parameters: 0.6 1.3 0.5 200 50 # 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/T0369/ # command:# Making conformation for sequence T0369 numbered 1 through 148 Created new target T0369 from T0369.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0369/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0369//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0369/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0369//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0369/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0369/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0369/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o5zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o5zA expands to /projects/compbio/data/pdb/1o5z.pdb.gz 1o5zA:# T0369 read from 1o5zA/merged-good-all-a2m # 1o5zA read from 1o5zA/merged-good-all-a2m # adding 1o5zA to template set # found chain 1o5zA in template set T0369 5 :QQALDRHVGVGVRTTRDLIR 1o5zA 93 :EEDVVKIYETMEPILNELDK # choosing archetypes in rotamer library T0369 36 :ISGKRSVYEVAVHLAVLLEA 1o5zA 114 :EIFSPSFFEVVTAMAFLYFA T0369 61 :TGAT 1o5zA 135 :KNVD T0369 80 :QLVDRLDQSWQYYQ 1o5zA 203 :EALKVMEDVARKKS T0369 103 :ETTYWG 1o5zA 218 :RMYVID T0369 122 :VHLYHHRSQLLDYLNLLGYDIK 1o5zA 258 :PHQIENAGVALKTLEATGLPLS Number of specific fragments extracted= 6 number of extra gaps= 0 total=6 Number of alignments=1 # 1o5zA read from 1o5zA/merged-good-all-a2m # found chain 1o5zA in template set Warning: unaligning (T0369)A63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o5zA)Y176 T0369 5 :QQALDRHVGVGVRTTRDL 1o5zA 93 :EEDVVKIYETMEPILNEL T0369 24 :R 1o5zA 112 :K T0369 35 :PISGKRSVYEVAVHLAV 1o5zA 113 :EEIFSPSFFEVVTAMAF T0369 54 :EADLRI 1o5zA 130 :LYFAEK T0369 64 :TADEMAQF 1o5zA 177 :TIEQIAWE T0369 73 :AVP 1o5zA 191 :ERV T0369 77 :LPEQLVDRLDQSWQYYQ 1o5zA 200 :RKREALKVMEDVARKKS T0369 97 :MADF 1o5zA 223 :DKDF T0369 101 :STETTYWGVTDS 1o5zA 245 :ENTFEDLVLTMN T0369 122 :VHLYHHRSQLLDYLNLLGYDIK 1o5zA 258 :PHQIENAGVALKTLEATGLPLS Number of specific fragments extracted= 10 number of extra gaps= 0 total=16 Number of alignments=2 # 1o5zA read from 1o5zA/merged-good-all-a2m # found chain 1o5zA in template set Warning: unaligning (T0369)H11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o5zA)V19 T0369 2 :TDWQQALDR 1o5zA 4 :LEVLRYLYH T0369 16 :VRTTRDLIRLIQPEDWDKRP 1o5zA 23 :LERISMLLSKLGNPHLEYKT T0369 39 :KRSVYEVAVHLAVLLEAD 1o5zA 48 :TNGKGSVANMVSNILVSQ T0369 65 :ADEMAQF 1o5zA 74 :SPHLSTF T0369 82 :VDRLDQSWQYYQDRLMADFSTET 1o5zA 93 :EEDVVKIYETMEPILNELDKEEI T0369 109 :VTDSTTGWLLE 1o5zA 116 :FSPSFFEVVTA T0369 130 :QLLDYLNLLGYD 1o5zA 127 :MAFLYFAEKNVD Number of specific fragments extracted= 7 number of extra gaps= 0 total=23 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rxqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0369 read from 1rxqA/merged-good-all-a2m # 1rxqA read from 1rxqA/merged-good-all-a2m # found chain 1rxqA in training set Warning: unaligning (T0369)D141 because last residue in template chain is (1rxqA)S178 T0369 3 :DWQQALDRHVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRIAT 1rxqA 22 :EQKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIRFK T0369 68 :MAQFYAVPV 1rxqA 84 :TEETPAIRP T0369 77 :LPE 1rxqA 94 :DEK T0369 80 :QLVDRLDQSWQYYQDRLMADFSTETTYWGVTD 1rxqA 115 :LLQELHGRWTALLRTLTDQQFKRGFYHPDTKE T0369 112 :STTGWLLEAAVHLYHHRSQLLDYLNLLGY 1rxqA 149 :TLENALGLYVWHSHHHIAHITELSRRMGW Number of specific fragments extracted= 5 number of extra gaps= 0 total=28 Number of alignments=4 # 1rxqA read from 1rxqA/merged-good-all-a2m # found chain 1rxqA in training set Warning: unaligning (T0369)D141 because last residue in template chain is (1rxqA)S178 T0369 4 :WQQALDRHVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRI 1rxqA 23 :QKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIR T0369 60 :ATGATADEMA 1rxqA 90 :IRPYDEKAWS T0369 70 :QFYAVPVLPEQLVDRLDQSWQYYQDRLMADFSTETTYWGVTD 1rxqA 105 :KTADPSGSLALLQELHGRWTALLRTLTDQQFKRGFYHPDTKE T0369 112 :STTGWLLEAAVHLYHHRSQLLDYLNLLGY 1rxqA 149 :TLENALGLYVWHSHHHIAHITELSRRMGW Number of specific fragments extracted= 4 number of extra gaps= 0 total=32 Number of alignments=5 # 1rxqA read from 1rxqA/merged-good-all-a2m # found chain 1rxqA in training set Warning: unaligning (T0369)D141 because last residue in template chain is (1rxqA)S178 T0369 2 :TDWQQALDRHVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRIATGATADEMAQF 1rxqA 21 :KEQKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIRFKLSLTEETPAI T0369 73 :AVPVLPEQLVDRLDQSWQYYQDRLMADFSTE 1rxqA 108 :DPSGSLALLQELHGRWTALLRTLTDQQFKRG T0369 104 :TTYWGVTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGY 1rxqA 141 :HPDTKEIITLENALGLYVWHSHHHIAHITELSRRMGW Number of specific fragments extracted= 3 number of extra gaps= 0 total=35 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ovlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ovlA expands to /projects/compbio/data/pdb/1ovl.pdb.gz 1ovlA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0369 read from 1ovlA/merged-good-all-a2m # 1ovlA read from 1ovlA/merged-good-all-a2m # adding 1ovlA to template set # found chain 1ovlA in template set T0369 3 :DWQQALDRHVGVGVRTTRDLIRLI 1ovlA 401 :QHIQQFYDLLTGSMEIIRGWAEKI T0369 27 :QPEDWD 1ovlA 431 :PKADQD T0369 41 :SVYEVAVHLAVLLEA 1ovlA 437 :LLFESAFLELFVLRL T0369 56 :DLRIATGATADEMA 1ovlA 489 :FSSNLQNMNIDISA T0369 71 :FYAVPV 1ovlA 512 :VTERHG T0369 77 :LPEQL 1ovlA 520 :EPKRV T0369 86 :DQSWQYYQDRLMADFSTETTYWGVTDSTTGW 1ovlA 525 :EELQNKIVNCLKDHVTFNNGGLNRPNYLSKL T0369 117 :LLEAAVHLY 1ovlA 562 :LRTLCTQGL T0369 130 :QLLDYLNLLG 1ovlA 571 :QRIFYLKLED T0369 140 :YDIK 1ovlA 582 :VPPP Number of specific fragments extracted= 10 number of extra gaps= 0 total=45 Number of alignments=7 # 1ovlA read from 1ovlA/merged-good-all-a2m # found chain 1ovlA in template set T0369 3 :DWQQALDRHVGVGVRTTRDLIRL 1ovlA 401 :QHIQQFYDLLTGSMEIIRGWAEK T0369 26 :IQPEDWD 1ovlA 430 :LPKADQD T0369 41 :SVYEVAVHLAVLLEADLRI 1ovlA 437 :LLFESAFLELFVLRLAYRS T0369 60 :ATGATADEMA 1ovlA 493 :LQNMNIDISA T0369 70 :QFYAVPVLPEQLVDRLDQSWQYYQDRLM 1ovlA 513 :TERHGLKEPKRVEELQNKIVNCLKDHVT T0369 98 :ADFST 1ovlA 542 :NNGGL T0369 108 :GVTD 1ovlA 547 :NRPN T0369 112 :STTGWLLEAAVHLYH 1ovlA 557 :GKLPELRTLCTQGLQ T0369 130 :QLLDYLNLLGYDIK 1ovlA 572 :RIFYLKLEDLVPPP Number of specific fragments extracted= 9 number of extra gaps= 0 total=54 Number of alignments=8 # 1ovlA read from 1ovlA/merged-good-all-a2m # found chain 1ovlA in template set T0369 2 :TDWQQALDRHVGVGVRTTRDLIRLIQP 1ovlA 400 :TQHIQQFYDLLTGSMEIIRGWAEKIPG T0369 31 :WDKRPISGKRSVYEVAVHLAVLLEADL 1ovlA 427 :FADLPKADQDLLFESAFLELFVLRLAY T0369 73 :AVPVLPEQLVDRLDQSWQYYQDRLMADF 1ovlA 516 :HGLKEPKRVEELQNKIVNCLKDHVTFNN T0369 105 :TYWGVTDSTTGWLL 1ovlA 544 :GGLNRPNYLSKLLG T0369 119 :EAAVHLYHHRSQLLDYLNLLGYDIK 1ovlA 561 :ELRTLCTQGLQRIFYLKLEDLVPPP Number of specific fragments extracted= 5 number of extra gaps= 0 total=59 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ezfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ezfA expands to /projects/compbio/data/pdb/1ezf.pdb.gz 1ezfA:# T0369 read from 1ezfA/merged-good-all-a2m # 1ezfA read from 1ezfA/merged-good-all-a2m # adding 1ezfA to template set # found chain 1ezfA in template set Warning: unaligning (T0369)D3 because first residue in template chain is (1ezfA)N38 T0369 4 :WQQALDRHVGVG 1ezfA 39 :SLKTCYKYLNQT T0369 19 :TRDLIRLIQ 1ezfA 54 :FAAVIQALD T0369 37 :SG 1ezfA 63 :GE T0369 42 :VYEVAVHLAVLLEADLRIAT 1ezfA 65 :MRNAVCIFYLVLRALDTLED T0369 62 :GATA 1ezfA 87 :TISV T0369 66 :DEMAQFYAVPVLPE 1ezfA 95 :PLLHNFHSFLYQPD T0369 80 :QLVDRLDQSWQYYQDRLMADFSTETTYWG 1ezfA 138 :KYQTVIADICRRMGIGMAEFLDKHVTSEQ T0369 109 :VTD 1ezfA 248 :KPE T0369 112 :STTGWLLEAAVHLYHHRSQLLDYLNL 1ezfA 254 :LAVQCLNELITNALHHIPDVITYLSR Number of specific fragments extracted= 9 number of extra gaps= 0 total=68 Number of alignments=10 # 1ezfA read from 1ezfA/merged-good-all-a2m # found chain 1ezfA in template set T0369 3 :DWQQALDRHVGVGVRTTRDLIRL 1ezfA 138 :KYQTVIADICRRMGIGMAEFLDK T0369 26 :IQ 1ezfA 162 :VT T0369 28 :PEDWD 1ezfA 165 :EQEWD T0369 40 :RSVYEVAVHLAVLLEADLRIATGATADEMA 1ezfA 170 :KYCHYVAGLVGIGLSRLFSASEFEDPLVGE T0369 77 :LPEQL 1ezfA 200 :DTERA T0369 83 :DRLDQSWQYYQD 1ezfA 215 :NIIRDYLEDQQG T0369 95 :RLMADFSTETTYWG 1ezfA 231 :WPQEVWSRYVKKLG T0369 109 :VTD 1ezfA 248 :KPE T0369 112 :ST 1ezfA 253 :DL T0369 114 :TGWLLEAAVHLYHHRSQLLDYLN 1ezfA 256 :VQCLNELITNALHHIPDVITYLS Number of specific fragments extracted= 10 number of extra gaps= 0 total=78 Number of alignments=11 # 1ezfA read from 1ezfA/merged-good-all-a2m # found chain 1ezfA in template set T0369 2 :TDWQQALDRHVGVGVRTTRDLIRL 1ezfA 137 :EKYQTVIADICRRMGIGMAEFLDK T0369 35 :PISGKRSVYEVAVHLAVLLEADL 1ezfA 161 :HVTSEQEWDKYCHYVAGLVGIGL T0369 58 :RIAT 1ezfA 185 :RLFS T0369 68 :MAQFYAVP 1ezfA 189 :ASEFEDPL T0369 76 :VLPEQLV 1ezfA 199 :EDTERAN T0369 83 :DRLDQSWQYYQ 1ezfA 215 :NIIRDYLEDQQ T0369 101 :STE 1ezfA 226 :GGR T0369 106 :YWGVTDSTTGWLLEAAVHLYHHRSQLLDYLNLL 1ezfA 248 :KPENIDLAVQCLNELITNALHHIPDVITYLSRL Number of specific fragments extracted= 8 number of extra gaps= 0 total=86 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f22A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f22A expands to /projects/compbio/data/pdb/2f22.pdb.gz 2f22A:Skipped atom 2, because occupancy 0.5 <= existing 0.500 in 2f22A Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 11, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 15, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 19, because occupancy 0.350 <= existing 0.400 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 21, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 102, because occupancy 0.330 <= existing 0.340 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 107, because occupancy 0.330 <= existing 0.340 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 110, because occupancy 0.330 <= existing 0.340 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 112, because occupancy 0.250 <= existing 0.250 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 113, because occupancy 0.250 <= existing 0.250 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 116, because occupancy 0.330 <= existing 0.340 in 2f22A Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 180, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 487, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 491, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 493, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 495, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 634, because occupancy 0.400 <= existing 0.600 in 2f22A Skipped atom 638, because occupancy 0.400 <= existing 0.600 in 2f22A Skipped atom 640, because occupancy 0.400 <= existing 0.600 in 2f22A Skipped atom 642, because occupancy 0.400 <= existing 0.600 in 2f22A Skipped atom 644, because occupancy 0.400 <= existing 0.600 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 864, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 866, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1083, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1149, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1155, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1157, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1159, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1161, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 2f22A # T0369 read from 2f22A/merged-good-all-a2m # 2f22A read from 2f22A/merged-good-all-a2m # adding 2f22A to template set # found chain 2f22A in template set T0369 12 :VGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRIATGATADEMAQFYAVPVLP 2f22A 6 :VLYAANMTNALAKEIPESKWDIQLIPELGTLRKLFIHIVRVRDVYRDGLKTGSIKFPGRLASDEHRL T0369 82 :VDRLDQSWQYYQDRLMA 2f22A 73 :LDELERSMEELVFEFKQ T0369 106 :YWG 2f22A 91 :TFN T0369 109 :VTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGYDIK 2f22A 100 :NYLSIMELLGTVIQHEGIHQGQYYVALKQSGINLP Number of specific fragments extracted= 4 number of extra gaps= 0 total=90 Number of alignments=13 # 2f22A read from 2f22A/merged-good-all-a2m # found chain 2f22A in template set T0369 12 :VGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRIATGATADEMA 2f22A 6 :VLYAANMTNALAKEIPESKWDIQLIPELGTLRKLFIHIVRVRDVYRDGLKTGSIKFPG T0369 70 :QFYAVPVLPEQLVDRLDQSWQYYQDRL 2f22A 65 :LASDEHRLLDELERSMEELVFEFKQTT T0369 101 :STETTYWGVTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGYDIK 2f22A 92 :FNSIKMGENYLSIMELLGTVIQHEGIHQGQYYVALKQSGINLP Number of specific fragments extracted= 3 number of extra gaps= 0 total=93 Number of alignments=14 # 2f22A read from 2f22A/merged-good-all-a2m # found chain 2f22A in template set T0369 11 :HVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRIATGATADEMAQFY 2f22A 5 :GVLYAANMTNALAKEIPESKWDIQLIPELGTLRKLFIHIVRVRDVYRDGLKTGSIKFPGRLA T0369 73 :AVPVLPEQLVDRLDQSWQYYQD 2f22A 68 :DEHRLLDELERSMEELVFEFKQ T0369 101 :STE 2f22A 91 :TFN T0369 107 :WGVTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGYDI 2f22A 98 :GENYLSIMELLGTVIQHEGIHQGQYYVALKQSGINL Number of specific fragments extracted= 4 number of extra gaps= 0 total=97 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xrsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xrsA expands to /projects/compbio/data/pdb/1xrs.pdb.gz 1xrsA:# T0369 read from 1xrsA/merged-good-all-a2m # 1xrsA read from 1xrsA/merged-good-all-a2m # adding 1xrsA to template set # found chain 1xrsA in template set T0369 3 :DWQQALDRHVGVGVRTTRDLIR 1xrsA 10 :NLVEKARAKAKAIAIDTQEFIE T0369 34 :R 1xrsA 50 :G T0369 35 :PISGKRSVYEVAVHLA 1xrsA 52 :DTDEVPLPNIVVDHIK T0369 52 :LLEADLRIATG 1xrsA 76 :AAMYIANAVLN T0369 63 :ATADEMAQ 1xrsA 89 :KTPQEIAQ T0369 71 :FYAVPV 1xrsA 105 :LTKLPM T0369 77 :LPEQLVDRL 1xrsA 112 :DLFEVKTKA T0369 86 :DQSWQYYQ 1xrsA 125 :KETVEKIK T0369 94 :DRLMADFSTETTYWG 1xrsA 136 :SIRESRFEEYGDKSG T0369 109 :VTDSTTGWLLEAAV 1xrsA 158 :ATGNIYEDITQAVA Number of specific fragments extracted= 10 number of extra gaps= 0 total=107 Number of alignments=16 # 1xrsA read from 1xrsA/merged-good-all-a2m # found chain 1xrsA in template set T0369 3 :DWQQALDRHVGVGVRTTRDLIRL 1xrsA 10 :NLVEKARAKAKAIAIDTQEFIEK T0369 32 :DKRPISGKRSVYEVAVHL 1xrsA 49 :DGVDTDEVPLPNIVVDHI T0369 50 :AVLLEADLRIATGATADEMA 1xrsA 76 :AAMYIANAVLNTGKTPQEIA T0369 70 :QFYAVPV 1xrsA 106 :TKLPMKD T0369 77 :LPEQLVDRLDQSWQYYQ 1xrsA 116 :VKTKALSMAKETVEKIK T0369 94 :DRLMADFSTETTYWG 1xrsA 136 :SIRESRFEEYGDKSG T0369 109 :VTDSTTGWLLEA 1xrsA 158 :ATGNIYEDITQA T0369 132 :LDYLNL 1xrsA 170 :VAAAKQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=115 Number of alignments=17 # 1xrsA read from 1xrsA/merged-good-all-a2m # found chain 1xrsA in template set T0369 2 :TDWQQALDRHVGVGVRTTRDLIRL 1xrsA 9 :FNLVEKARAKAKAIAIDTQEFIEK T0369 33 :KRPISGKRSVYEVAVHLAV 1xrsA 50 :GVDTDEVPLPNIVVDHIKE T0369 52 :LLEADL 1xrsA 79 :YIANAV T0369 58 :RIATGATA 1xrsA 96 :QAISAGEL T0369 67 :EMAQFY 1xrsA 104 :DLTKLP T0369 73 :AVPVLPEQLVDRLDQSWQYYQDRL 1xrsA 112 :DLFEVKTKALSMAKETVEKIKNNR T0369 97 :MADFSTE 1xrsA 139 :ESRFEEY T0369 106 :YWGVTDSTTGWLLEAAVH 1xrsA 155 :VIVATGNIYEDITQAVAA Number of specific fragments extracted= 8 number of extra gaps= 0 total=123 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r2rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r2rA expands to /projects/compbio/data/pdb/1r2r.pdb.gz 1r2rA:Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 422, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 821, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 823, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 1231, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 1678, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 1680, because occupancy 0.500 <= existing 0.500 in 1r2rA # T0369 read from 1r2rA/merged-good-all-a2m # 1r2rA read from 1r2rA/merged-good-all-a2m # adding 1r2rA to template set # found chain 1r2rA in template set T0369 13 :G 1r2rA 141 :K T0369 52 :LLEADLRIATG 1r2rA 142 :VVFEQTKVIAD T0369 63 :ATADE 1r2rA 155 :KDWSK T0369 68 :MAQFYAVPVLPEQLVDRLDQSWQYYQDRLMADFSTETTYW 1r2rA 168 :WAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRII T0369 108 :G 1r2rA 209 :G Number of specific fragments extracted= 5 number of extra gaps= 0 total=128 Number of alignments=19 # 1r2rA read from 1r2rA/merged-good-all-a2m # found chain 1r2rA in template set T0369 5 :QQALDRHVGVGVR 1r2rA 106 :DELIGQKVAHALS T0369 29 :EDWDKRP 1r2rA 132 :DEREAGI T0369 42 :VYEVAV 1r2rA 139 :TEKVVF T0369 51 :VLLEADLRIA 1r2rA 145 :EQTKVIADNV T0369 63 :ATADE 1r2rA 155 :KDWSK T0369 68 :MAQFYAVPVLPEQLVDRLDQSWQYYQDRLMADFSTETTYW 1r2rA 168 :WAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRII T0369 108 :GVTDS 1r2rA 209 :GGSVT Number of specific fragments extracted= 7 number of extra gaps= 0 total=135 Number of alignments=20 # 1r2rA read from 1r2rA/merged-good-all-a2m # found chain 1r2rA in template set T0369 53 :LEADLRIATGATADEMAQF 1r2rA 139 :TEKVVFEQTKVIADNVKDW T0369 73 :AVPVLPEQLVDRLDQSWQYYQDRLMADFSTE 1r2rA 173 :GKTATPQQAQEVHEKLRGWLKSNVSDAVAQS Number of specific fragments extracted= 2 number of extra gaps= 0 total=137 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bh4X/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bh4X expands to /projects/compbio/data/pdb/2bh4.pdb.gz 2bh4X:Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 285, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 293, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 729, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 733, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 735, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 737, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 785, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 787, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 791, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2bh4X # T0369 read from 2bh4X/merged-good-all-a2m # 2bh4X read from 2bh4X/merged-good-all-a2m # adding 2bh4X to template set # found chain 2bh4X in template set Warning: unaligning (T0369)S101 because of BadResidue code BAD_PEPTIDE in next template residue (2bh4X)K97 Warning: unaligning (T0369)T102 because of BadResidue code BAD_PEPTIDE at template residue (2bh4X)K97 T0369 62 :GATA 2bh4X 52 :GFKY T0369 66 :DE 2bh4X 57 :DG T0369 68 :MAQFYAVPVLPEQLVDRLDQSWQYYQDRLMADF 2bh4X 63 :AEKNPDMVWSEADLIEYVTDPKPWLVEKTGDSA T0369 103 :ETTYWGVTDSTTGWLLEAAVH 2bh4X 98 :TKKTFKLGKNQADVVAFLAQH Number of specific fragments extracted= 4 number of extra gaps= 1 total=141 Number of alignments=22 # 2bh4X read from 2bh4X/merged-good-all-a2m # found chain 2bh4X in template set Warning: unaligning (T0369)T102 because of BadResidue code BAD_PEPTIDE in next template residue (2bh4X)K97 Warning: unaligning (T0369)E103 because of BadResidue code BAD_PEPTIDE at template residue (2bh4X)K97 T0369 60 :ATGATADEMA 2bh4X 50 :VEGFKYGDGI T0369 70 :QFYAVPVLPEQLVDRLDQSWQYYQDRLMAD 2bh4X 65 :KNPDMVWSEADLIEYVTDPKPWLVEKTGDS T0369 101 :S 2bh4X 95 :A T0369 104 :TTYW 2bh4X 98 :TKKT T0369 108 :GVTDSTTGWLLEAAVH 2bh4X 103 :KLGKNQADVVAFLAQH Number of specific fragments extracted= 5 number of extra gaps= 1 total=146 Number of alignments=23 # 2bh4X read from 2bh4X/merged-good-all-a2m # found chain 2bh4X in template set T0369 17 :RTTRDLIRL 2bh4X 57 :DGILEVAEK T0369 35 :PISGKRSVYEVAVHLA 2bh4X 66 :NPDMVWSEADLIEYVT T0369 76 :VLPEQLVDR 2bh4X 82 :DPKPWLVEK T0369 100 :FSTE 2bh4X 91 :TGDS T0369 104 :TTYWGVTDSTTGWLLEAAVH 2bh4X 99 :KKTFKLGKNQADVVAFLAQH Number of specific fragments extracted= 5 number of extra gaps= 0 total=151 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8qB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y8qB expands to /projects/compbio/data/pdb/1y8q.pdb.gz 1y8qB:# T0369 read from 1y8qB/merged-good-all-a2m # 1y8qB read from 1y8qB/merged-good-all-a2m # adding 1y8qB to template set # found chain 1y8qB in template set Warning: unaligning (T0369)H48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1y8qB)L305 Warning: unaligning (T0369)A63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1y8qB)L305 T0369 3 :DWQQALDRHVGVGVRT 1y8qB 250 :DPVKLFTKLFKDDIRY T0369 23 :IRLI 1y8qB 266 :LLTM T0369 29 :EDWDKRPIS 1y8qB 270 :DKLWRKRKP T0369 38 :GKRSVYEVAV 1y8qB 280 :VPLDWAEVQS T0369 64 :TADEM 1y8qB 306 :GLKDQ T0369 74 :VPVLPEQLVDRLDQSWQYYQDRLMADFSTETTYWGVTD 1y8qB 311 :QVLDVKSYARLFSKSIETLRVHLAEKGDGAELIWDKDD T0369 112 :STTGWLLEAAV 1y8qB 350 :SAMDFVTSAAN T0369 133 :DYLNLLGYDIK 1y8qB 361 :LRMHIFSMNMK Number of specific fragments extracted= 8 number of extra gaps= 0 total=159 Number of alignments=25 # 1y8qB read from 1y8qB/merged-good-all-a2m # found chain 1y8qB in template set T0369 3 :DWQQALDRHVGVGVRTT 1y8qB 250 :DPVKLFTKLFKDDIRYL T0369 24 :RLI 1y8qB 267 :LTM T0369 29 :EDWDKRPISGKR 1y8qB 270 :DKLWRKRKPPVP T0369 63 :ATADEMA 1y8qB 282 :LDWAEVQ T0369 77 :LPEQLVDRLDQSWQYYQDRLMADFST 1y8qB 314 :DVKSYARLFSKSIETLRVHLAEKGDG T0369 103 :ETTYWGVTDSTTGWLLEAA 1y8qB 341 :ELIWDKDDPSAMDFVTSAA T0369 132 :LDYLNLLGYDIK 1y8qB 360 :NLRMHIFSMNMK Number of specific fragments extracted= 7 number of extra gaps= 0 total=166 Number of alignments=26 # 1y8qB read from 1y8qB/merged-good-all-a2m # found chain 1y8qB in template set Warning: unaligning (T0369)H48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1y8qB)L305 Warning: unaligning (T0369)A63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1y8qB)L305 T0369 5 :QQALDRHVGVGVRTT 1y8qB 252 :VKLFTKLFKDDIRYL T0369 24 :RLI 1y8qB 267 :LTM T0369 29 :EDW 1y8qB 270 :DKL T0369 32 :DKRPIS 1y8qB 275 :KRKPPV T0369 39 :KRSVYEVAV 1y8qB 281 :PLDWAEVQS T0369 64 :TADE 1y8qB 306 :GLKD T0369 73 :AVPVLPEQLVDRLDQSWQYYQDRLMADFSTE 1y8qB 310 :QQVLDVKSYARLFSKSIETLRVHLAEKGDGA T0369 104 :TTYWGVTDSTTGWLLEAA 1y8qB 342 :LIWDKDDPSAMDFVTSAA T0369 132 :LDYLNLLGYDI 1y8qB 360 :NLRMHIFSMNM Number of specific fragments extracted= 9 number of extra gaps= 0 total=175 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ufoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0369 read from 1ufoA/merged-good-all-a2m # 1ufoA read from 1ufoA/merged-good-all-a2m # found chain 1ufoA in training set T0369 4 :WQQALDRHVGVGVRTTRDLIRLIQ 1ufoA 81 :VYRVALGFKEEARRVAEEAERRFG T0369 41 :S 1ufoA 113 :S T0369 50 :AVLLEADLRIATGATA 1ufoA 114 :LGAFVAHLLLAEGFRP T0369 73 :AVPVLPE 1ufoA 140 :FPMKLPQ T0369 82 :VDRLDQSWQYYQ 1ufoA 188 :LARMEKTLEALR T0369 98 :ADFSTE 1ufoA 200 :PHYPEG T0369 109 :VTDS 1ufoA 217 :HTLT T0369 113 :TTGWLLEAAVHLY 1ufoA 223 :MARVGLAFLEHWL Number of specific fragments extracted= 8 number of extra gaps= 0 total=183 Number of alignments=28 # 1ufoA read from 1ufoA/merged-good-all-a2m # found chain 1ufoA in training set T0369 4 :WQQALDRHVGVGVRTTRDLIRLIQ 1ufoA 81 :VYRVALGFKEEARRVAEEAERRFG T0369 40 :RSVYEVAVHLAV 1ufoA 112 :GSLGAFVAHLLL T0369 60 :ATGATADE 1ufoA 124 :AEGFRPRG T0369 70 :QFYAVPV 1ufoA 140 :FPMKLPQ T0369 77 :LPEQL 1ufoA 166 :RGEAY T0369 82 :VDRLDQSWQYYQDRLMAD 1ufoA 188 :LARMEKTLEALRPHYPEG T0369 103 :ETTYW 1ufoA 206 :RLARF T0369 108 :GVTDST 1ufoA 216 :GHTLTP T0369 114 :TGWLLEAAVHLY 1ufoA 224 :ARVGLAFLEHWL Number of specific fragments extracted= 9 number of extra gaps= 0 total=192 Number of alignments=29 # 1ufoA read from 1ufoA/merged-good-all-a2m # found chain 1ufoA in training set T0369 2 :TDWQQALDRHVGVGVRTTRDLIRLIQ 1ufoA 79 :EEVYRVALGFKEEARRVAEEAERRFG T0369 40 :RSVYEVAVHLAV 1ufoA 112 :GSLGAFVAHLLL T0369 58 :RIATGATADEMAQFY 1ufoA 160 :QAPPATRGEAYGGVP T0369 78 :PEQL 1ufoA 188 :LARM T0369 90 :QYYQDRLMADFSTE 1ufoA 192 :EKTLEALRPHYPEG T0369 104 :TTYWGVTDSTTGWLLEAAVHLYH 1ufoA 214 :GAGHTLTPLMARVGLAFLEHWLE Number of specific fragments extracted= 6 number of extra gaps= 0 total=198 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vi0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0369 read from 1vi0A/merged-good-all-a2m # 1vi0A read from 1vi0A/merged-good-all-a2m # found chain 1vi0A in training set Warning: unaligning (T0369)L96 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1vi0A)D131 Warning: unaligning (T0369)M97 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1vi0A)D131 T0369 3 :DWQQALDRHVGVGVRTTRDLIR 1vi0A 49 :NKEDILISLFKEKMGQFIERME T0369 29 :EDWD 1vi0A 71 :EDIK T0369 38 :GKRSVYEVAV 1vi0A 75 :EKATAKEKLA T0369 51 :VLLEADLRIATGATA 1vi0A 85 :LVISKHFSLLAGDHN T0369 67 :E 1vi0A 102 :I T0369 68 :MAQFYAVPV 1vi0A 104 :TQLELRQSN T0369 79 :EQLVDRLDQSWQYYQDR 1vi0A 113 :LELRQKINEILKGYLNI T0369 98 :ADFSTE 1vi0A 132 :GILTEG T0369 104 :TTYWGVTDSTTGWLLEAAVHLYH 1vi0A 140 :SGEIKEGLDVRLARQMIFGTIDE T0369 130 :QL 1vi0A 163 :TV T0369 133 :DYLNLLGYDIK 1vi0A 165 :TTWVMNDQKYD T0369 144 :LDL 1vi0A 177 :VAL Number of specific fragments extracted= 12 number of extra gaps= 1 total=210 Number of alignments=31 # 1vi0A read from 1vi0A/merged-good-all-a2m # found chain 1vi0A in training set Warning: unaligning (T0369)Y92 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1vi0A)D131 Warning: unaligning (T0369)Q93 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1vi0A)D131 T0369 2 :TDWQQALDRHVGVGVRTTRDLIRL 1vi0A 48 :KNKEDILISLFKEKMGQFIERMEE T0369 31 :WD 1vi0A 73 :IK T0369 38 :GKRSVYEVAV 1vi0A 75 :EKATAKEKLA T0369 51 :VLLEADLRIATGATA 1vi0A 85 :LVISKHFSLLAGDHN T0369 67 :EMA 1vi0A 100 :LAI T0369 70 :QFYAVPV 1vi0A 106 :LELRQSN T0369 77 :LPEQLVDRLDQSWQY 1vi0A 115 :LRQKINEILKGYLNI T0369 94 :DRLMADF 1vi0A 132 :GILTEGI T0369 101 :STETT 1vi0A 140 :SGEIK T0369 108 :GVTDST 1vi0A 146 :GLDVRL T0369 114 :TGWLLEAAV 1vi0A 153 :RQMIFGTID T0369 129 :SQLLDY 1vi0A 162 :ETVTTW T0369 136 :NLLGYDIK 1vi0A 168 :VMNDQKYD T0369 144 :LDL 1vi0A 177 :VAL Number of specific fragments extracted= 14 number of extra gaps= 1 total=224 Number of alignments=32 # 1vi0A read from 1vi0A/merged-good-all-a2m # found chain 1vi0A in training set Warning: unaligning (T0369)Y92 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1vi0A)D131 Warning: unaligning (T0369)Q93 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1vi0A)D131 T0369 6 :QALDRHVGVGVRTTRDLIRL 1vi0A 52 :DILISLFKEKMGQFIERMEE T0369 36 :ISGKRSVYEVAVHLAVLLEADL 1vi0A 73 :IKEKATAKEKLALVISKHFSLL T0369 73 :AVPVLPEQLVDRLDQSWQY 1vi0A 111 :SNLELRQKINEILKGYLNI T0369 94 :DRLMADFSTE 1vi0A 132 :GILTEGIQSG T0369 104 :TTYWGVTDSTTGWLLEAAVHLY 1vi0A 144 :KEGLDVRLARQMIFGTIDETVT T0369 134 :YLNLLGYDIKL 1vi0A 166 :TWVMNDQKYDL Number of specific fragments extracted= 6 number of extra gaps= 1 total=230 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1io7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0369 read from 1io7A/merged-good-all-a2m # 1io7A read from 1io7A/merged-good-all-a2m # found chain 1io7A in training set T0369 5 :QQALDRHVGVGVRTTRDLIRLIQPED 1io7A 89 :PQKLQTLETFIRETTRSLLDSIDPRE T0369 41 :SVY 1io7A 116 :DIV T0369 47 :VHLA 1io7A 119 :KKLA T0369 51 :VLLEADLRIATGATADEMAQ 1io7A 124 :PLPIIVISKILGLPIEDKEK T0369 71 :FYAVPVLPEQLVDRLDQSWQYYQDRL 1io7A 154 :RLGKPGEIFELGKKYLELIGYVKDHL T0369 97 :MADFSTETTYWGVTDSTTGWLLEAA 1io7A 183 :TEVVSRVVNSNLSDIEKLGYIILLL T0369 122 :VHLYHHRSQLLDYLNLLGY 1io7A 212 :ETTTNLISNSVIDFTRFNL Number of specific fragments extracted= 7 number of extra gaps= 0 total=237 Number of alignments=34 # 1io7A read from 1io7A/merged-good-all-a2m # found chain 1io7A in training set T0369 6 :QALDRHVGVGVRTTRDLIRLIQPE 1io7A 90 :QKLQTLETFIRETTRSLLDSIDPR T0369 39 :KRSVYE 1io7A 114 :EDDIVK T0369 51 :VLLEADLRIATGATADEMA 1io7A 124 :PLPIIVISKILGLPIEDKE T0369 70 :QFYAVPVLPEQLVDRLDQSWQYYQDRLMA 1io7A 153 :FRLGKPGEIFELGKKYLELIGYVKDHLNS T0369 107 :W 1io7A 183 :T T0369 108 :GVTD 1io7A 191 :NSNL T0369 112 :STTGWLLEAA 1io7A 199 :KLGYIILLLI T0369 122 :VHLYHHRSQLLDYLNLLGY 1io7A 212 :ETTTNLISNSVIDFTRFNL Number of specific fragments extracted= 8 number of extra gaps= 0 total=245 Number of alignments=35 # 1io7A read from 1io7A/merged-good-all-a2m # found chain 1io7A in training set T0369 2 :TDWQQALDRHVG 1io7A 89 :PQKLQTLETFIR T0369 17 :RTTRDLIRLIQPED 1io7A 101 :ETTRSLLDSIDPRE T0369 40 :RSVYEVAVHLAVLLEADLRIATGATADEMAQF 1io7A 116 :DIVKKLAVPLPIIVISKILGLPIEDKEKFKEW T0369 73 :AVPVLPEQLVDRLDQSWQYYQDR 1io7A 156 :GKPGEIFELGKKYLELIGYVKDH T0369 100 :FSTE 1io7A 179 :LNSG T0369 104 :TTYWGVTDSTTGWLLEAA 1io7A 190 :VNSNLSDIEKLGYIILLL T0369 136 :NLL 1io7A 208 :IAG Number of specific fragments extracted= 7 number of extra gaps= 0 total=252 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g7sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2g7sA expands to /projects/compbio/data/pdb/2g7s.pdb.gz 2g7sA:Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 263, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 297, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 299, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 301, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 303, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 305, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 307, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 309, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 311, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 391, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 393, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 395, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 397, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 399, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 477, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 479, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 485, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 529, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 832, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 834, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 836, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 838, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 840, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 842, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 921, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 923, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 927, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1066, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1068, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1070, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1072, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1074, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1094, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1096, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1098, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1231, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1233, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1235, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1237, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1239, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1241, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1251, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1257, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1346, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1348, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1350, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1352, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1354, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1356, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1358, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1360, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1362, because occupancy 0.500 <= existing 0.500 in 2g7sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1453, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1455, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1457, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1459, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1463, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1469, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2g7sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1555, because occupancy 0.500 <= existing 0.500 in 2g7sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1557, because occupancy 0.500 <= existing 0.500 in 2g7sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1559, because occupancy 0.500 <= existing 0.500 in 2g7sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1561, because occupancy 0.500 <= existing 0.500 in 2g7sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1563, because occupancy 0.500 <= existing 0.500 in 2g7sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1565, because occupancy 0.500 <= existing 0.500 in 2g7sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1567, because occupancy 0.400 <= existing 0.400 in 2g7sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1569, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1579, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1581, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1583, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1585, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1587, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1589, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1601, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1603, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1615, because occupancy 0.500 <= existing 0.500 in 2g7sA Skipped atom 1617, because occupancy 0.500 <= existing 0.500 in 2g7sA # T0369 read from 2g7sA/merged-good-all-a2m # 2g7sA read from 2g7sA/merged-good-all-a2m # adding 2g7sA to template set # found chain 2g7sA in template set T0369 4 :WQQALDRHVGVGVRTTRDLIRLIQP 2g7sA 54 :VCKLVSQYRQEAEAGIAELEKNISD T0369 46 :AVHLAVLLEADLRIATGATADE 2g7sA 80 :LEQLRAYIGYWEGCIADATHPF T0369 68 :MA 2g7sA 104 :CA T0369 70 :QFYAVPVLPEQLVDRLDQSWQYYQDRLMADFSTE 2g7sA 107 :LASEIPVLPETVVLEVRAHFRSLSDWLTAVLERG T0369 104 :TTYWGVTDSTTGWLLEAAV 2g7sA 143 :QGRLVLTGTARANAEIFMA T0369 125 :YHHRS 2g7sA 162 :TVHGA Number of specific fragments extracted= 6 number of extra gaps= 0 total=258 Number of alignments=37 # 2g7sA read from 2g7sA/merged-good-all-a2m # found chain 2g7sA in template set T0369 4 :WQQALDRHVGVGVRTTRDLIRLIQP 2g7sA 54 :VCKLVSQYRQEAEAGIAELEKNISD T0369 42 :VYEVAV 2g7sA 79 :PLEQLR T0369 51 :VLLEADLRIATGATADEMA 2g7sA 85 :AYIGYWEGCIADATHPFCV T0369 70 :QFYAVPVLPEQLVDRLDQSWQYYQDRLMADF 2g7sA 107 :LASEIPVLPETVVLEVRAHFRSLSDWLTAVL T0369 101 :STETTYWGVTDSTTGWLLEAA 2g7sA 143 :QGRLVLTGTARANAEIFMATV T0369 128 :RSQLLD 2g7sA 164 :HGAMLS Number of specific fragments extracted= 6 number of extra gaps= 0 total=264 Number of alignments=38 # 2g7sA read from 2g7sA/merged-good-all-a2m # found chain 2g7sA in template set T0369 2 :TDWQQALDRHVGVGV 2g7sA 51 :SDLVCKLVSQYRQEA T0369 17 :RTTRDLIRLIQ 2g7sA 67 :AGIAELEKNIS T0369 40 :RSVYEVAVHLAVLLEADL 2g7sA 78 :DPLEQLRAYIGYWEGCIA T0369 68 :MAQFY 2g7sA 96 :DATHP T0369 73 :AVPVLPEQLVDRLDQSWQYYQDRLMADFSTE 2g7sA 110 :EIPVLPETVVLEVRAHFRSLSDWLTAVLERG T0369 104 :TTYWGVTDSTTGWLLEAAVHL 2g7sA 143 :QGRLVLTGTARANAEIFMATV T0369 127 :HR 2g7sA 164 :HG Number of specific fragments extracted= 7 number of extra gaps= 0 total=271 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n2aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1n2aA expands to /projects/compbio/data/pdb/1n2a.pdb.gz 1n2aA:# T0369 read from 1n2aA/merged-good-all-a2m # 1n2aA read from 1n2aA/merged-good-all-a2m # adding 1n2aA to template set # found chain 1n2aA in template set T0369 15 :GVRTTRDLIRLI 1n2aA 66 :GVAIMQYLADSV T0369 28 :PEDWDK 1n2aA 78 :PDRQLL T0369 35 :PISGKRSVYEVAVHLAVLLEADLRIAT 1n2aA 84 :APVNSISRYKTIEWLNYIATELHKGFT T0369 62 :GATADEM 1n2aA 114 :RPDTPEE T0369 77 :LPEQLVDRLDQSWQYYQDR 1n2aA 121 :YKPTVRAQLEKKLQYVNEA T0369 100 :FSTETTYWGVTDSTTGWLLEA 1n2aA 140 :LKDEHWICGQRFTIADAYLFT T0369 131 :LLDYLNLLGYDIK 1n2aA 161 :VLRWAYAVKLNLE Number of specific fragments extracted= 7 number of extra gaps= 0 total=278 Number of alignments=40 # 1n2aA read from 1n2aA/merged-good-all-a2m # found chain 1n2aA in template set T0369 15 :GVRTTRDLIRL 1n2aA 66 :GVAIMQYLADS T0369 28 :PED 1n2aA 78 :PDR T0369 32 :DKRPISGKRSVYEVAVHLAVLLEADLRIAT 1n2aA 81 :QLLAPVNSISRYKTIEWLNYIATELHKGFT T0369 62 :GATADEMAQ 1n2aA 116 :DTPEEYKPT T0369 77 :LPEQLVDRLDQSWQYYQD 1n2aA 125 :VRAQLEKKLQYVNEALKD T0369 105 :TYW 1n2aA 143 :EHW T0369 108 :GVTDSTTGWLLEAA 1n2aA 148 :GQRFTIADAYLFTV T0369 132 :LDYLNLLGYDIK 1n2aA 162 :LRWAYAVKLNLE Number of specific fragments extracted= 8 number of extra gaps= 0 total=286 Number of alignments=41 # 1n2aA read from 1n2aA/merged-good-all-a2m # found chain 1n2aA in template set T0369 15 :GVRTTRDLIRLIQ 1n2aA 66 :GVAIMQYLADSVP T0369 30 :DWDKRPISGKRSVYEVAVHLAVLLEADLRIATG 1n2aA 79 :DRQLLAPVNSISRYKTIEWLNYIATELHKGFTP T0369 68 :MAQFYAVPVLPEQLVDRLDQSWQYYQDR 1n2aA 112 :LFRPDTPEEYKPTVRAQLEKKLQYVNEA T0369 100 :FSTETTYWGVTDSTTGWLLEAA 1n2aA 140 :LKDEHWICGQRFTIADAYLFTV T0369 132 :LDYLNLLGYDIK 1n2aA 162 :LRWAYAVKLNLE Number of specific fragments extracted= 5 number of extra gaps= 0 total=291 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z8oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z8oA expands to /projects/compbio/data/pdb/1z8o.pdb.gz 1z8oA:# T0369 read from 1z8oA/merged-good-all-a2m # 1z8oA read from 1z8oA/merged-good-all-a2m # adding 1z8oA to template set # found chain 1z8oA in template set T0369 6 :QALDRHVGVGVRTTRDLIRLI 1z8oA 112 :RRVEAMRPRVEQITAELLDEV T0369 35 :PISGKRSVY 1z8oA 133 :GDSGVVDIV T0369 50 :AVLLEADLRIATGATADEMAQFYA 1z8oA 146 :HPLPIKVICELLGVDEKYRGEFGR T0369 74 :VPV 1z8oA 177 :MDP T0369 77 :LPEQLVDRLDQSWQYYQDRL 1z8oA 181 :RAEQRGQAAREVVNFILDLV T0369 98 :ADFSTETT 1z8oA 201 :ERRRTEPG T0369 108 :G 1z8oA 209 :D T0369 109 :VTD 1z8oA 226 :LSA T0369 112 :S 1z8oA 230 :E T0369 113 :TTGWLLEAAVHLYHHRSQLLDYLNLL 1z8oA 232 :TSIALVLLLAGFEASVSLIGIGTYLL Number of specific fragments extracted= 10 number of extra gaps= 0 total=301 Number of alignments=43 # 1z8oA read from 1z8oA/merged-good-all-a2m # found chain 1z8oA in template set T0369 6 :QALDRHVGVGVRTTRDLIRLIQ 1z8oA 112 :RRVEAMRPRVEQITAELLDEVG T0369 36 :ISGKRSVYEV 1z8oA 134 :DSGVVDIVDR T0369 50 :AVLLEADLRIATGATADEMAQFYAV 1z8oA 146 :HPLPIKVICELLGVDEKYRGEFGRW T0369 75 :PVLPEQLVDRLDQSWQYYQDRLMADFSTETTYW 1z8oA 179 :PERAEQRGQAAREVVNFILDLVERRRTEPGDDL T0369 108 :GVTDST 1z8oA 223 :DGRLSA T0369 114 :TGWLLEAAVHLYHHRSQLLDYLNL 1z8oA 233 :SIALVLLLAGFEASVSLIGIGTYL Number of specific fragments extracted= 6 number of extra gaps= 0 total=307 Number of alignments=44 # 1z8oA read from 1z8oA/merged-good-all-a2m # found chain 1z8oA in template set T0369 2 :TDWQQALDRHVG 1z8oA 111 :VRRVEAMRPRVE T0369 17 :RTTRDLIRLIQP 1z8oA 123 :QITAELLDEVGD T0369 37 :SGKRSVYEVAVH 1z8oA 135 :SGVVDIVDRFAH T0369 49 :LAVLLEADLRIATGATADEMAQF 1z8oA 148 :LPIKVICELLGVDEKYRGEFGRW T0369 73 :AVPVLPEQLVDRLDQSWQYYQDRLMADFSTE 1z8oA 177 :MDPERAEQRGQAAREVVNFILDLVERRRTEP T0369 104 :TTYWGVTDSTTGWLLEAAVHLYHHRSQLLDYLNL 1z8oA 223 :DGRLSADELTSIALVLLLAGFEASVSLIGIGTYL Number of specific fragments extracted= 6 number of extra gaps= 0 total=313 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sqgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0369 read from 1sqgA/merged-good-all-a2m # 1sqgA read from 1sqgA/merged-good-all-a2m # found chain 1sqgA in training set T0369 3 :DWQQALDRHVGVGVRTTRDL 1sqgA 39 :KDKALLQELCFGVLRTLSQL T0369 23 :IRLI 1sqgA 62 :INKL T0369 31 :WDKRPISGKRSV 1sqgA 66 :MARPMTGKQRTV T0369 48 :HLAVLLEADLRIATGATADE 1sqgA 78 :HYLIMVGLYQLLYTRIPPHA T0369 68 :MA 1sqgA 99 :LA T0369 70 :QFYAVPVLPEQLVDRLDQSWQYY 1sqgA 107 :IAIKRPQLKGLINGVLRQFQRQQ T0369 94 :DRLMADFSTETTYWG 1sqgA 130 :EELLAEFNASDARYL Number of specific fragments extracted= 7 number of extra gaps= 0 total=320 Number of alignments=46 # 1sqgA read from 1sqgA/merged-good-all-a2m # found chain 1sqgA in training set T0369 4 :WQQALDRHVGVGVRTTRDL 1sqgA 40 :DKALLQELCFGVLRTLSQL T0369 23 :IRLI 1sqgA 62 :INKL T0369 31 :WDKRPISGKRSVYEVAV 1sqgA 66 :MARPMTGKQRTVHYLIM T0369 53 :LEADLRIATGATADEMA 1sqgA 83 :VGLYQLLYTRIPPHAAL T0369 70 :QFYAVPVLPEQLVDRLDQS 1sqgA 107 :IAIKRPQLKGLINGVLRQF T0369 89 :WQYYQDRLMADF 1sqgA 150 :LKRLQKAYPEQW T0369 101 :STETTYW 1sqgA 169 :NQRPPMW T0369 108 :GVTDSTTGWLLE 1sqgA 180 :RTHHSRDSWLAL T0369 135 :LNLLGYD 1sqgA 192 :LDEAGMK Number of specific fragments extracted= 9 number of extra gaps= 0 total=329 Number of alignments=47 # 1sqgA read from 1sqgA/merged-good-all-a2m # found chain 1sqgA in training set T0369 2 :TDWQQALDRHVGVGVRTTRDLIRLI 1sqgA 41 :KALLQELCFGVLRTLSQLDWLINKL T0369 33 :KRPISGKRSVYEVAVHLAVLLEADLRIATGATADEMAQFY 1sqgA 67 :ARPMTGKQRTVHYLIMVGLYQLLYTRIPPHAALAETVEGA T0369 73 :AVPVLPEQLVDRLDQSWQY 1sqgA 110 :KRPQLKGLINGVLRQFQRQ T0369 93 :QDRLMADFSTETTYWGVTDSTTGWLLEA 1sqgA 129 :QEELLAEFNASDARYLHPSWLLKRLQKA Number of specific fragments extracted= 4 number of extra gaps= 0 total=333 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vb5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vb5A expands to /projects/compbio/data/pdb/1vb5.pdb.gz 1vb5A:# T0369 read from 1vb5A/merged-good-all-a2m # 1vb5A read from 1vb5A/merged-good-all-a2m # adding 1vb5A to template set # found chain 1vb5A in template set T0369 3 :DWQQALDRH 1vb5A 5 :RVLEILREM T0369 12 :VGVGVRTTRDLIRLIQPEDW 1vb5A 25 :AKKGAEAFLTLAEELDESLL T0369 41 :SVYEVAVHLAVLLE 1vb5A 47 :AIMELREEVVKVNP T0369 55 :ADLRIA 1vb5A 63 :ASLYNL T0369 69 :AQFYAVPVLPEQLVDRLDQSWQYYQD 1vb5A 69 :ARFIPVTNRRDILKSRALEFLRRMEE T0369 95 :RLMADFSTETTYWG 1vb5A 98 :ELASIGAQLIDDGD T0369 109 :VTDSTTGWLLEAAV 1vb5A 118 :FSSTVLEIIRTAKE T0369 131 :LLDYLNLLGYDIK 1vb5A 152 :LARELEFSGIEFE T0369 144 :L 1vb5A 167 :T Number of specific fragments extracted= 9 number of extra gaps= 0 total=342 Number of alignments=49 # 1vb5A read from 1vb5A/merged-good-all-a2m # found chain 1vb5A in template set T0369 3 :DWQQALDRH 1vb5A 5 :RVLEILREM T0369 12 :VGVGVRTTRDLIRLIQPEDWD 1vb5A 25 :AKKGAEAFLTLAEELDESLLE T0369 41 :SVYEVAVHLAVLLEADLRIA 1vb5A 47 :AIMELREEVVKVNPSMASLY T0369 67 :EMAQFYAVPVLPEQLVDRLDQSWQYYQDRLMA 1vb5A 67 :NLARFIPVTNRRDILKSRALEFLRRMEEAKRE T0369 99 :DFSTETTYW 1vb5A 102 :IGAQLIDDG T0369 108 :GVTDSTTGWLLEAAV 1vb5A 117 :SFSSTVLEIIRTAKE T0369 130 :QLLDYLNLLGYDIK 1vb5A 151 :HLARELEFSGIEFE Number of specific fragments extracted= 7 number of extra gaps= 0 total=349 Number of alignments=50 # 1vb5A read from 1vb5A/merged-good-all-a2m # found chain 1vb5A in template set T0369 2 :TDWQQALDRH 1vb5A 7 :LEILREMKRE T0369 12 :VGVGVRTTRDLIRLIQPEDWD 1vb5A 25 :AKKGAEAFLTLAEELDESLLE T0369 41 :SVYEVAVHLAV 1vb5A 47 :AIMELREEVVK T0369 52 :LLEADLRIAT 1vb5A 64 :SLYNLARFIP T0369 70 :QFYAVPVLPEQLVDR 1vb5A 74 :VTNRRDILKSRALEF T0369 85 :LDQSWQYYQDRLMADFSTE 1vb5A 92 :MEEAKRELASIGAQLIDDG T0369 106 :YWGVTDSTTGWLLEAAV 1vb5A 115 :THSFSSTVLEIIRTAKE T0369 129 :SQLLDYLNLLGYDI 1vb5A 150 :LHLARELEFSGIEF Number of specific fragments extracted= 8 number of extra gaps= 0 total=357 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lrv/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lrv expands to /projects/compbio/data/pdb/1lrv.pdb.gz 1lrv:Warning: there is no chain 1lrv will retry with 1lrvA # T0369 read from 1lrv/merged-good-all-a2m # 1lrv read from 1lrv/merged-good-all-a2m # adding 1lrv to template set # found chain 1lrv in template set Warning: unaligning (T0369)Q27 because of BadResidue code BAD_PEPTIDE in next template residue (1lrv)L124 Warning: unaligning (T0369)P28 because of BadResidue code BAD_PEPTIDE at template residue (1lrv)L124 T0369 16 :VRTTRDLIRLI 1lrv 112 :REVRITVADRL T0369 29 :EDWDKRPISG 1lrv 125 :EQLEQMAADR T0369 50 :AVLLEADLRI 1lrv 136 :YLVRAYVVQR T0369 63 :ATADEMAQFYAVPV 1lrv 146 :IPPGRLFRFMRDED T0369 86 :DQSWQYYQDRLMADFSTETTYWGVTDSTTGWLLE 1lrv 160 :RQVRKLVAKRLPEESLGLMTQDPEPEVRRIVASR Number of specific fragments extracted= 5 number of extra gaps= 1 total=362 Number of alignments=52 # 1lrv read from 1lrv/merged-good-all-a2m # found chain 1lrv in template set Warning: unaligning (T0369)Q27 because of BadResidue code BAD_PEPTIDE in next template residue (1lrv)L124 Warning: unaligning (T0369)P28 because of BadResidue code BAD_PEPTIDE at template residue (1lrv)L124 T0369 17 :RTTRDLIRLI 1lrv 113 :EVRITVADRL T0369 29 :EDWDKRPISGKR 1lrv 125 :EQLEQMAADRDY T0369 51 :VLLEADLRI 1lrv 137 :LVRAYVVQR T0369 63 :ATADEMAQFYAVPV 1lrv 146 :IPPGRLFRFMRDED T0369 82 :VDRLDQSWQY 1lrv 160 :RQVRKLVAKR T0369 95 :RLMADFST 1lrv 170 :LPEESLGL T0369 106 :YWGVTD 1lrv 178 :MTQDPE T0369 112 :STTGWLL 1lrv 185 :EVRRIVA Number of specific fragments extracted= 8 number of extra gaps= 1 total=370 Number of alignments=53 # 1lrv read from 1lrv/merged-good-all-a2m # found chain 1lrv in template set Warning: unaligning (T0369)Q27 because of BadResidue code BAD_PEPTIDE in next template residue (1lrv)L124 Warning: unaligning (T0369)P28 because of BadResidue code BAD_PEPTIDE at template residue (1lrv)L124 T0369 17 :RTTRDLIRLI 1lrv 113 :EVRITVADRL T0369 29 :EDWDK 1lrv 125 :EQLEQ T0369 51 :VLLEADLRIATGATADEMAQFY 1lrv 137 :LVRAYVVQRIPPGRLFRFMRDE T0369 74 :VPV 1lrv 159 :DRQ T0369 88 :SWQ 1lrv 162 :VRK T0369 95 :RLMADFSTETTYWGVTDSTTGWLLEAAV 1lrv 165 :LVAKRLPEESLGLMTQDPEPEVRRIVAS Number of specific fragments extracted= 6 number of extra gaps= 1 total=376 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fflA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fflA expands to /projects/compbio/data/pdb/2ffl.pdb.gz 2fflA:# T0369 read from 2fflA/merged-good-all-a2m # 2fflA read from 2fflA/merged-good-all-a2m # adding 2fflA to template set # found chain 2fflA in template set Warning: unaligning (T0369)V76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fflA)P558 T0369 6 :QALDRHVGVG 2fflA 463 :HEFRSLVDYA T0369 16 :VRTTRDLIRLIQPEDW 2fflA 486 :STMFLERLRDIPAEDM T0369 32 :DKRPISGKRSVYEVAVHLAVLLEADLRIA 2fflA 516 :GLSGPGGVVSVIDIMTHLARGLWLGSPGF T0369 73 :AVP 2fflA 545 :YVE T0369 80 :QLVDRLDQ 2fflA 591 :KVLALYEK T0369 88 :SWQYYQDRL 2fflA 612 :AAQTVSRSL T0369 102 :T 2fflA 621 :A T0369 104 :TTYWGVTDSTTGWLLEAA 2fflA 622 :VPIPSGTIPFLIRLLQIA T0369 128 :RSQLLDYLN 2fflA 645 :YQKLELLGD Number of specific fragments extracted= 9 number of extra gaps= 0 total=385 Number of alignments=55 # 2fflA read from 2fflA/merged-good-all-a2m # found chain 2fflA in template set Warning: unaligning (T0369)P75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fflA)T585 T0369 6 :QALDRHVGVGVR 2fflA 463 :HEFRSLVDYACE T0369 18 :TTRDLIRLIQPEDW 2fflA 488 :MFLERLRDIPAEDM T0369 32 :DKRPISGKRSVYEVAVHLAVLLEADLRI 2fflA 516 :GLSGPGGVVSVIDIMTHLARGLWLGSPG T0369 60 :ATGATADEMAQ 2fflA 568 :HRSVQCPVLYG T0369 73 :AV 2fflA 579 :SL T0369 77 :LPEQLVDRLDQS 2fflA 588 :VASKVLALYEKI T0369 89 :WQYYQDRLMADFSTE 2fflA 609 :KHIAAQTVSRSLAVP T0369 106 :YWGVTDSTTGWLLEAA 2fflA 624 :IPSGTIPFLIRLLQIA T0369 127 :H 2fflA 643 :H T0369 128 :RSQLLDYLNL 2fflA 645 :YQKLELLGDA Number of specific fragments extracted= 10 number of extra gaps= 0 total=395 Number of alignments=56 # 2fflA read from 2fflA/merged-good-all-a2m # found chain 2fflA in template set Warning: unaligning (T0369)P75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fflA)T585 T0369 5 :QQALDRHVGVGVRTTRD 2fflA 498 :AEDMLDWYRLGIQFSHR T0369 31 :WDKRPISGKRSVYEVAVHLAVLLEADL 2fflA 515 :SGLSGPGGVVSVIDIMTHLARGLWLGS T0369 58 :RIATGATADEMAQFY 2fflA 566 :IYHRSVQCPVLYGSL T0369 78 :PEQLVDRLDQSWQ 2fflA 589 :ASKVLALYEKILA T0369 91 :YYQDRLMADFST 2fflA 611 :IAAQTVSRSLAV T0369 105 :TYWGVTDSTTGWLLEAA 2fflA 623 :PIPSGTIPFLIRLLQIA Number of specific fragments extracted= 6 number of extra gaps= 0 total=401 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xo0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xo0A expands to /projects/compbio/data/pdb/1xo0.pdb.gz 1xo0A:# T0369 read from 1xo0A/merged-good-all-a2m # 1xo0A read from 1xo0A/merged-good-all-a2m # adding 1xo0A to template set # found chain 1xo0A in template set T0369 3 :DWQQALDRHVGVG 1xo0A 47 :SVCRSWAAWCKLN T0369 16 :VRTTRDLIRLI 1xo0A 68 :PEDVRDYLLYL T0369 38 :GKRSVYEVAVHLAVLLEADLR 1xo0A 81 :RGLAVKTIQQHLGQLNMLHRR T0369 61 :TGATADEM 1xo0A 102 :SGLPRPSD T0369 72 :Y 1xo0A 110 :S T0369 83 :DRLDQSWQYYQDRLMADFSTETTYWG 1xo0A 111 :NAVSLVMRRIRKENVDAGERAKQALA T0369 109 :VTDSTTGWLLEAA 1xo0A 151 :NSDRCQDIRNLAF Number of specific fragments extracted= 7 number of extra gaps= 0 total=408 Number of alignments=58 # 1xo0A read from 1xo0A/merged-good-all-a2m # found chain 1xo0A in template set T0369 77 :LPEQLVDRLDQSWQYYQDRL 1xo0A 41 :TWKMLLSVCRSWAAWCKLNN T0369 104 :TTYWGVTD 1xo0A 61 :RKWFPAEP T0369 112 :STTGWLLEAAV 1xo0A 70 :DVRDYLLYLQA T0369 123 :HLYHHRSQLLDYLNLLGYDIKLD 1xo0A 87 :TIQQHLGQLNMLHRRSGLPRPSD Number of specific fragments extracted= 4 number of extra gaps= 0 total=412 Number of alignments=59 # 1xo0A read from 1xo0A/merged-good-all-a2m # found chain 1xo0A in template set T0369 73 :AVPVLPEQLVDRLDQSWQYYQDRLMAD 1xo0A 33 :DRQAFSEHTWKMLLSVCRSWAAWCKLN T0369 102 :TETTYWGVTDSTTGWLLEAAV 1xo0A 60 :NRKWFPAEPEDVRDYLLYLQA T0369 124 :LYHHRSQLLDYLNLLGYD 1xo0A 88 :IQQHLGQLNMLHRRSGLP Number of specific fragments extracted= 3 number of extra gaps= 0 total=415 Number of alignments=60 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 60 Done printing distance constraints # command: