGG 1iscA 73 :HTFYWNCLAPNA T0360 95 :KGEVTPEEQAIAQNHPFVQQALQQQSAQA 1iscA 85 :GGEPTGKVAEAIAASFGSFADFKAQFTDA Number of specific fragments extracted= 5 number of extra gaps= 0 total=10 Number of alignments=2 # 1iscA read from 1iscA/merged-good-all-a2m # found chain 1iscA in template set T0360 19 :SKKKQTEMIADHIYGKYDVFKR 1iscA 30 :HHQTYVTNLNNLIKGTAFEGKS T0360 49 :DQDLIAA 1iscA 52 :LEEIIRS T0360 59 :YDAALIARVLANHC 1iscA 59 :SEGGVFNNAAQVWN T0360 74 :RPRYLKALARGG 1iscA 73 :HTFYWNCLAPNA T0360 95 :KGEVTPEEQAIAQNH 1iscA 85 :GGEPTGKVAEAIAAS Number of specific fragments extracted= 5 number of extra gaps= 0 total=15 Number of alignments=3 # 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 # T0360 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 Warning: unaligning (T0360)E131 because last residue in template chain is (1z7uA)N108 T0360 2 :T 1z7uA 4 :D T0360 4 :ETALGAALKSAVQTMSKKKQTEMIA 1z7uA 5 :KQTSINLALSTINGKWKLSLMDELF T0360 38 :FKRFK 1z7uA 30 :QGTKR T0360 49 :DQDLIAALPQYDAALIARVLANH 1z7uA 35 :NGELMRALDGITQRVLTDRLREM T0360 81 :LARGG 1z7uA 58 :EKDGL T0360 93 :RFKGEVTPEEQAIA 1z7uA 74 :RVEYTLTPEGYALY T0360 111 :FVQQALQQQSAQAAAETLSV 1z7uA 88 :DALSSLCHWGETFAQKKARL Number of specific fragments extracted= 7 number of extra gaps= 0 total=22 Number of alignments=4 # 1z7uA read from 1z7uA/merged-good-all-a2m # found chain 1z7uA in template set Warning: unaligning (T0360)T127 because last residue in template chain is (1z7uA)N108 T0360 2 :TQETALG 1z7uA 4 :DKQTSIN T0360 10 :ALKSAVQTMSKKKQTEMIA 1z7uA 11 :LALSTINGKWKLSLMDELF T0360 38 :FKRFK 1z7uA 30 :QGTKR T0360 49 :DQDLIAALPQYDAALIARVLANH 1z7uA 35 :NGELMRALDGITQRVLTDRLREM T0360 81 :LARGG 1z7uA 58 :EKDGL T0360 86 :KRFDLNNRFKGE 1z7uA 64 :HRESFNELPPRV T0360 98 :VTPEEQAIAQNHPFVQQALQQQSAQAAAE 1z7uA 79 :LTPEGYALYDALSSLCHWGETFAQKKARL Number of specific fragments extracted= 7 number of extra gaps= 0 total=29 Number of alignments=5 # 1z7uA read from 1z7uA/merged-good-all-a2m # found chain 1z7uA in template set T0360 3 :QETALGAALKSAVQTMSKKKQTEMIAD 1z7uA 4 :DKQTSINLALSTINGKWKLSLMDELFQ T0360 39 :KRFK 1z7uA 31 :GTKR T0360 49 :DQDLIAALPQYDAALIARVLANHCR 1z7uA 35 :NGELMRALDGITQRVLTDRLREMEK T0360 83 :RGG 1z7uA 60 :DGL T0360 93 :RFKGE 1z7uA 69 :NELPP T0360 98 :VTPEEQAIAQNHPFVQQALQQQSAQAAA 1z7uA 79 :LTPEGYALYDALSSLCHWGETFAQKKAR Number of specific fragments extracted= 6 number of extra gaps= 0 total=35 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k9uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1k9uA expands to /projects/compbio/data/pdb/1k9u.pdb.gz 1k9uA:Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 24, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 26, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 156, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 160, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 162, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 164, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 166, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 251, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 341, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 343, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 345, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 347, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 349, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 351, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 512, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 514, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 516, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 518, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 520, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 522, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 589, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 591, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 1k9uA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 1k9uA # T0360 read from 1k9uA/merged-good-all-a2m # 1k9uA read from 1k9uA/merged-good-all-a2m # adding 1k9uA to template set # found chain 1k9uA in template set Warning: unaligning (T0360)T2 because first residue in template chain is (1k9uA)D3 T0360 3 :QETALGAAL 1k9uA 4 :DMERIFKRF T0360 36 :DVFKRFK 1k9uA 13 :DTNGDGK T0360 49 :DQDLIAALPQYDAALIARVLANH 1k9uA 25 :LTDALRTLGSTSADEVQRMMAEI T0360 89 :DLNNR 1k9uA 48 :DTDGD T0360 96 :GEVTPEEQAIAQNHPFVQQALQQQ 1k9uA 53 :GFIDFNEFISFCNANPGLMKDVAK Number of specific fragments extracted= 5 number of extra gaps= 0 total=40 Number of alignments=7 # 1k9uA read from 1k9uA/merged-good-all-a2m # found chain 1k9uA in template set T0360 89 :DLNNR 1k9uA 13 :DTNGD T0360 96 :GEVTPEEQAIAQN 1k9uA 18 :GKISLSELTDALR T0360 109 :HPFVQQALQQQ 1k9uA 36 :SADEVQRMMAE T0360 120 :SAQAAAETLSVEAEAAESS 1k9uA 59 :EFISFCNANPGLMKDVAKV Number of specific fragments extracted= 4 number of extra gaps= 0 total=44 Number of alignments=8 # 1k9uA read from 1k9uA/merged-good-all-a2m # found chain 1k9uA in template set T0360 19 :SKKKQTEMIADHIYGKYD 1k9uA 4 :DMERIFKRFDTNGDGKIS T0360 49 :DQDLIAALPQYDAALIARVLANH 1k9uA 25 :LTDALRTLGSTSADEVQRMMAEI T0360 89 :DLNNR 1k9uA 48 :DTDGD T0360 96 :GEVTPEEQAIAQNHPFVQQALQQQ 1k9uA 53 :GFIDFNEFISFCNANPGLMKDVAK Number of specific fragments extracted= 4 number of extra gaps= 0 total=48 Number of alignments=9 # 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 # T0360 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 T0360 6 :ALGAALKSAVQTMSKKKQTEMI 2fswA 10 :CPVRKSMQIFAGKWTLLIIFQI T0360 38 :FKRFK 2fswA 32 :NRRII T0360 49 :DQDLIAALPQYDAALIARVLANHCR 2fswA 38 :YGELKRAIPGISEKMLIDELKFLCG T0360 83 :RGG 2fswA 63 :KGL T0360 86 :K 2fswA 76 :P T0360 93 :RFKGEVTP 2fswA 77 :RVEYSLTP T0360 105 :IAQNHPFVQQALQQQSAQ 2fswA 85 :LGEKVLPIIDEIAKFGME Number of specific fragments extracted= 7 number of extra gaps= 0 total=55 Number of alignments=10 # 2fswA read from 2fswA/merged-good-all-a2m # found chain 2fswA in template set T0360 7 :LGAALKSAVQTMSKKKQTEMI 2fswA 11 :PVRKSMQIFAGKWTLLIIFQI T0360 38 :FKRFK 2fswA 32 :NRRII T0360 49 :DQDLIAALPQYDAALIARVLANHC 2fswA 38 :YGELKRAIPGISEKMLIDELKFLC T0360 82 :ARGG 2fswA 62 :GKGL T0360 86 :KRFDL 2fswA 76 :PRVEY T0360 97 :EVTP 2fswA 81 :SLTP T0360 105 :IAQNHPFVQQALQQQSAQ 2fswA 85 :LGEKVLPIIDEIAKFGME Number of specific fragments extracted= 7 number of extra gaps= 0 total=62 Number of alignments=11 # 2fswA read from 2fswA/merged-good-all-a2m # found chain 2fswA in template set T0360 3 :QETALGAALKSAVQTMSKKKQTEMIAD 2fswA 7 :DEECPVRKSMQIFAGKWTLLIIFQINR T0360 40 :RFK 2fswA 34 :RII T0360 49 :DQDLIAALPQYDAALIARVLANHCR 2fswA 38 :YGELKRAIPGISEKMLIDELKFLCG Number of specific fragments extracted= 3 number of extra gaps= 0 total=65 Number of alignments=12 # 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 # T0360 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 (T0360)A54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M55 Warning: unaligning (T0360)L56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0360)A61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0360)L63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0360)K86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0360)Q107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0360)H109 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 Warning: unaligning (T0360)S129 because last residue in template chain is (1yyvA)E122 T0360 11 :LKSAVQTMSKKKQTEMIA 1yyvA 13 :GNLFAEQCPSREVLKHVT T0360 29 :DHIYG 1yyvA 36 :LILVA T0360 37 :VFKRFK 1yyvA 41 :LRDGTH T0360 49 :DQDLI 1yyvA 48 :FSDLR T0360 57 :PQYD 1yyvA 56 :GGVS T0360 64 :IARVLANHCR 1yyvA 63 :LAQSLQALEQ T0360 83 :RGG 1yyvA 73 :DGF T0360 87 :RFD 1yyvA 78 :RVS T0360 93 :RFKGEVTPEEQAIA 1yyvA 87 :HVEYSLTPLGEQVS T0360 110 :PFVQQALQQQSAQ 1yyvA 104 :AALADWIELNLPQ T0360 124 :AAETL 1yyvA 117 :VLAQR Number of specific fragments extracted= 11 number of extra gaps= 1 total=76 Number of alignments=13 # 1yyvA read from 1yyvA/merged-good-all-a2m # found chain 1yyvA in template set Warning: unaligning (T0360)A54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M55 Warning: unaligning (T0360)L56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0360)A61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0360)L63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0360)K86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0360)Q107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0360)H109 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 Warning: unaligning (T0360)S129 because last residue in template chain is (1yyvA)E122 T0360 9 :AALKSAVQTMSKKKQTEMIAD 1yyvA 20 :CPSREVLKHVTSRWGVLILVA T0360 37 :VFKRFK 1yyvA 41 :LRDGTH T0360 49 :DQDLI 1yyvA 48 :FSDLR T0360 57 :PQYD 1yyvA 56 :GGVS T0360 64 :IARVLANHC 1yyvA 63 :LAQSLQALE T0360 82 :ARGG 1yyvA 72 :QDGF T0360 87 :RFDLNNRFKGE 1yyvA 78 :RVSYPVVPPHV T0360 98 :VTPEEQAIA 1yyvA 92 :LTPLGEQVS T0360 110 :PFVQQA 1yyvA 104 :AALADW T0360 117 :QQQSAQAAAETL 1yyvA 110 :IELNLPQVLAQR Number of specific fragments extracted= 10 number of extra gaps= 1 total=86 Number of alignments=14 # 1yyvA read from 1yyvA/merged-good-all-a2m # found chain 1yyvA in template set Warning: unaligning (T0360)A54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M55 Warning: unaligning (T0360)L56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0360)A61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0360)L63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0360)Q107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0360)H109 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 T0360 13 :SAVQTMSKKKQTEMIADHIYGKY 1yyvA 23 :REVLKHVTSRWGVLILVALRDGT T0360 49 :DQDLI 1yyvA 48 :FSDLR T0360 57 :PQYD 1yyvA 56 :GGVS T0360 64 :IARVLANHCRRP 1yyvA 63 :LAQSLQALEQDG T0360 93 :RFKGE 1yyvA 82 :PVVPP T0360 98 :VTPEEQAIA 1yyvA 92 :LTPLGEQVS T0360 110 :PFVQQAL 1yyvA 104 :AALADWI T0360 129 :SVEAEAAESS 1yyvA 111 :ELNLPQVLAQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=94 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qdlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qdlA expands to /projects/compbio/data/pdb/1qdl.pdb.gz 1qdlA:# T0360 read from 1qdlA/merged-good-all-a2m # 1qdlA read from 1qdlA/merged-good-all-a2m # adding 1qdlA to template set # found chain 1qdlA in template set T0360 2 :TQETALGAALKSAVQTMSKKKQTEMIADH 1qdlA 248 :ADQEEDLKLELELMNSEKDKAEHLMLVDL T0360 48 :IDQDLIAAL 1qdlA 277 :ARNDLGKVC T0360 57 :PQ 1qdlA 287 :PG Number of specific fragments extracted= 3 number of extra gaps= 0 total=97 Number of alignments=16 # 1qdlA read from 1qdlA/merged-good-all-a2m # found chain 1qdlA in template set T0360 3 :QETALGAALKSAVQTMSKKKQTEMIADH 1qdlA 249 :DQEEDLKLELELMNSEKDKAEHLMLVDL T0360 48 :IDQDLIAALPQ 1qdlA 277 :ARNDLGKVCVP Number of specific fragments extracted= 2 number of extra gaps= 0 total=99 Number of alignments=17 # 1qdlA read from 1qdlA/merged-good-all-a2m # found chain 1qdlA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z1dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z1dA expands to /projects/compbio/data/pdb/1z1d.pdb.gz 1z1dA:# T0360 read from 1z1dA/merged-good-all-a2m # 1z1dA read from 1z1dA/merged-good-all-a2m # adding 1z1dA to template set # found chain 1z1dA in template set Warning: unaligning (T0360)T17 because first residue in template chain is (1z1dA)A202 T0360 18 :MSKKKQTEMIADHIYGKYDVF 1z1dA 203 :NGLTVAQNQVLNLIKACPRPE T0360 47 :GI 1z1dA 224 :GL T0360 49 :DQDLIAALPQYDAALIARVLANHCR 1z1dA 227 :FQDLKNQLKHMSVSSIKQAVDFLSN Number of specific fragments extracted= 3 number of extra gaps= 0 total=102 Number of alignments=18 # 1z1dA read from 1z1dA/merged-good-all-a2m # found chain 1z1dA in template set T0360 17 :TMSKKKQTEMIAD 1z1dA 206 :TVAQNQVLNLIKA T0360 35 :YDVFKRF 1z1dA 219 :CPRPEGL T0360 49 :DQDLIAALPQYDAALIARVLANHC 1z1dA 227 :FQDLKNQLKHMSVSSIKQAVDFLS Number of specific fragments extracted= 3 number of extra gaps= 0 total=105 Number of alignments=19 # 1z1dA read from 1z1dA/merged-good-all-a2m # found chain 1z1dA in template set Warning: unaligning (T0360)S13 because first residue in template chain is (1z1dA)A202 T0360 14 :AVQTMSKKKQTEMIADHIYGKYD 1z1dA 203 :NGLTVAQNQVLNLIKACPRPEGL T0360 49 :DQDLIAALPQYDAALIARVLANHCR 1z1dA 227 :FQDLKNQLKHMSVSSIKQAVDFLSN Number of specific fragments extracted= 2 number of extra gaps= 0 total=107 Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2arsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2arsA expands to /projects/compbio/data/pdb/2ars.pdb.gz 2arsA: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 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 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 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 # T0360 read from 2arsA/merged-good-all-a2m # 2arsA read from 2arsA/merged-good-all-a2m # adding 2arsA to template set # found chain 2arsA in template set T0360 56 :LPQYDAALIARVLANH 2arsA 202 :FVDVSIDEVRNALIRG T0360 77 :YLKAL 2arsA 218 :FSETL T0360 85 :GKRF 2arsA 224 :IDFR T0360 95 :KGEVTPEEQAIAQNHPFV 2arsA 228 :EDTITEKEESLARELFDK Number of specific fragments extracted= 4 number of extra gaps= 0 total=111 Number of alignments=21 # 2arsA read from 2arsA/merged-good-all-a2m # found chain 2arsA in template set T0360 55 :ALPQYDAALIARVLANHC 2arsA 201 :DFVDVSIDEVRNALIRGF T0360 78 :LKAL 2arsA 219 :SETL T0360 86 :KRF 2arsA 225 :DFR T0360 95 :KGEVTPEEQAIAQNHPFV 2arsA 228 :EDTITEKEESLARELFDK Number of specific fragments extracted= 4 number of extra gaps= 0 total=115 Number of alignments=22 # 2arsA read from 2arsA/merged-good-all-a2m # found chain 2arsA in template set T0360 57 :PQYDAALIARVLANHCR 2arsA 203 :VDVSIDEVRNALIRGFS T0360 79 :KAL 2arsA 220 :ETL T0360 84 :GGK 2arsA 223 :HID T0360 87 :RFD 2arsA 227 :RED T0360 97 :EVTPEEQAIAQNHPFVQ 2arsA 230 :TITEKEESLARELFDKK Number of specific fragments extracted= 5 number of extra gaps= 0 total=120 Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sfxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0360 read from 1sfxA/merged-good-all-a2m # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0360 1 :MTQETALGAALKSAVQTMSKK 1sfxA 1 :MSNPLGELVKALEKLSFKPSD T0360 22 :KQTEMIADH 1sfxA 23 :RIYSLLLER T0360 39 :KRFK 1sfxA 32 :GGMR T0360 49 :DQDLIAAL 1sfxA 36 :VSEIAREL T0360 58 :QYDAALIARVLANH 1sfxA 44 :DLSARFVRDRLKVL T0360 81 :LARGGKRFD 1sfxA 58 :LKRGFVRRE T0360 90 :L 1sfxA 68 :V T0360 91 :NNRF 1sfxA 70 :KGWV T0360 96 :GEV 1sfxA 74 :GYI T0360 99 :TPEE 1sfxA 81 :KPEK T0360 109 :HPFVQQALQQQSAQAAAET 1sfxA 85 :VLKEFKSSILGEIERIEKM Number of specific fragments extracted= 11 number of extra gaps= 0 total=131 Number of alignments=24 # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0360 1 :MTQETALGAALKSAVQTMS 1sfxA 1 :MSNPLGELVKALEKLSFKP T0360 20 :KKKQTEMIADH 1sfxA 21 :DVRIYSLLLER T0360 39 :KRFK 1sfxA 32 :GGMR T0360 49 :DQDLIAAL 1sfxA 36 :VSEIAREL T0360 58 :QYDAALIARVLANH 1sfxA 44 :DLSARFVRDRLKVL T0360 81 :LARGG 1sfxA 58 :LKRGF T0360 86 :KRFDLNNRFKGEV 1sfxA 64 :RREIVEKGWVGYI T0360 99 :T 1sfxA 81 :K T0360 110 :PFVQQALQQQSAQAAAETLS 1sfxA 82 :PEKVLKEFKSSILGEIERIE T0360 135 :A 1sfxA 102 :K Number of specific fragments extracted= 10 number of extra gaps= 0 total=141 Number of alignments=25 # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0360 2 :TQETALGAALKSAVQTMSKKKQTEMIADHIYGK 1sfxA 3 :NPLGELVKALEKLSFKPSDVRIYSLLLERGGMR T0360 49 :DQDLIAAL 1sfxA 36 :VSEIAREL T0360 58 :QYDAALIARVLAN 1sfxA 44 :DLSARFVRDRLKV T0360 80 :ALARGGKRFD 1sfxA 57 :LLKRGFVRRE T0360 91 :NNRFK 1sfxA 70 :KGWVG T0360 97 :E 1sfxA 75 :Y T0360 99 :TPE 1sfxA 81 :KPE T0360 105 :IAQNHPFVQQALQQQSAQA 1sfxA 84 :KVLKEFKSSILGEIERIEK Number of specific fragments extracted= 8 number of extra gaps= 0 total=149 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1efyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1efyA expands to /projects/compbio/data/pdb/1efy.pdb.gz 1efyA:# T0360 read from 1efyA/merged-good-all-a2m # 1efyA read from 1efyA/merged-good-all-a2m # adding 1efyA to template set # found chain 1efyA in template set T0360 6 :ALGAALKSAVQTMSKKKQTEMIADHIYGKYD 1efyA 715 :EVQQAVSDGGSESQILDLSNRFYTLIPHDFG Number of specific fragments extracted= 1 number of extra gaps= 0 total=150 Number of alignments=27 # 1efyA read from 1efyA/merged-good-all-a2m # found chain 1efyA in template set T0360 11 :LKSAVQTMSKKKQTEMIADH 1efyA 669 :IQDLIKMIFDVESMKKAMVE T0360 35 :YDVFKRFKPL 1efyA 689 :FEIDLQKMPL T0360 57 :PQYDAALIARVLANH 1efyA 699 :GKLSKRQIQSAYSIL T0360 75 :PRYLKALARGGK 1efyA 714 :NEVQQAVSDGGS T0360 110 :PFVQQALQQQ 1efyA 726 :ESQILDLSNR Number of specific fragments extracted= 5 number of extra gaps= 0 total=155 Number of alignments=28 # 1efyA read from 1efyA/merged-good-all-a2m # found chain 1efyA in template set T0360 62 :ALIARVLANHCRRPRYLKALAR 1efyA 667 :KPIQDLIKMIFDVESMKKAMVE T0360 88 :FDLNNRFKGEVTPEEQAIAQNHPFV 1efyA 691 :IDLQKMPLGKLSKRQIQSAYSILNE Number of specific fragments extracted= 2 number of extra gaps= 0 total=157 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w33A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w33A expands to /projects/compbio/data/pdb/1w33.pdb.gz 1w33A:Skipped atom 676, because occupancy 0.350 <= existing 0.650 in 1w33A Skipped atom 678, because occupancy 0.350 <= existing 0.650 in 1w33A Skipped atom 680, because occupancy 0.350 <= existing 0.650 in 1w33A Skipped atom 682, because occupancy 0.350 <= existing 0.650 in 1w33A # T0360 read from 1w33A/merged-good-all-a2m # 1w33A read from 1w33A/merged-good-all-a2m # adding 1w33A to template set # found chain 1w33A in template set T0360 1 :MTQETALGAALKSAVQTMSKKKQTEMIADHIYGKYDVFKRF 1w33A 116 :IDEDIQMKIKRTLYSSLDYKKENIEKLKEILEILKKNSEHY T0360 45 :ALGIDQDLIAAL 1w33A 167 :SWGIQFQIEQNL T0360 57 :PQYDAALIARVLANHCRRPRYLKAL 1w33A 186 :ENLSQEESKSLLMQIKSNLEIKQRL T0360 103 :QAIAQNHPFVQQALQQQSAQAAAETLSVEAEAAESSAAE 1w33A 211 :KKTLNETLKVYNQNTQDNEKILAEHFNKYYKDFDTLKPA Number of specific fragments extracted= 4 number of extra gaps= 0 total=161 Number of alignments=30 # 1w33A read from 1w33A/merged-good-all-a2m # found chain 1w33A in template set T0360 1 :MTQETALGAALKSAVQTMSKKKQTEMIADHIYGKYDVFKR 1w33A 116 :IDEDIQMKIKRTLYSSLDYKKENIEKLKEILEILKKNSEH T0360 45 :ALGIDQDLIAAL 1w33A 167 :SWGIQFQIEQNL T0360 57 :PQYDAALIARVLANH 1w33A 186 :ENLSQEESKSLLMQI T0360 100 :PEEQAIAQNHPFVQQALQQQSAQAAAETLSVEAEAAESS 1w33A 201 :KSNLEIKQRLKKTLNETLKVYNQNTQDNEKILAEHFNKY T0360 139 :AA 1w33A 247 :KP Number of specific fragments extracted= 5 number of extra gaps= 0 total=166 Number of alignments=31 # 1w33A read from 1w33A/merged-good-all-a2m # found chain 1w33A in template set T0360 10 :ALKSAVQTMSKKKQTEMIADHI 1w33A 145 :ILEILKKNSEHYNIIGRLIYHI T0360 45 :ALGIDQDLIAA 1w33A 167 :SWGIQFQIEQN T0360 56 :LPQYDAALIARVLANHCRRPRYLKAL 1w33A 185 :VENLSQEESKSLLMQIKSNLEIKQRL T0360 103 :QAIAQNHPFVQQALQQQSAQAAAETLSV 1w33A 211 :KKTLNETLKVYNQNTQDNEKILAEHFNK Number of specific fragments extracted= 4 number of extra gaps= 0 total=170 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x8bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x8bA expands to /projects/compbio/data/pdb/1x8b.pdb.gz 1x8bA:# T0360 read from 1x8bA/merged-good-all-a2m # 1x8bA read from 1x8bA/merged-good-all-a2m # adding 1x8bA to template set # found chain 1x8bA in template set T0360 48 :IDQDLIAAL 1x8bA 384 :LADAISENY T0360 57 :PQ 1x8bA 395 :MS T0360 59 :YDAALIARVLANHCRRPRYLKA 1x8bA 398 :FKEAELKDLLLQVGRGLRYIHS Number of specific fragments extracted= 3 number of extra gaps= 0 total=173 Number of alignments=33 # 1x8bA read from 1x8bA/merged-good-all-a2m # found chain 1x8bA in template set T0360 48 :IDQDLIAAL 1x8bA 384 :LADAISENY T0360 58 :Q 1x8bA 395 :M T0360 59 :YDAALIARVLANHCRRPRYLK 1x8bA 398 :FKEAELKDLLLQVGRGLRYIH Number of specific fragments extracted= 3 number of extra gaps= 0 total=176 Number of alignments=34 # 1x8bA read from 1x8bA/merged-good-all-a2m # found chain 1x8bA in template set T0360 48 :IDQDLIAALPQ 1x8bA 384 :LADAISENYRI T0360 59 :YDAALIARVLANHCRRPRYLKA 1x8bA 398 :FKEAELKDLLLQVGRGLRYIHS Number of specific fragments extracted= 2 number of extra gaps= 0 total=178 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c8mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c8mA expands to /projects/compbio/data/pdb/2c8m.pdb.gz 2c8mA:# T0360 read from 2c8mA/merged-good-all-a2m # 2c8mA read from 2c8mA/merged-good-all-a2m # adding 2c8mA to template set # found chain 2c8mA in template set T0360 57 :PQYDAALIARVLANH 2c8mA 203 :VDVSIDEVRNALIRG T0360 77 :YLKAL 2c8mA 218 :FSETL T0360 86 :KRF 2c8mA 225 :DFR T0360 95 :KGEVTPEEQAIAQNHPFV 2c8mA 228 :EDTITEKEESLARELFDK Number of specific fragments extracted= 4 number of extra gaps= 0 total=182 Number of alignments=36 # 2c8mA read from 2c8mA/merged-good-all-a2m # found chain 2c8mA in template set T0360 55 :ALPQYDAALIARVLANHC 2c8mA 201 :DFVDVSIDEVRNALIRGF T0360 78 :LKAL 2c8mA 219 :SETL T0360 87 :R 2c8mA 226 :F T0360 94 :FKGEVTPEEQAIAQNHPFV 2c8mA 227 :REDTITEKEESLARELFDK Number of specific fragments extracted= 4 number of extra gaps= 0 total=186 Number of alignments=37 # 2c8mA read from 2c8mA/merged-good-all-a2m # found chain 2c8mA in template set T0360 56 :LPQYDAALIARVLANHCR 2c8mA 202 :FVDVSIDEVRNALIRGFS T0360 79 :KAL 2c8mA 220 :ETL T0360 84 :GGKRF 2c8mA 223 :HIDFR T0360 95 :KGEVTPEEQAIAQNHPFV 2c8mA 228 :EDTITEKEESLARELFDK Number of specific fragments extracted= 4 number of extra gaps= 0 total=190 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v3wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0360 read from 1v3wA/merged-good-all-a2m # 1v3wA read from 1v3wA/merged-good-all-a2m # found chain 1v3wA in training set T0360 88 :FDLNNRFKGEVTPEEQAIAQNHPFVQQALQ 1v3wA 134 :LGVPGKVVRQLTEEEIEWTKKNAEIYVELA Number of specific fragments extracted= 1 number of extra gaps= 0 total=191 Number of alignments=39 # 1v3wA read from 1v3wA/merged-good-all-a2m # found chain 1v3wA in training set T0360 87 :RFDLNNRFKGEVTPEEQAIAQNHP 1v3wA 133 :VLGVPGKVVRQLTEEEIEWTKKNA T0360 122 :QAAAETLSVEAEA 1v3wA 157 :EIYVELAEKHIKG Number of specific fragments extracted= 2 number of extra gaps= 0 total=193 Number of alignments=40 # 1v3wA read from 1v3wA/merged-good-all-a2m # found chain 1v3wA in training set T0360 91 :NNRFKGEVTPEEQAIAQNHPFVQQAL 1v3wA 137 :PGKVVRQLTEEEIEWTKKNAEIYVEL Number of specific fragments extracted= 1 number of extra gaps= 0 total=194 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sgmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sgmA expands to /projects/compbio/data/pdb/1sgm.pdb.gz 1sgmA:# T0360 read from 1sgmA/merged-good-all-a2m # 1sgmA read from 1sgmA/merged-good-all-a2m # adding 1sgmA to template set # found chain 1sgmA in template set T0360 7 :LGAALKSAVQTMSKKKQTEMIADHIYGKYDVFKRFKPLALGI 1sgmA 67 :EHLIQQSMDESSDPVEAIQLFIKKTASQFDNTESIKGIPVGL T0360 52 :LIAALPQYD 1sgmA 109 :LASETALIS T0360 62 :ALIARVLANHCRRPR 1sgmA 118 :EPLRTVCMKVFKSWE T0360 77 :YLKALARG 1sgmA 135 :FARKLMEN T0360 92 :N 1sgmA 143 :G T0360 98 :VTPE 1sgmA 144 :FAEE T0360 102 :EQAIAQ 1sgmA 149 :ANQLGT Number of specific fragments extracted= 7 number of extra gaps= 0 total=201 Number of alignments=42 # 1sgmA read from 1sgmA/merged-good-all-a2m # found chain 1sgmA in template set T0360 5 :TALGAALKSAVQTMSKKKQTEMIADHIYGKYDVFKRFKPLALGI 1sgmA 65 :IVEHLIQQSMDESSDPVEAIQLFIKKTASQFDNTESIKGIPVGL T0360 52 :LIAALPQ 1sgmA 109 :LASETAL T0360 62 :ALIARVLANHCRRPR 1sgmA 118 :EPLRTVCMKVFKSWE T0360 77 :YLKAL 1sgmA 135 :FARKL T0360 82 :ARGGK 1sgmA 141 :ENGFA T0360 99 :TPEEQAIAQNHPFVQ 1sgmA 146 :EEEANQLGTLINSMI Number of specific fragments extracted= 6 number of extra gaps= 0 total=207 Number of alignments=43 # 1sgmA read from 1sgmA/merged-good-all-a2m # found chain 1sgmA in template set T0360 6 :ALGAALKSAVQTMSKKKQTEMIADHIYGKYDVFKRFKPLALGI 1sgmA 66 :VEHLIQQSMDESSDPVEAIQLFIKKTASQFDNTESIKGIPVGL T0360 52 :LIAALPQ 1sgmA 109 :LASETAL T0360 62 :ALIARVLANHCRRPR 1sgmA 118 :EPLRTVCMKVFKSWE T0360 77 :YLKALARG 1sgmA 135 :FARKLMEN T0360 97 :EVTPE 1sgmA 143 :GFAEE T0360 102 :EQAIA 1sgmA 149 :ANQLG Number of specific fragments extracted= 6 number of extra gaps= 0 total=213 Number of alignments=44 # 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 # T0360 read from 1r7jA/merged-good-all-a2m # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set Warning: unaligning (T0360)T17 because first residue in template chain is (1r7jA)K3 T0360 18 :MSKKKQTEMIADHIYGKYD 1r7jA 4 :KSKLEIIQAILEACKSGSP T0360 49 :DQDLIAAL 1r7jA 23 :KTRIMYGA T0360 58 :QYDAALIARVLANH 1r7jA 31 :NLSYALTGRYIKML T0360 81 :LARGGKRFD 1r7jA 45 :MDLEIIRQE T0360 91 :NN 1r7jA 54 :GK T0360 95 :KGEVTPEEQAIAQNHPFVQQALQQQSA 1r7jA 56 :QYMLTKKGEELLEDIRKFNEMRKNMDQ T0360 123 :AAAETLSVE 1r7jA 83 :LKEKINSVL Number of specific fragments extracted= 7 number of extra gaps= 0 total=220 Number of alignments=45 # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set Warning: unaligning (T0360)T17 because first residue in template chain is (1r7jA)K3 Warning: unaligning (T0360)E131 because last residue in template chain is (1r7jA)S92 T0360 18 :MSKKKQTEMIADHIYGKYD 1r7jA 4 :KSKLEIIQAILEACKSGSP T0360 49 :DQDLIAAL 1r7jA 23 :KTRIMYGA T0360 58 :QYDAALIARVLANH 1r7jA 31 :NLSYALTGRYIKML T0360 81 :LARGGKRF 1r7jA 45 :MDLEIIRQ T0360 91 :NNRFK 1r7jA 53 :EGKQY T0360 97 :EVTPEEQAIAQNHPFVQQALQQQSAQAAAETLSV 1r7jA 58 :MLTKKGEELLEDIRKFNEMRKNMDQLKEKINSVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=226 Number of alignments=46 # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set T0360 48 :IDQDLIAALPQ 1r7jA 9 :IIQAILEACKS T0360 59 :YDAALIARVLA 1r7jA 21 :SPKTRIMYGAN T0360 71 :HCRRPRYLKALAR 1r7jA 34 :YALTGRYIKMLMD T0360 84 :GGKRFD 1r7jA 48 :EIIRQE T0360 96 :G 1r7jA 54 :G T0360 97 :EVTPEEQAIAQNHPFVQQALQQQSAQAAAETLS 1r7jA 58 :MLTKKGEELLEDIRKFNEMRKNMDQLKEKINSV Number of specific fragments extracted= 6 number of extra gaps= 0 total=232 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mzbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0360 read from 1mzbA/merged-good-all-a2m # 1mzbA read from 1mzbA/merged-good-all-a2m # found chain 1mzbA in training set Warning: unaligning (T0360)V37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mzbA)Q30 Warning: unaligning (T0360)K39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mzbA)Q30 T0360 5 :TALGAALKSA 1mzbA 4 :NSELRKAGLK T0360 16 :QTMSKKKQTEMIA 1mzbA 14 :VTLPRVKILQMLD T0360 36 :D 1mzbA 27 :S T0360 40 :RFK 1mzbA 31 :RHM T0360 49 :DQDLIAAL 1mzbA 35 :AEDVYKAL T0360 57 :PQYDAALIARVLANH 1mzbA 47 :EDVGLATVYRVLTQF T0360 81 :LARGG 1mzbA 62 :EAAGL T0360 86 :KRFDLNN 1mzbA 68 :VRHNFDG T0360 93 :RFKGEVTPEEQAIAQNHP 1mzbA 97 :EVIEFMDAEIEKRQKEIV T0360 126 :ET 1mzbA 115 :RE Number of specific fragments extracted= 10 number of extra gaps= 0 total=242 Number of alignments=48 # 1mzbA read from 1mzbA/merged-good-all-a2m # found chain 1mzbA in training set Warning: unaligning (T0360)K39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mzbA)Q30 Warning: unaligning (T0360)F41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mzbA)Q30 T0360 5 :TALGAALKSAVQTMSKKKQTEMIA 1mzbA 3 :ENSELRKAGLKVTLPRVKILQMLD T0360 38 :F 1mzbA 27 :S T0360 42 :KPL 1mzbA 31 :RHM T0360 49 :DQDLIAAL 1mzbA 35 :AEDVYKAL T0360 57 :PQ 1mzbA 45 :AG T0360 59 :YDAALIARVLANH 1mzbA 49 :VGLATVYRVLTQF T0360 81 :LARG 1mzbA 62 :EAAG T0360 85 :GKRFDLNN 1mzbA 67 :VVRHNFDG T0360 93 :RFKGEVTPEEQ 1mzbA 97 :EVIEFMDAEIE T0360 118 :QQSAQAAAETLS 1mzbA 108 :KRQKEIVRERGF Number of specific fragments extracted= 10 number of extra gaps= 0 total=252 Number of alignments=49 # 1mzbA read from 1mzbA/merged-good-all-a2m # found chain 1mzbA in training set Warning: unaligning (T0360)H30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mzbA)Q30 Warning: unaligning (T0360)Y32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mzbA)Q30 T0360 4 :ETALGAALKSAVQTMSKKKQTEMIAD 1mzbA 2 :VENSELRKAGLKVTLPRVKILQMLDS T0360 33 :GKYD 1mzbA 31 :RHMS T0360 49 :DQDLIAALPQ 1mzbA 35 :AEDVYKALME T0360 59 :YDAALIARVLANHCR 1mzbA 49 :VGLATVYRVLTQFEA T0360 82 :ARGGKRFDLNNRFK 1mzbA 64 :AGLVVRHNFDGGHA T0360 96 :GEV 1mzbA 96 :GEV T0360 99 :TPEEQAIAQNHPFV 1mzbA 103 :DAEIEKRQKEIVRE Number of specific fragments extracted= 7 number of extra gaps= 0 total=259 Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dvoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dvoA expands to /projects/compbio/data/pdb/1dvo.pdb.gz 1dvoA:# T0360 read from 1dvoA/merged-good-all-a2m # 1dvoA read from 1dvoA/merged-good-all-a2m # adding 1dvoA to template set # found chain 1dvoA in template set T0360 3 :QETALGAALKSAVQTMSKKKQTEMIADHIYGKYD 1dvoA 56 :KKAQARQALSIYLNLPTLDEAVNTLKPWWPGLFD T0360 38 :FKRFKPLALGIDQDLIAAL 1dvoA 90 :GDTPRLLACGIRDVLLEDV T0360 57 :PQYDAALIARVLANHCRRPRYLKALARGGKRFDLNNRFKGEVTPEEQAIAQNHPFVQQALQQQSAQAAA 1dvoA 113 :IPLSHKKLRRAMKAITRSESYLCAMKAGACRYDTEGYVTEHISQEEEVYAAERLDKIRRQNRIKAELQA Number of specific fragments extracted= 3 number of extra gaps= 0 total=262 Number of alignments=51 # 1dvoA read from 1dvoA/merged-good-all-a2m # found chain 1dvoA in template set T0360 3 :QETALGAALKSAVQTMSKKKQTEMIADHIYGKYD 1dvoA 56 :KKAQARQALSIYLNLPTLDEAVNTLKPWWPGLFD T0360 38 :FKRFKPLALGIDQDLIAALP 1dvoA 90 :GDTPRLLACGIRDVLLEDVA T0360 58 :QYDAALIARVLANHCRRPRYLKALARGGKRFDLNNRFKGEVTPEEQAIAQNHPFVQQALQQQSAQAAA 1dvoA 114 :PLSHKKLRRAMKAITRSESYLCAMKAGACRYDTEGYVTEHISQEEEVYAAERLDKIRRQNRIKAELQA Number of specific fragments extracted= 3 number of extra gaps= 0 total=265 Number of alignments=52 # 1dvoA read from 1dvoA/merged-good-all-a2m # found chain 1dvoA in template set T0360 3 :QETALGAALKSAVQTMSKKKQTEMIADHIYGKYDVFKRFKPLALGIDQDLIAALPQ 1dvoA 55 :AKKAQARQALSIYLNLPTLDEAVNTLKPWWPGLFDGDTPRLLACGIRDVLLEDVAQ T0360 59 :YDAALIARVLANHCRRPRYLKALARGGKRFDLNNRFKGEVTPEEQAIAQNHPFVQQALQQQSAQ 1dvoA 115 :LSHKKLRRAMKAITRSESYLCAMKAGACRYDTEGYVTEHISQEEEVYAAERLDKIRRQNRIKAE Number of specific fragments extracted= 2 number of extra gaps= 0 total=267 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dpuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dpuA expands to /projects/compbio/data/pdb/1dpu.pdb.gz 1dpuA:# T0360 read from 1dpuA/merged-good-all-a2m # 1dpuA read from 1dpuA/merged-good-all-a2m # adding 1dpuA to template set # found chain 1dpuA in template set T0360 18 :MSKKKQTEMIAD 1dpuA 207 :VAQNQVLNLIKA T0360 35 :YDVFKR 1dpuA 219 :CPRPEG T0360 48 :I 1dpuA 225 :L T0360 49 :DQDLIAALPQYDAALIARVLANHCR 1dpuA 227 :FQDLKNQLKHMSVSSIKQAVDFLSN Number of specific fragments extracted= 4 number of extra gaps= 0 total=271 Number of alignments=54 # 1dpuA read from 1dpuA/merged-good-all-a2m # found chain 1dpuA in template set T0360 17 :TMSKKKQTEMIAD 1dpuA 206 :TVAQNQVLNLIKA T0360 35 :YDVFKRFK 1dpuA 219 :CPRPEGLN T0360 49 :DQDLIAALPQYDAALIARVLANHC 1dpuA 227 :FQDLKNQLKHMSVSSIKQAVDFLS Number of specific fragments extracted= 3 number of extra gaps= 0 total=274 Number of alignments=55 # 1dpuA read from 1dpuA/merged-good-all-a2m # found chain 1dpuA in template set Warning: unaligning (T0360)S13 because first residue in template chain is (1dpuA)A202 T0360 14 :AVQTMSKKKQTEMIADHIYGKYD 1dpuA 203 :NGLTVAQNQVLNLIKACPRPEGL T0360 49 :DQDLIAALPQYDAALIARVLANHCR 1dpuA 227 :FQDLKNQLKHMSVSSIKQAVDFLSN Number of specific fragments extracted= 2 number of extra gaps= 0 total=276 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ucrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0360 read from 1ucrA/merged-good-all-a2m # 1ucrA read from 1ucrA/merged-good-all-a2m # found chain 1ucrA in training set T0360 22 :KQTEMIADHIYG 1ucrA 3 :EAKQKVVDFLNS T0360 37 :VFKR 1ucrA 18 :SKSK T0360 49 :DQDLIAALPQYDAALIARVLANHCR 1ucrA 24 :FNDFTDLFPDMKQREVKKILTALVN Number of specific fragments extracted= 3 number of extra gaps= 0 total=279 Number of alignments=57 # 1ucrA read from 1ucrA/merged-good-all-a2m # found chain 1ucrA in training set Warning: unaligning (T0360)Y35 because of BadResidue code BAD_PEPTIDE in next template residue (1ucrA)G17 Warning: unaligning (T0360)D36 because of BadResidue code BAD_PEPTIDE at template residue (1ucrA)G17 T0360 22 :KQTEMIADHIYGK 1ucrA 3 :EAKQKVVDFLNSK T0360 37 :VFKRFK 1ucrA 18 :SKSKFY T0360 49 :DQDLIAALPQYDAALIARVLANHCR 1ucrA 24 :FNDFTDLFPDMKQREVKKILTALVN Number of specific fragments extracted= 3 number of extra gaps= 1 total=282 Number of alignments=58 # 1ucrA read from 1ucrA/merged-good-all-a2m # found chain 1ucrA in training set Warning: unaligning (T0360)Y35 because of BadResidue code BAD_PEPTIDE in next template residue (1ucrA)G17 Warning: unaligning (T0360)D36 because of BadResidue code BAD_PEPTIDE at template residue (1ucrA)G17 T0360 22 :KQTEMIADHIYGK 1ucrA 3 :EAKQKVVDFLNSK T0360 37 :VFKRFK 1ucrA 18 :SKSKFY T0360 49 :DQDLIAALPQYDAALIARVLANHCR 1ucrA 24 :FNDFTDLFPDMKQREVKKILTALVN Number of specific fragments extracted= 3 number of extra gaps= 1 total=285 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pmzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pmzA expands to Error: no filename for 1pmzA 1pmzA expands to Error: no filename for 1pmzA 1pmzA expands to Error: no filename for 1pmzA # T0360 read from 1pmzA/merged-good-all-a2m # 1pmzA read from 1pmzA/merged-good-all-a2m # adding 1pmzA to template set Error: can't find template for 1pmzA or 1pmzA, so skipping it. # 1pmzA read from 1pmzA/merged-good-all-a2m # adding 1pmzA to template set Error: can't find template for 1pmzA or 1pmzA, so skipping it. # 1pmzA read from 1pmzA/merged-good-all-a2m # adding 1pmzA to template set Error: can't find template for 1pmzA or 1pmzA, so skipping it. # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0360//projects/compbio/experiments/protein-predict/casp7/T0360/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0360//projects/compbio/experiments/protein-predict/casp7/T0360/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0360/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0360/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((T0360)L52.CB, (T0360)I64.CB) [> 3.6030 = 6.0050 < 7.8065] w=1.0000 to align # Constraint # added constraint: constraint((T0360)I53.CB, (T0360)I64.CB) [> 3.5803 = 5.9672 < 7.7573] w=0.9945 to align # Constraint # added constraint: constraint((T0360)D49.CB, (T0360)I64.CB) [> 3.9865 = 6.6442 < 8.6374] w=0.8904 to align # Constraint # added constraint: constraint((T0360)Q23.CB, (T0360)V67.CB) [> 3.1507 = 5.2512 < 6.8266] w=0.8681 to align # Constraint # added constraint: constraint((T0360)K20.CB, (T0360)N70.CB) [> 4.1016 = 6.8360 < 8.8868] w=0.8402 to align # Constraint # added constraint: constraint((T0360)D49.CB, (T0360)L68.CB) [> 4.1256 = 6.8760 < 8.9388] w=0.8331 to align # Constraint # added constraint: constraint((T0360)T24.CB, (T0360)H71.CB) [> 3.8973 = 6.4955 < 8.4441] w=0.8209 to align # Constraint # added constraint: constraint((T0360)I27.CB, (T0360)L52.CB) [> 4.2790 = 7.1317 < 9.2712] w=0.7391 to align # Constraint # added constraint: constraint((T0360)Q23.CB, (T0360)H71.CB) [> 3.9723 = 6.6205 < 8.6066] w=0.6870 to align # Constraint # added constraint: constraint((T0360)K20.CB, (T0360)H71.CB) [> 4.0841 = 6.8068 < 8.8488] w=0.6398 to align # Constraint # added constraint: constraint((T0360)M26.CB, (T0360)L56.CB) [> 3.8894 = 6.4823 < 8.4270] w=0.6397 to align # Constraint # added constraint: constraint((T0360)M26.CB, (T0360)L52.CB) [> 3.7815 = 6.3025 < 8.1932] w=0.6351 to align # Constraint # added constraint: constraint((T0360)M26.CB, (T0360)A55.CB) [> 3.3235 = 5.5391 < 7.2009] w=0.6088 to align # Constraint # added constraint: constraint((T0360)Q23.CB, (T0360)L56.CB) [> 4.1708 = 6.9513 < 9.0366] w=0.6088 to align # Constraint # added constraint: constraint((T0360)I27.CB, (T0360)H71.CB) [> 4.4989 = 7.4982 < 9.7476] w=0.5963 to align # Constraint # added constraint: constraint((T0360)Q23.CB, (T0360)L68.CB) [> 4.3225 = 7.2041 < 9.3653] w=0.5860 to align # Constraint # added constraint: constraint((T0360)Q23.CB, (T0360)L52.CB) [> 3.9879 = 6.6465 < 8.6404] w=0.5794 to align # Constraint # added constraint: constraint((T0360)K22.CB, (T0360)L56.CB) [> 3.8808 = 6.4681 < 8.4085] w=0.5794 to align # Constraint # added constraint: constraint((T0360)Q23.CB, (T0360)I64.CB) [> 4.0464 = 6.7440 < 8.7672] w=0.5444 to align # Constraint # added constraint: constraint((T0360)D49.CB, (T0360)A65.CB) [> 3.8332 = 6.3887 < 8.3053] w=0.5319 to align # Constraint # added constraint: constraint((T0360)L52.CB, (T0360)L68.CB) [> 4.3144 = 7.1907 < 9.3479] w=0.4211 to align # Constraint # added constraint: constraint((T0360)H71.CB, (T0360)G85.CA) [> 3.1519 = 5.2531 < 6.8291] w=0.3724 to align # Constraint # added constraint: constraint((T0360)H71.CB, (T0360)G84.CA) [> 4.0810 = 6.8016 < 8.8421] w=0.3724 to align # Constraint # added constraint: constraint((T0360)G85.CA, (T0360)V98.CB) [> 3.3016 = 5.5027 < 7.1535] w=0.3551 to align # Constraint # added constraint: constraint((T0360)K42.CB, (T0360)L52.CB) [> 3.5476 = 5.9126 < 7.6864] w=0.3516 to align # Constraint # added constraint: constraint((T0360)K42.CB, (T0360)D51.CB) [> 2.7245 = 4.5409 < 5.9031] w=0.3516 to align # Constraint # added constraint: constraint((T0360)N70.CB, (T0360)R83.CB) [> 3.7711 = 6.2852 < 8.1708] w=0.3512 to align # Constraint # added constraint: constraint((T0360)I27.CB, (T0360)V67.CB) [> 3.1576 = 5.2627 < 6.8416] w=0.3375 to align # Constraint # added constraint: constraint((T0360)T17.CB, (T0360)V67.CB) [> 4.1143 = 6.8572 < 8.9144] w=0.3102 to align # Constraint # added constraint: constraint((T0360)H30.CB, (T0360)A55.CB) [> 4.1816 = 6.9694 < 9.0602] w=0.2981 to align # Constraint # added constraint: constraint((T0360)L81.CB, (T0360)A106.CB) [> 2.7780 = 4.6300 < 6.0190] w=0.2979 to align # Constraint # added constraint: constraint((T0360)L81.CB, (T0360)I105.CB) [> 4.0444 = 6.7406 < 8.7628] w=0.2979 to align # Constraint # added constraint: constraint((T0360)I31.CB, (T0360)L52.CB) [> 4.3060 = 7.1767 < 9.3296] w=0.2967 to align # Constraint # added constraint: constraint((T0360)A69.CB, (T0360)R87.CB) [> 4.3718 = 7.2863 < 9.4722] w=0.2791 to align # Constraint # added constraint: constraint((T0360)L81.CB, (T0360)Q103.CB) [> 3.3932 = 5.6554 < 7.3520] w=0.2649 to align # Constraint # added constraint: constraint((T0360)I27.CB, (T0360)I64.CB) [> 4.5023 = 7.5038 < 9.7549] w=0.2369 to align # Constraint # added constraint: constraint((T0360)C72.CB, (T0360)G85.CA) [> 4.1381 = 6.8968 < 8.9659] w=0.2325 to align # Constraint # added constraint: constraint((T0360)L68.CB, (T0360)L81.CB) [> 3.6939 = 6.1565 < 8.0034] w=0.2161 to align # Constraint # added constraint: constraint((T0360)A69.CB, (T0360)L81.CB) [> 3.3979 = 5.6632 < 7.3621] w=0.2161 to align # Constraint # added constraint: constraint((T0360)N70.CB, (T0360)L81.CB) [> 4.3462 = 7.2437 < 9.4168] w=0.2161 to align # Constraint # added constraint: constraint((T0360)Q50.CB, (T0360)A61.CB) [> 4.0695 = 6.7825 < 8.8172] w=0.2129 to align # Constraint # added constraint: constraint((T0360)K34.CB, (T0360)L90.CB) [> 3.6883 = 6.1471 < 7.9913] w=0.2114 to align # Constraint # added constraint: constraint((T0360)P43.CB, (T0360)F88.CB) [> 3.8984 = 6.4974 < 8.4466] w=0.2114 to align # Constraint # added constraint: constraint((T0360)I27.CB, (T0360)L68.CB) [> 4.4070 = 7.3450 < 9.5486] w=0.2112 to align # Constraint # added constraint: constraint((T0360)L68.CB, (T0360)R87.CB) [> 4.5650 = 7.6083 < 9.8908] w=0.2020 to align # Constraint # added constraint: constraint((T0360)L52.CB, (T0360)L90.CB) [> 4.3146 = 7.1911 < 9.3484] w=0.2009 to align # Constraint # added constraint: constraint((T0360)K86.CB, (T0360)V98.CB) [> 4.4858 = 7.4764 < 9.7193] w=0.2009 to align # Constraint # added constraint: constraint((T0360)L78.CB, (T0360)A106.CB) [> 2.7904 = 4.6506 < 6.0458] w=0.1982 to align # Constraint # added constraint: constraint((T0360)A14.CB, (T0360)R83.CB) [> 3.1457 = 5.2428 < 6.8157] w=0.1971 to align # Constraint # added constraint: constraint((T0360)H71.CB, (T0360)E102.CB) [> 4.1649 = 6.9415 < 9.0239] w=0.1967 to align # Constraint # added constraint: constraint((T0360)F41.CB, (T0360)A55.CB) [> 4.5757 = 7.6262 < 9.9141] w=0.1909 to align # Constraint # added constraint: constraint((T0360)G84.CA, (T0360)V98.CB) [> 3.1767 = 5.2945 < 6.8829] w=0.1872 to align # Constraint # added constraint: constraint((T0360)A14.CB, (T0360)T24.CB) [> 3.8206 = 6.3677 < 8.2780] w=0.1824 to align # Constraint # added constraint: constraint((T0360)K86.CB, (T0360)E97.CB) [> 3.5852 = 5.9754 < 7.7680] w=0.1818 to align # Constraint # added constraint: constraint((T0360)C72.CB, (T0360)G84.CA) [> 3.9562 = 6.5937 < 8.5718] w=0.1812 to align # Constraint # added constraint: constraint((T0360)P75.CB, (T0360)P110.CB) [> 3.8254 = 6.3756 < 8.2883] w=0.1763 to align # Constraint # added constraint: constraint((T0360)P43.CB, (T0360)K86.CB) [> 3.8330 = 6.3883 < 8.3048] w=0.1653 to align # Constraint # added constraint: constraint((T0360)P43.CB, (T0360)R87.CB) [> 2.7186 = 4.5311 < 5.8904] w=0.1653 to align # Constraint # added constraint: constraint((T0360)P43.CB, (T0360)V98.CB) [> 4.1615 = 6.9358 < 9.0165] w=0.1653 to align # Constraint # added constraint: constraint((T0360)L44.CB, (T0360)L68.CB) [> 4.3498 = 7.2497 < 9.4246] w=0.1653 to align # Constraint # added constraint: constraint((T0360)L44.CB, (T0360)H71.CB) [> 4.5601 = 7.6002 < 9.8802] w=0.1653 to align # Constraint # added constraint: constraint((T0360)L44.CB, (T0360)C72.CB) [> 4.1589 = 6.9316 < 9.0110] w=0.1653 to align # Constraint # added constraint: constraint((T0360)L44.CB, (T0360)R87.CB) [> 3.7049 = 6.1748 < 8.0273] w=0.1653 to align # Constraint # added constraint: constraint((T0360)L44.CB, (T0360)F88.CB) [> 4.3243 = 7.2071 < 9.3693] w=0.1653 to align # Constraint # added constraint: constraint((T0360)A45.CB, (T0360)R87.CB) [> 2.9799 = 4.9666 < 6.4565] w=0.1653 to align # Constraint # added constraint: constraint((T0360)A45.CB, (T0360)F88.CB) [> 3.6739 = 6.1231 < 7.9600] w=0.1653 to align # Constraint # added constraint: constraint((T0360)A45.CB, (T0360)D89.CB) [> 2.4766 = 4.1277 < 5.3661] w=0.1653 to align # Constraint # added constraint: constraint((T0360)A45.CB, (T0360)R93.CB) [> 4.7900 = 7.9833 < 10.3784] w=0.1653 to align # Constraint # added constraint: constraint((T0360)A45.CB, (T0360)K95.CB) [> 2.4602 = 4.1003 < 5.3304] w=0.1653 to align # Constraint # added constraint: constraint((T0360)L46.CB, (T0360)R87.CB) [> 3.9617 = 6.6028 < 8.5837] w=0.1653 to align # Constraint # added constraint: constraint((T0360)P43.CB, (T0360)G85.CA) [> 4.0613 = 6.7688 < 8.7994] w=0.1653 to align # Constraint # added constraint: constraint((T0360)P43.CB, (T0360)A80.CB) [> 3.5154 = 5.8589 < 7.6166] w=0.1653 to align # Constraint # added constraint: constraint((T0360)P43.CB, (T0360)Y77.CB) [> 4.4261 = 7.3768 < 9.5899] w=0.1653 to align # Constraint # added constraint: constraint((T0360)F41.CB, (T0360)Y77.CB) [> 3.5140 = 5.8566 < 7.6136] w=0.1653 to align # Constraint # added constraint: constraint((T0360)F41.CB, (T0360)R76.CB) [> 4.4778 = 7.4630 < 9.7019] w=0.1653 to align # Constraint # added constraint: constraint((T0360)F41.CB, (T0360)R74.CB) [> 4.4029 = 7.3382 < 9.5396] w=0.1653 to align # Constraint # added constraint: constraint((T0360)R40.CB, (T0360)R76.CB) [> 3.7562 = 6.2603 < 8.1383] w=0.1653 to align # Constraint # added constraint: constraint((T0360)G33.CA, (T0360)L90.CB) [> 4.0025 = 6.6708 < 8.6720] w=0.1653 to align # Constraint # added constraint: constraint((T0360)I31.CB, (T0360)A55.CB) [> 4.3336 = 7.2226 < 9.3894] w=0.1653 to align # Constraint # added constraint: constraint((T0360)A82.CB, (T0360)A106.CB) [> 4.7480 = 7.9133 < 10.2873] w=0.1653 to align # Constraint # added constraint: constraint((T0360)A82.CB, (T0360)Q103.CB) [> 3.3417 = 5.5694 < 7.2403] w=0.1653 to align # Constraint # added constraint: constraint((T0360)K79.CB, (T0360)P110.CB) [> 3.9748 = 6.6247 < 8.6120] w=0.1653 to align # Constraint # added constraint: constraint((T0360)K79.CB, (T0360)A106.CB) [> 4.6796 = 7.7994 < 10.1392] w=0.1653 to align # Constraint # added constraint: constraint((T0360)L46.CB, (T0360)K95.CB) [> 3.9238 = 6.5396 < 8.5015] w=0.1653 to align # Constraint # added constraint: constraint((T0360)I48.CB, (T0360)D89.CB) [> 3.6649 = 6.1082 < 7.9406] w=0.1653 to align # Constraint # added constraint: constraint((T0360)I48.CB, (T0360)L90.CB) [> 4.3540 = 7.2567 < 9.4337] w=0.1653 to align # Constraint # added constraint: constraint((T0360)D51.CB, (T0360)D89.CB) [> 4.1505 = 6.9176 < 8.9928] w=0.1653 to align # Constraint # added constraint: constraint((T0360)D51.CB, (T0360)L90.CB) [> 3.9632 = 6.6053 < 8.5868] w=0.1653 to align # Constraint # added constraint: constraint((T0360)A55.CB, (T0360)L90.CB) [> 4.2778 = 7.1297 < 9.2686] w=0.1653 to align # Constraint # added constraint: constraint((T0360)R73.CB, (T0360)H109.CB) [> 4.3879 = 7.3132 < 9.5072] w=0.1653 to align # Constraint # added constraint: constraint((T0360)R74.CB, (T0360)Q113.CB) [> 4.6627 = 7.7712 < 10.1026] w=0.1653 to align # Constraint # added constraint: constraint((T0360)P75.CB, (T0360)Q113.CB) [> 3.5859 = 5.9765 < 7.7695] w=0.1653 to align # Constraint # added constraint: constraint((T0360)L78.CB, (T0360)Q107.CB) [> 4.6921 = 7.8201 < 10.1662] w=0.1653 to align # Constraint # added constraint: constraint((T0360)L78.CB, (T0360)H109.CB) [> 3.4170 = 5.6951 < 7.4036] w=0.1653 to align # Constraint # added constraint: constraint((T0360)M26.CB, (T0360)Y35.CB) [> 3.8277 = 6.3794 < 8.2933] w=0.1644 to align # Constraint # added constraint: constraint((T0360)T24.CB, (T0360)H109.CB) [> 3.7976 = 6.3293 < 8.2281] w=0.1564 to align # Constraint # added constraint: constraint((T0360)E25.CB, (T0360)F38.CB) [> 3.9814 = 6.6357 < 8.6264] w=0.1557 to align # Constraint # added constraint: constraint((T0360)A55.CB, (T0360)V67.CB) [> 3.7473 = 6.2455 < 8.1191] w=0.1550 to align # Constraint # added constraint: constraint((T0360)D36.CB, (T0360)A55.CB) [> 4.5916 = 7.6527 < 9.9485] w=0.1549 to align # Constraint # added constraint: constraint((T0360)F88.CB, (T0360)E97.CB) [> 3.8302 = 6.3837 < 8.2988] w=0.1549 to align # Constraint # added constraint: constraint((T0360)M26.CB, (T0360)V67.CB) [> 2.8092 = 4.6819 < 6.0865] w=0.1548 to align # Constraint # added constraint: constraint((T0360)G85.CA, (T0360)E102.CB) [> 2.4647 = 4.1079 < 5.3403] w=0.1544 to align # Constraint # added constraint: constraint((T0360)H71.CB, (T0360)A80.CB) [> 3.5591 = 5.9318 < 7.7114] w=0.1540 to align # Constraint # added constraint: constraint((T0360)N70.CB, (T0360)K79.CB) [> 3.6267 = 6.0445 < 7.8579] w=0.1540 to align # Constraint # added constraint: constraint((T0360)K42.CB, (T0360)A55.CB) [> 4.4252 = 7.3753 < 9.5879] w=0.1531 to align # Constraint # added constraint: constraint((T0360)M26.CB, (T0360)K42.CB) [> 4.3588 = 7.2646 < 9.4440] w=0.1531 to align # Constraint # added constraint: constraint((T0360)A14.CB, (T0360)H71.CB) [> 4.6296 = 7.7160 < 10.0308] w=0.1495 to align # Constraint # added constraint: constraint((T0360)A55.CB, (T0360)H71.CB) [> 3.0722 = 5.1203 < 6.6564] w=0.1495 to align # Constraint # added constraint: constraint((T0360)I27.CB, (T0360)A106.CB) [> 4.1553 = 6.9256 < 9.0032] w=0.1435 to align # Constraint # added constraint: constraint((T0360)L78.CB, (T0360)Q103.CB) [> 3.8235 = 6.3726 < 8.2843] w=0.1326 to align # Constraint # added constraint: constraint((T0360)M26.CB, (T0360)I64.CB) [> 4.5390 = 7.5650 < 9.8345] w=0.1325 to align # Constraint # added constraint: constraint((T0360)M26.CB, (T0360)Y59.CB) [> 4.2495 = 7.0824 < 9.2072] w=0.1325 to align # Constraint # added constraint: constraint((T0360)I27.CB, (T0360)L63.CB) [> 4.2207 = 7.0345 < 9.1449] w=0.1262 to align # Constraint # added constraint: constraint((T0360)T24.CB, (T0360)R66.CB) [> 4.6395 = 7.7324 < 10.0522] w=0.1262 to align # Constraint # added constraint: constraint((T0360)T24.CB, (T0360)Y35.CB) [> 3.7919 = 6.3199 < 8.2158] w=0.1159 to align # Constraint # added constraint: constraint((T0360)T17.CB, (T0360)R73.CB) [> 4.5591 = 7.5985 < 9.8781] w=0.1102 to align # Constraint # added constraint: constraint((T0360)M26.CB, (T0360)L63.CB) [> 3.9744 = 6.6241 < 8.6113] w=0.1102 to align # Constraint # added constraint: constraint((T0360)I31.CB, (T0360)L90.CB) [> 2.5492 = 4.2487 < 5.5233] w=0.1102 to align # Constraint # added constraint: constraint((T0360)L11.CB, (T0360)D49.CB) [> 3.2992 = 5.4988 < 7.1484] w=0.1054 to align # Constraint # added constraint: constraint((T0360)I48.CB, (T0360)Y77.CB) [> 3.6529 = 6.0882 < 7.9147] w=0.1051 to align # Constraint # added constraint: constraint((T0360)I27.CB, (T0360)Y59.CB) [> 4.2137 = 7.0228 < 9.1297] w=0.1044 to align # Constraint # added constraint: constraint((T0360)C72.CB, (T0360)A82.CB) [> 3.6469 = 6.0781 < 7.9016] w=0.1041 to align # Constraint # added constraint: constraint((T0360)I53.CB, (T0360)L68.CB) [> 2.8145 = 4.6908 < 6.0981] w=0.1041 to align # Constraint # added constraint: constraint((T0360)L7.CB, (T0360)D49.CB) [> 4.7597 = 7.9328 < 10.3126] w=0.0996 to align # Constraint # added constraint: constraint((T0360)A80.CB, (T0360)I105.CB) [> 3.6209 = 6.0348 < 7.8453] w=0.0996 to align # Constraint # added constraint: constraint((T0360)I48.CB, (T0360)L78.CB) [> 3.7779 = 6.2965 < 8.1854] w=0.0996 to align # Constraint # added constraint: constraint((T0360)A45.CB, (T0360)L81.CB) [> 4.4402 = 7.4004 < 9.6205] w=0.0996 to align # Constraint # added constraint: constraint((T0360)I31.CB, (T0360)I48.CB) [> 3.2345 = 5.3908 < 7.0081] w=0.0991 to align # Constraint # added constraint: constraint((T0360)I31.CB, (T0360)G47.CA) [> 3.7697 = 6.2829 < 8.1677] w=0.0991 to align # Constraint # added constraint: constraint((T0360)H71.CB, (T0360)A106.CB) [> 4.3324 = 7.2208 < 9.3870] w=0.0828 to align # Constraint # added constraint: constraint((T0360)L52.CB, (T0360)V67.CB) [> 2.7936 = 4.6560 < 6.0528] w=0.0766 to align # Constraint # added constraint: constraint((T0360)I53.CB, (T0360)L63.CB) [> 4.7569 = 7.9282 < 10.3066] w=0.0746 to align # Constraint # added constraint: constraint((T0360)I48.CB, (T0360)V67.CB) [> 4.4580 = 7.4300 < 9.6590] w=0.0732 to align # Constraint # added constraint: constraint((T0360)I27.CB, (T0360)R66.CB) [> 2.4021 = 4.0036 < 5.2046] w=0.0711 to align # Constraint # added constraint: constraint((T0360)K20.CB, (T0360)P75.CB) [> 4.6348 = 7.7247 < 10.0421] w=0.0711 to align # Constraint # added constraint: constraint((T0360)L52.CB, (T0360)L63.CB) [> 3.9643 = 6.6071 < 8.5893] w=0.0711 to align # Constraint # added constraint: constraint((T0360)K42.CB, (T0360)F94.CB) [> 4.5131 = 7.5219 < 9.7784] w=0.0652 to align # Constraint # added constraint: constraint((T0360)L68.CB, (T0360)K86.CB) [> 3.8249 = 6.3749 < 8.2874] w=0.0608 to align # Constraint # added constraint: constraint((T0360)I27.CB, (T0360)K86.CB) [> 4.0626 = 6.7709 < 8.8022] w=0.0608 to align # Constraint # added constraint: constraint((T0360)K34.CB, (T0360)N91.CB) [> 3.6063 = 6.0106 < 7.8137] w=0.0606 to align # Constraint # added constraint: constraint((T0360)K34.CB, (T0360)D89.CB) [> 4.5536 = 7.5894 < 9.8662] w=0.0606 to align # Constraint # added constraint: constraint((T0360)K42.CB, (T0360)L90.CB) [> 4.0228 = 6.7047 < 8.7162] w=0.0605 to align # Constraint # added constraint: constraint((T0360)T24.CB, (T0360)A80.CB) [> 4.2900 = 7.1500 < 9.2951] w=0.0578 to align # Constraint # added constraint: constraint((T0360)L68.CB, (T0360)Y77.CB) [> 3.6112 = 6.0186 < 7.8242] w=0.0568 to align # Constraint # added constraint: constraint((T0360)K21.CB, (T0360)R76.CB) [> 4.7363 = 7.8938 < 10.2620] w=0.0551 to align # Constraint # added constraint: constraint((T0360)Y35.CB, (T0360)F88.CB) [> 4.1780 = 6.9633 < 9.0523] w=0.0551 to align # Constraint # added constraint: constraint((T0360)Y35.CB, (T0360)L44.CB) [> 4.1795 = 6.9658 < 9.0555] w=0.0551 to align # Constraint # added constraint: constraint((T0360)Y32.CB, (T0360)L90.CB) [> 3.1155 = 5.1926 < 6.7503] w=0.0551 to align # Constraint # added constraint: constraint((T0360)Y32.CB, (T0360)A55.CB) [> 4.6289 = 7.7148 < 10.0292] w=0.0551 to align # Constraint # added constraint: constraint((T0360)A28.CB, (T0360)I64.CB) [> 4.5896 = 7.6493 < 9.9441] w=0.0551 to align # Constraint # added constraint: constraint((T0360)R73.CB, (T0360)K86.CB) [> 3.4284 = 5.7140 < 7.4282] w=0.0513 to align # Constraint # added constraint: constraint((T0360)I27.CB, (T0360)A45.CB) [> 3.7649 = 6.2748 < 8.1572] w=0.0498 to align # Constraint # added constraint: constraint((T0360)L11.CB, (T0360)A28.CB) [> 4.7035 = 7.8391 < 10.1909] w=0.0498 to align # Constraint # added constraint: constraint((T0360)A45.CB, (T0360)H109.CB) [> 4.4417 = 7.4029 < 9.6237] w=0.0498 to align # Constraint # added constraint: constraint((T0360)I48.CB, (T0360)E102.CB) [> 3.7581 = 6.2636 < 8.1426] w=0.0498 to align # Constraint # added constraint: constraint((T0360)I48.CB, (T0360)I105.CB) [> 3.6103 = 6.0173 < 7.8224] w=0.0498 to align # Constraint # added constraint: constraint((T0360)L52.CB, (T0360)E102.CB) [> 3.3821 = 5.6369 < 7.3280] w=0.0498 to align # Constraint # added constraint: constraint((T0360)A28.CB, (T0360)L46.CB) [> 4.1804 = 6.9674 < 9.0576] w=0.0498 to align # Constraint # added constraint: constraint((T0360)I31.CB, (T0360)L46.CB) [> 4.5297 = 7.5494 < 9.8143] w=0.0498 to align # Constraint # added constraint: constraint((T0360)H30.CB, (T0360)G47.CA) [> 3.6675 = 6.1125 < 7.9462] w=0.0498 to align # Constraint # added constraint: constraint((T0360)H30.CB, (T0360)L46.CB) [> 4.4402 = 7.4003 < 9.6204] w=0.0498 to align # Constraint # added constraint: constraint((T0360)L68.CB, (T0360)F88.CB) [> 4.7592 = 7.9321 < 10.3117] w=0.0498 to align # Constraint # added constraint: constraint((T0360)K34.CB, (T0360)G47.CA) [> 3.0928 = 5.1547 < 6.7011] w=0.0493 to align # Constraint # added constraint: constraint((T0360)D36.CB, (T0360)G47.CA) [> 2.8924 = 4.8207 < 6.2670] w=0.0493 to align # Constraint # added constraint: constraint((T0360)F38.CB, (T0360)G47.CA) [> 2.7941 = 4.6568 < 6.0539] w=0.0493 to align # Constraint # added constraint: constraint((T0360)K86.CB, (T0360)T99.CB) [> 3.4700 = 5.7834 < 7.5184] w=0.0466 to align # Constraint # added constraint: constraint((T0360)F41.CB, (T0360)F88.CB) [> 4.4939 = 7.4899 < 9.7368] w=0.0461 to align # Constraint # added constraint: constraint((T0360)I27.CB, (T0360)L44.CB) [> 4.3045 = 7.1741 < 9.3263] w=0.0461 to align # Constraint # added constraint: constraint((T0360)M26.CB, (T0360)L44.CB) [> 4.7487 = 7.9144 < 10.2887] w=0.0461 to align # Constraint # added constraint: constraint((T0360)L11.CB, (T0360)G85.CA) [> 3.5818 = 5.9697 < 7.7606] w=0.0461 to align # Constraint # added constraint: constraint((T0360)L7.CB, (T0360)G85.CA) [> 4.3339 = 7.2232 < 9.3902] w=0.0461 to align # Constraint # added constraint: constraint((T0360)L44.CB, (T0360)A55.CB) [> 4.5418 = 7.5697 < 9.8406] w=0.0461 to align # Constraint # added constraint: constraint((T0360)M26.CB, (T0360)H71.CB) [> 3.6563 = 6.0938 < 7.9220] w=0.0447 to align # Constraint # added constraint: constraint((T0360)D89.CB, (T0360)V98.CB) [> 3.6643 = 6.1071 < 7.9393] w=0.0421 to align # Constraint # added constraint: constraint((T0360)K42.CB, (T0360)D89.CB) [> 4.1091 = 6.8486 < 8.9031] w=0.0357 to align # Constraint # added constraint: constraint((T0360)I27.CB, (T0360)A55.CB) [> 4.4499 = 7.4165 < 9.6414] w=0.0352 to align # Constraint # added constraint: constraint((T0360)M26.CB, (T0360)I48.CB) [> 3.5928 = 5.9879 < 7.7843] w=0.0345 to align # Constraint # added constraint: constraint((T0360)A14.CB, (T0360)A80.CB) [> 2.6019 = 4.3366 < 5.6375] w=0.0330 to align # Constraint # added constraint: constraint((T0360)L7.CB, (T0360)P75.CB) [> 3.4942 = 5.8236 < 7.5707] w=0.0330 to align # Constraint # added constraint: constraint((T0360)Y77.CB, (T0360)I105.CB) [> 4.0529 = 6.7548 < 8.7812] w=0.0330 to align # Constraint # added constraint: constraint((T0360)L56.CB, (T0360)A65.CB) [> 3.6805 = 6.1342 < 7.9744] w=0.0330 to align # Constraint # added constraint: constraint((T0360)G47.CA, (T0360)C72.CB) [> 4.7994 = 7.9991 < 10.3988] w=0.0330 to align # Constraint # added constraint: constraint((T0360)G47.CA, (T0360)L68.CB) [> 4.0814 = 6.8024 < 8.8431] w=0.0330 to align # Constraint # added constraint: constraint((T0360)L46.CB, (T0360)C72.CB) [> 3.9697 = 6.6163 < 8.6011] w=0.0330 to align # Constraint # added constraint: constraint((T0360)L46.CB, (T0360)H71.CB) [> 3.2027 = 5.3379 < 6.9393] w=0.0330 to align # Constraint # added constraint: constraint((T0360)L46.CB, (T0360)L68.CB) [> 3.2260 = 5.3767 < 6.9897] w=0.0330 to align # Constraint # added constraint: constraint((T0360)Y32.CB, (T0360)D89.CB) [> 3.9430 = 6.5717 < 8.5432] w=0.0249 to align # Constraint # added constraint: constraint((T0360)L68.CB, (T0360)A80.CB) [> 3.3497 = 5.5828 < 7.2577] w=0.0249 to align # Constraint # added constraint: constraint((T0360)M26.CB, (T0360)L68.CB) [> 3.9640 = 6.6067 < 8.5887] w=0.0223 to align # Constraint # added constraint: constraint((T0360)L44.CB, (T0360)Y59.CB) [> 3.9358 = 6.5597 < 8.5276] w=0.0095 to align # Constraint # added constraint: constraint((T0360)L52.CB, (T0360)Y77.CB) [> 3.5867 = 5.9778 < 7.7712] w=0.0055 to align # Constraint # added constraint: constraint((T0360)L52.CB, (T0360)L78.CB) [> 4.4114 = 7.3524 < 9.5581] w=0.0055 to align # Constraint # added constraint: constraint((T0360)A61.CB, (T0360)L78.CB) [> 4.1533 = 6.9222 < 8.9989] w=0.0055 to align # Constraint # added constraint: constraint((T0360)A61.CB, (T0360)H71.CB) [> 4.6131 = 7.6885 < 9.9950] w=0.0055 to align # Constraint # added constraint: constraint((T0360)A55.CB, (T0360)L68.CB) [> 4.5947 = 7.6578 < 9.9551] w=0.0055 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0360/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0360/decoys/ # ReadConformPDB reading from PDB file XXXX_0001.pdb.gz looking for model 1 Error: Reading chain '' from PDB file XXXX_0001.pdb.gz failed---no such chain. # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # 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 T0360 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0360 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0360 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # 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 T0360 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 T0360 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 T0360 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 T0360 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 T0360 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 T0360 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 T0360 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 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 T0360 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 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 37 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 74 # 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 74 # 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 102 # 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 127 # 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 125 # 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 109 # 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 # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 T0360 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 T0360 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 T0360 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: atoms too close: (T0360)Q50.C and (T0360)D51.N only 0.000 apart, marking (T0360)D51.N as missing WARNING: atoms too close: (T0360)D51.N and (T0360)D51.CA only 0.000 apart, marking (T0360)D51.CA as missing WARNING: atoms too close: (T0360)Q50.C and (T0360)D51.CA only 0.000 apart, marking (T0360)D51.CA as missing WARNING: atoms too close: (T0360)D51.CA and (T0360)D51.CB only 0.000 apart, marking (T0360)D51.CB as missing WARNING: atoms too close: (T0360)D51.N and (T0360)D51.CB only 0.000 apart, marking (T0360)D51.CB as missing WARNING: atoms too close: (T0360)Q50.C and (T0360)D51.CB only 0.000 apart, marking (T0360)D51.CB as missing WARNING: atoms too close: (T0360)D51.CB and (T0360)D51.CG only 0.000 apart, marking (T0360)D51.CG as missing WARNING: atoms too close: (T0360)D51.CA and (T0360)D51.CG only 0.000 apart, marking (T0360)D51.CG as missing WARNING: atoms too close: (T0360)D51.N and (T0360)D51.CG only 0.000 apart, marking (T0360)D51.CG as missing WARNING: atoms too close: (T0360)Q50.C and (T0360)D51.CG only 0.000 apart, marking (T0360)D51.CG as missing WARNING: atoms too close: (T0360)D51.CG and (T0360)D51.OD1 only 0.000 apart, marking (T0360)D51.OD1 as missing WARNING: atoms too close: (T0360)D51.CB and (T0360)D51.OD1 only 0.000 apart, marking (T0360)D51.OD1 as missing WARNING: atoms too close: (T0360)D51.CA and (T0360)D51.OD1 only 0.000 apart, marking (T0360)D51.OD1 as missing WARNING: atoms too close: (T0360)D51.N and (T0360)D51.OD1 only 0.000 apart, marking (T0360)D51.OD1 as missing WARNING: atoms too close: (T0360)Q50.C and (T0360)D51.OD1 only 0.000 apart, marking (T0360)D51.OD1 as missing WARNING: atoms too close: (T0360)D51.OD1 and (T0360)D51.OD2 only 0.000 apart, marking (T0360)D51.OD2 as missing WARNING: atoms too close: (T0360)D51.CG and (T0360)D51.OD2 only 0.000 apart, marking (T0360)D51.OD2 as missing WARNING: atoms too close: (T0360)D51.CB and (T0360)D51.OD2 only 0.000 apart, marking (T0360)D51.OD2 as missing WARNING: atoms too close: (T0360)D51.CA and (T0360)D51.OD2 only 0.000 apart, marking (T0360)D51.OD2 as missing WARNING: atoms too close: (T0360)D51.N and (T0360)D51.OD2 only 0.000 apart, marking (T0360)D51.OD2 as missing WARNING: atoms too close: (T0360)Q50.C and (T0360)D51.OD2 only 0.000 apart, marking (T0360)D51.OD2 as missing WARNING: atoms too close: (T0360)D51.OD2 and (T0360)D51.O only 0.000 apart, marking (T0360)D51.O as missing WARNING: atoms too close: (T0360)D51.OD1 and (T0360)D51.O only 0.000 apart, marking (T0360)D51.O as missing WARNING: atoms too close: (T0360)D51.CG and (T0360)D51.O only 0.000 apart, marking (T0360)D51.O as missing WARNING: atoms too close: (T0360)D51.CB and (T0360)D51.O only 0.000 apart, marking (T0360)D51.O as missing WARNING: atoms too close: (T0360)D51.CA and (T0360)D51.O only 0.000 apart, marking (T0360)D51.O as missing WARNING: atoms too close: (T0360)D51.N and (T0360)D51.O only 0.000 apart, marking (T0360)D51.O as missing WARNING: atoms too close: (T0360)Q50.C and (T0360)D51.O only 0.000 apart, marking (T0360)D51.O as missing WARNING: atoms too close: (T0360)D51.O and (T0360)D51.C only 0.000 apart, marking (T0360)D51.C as missing WARNING: atoms too close: (T0360)D51.OD2 and (T0360)D51.C only 0.000 apart, marking (T0360)D51.C as missing WARNING: atoms too close: (T0360)D51.OD1 and (T0360)D51.C only 0.000 apart, marking (T0360)D51.C as missing WARNING: atoms too close: (T0360)D51.CG and (T0360)D51.C only 0.000 apart, marking (T0360)D51.C as missing WARNING: atoms too close: (T0360)D51.CB and (T0360)D51.C only 0.000 apart, marking (T0360)D51.C as missing WARNING: atoms too close: (T0360)D51.CA and (T0360)D51.C only 0.000 apart, marking (T0360)D51.C as missing WARNING: atoms too close: (T0360)D51.N and (T0360)D51.C only 0.000 apart, marking (T0360)D51.C as missing WARNING: atoms too close: (T0360)Q50.C and (T0360)D51.C only 0.000 apart, marking (T0360)D51.C as missing # WARNING: incomplete conformation T0360 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 T0360 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 T0360 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 T0360 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 T0360 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 T0360 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 T0360 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 T0360 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 132 # 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 T0360 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 T0360 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 T0360 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 T0360 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 129 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 34 # 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 98 # 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 128 # 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 129 # 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 109 # 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 T0360 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 T0360 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 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 270, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz # WARNING: incomplete conformation T0360 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 T0360 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 Skipped atom 55, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 68, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 # WARNING: incomplete conformation T0360 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 Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 270, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz # WARNING: incomplete conformation T0360 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 T0360 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 Skipped atom 55, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 68, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # 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 80 # 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 # 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 125 # 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 # Found a chain break before 24 # copying to AlignedFragments data structure # 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 84 # 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 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 75 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 T0360 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 139 # 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 125 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 55 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # 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 T0360 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 T0360 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 T0360 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 T0360 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 T0360 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 T0360 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 T0360 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 T0360 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 T0360 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 T0360 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 Skipped atom 75, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 88, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 137, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 255, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 317, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # 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 136 # 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 # 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 # 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 136 # 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 46 # 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 # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # 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 136 # 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 137 # 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 138 # 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 136 # 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 100 # 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 135 # 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 111 # 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 136 # 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 121 # 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 # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 T0360 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 T0360 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 T0360 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 T0360 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 T0360 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 # Found a chain break before 140 # 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 # Found a chain break before 140 # 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 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 140 # 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 T0360 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 T0360 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 21 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # 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 # Found a chain break before 55 # copying to AlignedFragments data structure # 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 106 # 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 42 # 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 42 # 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 42 # 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 134 # 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 136 # 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 # 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 18 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 21 # 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 56 # 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 58 # 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 35 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 T0360 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 # WARNING: incomplete conformation T0360 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 T0360 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 T0360 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 T0360 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 96 # 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 T0360 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 T0360 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 T0360 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 T0360 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 31 # 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 60 # 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 40 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 57 # copying to AlignedFragments data structure # 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 # Found a chain break before 36 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 26 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 T0360 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 39 # 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 110 # 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 130 # 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 126 # 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 109 # 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 140 # 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 T0360 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 T0360 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 T0360 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 T0360 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 T0360 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # 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 93 # 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 # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # 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 138 # 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 138 # 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 138 # 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 138 # 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 138 # 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 T0360 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 T0360 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 T0360 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 # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # 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 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 T0360 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 T0360 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0360 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 T0360 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 T0360 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 T0360 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 T0360 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 1.3778 model score 2.1181 model score 2.4539 model score 2.4708 model score 1.4409 model score 1.4120 model score 1.4488 model score 1.5062 model score 1.4099 model score 1.4411 model score 1.4899 model score 1.4714 model score 1.2696 model score 2.5000 model score 1.5843 model score 1.2564 model score 1.6542 model score 1.6452 model score 1.6114 model score 1.3258 model score 1.3258 model score 1.5054 model score 1.5094 model score 1.6643 model score 1.4266 model score 0.2502 model score 0.1393 model score 0.1759 model score 0.1831 model score 0.1735 model score 0.1787 model score 0.6273 model score 0.1425 model score 1.1723 model score 1.7476 model score 1.8553 model score 1.8388 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.1735 model score 0.1760 model score 0.6315 model score 0.5264 model score 0.4548 model score 0.1813 model score 0.1735 model score 0.6273 model score 0.1760 model score 0.1759 model score 0.8792 model score 1.7941 model score 1.7415 model score 1.8561 model score 1.8664 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 1.8696 model score 2.2285 model score 1.7173 model score 2.2620 model score 1.8668 model score 0.1575 model score 0.7727 model score 1.9234 model score 1.6831 model score 1.2653 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.1855 model score 1.9507 model score 2.0664 model score 2.9044 model score 1.5393 model score 0.2534 model score 0.1554 model score 0.3900 model score 1.1805 model score 0.2534 model score 0.2560 model score 0.2560 model score 0.2560 model score 1.4346 model score 1.2532 model score 1.2682 model score 1.9062 model score 1.3977 model score 0.5714 model score 1.5395 model score 1.9705 model score 0.8917 model score 1.8257 model score 1.2771 model score 0.1797 model score 0.1801 model score 1.8597 model score 2.4318 model score 2.6939 model score 0.1801 model score 0.2810 model score 1.8909 model score 2.4195 model score 2.6939 model score 0.1731 model score 0.4958 model score 0.9952 model score 0.5506 model score 0.3475 model score 1.6066 model score 2.1801 model score 2.1063 model score 2.1776 model score 1.8457 model score 2.2971 model score 0.1866 model score 0.1865 model score 0.1863 model score 0.1859 model score 0.1864 model score 0.1866 model score 0.1866 model score 0.1778 model score 1.2106 model score 0.1741 model score 0.1910 model score 0.2302 model score 0.2051 model score 0.2302 model score 0.1865 model score 0.1969 model score 0.2067 model score 0.1673 model score 0.1673 model score 0.2067 model score 0.2419 model score 0.1865 model score 0.2619 model score 0.2051 model score 0.2302 model score 0.2302 model score 0.1641 model score 0.1988 model score 0.4202 model score 1.6066 model score 0.3455 model score 0.2161 model score 0.1965 model score 0.2161 model score 0.4016 model score 0.8193 model score 0.1868 model score 0.1754 model score 0.1868 model score 0.3625 model score 0.2619 model score 0.1386 model score 0.5807 model score 0.6807 model score 0.2749 model score 0.3959 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 0.4352 model score 0.1414 model score 1.8766 model score 0.5883 model score 0.4104 model score 1.6066 model score 2.1751 model score 1.6441 model score 1.9337 model score 2.2132 model score 1.6066 model score 1.7214 model score 2.1338 model score 0.5520 model score 1.2712 model score 1.6269 model score 1.7139 model score 1.6887 model score 1.7982 model score 2.1144 model score 1.2771 model score 0.1455 model score 1.2771 model score 0.1835 model score 0.2161 model score 0.1880 model score 0.1709 model score 0.1585 model score 0.2595 model score 0.3042 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.3298 model score 0.4562 model score 1.4621 model score 2.0543 model score 1.8118 model score 2.1555 model score 1.7760 model score 2.2361 model score 1.4503 model score 2.2067 model score 0.1766 model score 0.9731 model score 1.5358 model score 1.8420 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USE_META, weight: 0.3175 cost: 2.2361 min: 0.1386 max: 2.9044 USE_META, weight: 0.5732 cost: 1.4503 min: 0.1386 max: 2.9044 USE_META, weight: 0.3270 cost: 2.2067 min: 0.1386 max: 2.9044 USE_META, weight: 0.9876 cost: 0.1766 min: 0.1386 max: 2.9044 USE_META, weight: 0.7284 cost: 0.9731 min: 0.1386 max: 2.9044 USE_META, weight: 0.5454 cost: 1.5358 min: 0.1386 max: 2.9044 USE_META, weight: 0.4457 cost: 1.8420 min: 0.1386 max: 2.9044 USE_META, weight: 0.5041 cost: 1.6625 min: 0.1386 max: 2.9044 USE_META, weight: 0.9836 cost: 0.1891 min: 0.1386 max: 2.9044 USE_META, weight: 0.9804 cost: 0.1989 min: 0.1386 max: 2.9044 USE_META, weight: 0.9759 cost: 0.2126 min: 0.1386 max: 2.9044 USE_META, weight: 0.6198 cost: 1.3069 min: 0.1386 max: 2.9044 USE_META, weight: 0.3692 cost: 2.0770 min: 0.1386 max: 2.9044 USE_META, weight: 0.9854 cost: 0.1834 min: 0.1386 max: 2.9044 USE_META, weight: 0.9620 cost: 0.2554 min: 0.1386 max: 2.9044 USE_META, weight: 0.2787 cost: 2.3551 min: 0.1386 max: 2.9044 USE_META, weight: 0.4348 cost: 1.8754 min: 0.1386 max: 2.9044 USE_META, weight: 0.4159 cost: 1.9336 min: 0.1386 max: 2.9044 USE_META, weight: 0.4165 cost: 1.9318 min: 0.1386 max: 2.9044 USE_META, weight: 0.8076 cost: 0.7299 min: 0.1386 max: 2.9044 USE_META, weight: 0.9423 cost: 0.3160 min: 0.1386 max: 2.9044 USE_EVALUE, weight: 0.4303 eval: 7.9961 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.4303 eval: 7.9961 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.4303 eval: 7.9961 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.3470 eval: 9.1666 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.3470 eval: 9.1666 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.3470 eval: 9.1666 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1043 eval: 12.5720 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1043 eval: 12.5720 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1043 eval: 12.5720 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.6475 eval: 4.9483 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.6475 eval: 4.9483 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.6475 eval: 4.9483 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.4054 eval: 8.3465 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.4054 eval: 8.3465 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.4054 eval: 8.3465 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.2163 eval: 11.0000 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.2163 eval: 11.0000 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.8951 eval: 1.4724 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.8951 eval: 1.4724 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.8951 eval: 1.4724 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.2389 eval: 10.6840 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.2389 eval: 10.6840 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.2389 eval: 10.6840 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.4516 eval: 7.6979 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.4516 eval: 7.6979 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.4516 eval: 7.6979 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1724 eval: 11.6170 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1724 eval: 11.6170 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1724 eval: 11.6170 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.9043 eval: 1.3428 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.9043 eval: 1.3428 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.9043 eval: 1.3428 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.4430 eval: 7.8188 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.4430 eval: 7.8188 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.4430 eval: 7.8188 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.6931 eval: 4.3080 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.6931 eval: 4.3080 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.6931 eval: 4.3080 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.3791 eval: 8.7149 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.3791 eval: 8.7149 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.3791 eval: 8.7149 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1995 eval: 11.2370 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1995 eval: 11.2370 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1995 eval: 11.2370 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1000 eval: 12.6330 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1000 eval: 12.6330 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1000 eval: 12.6330 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.8366 eval: 2.2935 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.8366 eval: 2.2935 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.8366 eval: 2.2935 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.6266 eval: 5.2417 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.6266 eval: 5.2417 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.6266 eval: 5.2417 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1114 eval: 12.4730 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1114 eval: 12.4730 min: 0.0000 max: 12.6330 USE_EVALUE, weight: 0.1114 eval: 12.4730 min: 0.0000 max: 12.6330 Number of contacts in models: 241 Number of contacts in alignments: 59 NUMB_ALIGNS: 59 Adding 6317 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: -204.2495, CN propb: -204.2495 weights: 0.3671 constraints: 197 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 197 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 197 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 6120 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 6120 # 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 6317 # command: