# 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:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 59 Adding 984 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -217.9095, CN propb: -217.9095 weights: 0.1910 constraints: 195 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 195 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 195 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 789 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 789 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 984 # command: