# 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/T0284/ # command:# Making conformation for sequence T0284 numbered 1 through 287 Created new target T0284 from T0284.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0284/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0284//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0284/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0284//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0284/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0284/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0284/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2czdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2czdA expands to /projects/compbio/data/pdb/2czd.pdb.gz 2czdA:# T0284 read from 2czdA/merged-good-all-a2m # 2czdA read from 2czdA/merged-good-all-a2m # adding 2czdA to template set # found chain 2czdA in template set Warning: unaligning (T0284)A257 because last residue in template chain is (2czdA)R206 T0284 22 :CYHTASVFDPMSA 2czdA 2 :IVLALDVYEGERA # choosing archetypes in rotamer library T0284 35 :RIAADL 2czdA 16 :KIAKSV T0284 42 :FECGILG 2czdA 25 :ISMIKVN T0284 70 :FVE 2czdA 34 :LIL T0284 73 :QATRIGRVARLPVIADADHG 2czdA 42 :IIRRLKEETGVEIIADLKLA T0284 94 :GNALNVMRTVVELERAGIAALTIEDTLL 2czdA 62 :DIPNTNRLIARKVFGAGADYVIVHTFVG T0284 139 :VGKIRAALEAR 2czdA 90 :RDSVMAVKELG T0284 153 :ALTIIAR 2czdA 101 :EIIMVVE T0284 160 :TNAELID 2czdA 109 :SHPGALE T0284 167 :VDAVIQRTLAYQ 2czdA 121 :TDRFIEVANEIE T0284 182 :ADGICLVGVR 2czdA 133 :PFGVIAPGTR T0284 193 :FAHLEAIAEHLH 2czdA 143 :PERIGYIRDRLK T0284 205 :IPLMLVTYGNPQL 2czdA 157 :IKILAPGIGAQGG T0284 219 :DDARLARLGVRVVVNGHAAY 2czdA 170 :KAKDAVKAGADYIIVGRAIY T0284 245 :TYDCLREERGAV 2czdA 194 :PREAAKAIYDEI Number of specific fragments extracted= 15 number of extra gaps= 0 total=15 Number of alignments=1 # 2czdA read from 2czdA/merged-good-all-a2m # found chain 2czdA in template set Warning: unaligning (T0284)A257 because last residue in template chain is (2czdA)R206 T0284 22 :CYHTASVFDPMSA 2czdA 2 :IVLALDVYEGERA T0284 35 :RIAADL 2czdA 16 :KIAKSV T0284 42 :FECGIL 2czdA 25 :ISMIKV T0284 49 :GSVAS 2czdA 31 :NWPLI T0284 57 :LA 2czdA 36 :LG T0284 59 :APD 2czdA 39 :GVD T0284 73 :QATRIGRVARLPVIADADHG 2czdA 42 :IIRRLKEETGVEIIADLKLA T0284 94 :GNALNVMRTVVELERAGIAALTIEDTLL 2czdA 62 :DIPNTNRLIARKVFGAGADYVIVHTFVG T0284 139 :VGKIRAALE 2czdA 90 :RDSVMAVKE T0284 152 :PA 2czdA 99 :LG T0284 154 :LTIIAR 2czdA 102 :IIMVVE T0284 160 :TNAELID 2czdA 109 :SHPGALE T0284 167 :VDAVIQRTLAY 2czdA 121 :TDRFIEVANEI T0284 182 :ADGICLVGVR 2czdA 133 :PFGVIAPGTR T0284 193 :FAHLEAIAEHLH 2czdA 143 :PERIGYIRDRLK T0284 205 :IPLMLVTYGNPQL 2czdA 157 :IKILAPGIGAQGG T0284 219 :DDARLARLGVRVVVNGHAAY 2czdA 170 :KAKDAVKAGADYIIVGRAIY T0284 245 :TYDCLREERGAV 2czdA 194 :PREAAKAIYDEI Number of specific fragments extracted= 18 number of extra gaps= 0 total=33 Number of alignments=2 # 2czdA read from 2czdA/merged-good-all-a2m # found chain 2czdA in template set T0284 22 :CYHTASVFDPMSA 2czdA 2 :IVLALDVYEGERA T0284 35 :RIAADL 2czdA 16 :KIAKSV T0284 41 :GFECGILGGSVASLQ 2czdA 24 :YISMIKVNWPLILGS T0284 73 :QATRIGRVARLPVIADADHG 2czdA 42 :IIRRLKEETGVEIIADLKLA T0284 94 :GNALNVMRTVVELERAGIAALTIEDTLLP 2czdA 62 :DIPNTNRLIARKVFGAGADYVIVHTFVGR T0284 140 :GKIRAALEAR 2czdA 91 :DSVMAVKELG T0284 153 :ALTIIARTN 2czdA 101 :EIIMVVEMS T0284 162 :A 2czdA 113 :A T0284 166 :DVDAVIQRTLAY 2czdA 120 :LTDRFIEVANEI T0284 182 :ADGICLVGVR 2czdA 133 :PFGVIAPGTR T0284 193 :FAHLEAIAEHLHI 2czdA 143 :PERIGYIRDRLKE T0284 206 :PLMLVTYGNPQLRDDARLARLGVRVVVNGHAAY 2czdA 157 :IKILAPGIGAQGGKAKDAVKAGADYIIVGRAIY T0284 239 :FAAIKATYDC 2czdA 195 :REAAKAIYDE Number of specific fragments extracted= 13 number of extra gaps= 0 total=46 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b4kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b4kA expands to /projects/compbio/data/pdb/1b4k.pdb.gz 1b4kA:# T0284 read from 1b4kA/merged-good-all-a2m # 1b4kA read from 1b4kA/merged-good-all-a2m # adding 1b4kA to template set # found chain 1b4kA in template set T0284 23 :YHTASVFD 1b4kA 39 :ILPVFVLD T0284 31 :PMSARIAADLGFECGILG 1b4kA 69 :LIEAEEWVALGIPALALF T0284 56 :VLAAPDFALIT 1b4kA 93 :KKSLDAAEAYN T0284 69 :EFVEQATRIGRVA 1b4kA 107 :IAQRATRALRERF T0284 82 :RLPVIADAD 1b4kA 121 :ELGIITDVA T0284 92 :GYG 1b4kA 135 :THG T0284 96 :ALNVMRTVVELERAGIAALTIEDTL 1b4kA 154 :IDVLVRQALSHAEAGAQVVAPSDMM T0284 140 :GKIRAALEAR 1b4kA 180 :GRIGAIREAL T0284 150 :VDPALTIIA 1b4kA 193 :GHTNVRIMA T0284 159 :RTNAELI 1b4kA 205 :KYASAYY T0284 166 :DVDAVIQRTLAYQEAGADGICLV 1b4kA 238 :NSDEALHEVAADLAEGADMVMVK T0284 189 :GVRDFAHLEAIAEHLHIPLMLVTY 1b4kA 262 :GMPYLDIVRRVKDEFRAPTFVYQV T0284 219 :DD 1b4kA 286 :SG T0284 221 :ARLARLGVRVVVNGHAAYFA 1b4kA 311 :TAFKRAGADGILTYFAKQAA T0284 243 :KA 1b4kA 331 :EQ Number of specific fragments extracted= 15 number of extra gaps= 0 total=61 Number of alignments=4 # 1b4kA read from 1b4kA/merged-good-all-a2m # found chain 1b4kA in template set T0284 10 :RAMFRALLDS 1b4kA 65 :IDQLLIEAEE T0284 37 :AADLGFECGILG 1b4kA 75 :WVALGIPALALF T0284 57 :LA 1b4kA 96 :LD T0284 59 :APDF 1b4kA 103 :NPEG T0284 69 :EFVEQATRIGR 1b4kA 107 :IAQRATRALRE T0284 80 :VARLPVIADADH 1b4kA 119 :FPELGIITDVAL T0284 93 :YG 1b4kA 133 :FT T0284 96 :ALNVMRTVVELERAGIAALTIEDTL 1b4kA 154 :IDVLVRQALSHAEAGAQVVAPSDMM T0284 136 :EEGVGKIRAALEARVDPALTIIA 1b4kA 179 :DGRIGAIREALESAGHTNVRIMA T0284 159 :RTNAELIDV 1b4kA 205 :KYASAYYGP T0284 168 :DAVIQRTLAYQEAGADGICLVG 1b4kA 240 :DEALHEVAADLAEGADMVMVKP T0284 190 :VRDFAHLEAIAEHLHIPLMLVTY 1b4kA 263 :MPYLDIVRRVKDEFRAPTFVYQV T0284 217 :LRDDA 1b4kA 286 :SGEYA T0284 222 :RLARLGVRVVVNGH 1b4kA 312 :AFKRAGADGILTYF T0284 245 :TYDCLREE 1b4kA 326 :AKQAAEQL Number of specific fragments extracted= 15 number of extra gaps= 0 total=76 Number of alignments=5 # 1b4kA read from 1b4kA/merged-good-all-a2m # found chain 1b4kA in template set T0284 31 :PMSARIAADLGFECGILGGSV 1b4kA 69 :LIEAEEWVALGIPALALFPVT T0284 56 :VLAAPDFALITLS 1b4kA 93 :KKSLDAAEAYNPE T0284 69 :EFVEQATRIGRVA 1b4kA 107 :IAQRATRALRERF T0284 82 :RLPVIADA 1b4kA 121 :ELGIITDV T0284 90 :DHGYG 1b4kA 144 :DDGYV T0284 95 :NALNVMRTVVELERAGIAALTIEDTLLP 1b4kA 153 :SIDVLVRQALSHAEAGAQVVAPSDMMDG T0284 138 :GVGKIRAALEARVDPALTIIARTNAELI 1b4kA 181 :RIGAIREALESAGHTNVRIMAYSAKYAS T0284 167 :VDAVIQRTLAYQEAGADGICLVGVRD 1b4kA 239 :SDEALHEVAADLAEGADMVMVKPGMP T0284 193 :FAHLEAIAEHLHIPLMLVTY 1b4kA 266 :LDIVRRVKDEFRAPTFVYQV T0284 242 :IKATYDCLREERGAVASDLTAS 1b4kA 286 :SGEYAMHMGAIQNGWLAESVIL T0284 273 :EEYQAW 1b4kA 308 :ESLTAF Number of specific fragments extracted= 11 number of extra gaps= 0 total=87 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h5yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h5yA expands to /projects/compbio/data/pdb/1h5y.pdb.gz 1h5yA:Skipped atom 208, because occupancy 0.5 <= existing 0.500 in 1h5yA Skipped atom 210, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 212, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 214, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 216, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 218, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 1h5yA # T0284 read from 1h5yA/merged-good-all-a2m # 1h5yA read from 1h5yA/merged-good-all-a2m # adding 1h5yA to template set # found chain 1h5yA in template set T0284 24 :HTASVFD 1h5yA 6 :RIIPCLD T0284 31 :PMSARIAADLGFE 1h5yA 36 :VEMAVRYEEEGAD T0284 44 :CGILG 1h5yA 50 :IAILD T0284 57 :LAAPDF 1h5yA 56 :TAAPEG T0284 67 :LSEFVEQATRIGRVARLPVIADA 1h5yA 62 :RATFIDSVKRVAEAVSIPVLVGG T0284 92 :GYGNALN 1h5yA 85 :GVRSLED T0284 103 :VVELERAGIAALTIE 1h5yA 92 :ATTLFRAGADKVSVN T0284 137 :EGV 1h5yA 108 :AAV T0284 140 :GKIRAALEAR 1h5yA 114 :QLVALLAREF T0284 151 :DPA 1h5yA 124 :GSQ T0284 154 :LTIIARTNAEL 1h5yA 130 :VAIDAKWNGEY T0284 169 :AVIQRTLAYQEAGADGICLVGV 1h5yA 155 :DAVKWAKEVEELGAGEILLTSI T0284 192 :DFAHLEAIAEHLHIPL 1h5yA 186 :DVELIRRVADSVRIPV T0284 209 :LVTYGNPQLRDDARLARLGVRVVVNGHAAYF 1h5yA 202 :IASGGAGRVEHFYEAAAAGADAVLAASLFHF T0284 242 :IKATYDCLRE 1h5yA 237 :IAQVKRYLKE Number of specific fragments extracted= 15 number of extra gaps= 0 total=102 Number of alignments=7 # 1h5yA read from 1h5yA/merged-good-all-a2m # found chain 1h5yA in template set T0284 22 :CYHTASVF 1h5yA 7 :IIPCLDID T0284 31 :PMSARIAADLGFE 1h5yA 36 :VEMAVRYEEEGAD T0284 44 :CGILG 1h5yA 50 :IAILD T0284 57 :LAAPDF 1h5yA 56 :TAAPEG T0284 67 :LSEFVEQATRIGRVARLPVIADADH 1h5yA 62 :RATFIDSVKRVAEAVSIPVLVGGGV T0284 94 :GNALN 1h5yA 87 :RSLED T0284 103 :VVELERAGIAALTIED 1h5yA 92 :ATTLFRAGADKVSVNT T0284 137 :EGV 1h5yA 108 :AAV T0284 140 :GKIRAALEARVDPA 1h5yA 114 :QLVALLAREFGSQS T0284 154 :LTIIARTNAEL 1h5yA 130 :VAIDAKWNGEY T0284 169 :AVIQRTLAYQEAGADGICLVGVR 1h5yA 155 :DAVKWAKEVEELGAGEILLTSID T0284 192 :DFAHLEAIAEHLHIPLMLVTY 1h5yA 186 :DVELIRRVADSVRIPVIASGG T0284 217 :LRDDARLARL 1h5yA 207 :AGRVEHFYEA T0284 227 :GVRVVVNGHAAY 1h5yA 220 :GADAVLAASLFH T0284 245 :TYDCLREERGAVA 1h5yA 237 :IAQVKRYLKERGV Number of specific fragments extracted= 15 number of extra gaps= 0 total=117 Number of alignments=8 # 1h5yA read from 1h5yA/merged-good-all-a2m # found chain 1h5yA in template set T0284 32 :MSARIAADLGFECGILGGS 1h5yA 37 :EMAVRYEEEGADEIAILDI T0284 57 :LAAPDF 1h5yA 56 :TAAPEG T0284 67 :LSEFVEQATRIGRVARLPVIA 1h5yA 62 :RATFIDSVKRVAEAVSIPVLV T0284 92 :GYG 1h5yA 83 :GGG T0284 95 :NALN 1h5yA 88 :SLED T0284 103 :VVELERAGIAALTI 1h5yA 92 :ATTLFRAGADKVSV T0284 134 :CVEEGV 1h5yA 106 :NTAAVR T0284 140 :GKIRAALEARVDPALTIIARTN 1h5yA 114 :QLVALLAREFGSQSTVVAIDAK T0284 170 :VIQRTLAYQEAGADGICLVGVRD 1h5yA 156 :AVKWAKEVEELGAGEILLTSIDR T0284 193 :FAHLEAIAEHLHIPLMLVTYG 1h5yA 187 :VELIRRVADSVRIPVIASGGA T0284 218 :RDDARLAR 1h5yA 208 :GRVEHFYE T0284 226 :LGVRVVVNGHAAY 1h5yA 219 :AGADAVLAASLFH T0284 253 :RGAVASDLTASELSKKY 1h5yA 232 :FRVLSIAQVKRYLKERG Number of specific fragments extracted= 13 number of extra gaps= 0 total=130 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kfcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kfcA expands to /projects/compbio/data/pdb/1kfc.pdb.gz 1kfcA:# T0284 read from 1kfcA/merged-good-all-a2m # 1kfcA read from 1kfcA/merged-good-all-a2m # adding 1kfcA to template set # found chain 1kfcA in template set Warning: unaligning (T0284)D192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kfcA)L193 T0284 8 :ELRAMFRALLDSSRCYHTASV 1kfcA 3 :RYENLFAQLNDRREGAFVPFV T0284 29 :FDPMSARIAADLGFECGIL 1kfcA 32 :QSLKIIDTLIDAGADALEL T0284 49 :GSV 1kfcA 51 :GVP T0284 53 :SLQVLA 1kfcA 70 :RAFAAG T0284 65 :ITLSEFVEQATRIGRVA 1kfcA 76 :VTPAQCFEMLAIIREKH T0284 82 :RLPVIADAD 1kfcA 94 :TIPIGLLMY T0284 94 :GNA 1kfcA 109 :NGI T0284 100 :MRTVVELERAGIAALTIED 1kfcA 112 :DAFYARCEQVGVDSVLVAD T0284 133 :ICVEEGVGKIRAALEA 1kfcA 131 :VPVEESAPFRQAALRH T0284 153 :ALTIIARTNAELI 1kfcA 147 :NIAPIFICPPNAD T0284 168 :DAVIQRTLAY 1kfcA 160 :DDLLRQVASY T0284 181 :GADGICLV 1kfcA 170 :GRGYTYLL T0284 193 :FAHLEAIAEH 1kfcA 194 :HHLIEKLKEY T0284 204 :HIPLMLVTYGNPQLRDDARLARLGVRVVVNGH 1kfcA 204 :HAAPALQGFGISSPEQVSAAVRAGAAGAISGS T0284 240 :AAIKATYD 1kfcA 236 :AIVKIIEK T0284 248 :CLREERGAVASDLT 1kfcA 251 :MLAELRSFVSAMKA Number of specific fragments extracted= 16 number of extra gaps= 0 total=146 Number of alignments=10 # 1kfcA read from 1kfcA/merged-good-all-a2m # found chain 1kfcA in template set Warning: unaligning (T0284)D192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kfcA)L193 T0284 7 :HELRAMFRALLDSSRCYHTASV 1kfcA 2 :ERYENLFAQLNDRREGAFVPFV T0284 29 :FDPMSARIAADLGFECGIL 1kfcA 32 :QSLKIIDTLIDAGADALEL T0284 49 :GSVA 1kfcA 51 :GVPF T0284 53 :SLQVLA 1kfcA 70 :RAFAAG T0284 65 :ITLSEFVEQATRIGR 1kfcA 76 :VTPAQCFEMLAIIRE T0284 80 :VARLPVIADAD 1kfcA 92 :HPTIPIGLLMY T0284 96 :ALNVM 1kfcA 103 :ANLVF T0284 101 :RTVVELERAGIAALTIED 1kfcA 113 :AFYARCEQVGVDSVLVAD T0284 133 :ICVEEGVGKIRAALE 1kfcA 131 :VPVEESAPFRQAALR T0284 152 :PALTIIARTNAELI 1kfcA 146 :HNIAPIFICPPNAD T0284 168 :DAVIQRTLA 1kfcA 160 :DDLLRQVAS T0284 180 :AG 1kfcA 169 :YG T0284 182 :ADGICL 1kfcA 172 :GYTYLL T0284 193 :FAHLEAIAEH 1kfcA 194 :HHLIEKLKEY T0284 204 :HIPLMLVTYGNPQLRDDARLARLGVRVVVNGHAAYFAA 1kfcA 204 :HAAPALQGFGISSPEQVSAAVRAGAAGAISGSAIVKII T0284 242 :IKATYDCLREERGAVA 1kfcA 252 :LAELRSFVSAMKAASR Number of specific fragments extracted= 16 number of extra gaps= 0 total=162 Number of alignments=11 # 1kfcA read from 1kfcA/merged-good-all-a2m # found chain 1kfcA in template set Warning: unaligning (T0284)G189 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kfcA)L193 T0284 4 :ASHHELRAMFRA 1kfcA 2 :ERYENLFAQLND T0284 19 :SSR 1kfcA 14 :RRE T0284 22 :CYHTASVF 1kfcA 21 :PFVTLGDP T0284 30 :DPMSARIAADLGFECGILG 1kfcA 33 :SLKIIDTLIDAGADALELG T0284 51 :VASLQ 1kfcA 65 :QNANL T0284 63 :ALITLSEFVEQATRIGRVA 1kfcA 74 :AGVTPAQCFEMLAIIREKH T0284 82 :RLPVIADA 1kfcA 94 :TIPIGLLM T0284 96 :ALNVM 1kfcA 103 :ANLVF T0284 101 :RTVVELERAGIAALTIED 1kfcA 113 :AFYARCEQVGVDSVLVAD T0284 133 :ICVEEGVGKIRAALEA 1kfcA 131 :VPVEESAPFRQAALRH T0284 153 :ALTIIARTN 1kfcA 147 :NIAPIFICP T0284 167 :VDAVIQRTL 1kfcA 159 :DDDLLRQVA T0284 179 :EAGADGICLV 1kfcA 168 :SYGRGYTYLL T0284 193 :FAHLEAIAE 1kfcA 194 :HHLIEKLKE T0284 203 :LHIPLMLVTY 1kfcA 203 :YHAAPALQGF T0284 216 :QLRDDARLARL 1kfcA 213 :GISSPEQVSAA T0284 227 :GVRVVVNGHAAYFAAIKA 1kfcA 227 :GAAGAISGSAIVKIIEKN T0284 245 :TYDCLREERG 1kfcA 251 :MLAELRSFVS Number of specific fragments extracted= 18 number of extra gaps= 0 total=180 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1igs/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1igs expands to /projects/compbio/data/pdb/1igs.pdb.gz 1igs:Warning: there is no chain 1igs will retry with 1igsA # T0284 read from 1igs/merged-good-all-a2m # 1igs read from 1igs/merged-good-all-a2m # adding 1igs to template set # found chain 1igs in template set T0284 8 :ELRAMFRALLDSSRCYHTASVFD 1igs 32 :SLNERILEFNKRNITAIIAEYKR T0284 31 :PMSARIAADL 1igs 67 :IEYSKFMERY T0284 42 :FECGIL 1igs 77 :AVGLSI T0284 57 :LAAPDFALITLSEF 1igs 83 :LTEEKYFNGSYETL T0284 75 :TRIGRVARLPVIADADH 1igs 97 :RKIASSVSIPILMKDFI T0284 100 :MRTVVELERAGIAALTIEDTLLPA 1igs 116 :ESQIDDAYNLGADTVLLIVKILTE T0284 136 :EEGVGKIRAALEARV 1igs 140 :RELESLLEYARSYGM T0284 153 :ALTIIART 1igs 155 :EPLIEIND T0284 168 :DAVIQRTLA 1igs 163 :ENDLDIALR T0284 180 :AGADGICLVGV 1igs 172 :IGARFIGINSR T0284 191 :RDFAHLEAIAEHLH 1igs 189 :INKENQRKLISMIP T0284 205 :I 1igs 205 :V T0284 207 :LMLVTYGNPQLRDDARLARLGVRVVVNGHAAYF 1igs 206 :VKVAESGISERNEIEELRKLGVNAFLIGSSLMR Number of specific fragments extracted= 13 number of extra gaps= 0 total=193 Number of alignments=13 # 1igs read from 1igs/merged-good-all-a2m # found chain 1igs in template set T0284 4 :ASHHELRAMFRALLDSSRCYHTASVFD 1igs 28 :RPIISLNERILEFNKRNITAIIAEYKR T0284 31 :PMSARIAADL 1igs 67 :IEYSKFMERY T0284 42 :FECGIL 1igs 77 :AVGLSI T0284 57 :LAAPDFALITLSE 1igs 83 :LTEEKYFNGSYET T0284 74 :ATRIGRVARLPVIADADH 1igs 96 :LRKIASSVSIPILMKDFI T0284 100 :MRTVVELERAGIAALTIEDTLLPA 1igs 116 :ESQIDDAYNLGADTVLLIVKILTE T0284 136 :EEGVGKIRAALE 1igs 140 :RELESLLEYARS T0284 152 :PA 1igs 152 :YG T0284 154 :LTIIART 1igs 156 :PLIEIND T0284 168 :DAVIQRTL 1igs 163 :ENDLDIAL T0284 179 :EAGADGICLVGVR 1igs 171 :RIGARFIGINSRD T0284 192 :DFAHLEAIAEHLH 1igs 190 :NKENQRKLISMIP T0284 205 :I 1igs 205 :V T0284 207 :LMLVTYGNPQLRDDARLARLGVRVVVNGHAAYF 1igs 206 :VKVAESGISERNEIEELRKLGVNAFLIGSSLMR T0284 261 :TASELSK 1igs 239 :NPEKIKE Number of specific fragments extracted= 15 number of extra gaps= 0 total=208 Number of alignments=14 # 1igs read from 1igs/merged-good-all-a2m # found chain 1igs in template set T0284 9 :LRAMFRALLDSSRCYHTASVFD 1igs 33 :LNERILEFNKRNITAIIAEYKR T0284 31 :PMSARIAADL 1igs 67 :IEYSKFMERY T0284 42 :FECGIL 1igs 77 :AVGLSI T0284 57 :LAAPDFALIT 1igs 83 :LTEEKYFNGS T0284 71 :VEQATRIGRVARLPVIADA 1igs 93 :YETLRKIASSVSIPILMKD T0284 100 :MRTVVELERAGIAALTIEDTLLP 1igs 116 :ESQIDDAYNLGADTVLLIVKILT T0284 135 :VEEGVGKIRAALEARV 1igs 139 :ERELESLLEYARSYGM T0284 153 :ALTIIAR 1igs 155 :EPLIEIN T0284 167 :VDAVI 1igs 162 :DENDL T0284 175 :LAYQEAGADGICLVGVRD 1igs 167 :DIALRIGARFIGINSRDL T0284 193 :FAHLEAIAEHLHI 1igs 191 :KENQRKLISMIPS T0284 206 :PLMLVTYGNPQLRDDARLARLGVRVVVNGHAAYF 1igs 205 :VVKVAESGISERNEIEELRKLGVNAFLIGSSLMR Number of specific fragments extracted= 12 number of extra gaps= 0 total=220 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w8sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w8sA expands to /projects/compbio/data/pdb/1w8s.pdb.gz 1w8sA:Skipped atom 267, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 269, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 271, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 273, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 790, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 792, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1672, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1674, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1676, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1678, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1680, because occupancy 0.350 <= existing 0.650 in 1w8sA # T0284 read from 1w8sA/merged-good-all-a2m # 1w8sA read from 1w8sA/merged-good-all-a2m # adding 1w8sA to template set # found chain 1w8sA in template set T0284 9 :LRAMFRALLDSSRCYHTASVFDP 1w8sA 4 :LTEKFLRIFARRGKSIILAYDHG T0284 33 :SA 1w8sA 27 :IE T0284 35 :RIAADLGFECGILG 1w8sA 48 :RLARDAGFDGVVFQ T0284 67 :LSEFVE 1w8sA 62 :RGIAEK T0284 80 :VA 1w8sA 68 :YY T0284 82 :RLPVIADAD 1w8sA 72 :SVPLILKLN T0284 91 :H 1w8sA 84 :T T0284 93 :YGN 1w8sA 86 :YNG T0284 103 :VVELERAGIAALTIE 1w8sA 98 :VEEAVSLGASAVGYT T0284 120 :L 1w8sA 115 :P T0284 126 :GRKS 1w8sA 116 :GSGF T0284 135 :VEEGVGKIRAALEAR 1w8sA 120 :EWKMFEELARIKRDA T0284 150 :V 1w8sA 137 :F T0284 153 :ALTIIARTNAELID 1w8sA 138 :DLPLVVESFPRGGK T0284 167 :VDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLH 1w8sA 158 :PEIVAYAARIALELGADAMKIKYTGDPKTFSWAVKVAG T0284 205 :IPLMLVTYGNPQ 1w8sA 197 :VPVLMSGGPKTK T0284 219 :DD 1w8sA 209 :TE T0284 221 :ARLARLGVRVVVNGHAAY 1w8sA 218 :EGVLEAGALGIAVGRNVW T0284 245 :TYDCLREERGAV 1w8sA 240 :ALKFARALAELV Number of specific fragments extracted= 19 number of extra gaps= 0 total=239 Number of alignments=16 # 1w8sA read from 1w8sA/merged-good-all-a2m # found chain 1w8sA in template set Warning: unaligning (T0284)E8 because first residue in template chain is (1w8sA)N3 Warning: unaligning (T0284)A257 because last residue in template chain is (1w8sA)Y252 T0284 9 :LRAMFRALLDSSRCYHTASVFDP 1w8sA 4 :LTEKFLRIFARRGKSIILAYDHG T0284 32 :MSARIAADLGFECGIL 1w8sA 45 :YILRLARDAGFDGVVF T0284 49 :GSVASLQ 1w8sA 61 :QRGIAEK T0284 80 :VARLPVIADA 1w8sA 70 :DGSVPLILKL T0284 90 :DHG 1w8sA 90 :PVS T0284 93 :YGNALNV 1w8sA 95 :NCSVEEA T0284 107 :ERAGIAALTIEDTLL 1w8sA 102 :VSLGASAVGYTIYPG T0284 125 :FGR 1w8sA 117 :SGF T0284 135 :VEEGVGKIRAALEA 1w8sA 120 :EWKMFEELARIKRD T0284 149 :RVDPALTIIARTNAELID 1w8sA 136 :KFDLPLVVESFPRGGKVV T0284 167 :VDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLH 1w8sA 158 :PEIVAYAARIALELGADAMKIKYTGDPKTFSWAVKVAG T0284 205 :IPLMLVTYGNPQLR 1w8sA 197 :VPVLMSGGPKTKTE T0284 219 :DDARLARLGVRVVVNGHAAY 1w8sA 216 :QVEGVLEAGALGIAVGRNVW T0284 245 :TYDCLREERGAV 1w8sA 240 :ALKFARALAELV Number of specific fragments extracted= 14 number of extra gaps= 0 total=253 Number of alignments=17 # 1w8sA read from 1w8sA/merged-good-all-a2m # found chain 1w8sA in template set T0284 9 :LRAMFRALLDSSRCYHTASVFDPM 1w8sA 4 :LTEKFLRIFARRGKSIILAYDHGI T0284 34 :ARIAADLGFECGILGGSVASLQ 1w8sA 47 :LRLARDAGFDGVVFQRGIAEKY T0284 57 :L 1w8sA 69 :Y T0284 82 :RLPVIADA 1w8sA 72 :SVPLILKL T0284 103 :VVELERAGIAALTIEDT 1w8sA 98 :VEEAVSLGASAVGYTIY T0284 123 :AQFGR 1w8sA 115 :PGSGF T0284 135 :VEEGVGKIRAALEARVDPALTIIARTNAELI 1w8sA 120 :EWKMFEELARIKRDAVKFDLPLVVESFPRGG T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHL 1w8sA 157 :APEIVAYAARIALELGADAMKIKYTGDPKTFSWAVKVA T0284 204 :HIPLMLVTYGNPQ 1w8sA 196 :KVPVLMSGGPKTK T0284 219 :DDARLAR 1w8sA 209 :TEEDFLK T0284 226 :LGVRVVVNGHAAY 1w8sA 223 :AGALGIAVGRNVW T0284 239 :FAAIKATYDCL 1w8sA 241 :LKFARALAELV Number of specific fragments extracted= 12 number of extra gaps= 0 total=265 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o5kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1o5kA/merged-good-all-a2m # 1o5kA read from 1o5kA/merged-good-all-a2m # found chain 1o5kA in training set Warning: unaligning (T0284)I185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o5kA)E162 Warning: unaligning (T0284)L187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o5kA)E162 Warning: unaligning (T0284)V232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o5kA)S207 Warning: unaligning (T0284)N233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o5kA)S207 T0284 21 :RCYHTASVFD 1o5kA 3 :RGVGTAIVTP T0284 31 :PMSARIAADLGFECGILGGSVASLQ 1o5kA 24 :ERLVRYQLENGVNALIVLGTTGESP T0284 64 :LITLSEFVEQATRIGRVA 1o5kA 49 :TVNEDEREKLVSRTLEIV T0284 82 :RLPVIADA 1o5kA 69 :KIPVIVGA T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLLPA 1o5kA 77 :GTNSTEKTLKLVKQAEKLGANGVLVVTPYYNK T0284 129 :S 1o5kA 109 :P T0284 135 :VEEGV 1o5kA 110 :TQEGL T0284 140 :GKIRAALEAR 1o5kA 116 :QHYKYISERT T0284 150 :VD 1o5kA 127 :LG T0284 155 :TIIARTNAEL 1o5kA 129 :IVVYNVPGRT T0284 166 :D 1o5kA 139 :G T0284 167 :VDAVIQRTLA 1o5kA 144 :PETAARIAAD T0284 181 :GADG 1o5kA 156 :NVVG T0284 188 :V 1o5kA 163 :A T0284 190 :VRDFAHLEAIAEHL 1o5kA 164 :NPDIDQIDRTVSLT T0284 204 :HI 1o5kA 183 :DF T0284 209 :LVTYGNPQL 1o5kA 185 :MVWSGNDDR T0284 220 :DARLARLGVRVV 1o5kA 194 :TFYLLCAGGDGV T0284 234 :GHAAYF 1o5kA 208 :VVSNVA T0284 242 :IKATYDCLREERG 1o5kA 214 :PKQMVELCAEYFS T0284 255 :AVASDLTASELS 1o5kA 235 :VHRKLRPLMKAL Number of specific fragments extracted= 21 number of extra gaps= 1 total=286 Number of alignments=19 # 1o5kA read from 1o5kA/merged-good-all-a2m # found chain 1o5kA in training set Warning: unaligning (T0284)I185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o5kA)E162 Warning: unaligning (T0284)L187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o5kA)E162 Warning: unaligning (T0284)V232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o5kA)S207 Warning: unaligning (T0284)N233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o5kA)S207 T0284 21 :RCYHTASVFD 1o5kA 3 :RGVGTAIVTP T0284 31 :PMSARIAADLGFECGILGGSVASL 1o5kA 24 :ERLVRYQLENGVNALIVLGTTGES T0284 63 :ALITLSEFVEQATRIGR 1o5kA 48 :PTVNEDEREKLVSRTLE T0284 80 :VARLPVIADA 1o5kA 67 :DGKIPVIVGA T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLLPA 1o5kA 77 :GTNSTEKTLKLVKQAEKLGANGVLVVTPYYNK T0284 133 :ICVEEGVGKIRAALE 1o5kA 109 :PTQEGLYQHYKYISE T0284 149 :RVDPALTII 1o5kA 124 :RTDLGIVVY T0284 159 :RTNAELI 1o5kA 133 :NVPGRTG T0284 166 :DVDAVIQRTLA 1o5kA 143 :LPETAARIAAD T0284 181 :GADG 1o5kA 156 :NVVG T0284 188 :VG 1o5kA 163 :AN T0284 191 :RDFAHLEAIAEHL 1o5kA 165 :PDIDQIDRTVSLT T0284 205 :I 1o5kA 184 :F T0284 209 :LVTYGNPQ 1o5kA 185 :MVWSGNDD T0284 219 :DDARLARLGVRVV 1o5kA 193 :RTFYLLCAGGDGV T0284 234 :GHA 1o5kA 208 :VVS T0284 242 :IKATYDCLREERGA 1o5kA 214 :PKQMVELCAEYFSG T0284 261 :TASELSK 1o5kA 228 :NLEKSRE T0284 274 :EYQAWARD 1o5kA 235 :VHRKLRPL Number of specific fragments extracted= 19 number of extra gaps= 1 total=305 Number of alignments=20 # 1o5kA read from 1o5kA/merged-good-all-a2m # found chain 1o5kA in training set Warning: unaligning (T0284)C186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o5kA)E162 Warning: unaligning (T0284)V188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o5kA)E162 Warning: unaligning (T0284)V232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o5kA)S207 Warning: unaligning (T0284)N233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o5kA)S207 T0284 31 :PMSARIAADLGFECGILGGSVAS 1o5kA 24 :ERLVRYQLENGVNALIVLGTTGE T0284 62 :FALITLSEFVEQATRIGRVA 1o5kA 47 :SPTVNEDEREKLVSRTLEIV T0284 82 :RLPVIADADH 1o5kA 69 :KIPVIVGAGT T0284 94 :GNALNVMRTVVELERAGIAALTIEDTLLPA 1o5kA 79 :NSTEKTLKLVKQAEKLGANGVLVVTPYYNK T0284 133 :ICVEEGVGKIRAALEAR 1o5kA 109 :PTQEGLYQHYKYISERT T0284 152 :PALTIIARTNAELI 1o5kA 126 :DLGIVVYNVPGRTG T0284 166 :DVDAVIQRTLA 1o5kA 143 :LPETAARIAAD T0284 182 :ADGI 1o5kA 156 :NVVG T0284 189 :GVRDFAHLEAIAEHL 1o5kA 163 :ANPDIDQIDRTVSLT T0284 208 :MLVTYGNPQ 1o5kA 184 :FMVWSGNDD T0284 222 :RLARLGVRVV 1o5kA 196 :YLLCAGGDGV T0284 234 :GHA 1o5kA 208 :VVS T0284 242 :IKATYDCLREERGAV 1o5kA 214 :PKQMVELCAEYFSGN T0284 258 :SDLTASELSKKYTF 1o5kA 229 :LEKSREVHRKLRPL Number of specific fragments extracted= 14 number of extra gaps= 1 total=319 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xkyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xkyA expands to /projects/compbio/data/pdb/1xky.pdb.gz 1xkyA:# T0284 read from 1xkyA/merged-good-all-a2m # 1xkyA read from 1xkyA/merged-good-all-a2m # adding 1xkyA to template set # found chain 1xkyA in template set Warning: unaligning (T0284)I165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)I145 Warning: unaligning (T0284)V231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xkyA)V205 Warning: unaligning (T0284)V232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)V205 Warning: unaligning (T0284)N233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)S206 T0284 22 :CYHTASVFD 1xkyA 6 :TIATAMVTP T0284 31 :PMSARIAADLGFECGILGGSVAS 1xkyA 27 :TKLVNYLIDNGTTAIVVGGTTGE T0284 62 :FALITLSEFVEQATRIGRVA 1xkyA 50 :SPTLTSEEKVALYRHVVSVV T0284 82 :RLPVIADA 1xkyA 72 :RVPVIAGT T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLL 1xkyA 80 :GSNNTHASIDLTKKATEVGVDAVMLVAPYY T0284 127 :RKS 1xkyA 110 :NKP T0284 134 :CVEEGVGKIRAALEAR 1xkyA 113 :SQEGMYQHFKAIAEST T0284 153 :ALTIIA 1xkyA 129 :PLPVML T0284 159 :RTNAEL 1xkyA 136 :NVPGRS T0284 166 :DVDA 1xkyA 146 :SVDT T0284 174 :TLAYQEA 1xkyA 150 :VVRLSEI T0284 181 :GADGICLVGVR 1xkyA 158 :NIVAIKDAGGD T0284 193 :FAHLEAIAEHLH 1xkyA 169 :VLTMTEIIEKTA T0284 205 :IPL 1xkyA 183 :FAV T0284 210 :VTYGNPQ 1xkyA 186 :YSGDDGL T0284 220 :DARLARLGVRV 1xkyA 193 :TLPAMAVGAKG T0284 234 :GHAAYFA 1xkyA 207 :VASHVIG T0284 243 :KATYDCLREERG 1xkyA 214 :NEMQEMIAAFQA T0284 255 :AVAS 1xkyA 234 :LHQL Number of specific fragments extracted= 19 number of extra gaps= 2 total=338 Number of alignments=22 # 1xkyA read from 1xkyA/merged-good-all-a2m # found chain 1xkyA in template set Warning: unaligning (T0284)V231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xkyA)V205 Warning: unaligning (T0284)V232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)V205 Warning: unaligning (T0284)N233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)S206 T0284 21 :RCYHTASVFD 1xkyA 5 :GTIATAMVTP T0284 31 :PMSARIAADLGFECGIL 1xkyA 27 :TKLVNYLIDNGTTAIVV T0284 49 :GSVASLQ 1xkyA 44 :GGTTGES T0284 63 :ALITLSEFVEQATRIGR 1xkyA 51 :PTLTSEEKVALYRHVVS T0284 80 :VARLPVIADA 1xkyA 70 :DKRVPVIAGT T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLLPA 1xkyA 80 :GSNNTHASIDLTKKATEVGVDAVMLVAPYYNK T0284 133 :ICVEEGVGKIRAALEA 1xkyA 112 :PSQEGMYQHFKAIAES T0284 152 :PALTIIARTNAELI 1xkyA 129 :PLPVMLYNVPGRSI T0284 166 :DVD 1xkyA 146 :SVD T0284 173 :RTLAYQEA 1xkyA 149 :TVVRLSEI T0284 181 :GADGICLVG 1xkyA 158 :NIVAIKDAG T0284 191 :RDFAHLEAIAEHLH 1xkyA 167 :GDVLTMTEIIEKTA T0284 205 :IPLML 1xkyA 183 :FAVYS T0284 215 :PQLRDDARLARLGVRV 1xkyA 188 :GDDGLTLPAMAVGAKG T0284 234 :GHAAYF 1xkyA 207 :VASHVI T0284 242 :IKATYDCLREERG 1xkyA 213 :GNEMQEMIAAFQA T0284 270 :TFPEEYQAWARDYME 1xkyA 226 :GEFKKAQKLHQLLVR Number of specific fragments extracted= 17 number of extra gaps= 1 total=355 Number of alignments=23 # 1xkyA read from 1xkyA/merged-good-all-a2m # found chain 1xkyA in template set Warning: unaligning (T0284)V230 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xkyA)V205 Warning: unaligning (T0284)V231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)V205 Warning: unaligning (T0284)V232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)S206 T0284 31 :PMSARIAADLGFECGILGGSVA 1xkyA 27 :TKLVNYLIDNGTTAIVVGGTTG T0284 61 :DFALITLSEFVEQATRIGRVA 1xkyA 49 :ESPTLTSEEKVALYRHVVSVV T0284 82 :RLPVIA 1xkyA 72 :RVPVIA T0284 90 :DHGYGNALNVMRTVVELERAGIAALTIEDTLLPA 1xkyA 78 :GTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNK T0284 133 :ICVEEGVGKIRAALEAR 1xkyA 112 :PSQEGMYQHFKAIAEST T0284 152 :PALTIIARTNAELI 1xkyA 129 :PLPVMLYNVPGRSI T0284 166 :DVD 1xkyA 146 :SVD T0284 173 :RTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTYGNP 1xkyA 149 :TVVRLSEIENIVAIKDAGGDVLTMTEIIEKTADDFAVYSGDDG T0284 220 :DARLARLGVR 1xkyA 194 :LPAMAVGAKG T0284 233 :NGHAA 1xkyA 207 :VASHV T0284 241 :AIKATYDCLREERGAV 1xkyA 212 :IGNEMQEMIAAFQAGE T0284 257 :ASDLTASELSK 1xkyA 230 :KAQKLHQLLVR Number of specific fragments extracted= 12 number of extra gaps= 1 total=367 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zlpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0284/1zlpA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0284/1zlpA/merged-good-all-a2m.gz for input Trying 1zlpA/merged-good-all-a2m Error: Couldn't open file 1zlpA/merged-good-all-a2m or 1zlpA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q7zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1q7zA/merged-good-all-a2m # 1q7zA read from 1q7zA/merged-good-all-a2m # found chain 1q7zA in training set T0284 5 :SHHELRAMFRA 1q7zA 3 :NRREVSKLLSE T0284 21 :RCYHTASVFDPMSA 1q7zA 14 :RVLLLDGAYGTEFM T0284 35 :RIAADLGFECGILG 1q7zA 51 :RSYIESGSDVILTN T0284 49 :GSVASLQVLAAPDF 1q7zA 68 :ATRMKLRKHGLEDK T0284 67 :LSEFVEQATRIGR 1q7zA 82 :LDPIVRNAVRIAR T0284 80 :VARLPVIADAD 1q7zA 97 :AGEKLVFGDIG T0284 91 :HG 1q7zA 109 :TG T0284 93 :YGN 1q7zA 116 :LGS T0284 96 :ALNVMRTVVELERAGIAALTIED 1q7zA 125 :YENFRETVEIMVEEGVDGIIFET T0284 135 :VEEGVGKIRAALEAR 1q7zA 148 :FSDILELKAAVLAAR T0284 150 :VDPALTIIARTNAELI 1q7zA 164 :VSRDVFLIAHMTFDEK T0284 167 :VDAVIQRTLAYQEAGADGICLVGVR 1q7zA 339 :EEIVIKEAKTQVEKGAEVLDVNFGI T0284 192 :DFAHLEAIAEHL 1q7zA 368 :DVRYVEKIVQTL T0284 204 :HIPLMLV 1q7zA 384 :NVPLSLD T0284 212 :Y 1q7zA 391 :I T0284 218 :RDD 1q7zA 392 :QNV T0284 221 :ARLARLGVRVVVN 1q7zA 425 :NLLKKYGGTLIVL T0284 243 :KATYDCLREERGAVASD 1q7zA 448 :EERKEYFEKALKILERH Number of specific fragments extracted= 18 number of extra gaps= 0 total=385 Number of alignments=25 # 1q7zA read from 1q7zA/merged-good-all-a2m # found chain 1q7zA in training set T0284 5 :SHHELRAMFRA 1q7zA 3 :NRREVSKLLSE T0284 21 :RCYHTASVFDPMS 1q7zA 14 :RVLLLDGAYGTEF T0284 34 :ARIAADLGFECGILG 1q7zA 50 :HRSYIESGSDVILTN T0284 49 :GSVASLQVLAAPDF 1q7zA 68 :ATRMKLRKHGLEDK T0284 67 :LSEFVEQATRIGR 1q7zA 82 :LDPIVRNAVRIAR T0284 80 :VARLPVIADADH 1q7zA 97 :AGEKLVFGDIGP T0284 92 :G 1q7zA 110 :G T0284 93 :YG 1q7zA 114 :YP T0284 95 :N 1q7zA 117 :G T0284 96 :ALNVMRTVVELERAGIAALTIEDTL 1q7zA 125 :YENFRETVEIMVEEGVDGIIFETFS T0284 137 :EGVGKIRAALEA 1q7zA 150 :DILELKAAVLAA T0284 149 :RVDPALTIIARTNAELID 1q7zA 163 :EVSRDVFLIAHMTFDEKG T0284 168 :DAVIQRTLAYQEAGADGICLVGVR 1q7zA 340 :EIVIKEAKTQVEKGAEVLDVNFGI T0284 192 :DFAHLEAIAEHL 1q7zA 368 :DVRYVEKIVQTL T0284 204 :HIPLMLVT 1q7zA 384 :NVPLSLDI T0284 218 :RDDA 1q7zA 392 :QNVD T0284 222 :RLARLGVRVVVNGH 1q7zA 426 :LLKKYGGTLIVLLM T0284 256 :VAS 1q7zA 440 :GKD T0284 259 :DLTASELSKKY 1q7zA 444 :PKSFEERKEYF T0284 272 :PEEYQAWARD 1q7zA 455 :EKALKILERH Number of specific fragments extracted= 20 number of extra gaps= 0 total=405 Number of alignments=26 # 1q7zA read from 1q7zA/merged-good-all-a2m # found chain 1q7zA in training set T0284 6 :HHELRAMFRALLDSSRCYHTASVFD 1q7zA 86 :VRNAVRIARRAAGEKLVFGDIGPTG T0284 31 :PMSARIAADLGFECGIL 1q7zA 129 :RETVEIMVEEGVDGIIF T0284 49 :GSVASL 1q7zA 156 :AAVLAA T0284 56 :VLAAP 1q7zA 197 :ELDID T0284 63 :ALITLSEFVEQATRIGRVARLPVIADADHG 1q7zA 207 :CSLGPEEILPIFQELSQYTDKFLVVEPNAG T0284 93 :YG 1q7zA 247 :YP T0284 95 :NALNVMRTVVELERAGIAAL 1q7zA 250 :KPHDFAVHIDSYYELGVNIF T0284 123 :AQFGRK 1q7zA 271 :GCCGTT T0284 139 :VGKIRAALEARVD 1q7zA 277 :PEHVKLFRKVLGN T0284 152 :PALTIIA 1q7zA 313 :DHFVVIG T0284 159 :RTNAELI 1q7zA 321 :RINPAGR T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRD 1q7zA 338 :NEEIVIKEAKTQVEKGAEVLDVNFGIE T0284 193 :FAHLEAIAEHL 1q7zA 417 :EEELEMKINLL T0284 204 :HIPLMLVTYGNPQLRDDARLAR 1q7zA 431 :GGTLIVLLMGKDVPKSFEERKE T0284 241 :AIKATYDCLREE 1q7zA 453 :YFEKALKILERH Number of specific fragments extracted= 15 number of extra gaps= 0 total=420 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rvgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rvgA expands to /projects/compbio/data/pdb/1rvg.pdb.gz 1rvgA:Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1326, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1328, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1330, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1336, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1346, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1348, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1350, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1352, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1354, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1356, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1358, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1360, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1362, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1364, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1581, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1583, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1585, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1587, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1589, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1601, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1603, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1615, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1617, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1621, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1623, because occupancy 0.500 <= existing 0.500 in 1rvgA # T0284 read from 1rvgA/merged-good-all-a2m # 1rvgA read from 1rvgA/merged-good-all-a2m # adding 1rvgA to template set # found chain 1rvgA in template set T0284 10 :RAMFRALLDSSRCYHTASVFDPMSA 1rvgA 6 :LEILKKAREEGYGVGAFNVNNMEFL T0284 35 :RIAADLGFECGILGGSVA 1rvgA 35 :EAAEEQRSPVILALSEGA T0284 54 :LQ 1rvgA 53 :MK T0284 57 :LA 1rvgA 55 :YG T0284 67 :LSEFVEQATRIGRVARLPVIADADHG 1rvgA 57 :GRALTLMAVELAKEARVPVAVHLDHG T0284 94 :GNALN 1rvgA 83 :SSYES T0284 103 :VVELERAGIAALTIEDTLLP 1rvgA 88 :VLRALRAGFTSVMIDKSHED T0284 135 :VEEGVGKIRAALEARVDPALTIIART 1rvgA 108 :FETNVRETRRVVEAAHAVGVTVEAEL T0284 161 :NAELIDVDAVIQ 1rvgA 149 :DALLTNPEEARI T0284 176 :AYQEAGADGICLV 1rvgA 161 :FMERTGADYLAVA T0284 189 :GV 1rvgA 175 :GT T0284 192 :DFAHLEAIAEHLHIPL 1rvgA 190 :DHARLERIARLVPAPL T0284 210 :VTYGNPQLRDD 1rvgA 206 :VLHGASAVPPE T0284 221 :ARLARLGVRVVVNGHAAYFAAIKATYDC 1rvgA 240 :KKAISLGIAKINTDTDLRLAFTALIREA T0284 253 :RG 1rvgA 268 :LN T0284 264 :ELSKKYTFPEEYQAWARD 1rvgA 270 :KNPKEFDPRKYLGPAREA Number of specific fragments extracted= 16 number of extra gaps= 0 total=436 Number of alignments=28 # 1rvgA read from 1rvgA/merged-good-all-a2m # found chain 1rvgA in template set T0284 9 :LRAMFRALLDSSRCYHTASVFDPMSARI 1rvgA 5 :GLEILKKAREEGYGVGAFNVNNMEFLQA T0284 37 :AADLGFECGILGGSVASL 1rvgA 37 :AEEQRSPVILALSEGAMK T0284 57 :LA 1rvgA 55 :YG T0284 67 :LSEFVEQATRIGRVARLPVIADADHG 1rvgA 57 :GRALTLMAVELAKEARVPVAVHLDHG T0284 94 :GNALNV 1rvgA 83 :SSYESV T0284 104 :VELERAGIAALTIEDTLL 1rvgA 89 :LRALRAGFTSVMIDKSHE T0284 134 :CVEEGVGKIRAALEARVDPALTIIART 1rvgA 107 :DFETNVRETRRVVEAAHAVGVTVEAEL T0284 161 :NAELIDVDAVIQRTLA 1rvgA 149 :DALLTNPEEARIFMER T0284 180 :AGADGICLVGVR 1rvgA 165 :TGADYLAVAIGT T0284 192 :DFAHLEAIAEHLHIPLMLVTYGNPQLRDDA 1rvgA 190 :DHARLERIARLVPAPLVLHGASAVPPELVE T0284 222 :RLARLGVRVVVNGHAAYFAA 1rvgA 241 :KAISLGIAKINTDTDLRLAF T0284 246 :YDCLREERGAVASDLTASELSK 1rvgA 261 :TALIREALNKNPKEFDPRKYLG T0284 273 :EEYQAWARDYME 1rvgA 283 :PAREAVKEVVKS Number of specific fragments extracted= 13 number of extra gaps= 0 total=449 Number of alignments=29 # 1rvgA read from 1rvgA/merged-good-all-a2m # found chain 1rvgA in template set T0284 9 :LRAMFRALLDSSRCYHTASVFDPMSARIAADL 1rvgA 5 :GLEILKKAREEGYGVGAFNVNNMEFLQAVLEA T0284 41 :GFECGILGGSVASLQV 1rvgA 41 :RSPVILALSEGAMKYG T0284 67 :LSEFVEQATRIGRVARLPVIADADHGYG 1rvgA 57 :GRALTLMAVELAKEARVPVAVHLDHGSS T0284 100 :MRTVVELERAGIAALTIEDTLLP 1rvgA 85 :YESVLRALRAGFTSVMIDKSHED T0284 135 :VEEGVGKIRAALEARVDPALTIIART 1rvgA 108 :FETNVRETRRVVEAAHAVGVTVEAEL T0284 161 :NAELIDVDAVIQR 1rvgA 149 :DALLTNPEEARIF T0284 177 :YQEAGADGICLVGVRD 1rvgA 162 :MERTGADYLAVAIGTS T0284 193 :FAHLEAIAEHLHIPLMLVTY 1rvgA 191 :HARLERIARLVPAPLVLHGA T0284 213 :GNPQLRDDARLA 1rvgA 229 :GEAAGIHPEDIK T0284 225 :RLGVRVVVNGHAAYFAAIKATYDCLREERGAVASDLTASELSK 1rvgA 244 :SLGIAKINTDTDLRLAFTALIREALNKNPKEFDPRKYLGPARE Number of specific fragments extracted= 10 number of extra gaps= 0 total=459 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f8iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0284/1f8iA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0284/1f8iA/merged-good-all-a2m.gz for input Trying 1f8iA/merged-good-all-a2m Error: Couldn't open file 1f8iA/merged-good-all-a2m or 1f8iA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1muwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1muwA/merged-good-all-a2m # 1muwA read from 1muwA/merged-good-all-a2m # found chain 1muwA in training set Warning: unaligning (T0284)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1muwA)H53 Warning: unaligning (T0284)G48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1muwA)H53 Warning: unaligning (T0284)A182 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1muwA)I175 T0284 30 :DPMSARIAADLGFECGI 1muwA 35 :PVETVQRLAELGAHGVT T0284 53 :SLQVLAA 1muwA 56 :DLIPFGS T0284 66 :TLSEFVEQATRIGRVA 1muwA 63 :SDTERESHIKRFRQAL T0284 82 :RLPVIADA 1muwA 84 :TVPMATTN T0284 90 :DHGYG 1muwA 100 :DGGFT T0284 95 :N 1muwA 106 :N T0284 96 :ALNVMRTVVELERAGIAALTIEDTLL 1muwA 115 :LRKTIRNIDLAVELGAKTYVAWGGRE T0284 125 :FGRKSTD 1muwA 141 :GAESGAA T0284 133 :ICVEEGVGKIRAAL 1muwA 148 :KDVRVALDRMKEAF T0284 168 :DAVIQRTLA 1muwA 162 :DLLGEYVTS T0284 180 :AG 1muwA 171 :QG T0284 183 :DGICLVGV 1muwA 176 :RFAIEPKP T0284 191 :RDFAHLEAIAEHLHIPLM 1muwA 193 :PTVGHALAFIERLERPEL T0284 210 :VTYGNP 1muwA 211 :YGVNPE T0284 216 :QLRDD 1muwA 223 :AGLNF T0284 221 :ARLARLGV 1muwA 272 :DLLESAGY T0284 229 :RVVVNGHA 1muwA 283 :RHFDFKPP T0284 238 :YFAAIKATYDCLREERGAVASDLTASELSKKYTFPEEYQ 1muwA 298 :VWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDE Number of specific fragments extracted= 18 number of extra gaps= 2 total=477 Number of alignments=31 # 1muwA read from 1muwA/merged-good-all-a2m # found chain 1muwA in training set Warning: unaligning (T0284)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1muwA)H53 Warning: unaligning (T0284)G48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1muwA)H53 Warning: unaligning (T0284)A182 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1muwA)I175 T0284 31 :PMSARIAADLGFECGI 1muwA 36 :VETVQRLAELGAHGVT T0284 49 :GSVA 1muwA 54 :DDDL T0284 55 :QVLAAP 1muwA 58 :IPFGSS T0284 67 :LSEFVEQATRIGRVAR 1muwA 64 :DTERESHIKRFRQALD T0284 83 :LPVIADA 1muwA 85 :VPMATTN T0284 90 :DHGYG 1muwA 100 :DGGFT T0284 95 :N 1muwA 107 :D T0284 96 :ALNVMRTVVELERAGIAALTIEDTLL 1muwA 115 :LRKTIRNIDLAVELGAKTYVAWGGRE T0284 125 :FGRKSTD 1muwA 141 :GAESGAA T0284 133 :ICVEEGVGKIRAAL 1muwA 148 :KDVRVALDRMKEAF T0284 168 :DAVIQRTL 1muwA 162 :DLLGEYVT T0284 179 :EAG 1muwA 170 :SQG T0284 183 :DGICLVGVR 1muwA 176 :RFAIEPKPN T0284 192 :DFAHLEAIAEHLHIP 1muwA 194 :TVGHALAFIERLERP T0284 208 :MLVT 1muwA 211 :YGVN T0284 222 :RLARLGVR 1muwA 273 :LLESAGYE T0284 230 :VVVNGH 1muwA 283 :RHFDFK T0284 236 :A 1muwA 297 :G T0284 241 :AIKATYDCLREERG 1muwA 298 :VWASAAGCMRNYLI T0284 262 :ASELSKKYTFPEEYQAWARDYME 1muwA 313 :KERAAAFRADPEVQEALRASRLD Number of specific fragments extracted= 20 number of extra gaps= 2 total=497 Number of alignments=32 # 1muwA read from 1muwA/merged-good-all-a2m # found chain 1muwA in training set Warning: unaligning (T0284)R218 because of BadResidue code BAD_PEPTIDE in next template residue (1muwA)G345 Warning: unaligning (T0284)D219 because of BadResidue code BAD_PEPTIDE at template residue (1muwA)G345 T0284 2 :HRASHHELRAMFRALLDSSR 1muwA 63 :SDTERESHIKRFRQALDATG T0284 22 :CYHTASVFD 1muwA 86 :PMATTNLFT T0284 31 :PMSARIAADLGFECGILGGS 1muwA 119 :IRNIDLAVELGAKTYVAWGG T0284 56 :VLAAPDFALITLSEFVEQATRIGRVARL 1muwA 139 :REGAESGAAKDVRVALDRMKEAFDLLGE T0284 90 :DHGYGNALNVMRTVVELERAGIAALTIEDTLLPAQF 1muwA 258 :RFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTE T0284 134 :CVEEGVGKIRAALEARV 1muwA 294 :DIDGVWASAAGCMRNYL T0284 169 :AVIQRTLAYQE 1muwA 311 :ILKERAAAFRA T0284 193 :FAHLEAIAEHLHI 1muwA 322 :DPEVQEALRASRL T0284 209 :LVTYGNPQL 1muwA 335 :DELAQPTAA T0284 220 :DARLARL 1muwA 346 :VQELLAD T0284 254 :GAVASDLTASELSKKYTFPEEYQAWARD 1muwA 353 :RTAFEDFDVDAAAARGMAFERLDQLAMD Number of specific fragments extracted= 11 number of extra gaps= 1 total=508 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s2uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0284/1s2uA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0284/1s2uA/merged-good-all-a2m.gz for input Trying 1s2uA/merged-good-all-a2m Error: Couldn't open file 1s2uA/merged-good-all-a2m or 1s2uA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rhcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1rhcA/merged-good-all-a2m # 1rhcA read from 1rhcA/merged-good-all-a2m # found chain 1rhcA in training set Warning: unaligning (T0284)R159 because of BadResidue code BAD_PEPTIDE in next template residue (1rhcA)I73 Warning: unaligning (T0284)T160 because of BadResidue code BAD_PEPTIDE at template residue (1rhcA)I73 T0284 21 :RCYHTAS 1rhcA 3 :TQIGYFA T0284 90 :DHGYGNALNVMRTVVELERAGIAALTIEDTLL 1rhcA 10 :SLEQYRPMDALEQAIRAEKVGFDSVWVDDHFH T0284 124 :QFGRKSTD 1rhcA 42 :PWYHDNAQ T0284 135 :VEEGVGKIRAALEAR 1rhcA 50 :SAQAWAWMGAALQAT T0284 152 :PALTIIA 1rhcA 65 :KKVFIST T0284 171 :IQRTLAYQEA 1rhcA 177 :PKGAKLAGMY T0284 182 :ADGICLVGVR 1rhcA 187 :GDHLMTVAAA T0284 193 :FAH 1rhcA 197 :PST T0284 196 :LEAIAEHLH 1rhcA 208 :FEEGAREAG T0284 205 :IPL 1rhcA 222 :MEH T0284 208 :MLVTYGNPQLRDD 1rhcA 226 :MLIWYSVDPDYDK T0284 221 :ARLARLGVRVVVNGHAAYFA 1rhcA 295 :ERFKEAGINHFCLGNSSPDV T0284 243 :KATYDCLREERGAVA 1rhcA 315 :NFGIDIFKEVIPAVR Number of specific fragments extracted= 13 number of extra gaps= 1 total=521 Number of alignments=34 # 1rhcA read from 1rhcA/merged-good-all-a2m # found chain 1rhcA in training set Warning: unaligning (T0284)R159 because of BadResidue code BAD_PEPTIDE in next template residue (1rhcA)I73 T0284 82 :RLPVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1rhcA 2 :KTQIGYFASLEQYRPMDALEQAIRAEKVGFDSVWVDDHFHP T0284 125 :FGRKS 1rhcA 43 :WYHDN T0284 133 :ICVEEGVGKIRAALEA 1rhcA 48 :AQSAQAWAWMGAALQA T0284 152 :PALTIIA 1rhcA 65 :KKVFIST T0284 160 :TNAELI 1rhcA 74 :TCPIMR T0284 166 :DV 1rhcA 81 :NP T0284 172 :QRTLAYQEA 1rhcA 178 :KGAKLAGMY T0284 182 :ADGICLVGVR 1rhcA 187 :GDHLMTVAAA T0284 193 :FAHLEAIAEHLH 1rhcA 205 :IPKFEEGAREAG T0284 205 :IPLMLVTYGNPQLRDDA 1rhcA 223 :EHAMLIWYSVDPDYDKA T0284 222 :RLARLGVRVVVNGHA 1rhcA 296 :RFKEAGINHFCLGNS T0284 242 :IKATYDCLREERGAVA 1rhcA 314 :VNFGIDIFKEVIPAVR Number of specific fragments extracted= 12 number of extra gaps= 1 total=533 Number of alignments=35 # 1rhcA read from 1rhcA/merged-good-all-a2m # found chain 1rhcA in training set Warning: unaligning (T0284)S27 because of BadResidue code BAD_PEPTIDE in next template residue (1rhcA)I73 Warning: unaligning (T0284)V28 because of BadResidue code BAD_PEPTIDE at template residue (1rhcA)I73 T0284 6 :H 1rhcA 53 :A T0284 10 :RAMFRALLDS 1rhcA 54 :WAWMGAALQA T0284 20 :SRCYHTA 1rhcA 65 :KKVFIST T0284 29 :FD 1rhcA 74 :TC T0284 31 :PMSARIAADL 1rhcA 83 :AIVAQTFATL T0284 41 :GFECGILG 1rhcA 98 :GRVGVAVG T0284 49 :GSVASLQV 1rhcA 107 :GEAMNEVP T0284 62 :FALITLSEFVEQATRIGRVARL 1rhcA 117 :GEWPSVPVRQDMTVEAVKVMRM T0284 84 :PVIA 1rhcA 189 :HLMT T0284 89 :AD 1rhcA 193 :VA T0284 94 :GNALNVMR 1rhcA 195 :AAPSTLKN T0284 102 :TVVELER 1rhcA 204 :TIPKFEE T0284 109 :AGI 1rhcA 215 :AGK T0284 112 :AALTIEDTLLPA 1rhcA 224 :HAMLIWYSVDPD T0284 126 :GRKSTDLICVEEGVGKI 1rhcA 253 :SMFKYKVYDPKEVQLHA T0284 143 :RAALEAR 1rhcA 275 :DTIKENY T0284 167 :VDAVIQRTLAYQEAGADGICLVGVRD 1rhcA 287 :AEEMIKEIERFKEAGINHFCLGNSSP T0284 193 :FAHLEAIAEHLH 1rhcA 318 :IDIFKEVIPAVR Number of specific fragments extracted= 18 number of extra gaps= 1 total=551 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gzgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gzgA expands to /projects/compbio/data/pdb/1gzg.pdb.gz 1gzgA:Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 268, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 419, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 421, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 423, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 425, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 427, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 429, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 1241, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1243, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1245, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1247, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1249, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1251, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1253, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1255, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1257, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1259, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1261, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1453, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1455, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1457, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1459, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1461, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1463, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1465, because occupancy 0.200 <= existing 0.800 in 1gzgA Skipped atom 1491, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 1493, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 1495, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 1497, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 1499, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 1501, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2021, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2023, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2025, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2027, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2029, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2031, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2033, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2035, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2116, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2118, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2120, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2122, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2124, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2126, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2128, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2130, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2132, because occupancy 0.300 <= existing 0.700 in 1gzgA Skipped atom 2162, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2164, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2166, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2168, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2170, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2172, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2174, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2176, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2178, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2180, because occupancy 0.500 <= existing 0.500 in 1gzgA Skipped atom 2182, because occupancy 0.500 <= existing 0.500 in 1gzgA # T0284 read from 1gzgA/merged-good-all-a2m # 1gzgA read from 1gzgA/merged-good-all-a2m # adding 1gzgA to template set # found chain 1gzgA in template set Warning: unaligning (T0284)R159 because of BadResidue code BAD_PEPTIDE at template residue (1gzgA)K205 Warning: unaligning (T0284)L187 because of BadResidue code BAD_PEPTIDE in next template residue (1gzgA)K260 Warning: unaligning (T0284)V188 because of BadResidue code BAD_PEPTIDE at template residue (1gzgA)K260 T0284 23 :YHTASVFD 1gzgA 39 :ILPVFVLD T0284 31 :PMSARIAADLGFECGILG 1gzgA 69 :LIEAEEWVALGIPALALF T0284 56 :VLAAPDFALIT 1gzgA 93 :KKSLDAAEAYN T0284 69 :EFVEQATRIGRVA 1gzgA 107 :IAQRATRALRERF T0284 82 :RLPVIADAD 1gzgA 121 :ELGIITDVA T0284 92 :GYG 1gzgA 135 :THG T0284 96 :ALNVMRTVVELERAGIAALTIEDTL 1gzgA 154 :IDVLVRQALSHAEAGAQVVAPSDMM T0284 140 :GKIRAALEAR 1gzgA 180 :GRIGAIREAL T0284 150 :VDPALTIIA 1gzgA 193 :GHTNVRVMA T0284 160 :TNAELI 1gzgA 206 :YASAYY T0284 166 :DVDAVIQRTLAYQEAGADGIC 1gzgA 238 :NSDEALHEVAADLAEGADMVM T0284 189 :GVRDFAHLEAIAEHLHIPLMLVTY 1gzgA 262 :GMPYLDIVRRVKDEFRAPTFVYQV T0284 219 :DD 1gzgA 286 :SG T0284 221 :ARLARLGVRVVVNGHAAYFA 1gzgA 311 :TAFKRAGADGILTYFAKQAA T0284 247 :DC 1gzgA 331 :EQ Number of specific fragments extracted= 15 number of extra gaps= 2 total=566 Number of alignments=37 # 1gzgA read from 1gzgA/merged-good-all-a2m # found chain 1gzgA in template set Warning: unaligning (T0284)R159 because of BadResidue code BAD_PEPTIDE at template residue (1gzgA)K205 Warning: unaligning (T0284)L187 because of BadResidue code BAD_PEPTIDE in next template residue (1gzgA)K260 Warning: unaligning (T0284)V188 because of BadResidue code BAD_PEPTIDE at template residue (1gzgA)K260 Warning: unaligning (T0284)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gzgA)P261 T0284 10 :RAMFRALLDS 1gzgA 65 :IDQLLIEAEE T0284 37 :AADLGFECGILG 1gzgA 75 :WVALGIPALALF T0284 57 :LA 1gzgA 96 :LD T0284 59 :APDF 1gzgA 103 :NPEG T0284 70 :FVEQATRIGR 1gzgA 108 :AQRATRALRE T0284 80 :VARLPVIADADH 1gzgA 119 :FPELGIITDVAL T0284 93 :YG 1gzgA 133 :FT T0284 96 :ALNVMRTVVELERAGIAALTIEDTL 1gzgA 154 :IDVLVRQALSHAEAGAQVVAPSDMM T0284 136 :EEGVGKIRAALEARVDPALTIIA 1gzgA 179 :DGRIGAIREALESAGHTNVRVMA T0284 160 :TNAELIDV 1gzgA 206 :YASAYYGP T0284 168 :DAVIQRTLAYQEAGADGIC 1gzgA 240 :DEALHEVAADLAEGADMVM T0284 190 :VRDFAHLEAIAEHLHIPLMLVTY 1gzgA 263 :MPYLDIVRRVKDEFRAPTFVYQV T0284 218 :RDDA 1gzgA 287 :GEYA T0284 222 :RLARLGVRVVVNGH 1gzgA 312 :AFKRAGADGILTYF T0284 245 :TYDCLREER 1gzgA 326 :AKQAAEQLR Number of specific fragments extracted= 15 number of extra gaps= 2 total=581 Number of alignments=38 # 1gzgA read from 1gzgA/merged-good-all-a2m # found chain 1gzgA in template set Warning: unaligning (T0284)N161 because of BadResidue code BAD_PEPTIDE in next template residue (1gzgA)K205 Warning: unaligning (T0284)A162 because of BadResidue code BAD_PEPTIDE at template residue (1gzgA)K205 Warning: unaligning (T0284)L187 because of BadResidue code BAD_PEPTIDE in next template residue (1gzgA)K260 Warning: unaligning (T0284)V188 because of BadResidue code BAD_PEPTIDE at template residue (1gzgA)K260 Warning: unaligning (T0284)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gzgA)P261 T0284 31 :PMSARIAADLGFECGILGGSV 1gzgA 69 :LIEAEEWVALGIPALALFPVT T0284 56 :VLAAPDFALITL 1gzgA 93 :KKSLDAAEAYNP T0284 70 :FVEQATRIGRVA 1gzgA 108 :AQRATRALRERF T0284 82 :RLPVIADA 1gzgA 121 :ELGIITDV T0284 90 :DHGYG 1gzgA 144 :DDGYV T0284 95 :NALNVMRTVVELERAGIAALTIEDTLLP 1gzgA 153 :SIDVLVRQALSHAEAGAQVVAPSDMMDG T0284 138 :GVGKIRAALEARVDPALTIIART 1gzgA 181 :RIGAIREALESAGHTNVRVMAYS T0284 163 :ELI 1gzgA 206 :YAS T0284 167 :VDAVIQRTLAYQEAGADGIC 1gzgA 239 :SDEALHEVAADLAEGADMVM T0284 190 :VRD 1gzgA 262 :GMP T0284 193 :FAHLEAIAEHLHIPLMLVTY 1gzgA 266 :LDIVRRVKDEFRAPTFVYQV T0284 213 :GNPQLR 1gzgA 299 :GWLAES T0284 220 :DARLARLGVRVVVNGHAAYF 1gzgA 310 :LTAFKRAGADGILTYFAKQA Number of specific fragments extracted= 13 number of extra gaps= 2 total=594 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1thfD/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1thfD/merged-good-all-a2m # 1thfD read from 1thfD/merged-good-all-a2m # found chain 1thfD in training set T0284 21 :RCYHTASV 1thfD 5 :RIIACLDV T0284 31 :PMSARIAADLGFE 1thfD 33 :VELGKFYSEIGID T0284 44 :CGILG 1thfD 47 :LVFLD T0284 61 :DFALITLSEFVEQATRIGRVARLPVIADAD 1thfD 53 :TASVEKRKTMLELVEKVAEQIDIPFTVGGG T0284 93 :YGNAL 1thfD 83 :IHDFE T0284 102 :TVVELERAGIAALTIE 1thfD 88 :TASELILRGADKVSIN T0284 136 :EEGV 1thfD 104 :TAAV T0284 140 :GKIRAALEA 1thfD 111 :SLITQIAQT T0284 150 :VDPALTIIA 1thfD 120 :FGSQAVVVA T0284 159 :RTNAEL 1thfD 133 :RVDGEF T0284 166 :D 1thfD 146 :K T0284 167 :VDAV 1thfD 153 :LRDW T0284 174 :TLAYQEAGADGICLVGV 1thfD 157 :VVEVEKRGAGEILLTSI T0284 192 :DFAHLEAIAEHLHIPL 1thfD 183 :DTEMIRFVRPLTTLPI T0284 209 :LVTYGNPQLRDDARLARLGVRVVVNGHAAYF 1thfD 199 :IASGGAGKMEHFLEAFLAGADAALAASVFHF T0284 245 :TYDCLREERG 1thfD 234 :VRELKEYLKK Number of specific fragments extracted= 16 number of extra gaps= 0 total=610 Number of alignments=40 # 1thfD read from 1thfD/merged-good-all-a2m # found chain 1thfD in training set T0284 22 :CYHTASV 1thfD 6 :IIACLDV T0284 30 :DPMSARIAADLGFE 1thfD 32 :PVELGKFYSEIGID T0284 44 :CGILG 1thfD 47 :LVFLD T0284 61 :DFALITLSEFVEQATRIGRVARLPVIADADH 1thfD 53 :TASVEKRKTMLELVEKVAEQIDIPFTVGGGI T0284 94 :GNALN 1thfD 84 :HDFET T0284 103 :VVELERAGIAALTIEDT 1thfD 89 :ASELILRGADKVSINTA T0284 138 :GV 1thfD 106 :AV T0284 140 :GKIRAALEARVDPA 1thfD 111 :SLITQIAQTFGSQA T0284 154 :LTIIAR 1thfD 127 :VAIDAK T0284 160 :TNA 1thfD 134 :VDG T0284 170 :VIQRTLAYQEAGADGICLVGVR 1thfD 153 :LRDWVVEVEKRGAGEILLTSID T0284 192 :DFAHLEAIAEHLHIPLMLVTY 1thfD 183 :DTEMIRFVRPLTTLPIIASGG T0284 214 :NP 1thfD 204 :AG T0284 219 :DDARLARL 1thfD 206 :KMEHFLEA T0284 227 :GVRVVVNGHAAY 1thfD 217 :GADAALAASVFH T0284 245 :TYDCLREERGAVA 1thfD 234 :VRELKEYLKKHGV Number of specific fragments extracted= 16 number of extra gaps= 0 total=626 Number of alignments=41 # 1thfD read from 1thfD/merged-good-all-a2m # found chain 1thfD in training set T0284 31 :PMSARIAADLGFECGILGG 1thfD 33 :VELGKFYSEIGIDELVFLD T0284 57 :LA 1thfD 52 :IT T0284 62 :FALITLSEFVEQATRIGRVARLPVIADA 1thfD 54 :ASVEKRKTMLELVEKVAEQIDIPFTVGG T0284 94 :G 1thfD 82 :G T0284 95 :N 1thfD 85 :D T0284 100 :MRTVVELERAGIAALTIE 1thfD 86 :FETASELILRGADKVSIN T0284 136 :EEGV 1thfD 104 :TAAV T0284 140 :GKIRAALEAR 1thfD 111 :SLITQIAQTF T0284 151 :DPALTIIAR 1thfD 121 :GSQAVVVAI T0284 167 :V 1thfD 153 :L T0284 171 :IQRTLAYQEAGADGICLVGVRD 1thfD 154 :RDWVVEVEKRGAGEILLTSIDR T0284 193 :FAHLEAIAEHLHIPLMLVTYG 1thfD 184 :TEMIRFVRPLTTLPIIASGGA T0284 218 :RDDARLAR 1thfD 205 :GKMEHFLE T0284 226 :LGVRVVVNGHAA 1thfD 216 :AGADAALAASVF T0284 252 :ERGAVASDLTASELSKKY 1thfD 228 :HFREIDVRELKEYLKKHG Number of specific fragments extracted= 15 number of extra gaps= 0 total=641 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s2wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1s2wA/merged-good-all-a2m # 1s2wA read from 1s2wA/merged-good-all-a2m # found chain 1s2wA in training set Warning: unaligning (T0284)L57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s2wA)W64 Warning: unaligning (T0284)L67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s2wA)W64 Warning: unaligning (T0284)L121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s2wA)G127 Warning: unaligning (T0284)K268 because last residue in template chain is (1s2wA)L278 T0284 7 :HELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQ 1s2wA 5 :VKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQ T0284 68 :SEFVEQATRIGRVARLPVIADADHGYGNALNVMRTVVELERAGIAALTIEDTL 1s2wA 65 :TQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKL T0284 128 :KSTDLICVEEGVGKIRAALEARVDPALTIIARTNAELID 1s2wA 128 :RAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAG T0284 167 :VDAVIQRTLAYQEAGADGICLV 1s2wA 169 :LDEALKRAEAYRNAGADAILMH T0284 189 :GVRDFAHLEAIAEHLH 1s2wA 192 :KKADPSDIEAFMKAWN T0284 205 :IPL 1s2wA 210 :GPV T0284 209 :LVTYGNPQLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERG 1s2wA 213 :VIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYD T0284 255 :AVASDLTASELSK 1s2wA 265 :VEDKIVSVKEIFR Number of specific fragments extracted= 8 number of extra gaps= 0 total=649 Number of alignments=43 # 1s2wA read from 1s2wA/merged-good-all-a2m # found chain 1s2wA in training set Warning: unaligning (T0284)L57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s2wA)W64 Warning: unaligning (T0284)L67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s2wA)W64 Warning: unaligning (T0284)L121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s2wA)G127 Warning: unaligning (T0284)K268 because last residue in template chain is (1s2wA)L278 T0284 8 :ELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQ 1s2wA 6 :KKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQ T0284 68 :SEFVEQATRIGRVARLPVIADADHGYGNALNVMRTVVELERAGIAALTIEDTL 1s2wA 65 :TQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKL T0284 128 :KSTDLICVEEGVGKIRAALEARVDPALTIIARTNAELI 1s2wA 128 :RAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIA T0284 166 :DVDAVIQRTLAYQEAGADGICLVG 1s2wA 168 :GLDEALKRAEAYRNAGADAILMHS T0284 190 :VRDFAHLEAIAEHLH 1s2wA 193 :KADPSDIEAFMKAWN T0284 205 :IPLMLVTYGNPQL 1s2wA 210 :GPVVIVPTKYYKT T0284 219 :DDARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVAS 1s2wA 223 :PTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSL T0284 259 :DLTASELSK 1s2wA 269 :IVSVKEIFR Number of specific fragments extracted= 8 number of extra gaps= 0 total=657 Number of alignments=44 # 1s2wA read from 1s2wA/merged-good-all-a2m # found chain 1s2wA in training set Warning: unaligning (T0284)L57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s2wA)W64 Warning: unaligning (T0284)L67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s2wA)W64 Warning: unaligning (T0284)L121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s2wA)G127 Warning: unaligning (T0284)T130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s2wA)G127 Warning: unaligning (T0284)E274 because last residue in template chain is (1s2wA)L278 T0284 9 :LRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQ 1s2wA 7 :KTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQ T0284 68 :SEFVEQATRIGRVARLPVIADADHGYGNALNVMRTVVELERAGIAALTIEDTL 1s2wA 65 :TQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKL T0284 131 :D 1s2wA 128 :R T0284 132 :LICVEEGVGKIRAALEARVDPALTIIARTNAELI 1s2wA 132 :LADIEEFALKIKACKDSQTDPDFCIVARVEAFIA T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRD 1s2wA 168 :GLDEALKRAEAYRNAGADAILMHSKKA T0284 193 :FAHLEAIAEHL 1s2wA 196 :PSDIEAFMKAW T0284 204 :HIPLMLVTYGNPQLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVASDLTASELSKKYTFPE 1s2wA 208 :NQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFR Number of specific fragments extracted= 7 number of extra gaps= 0 total=664 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wv2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wv2A expands to /projects/compbio/data/pdb/1wv2.pdb.gz 1wv2A:# T0284 read from 1wv2A/merged-good-all-a2m # 1wv2A read from 1wv2A/merged-good-all-a2m # adding 1wv2A to template set # found chain 1wv2A in template set Warning: unaligning (T0284)T66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wv2A)I1069 Warning: unaligning (T0284)L67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wv2A)I1069 Warning: unaligning (T0284)F271 because last residue in template chain is (1wv2A)K1251 T0284 21 :RCYHTASVFD 1wv2A 1019 :GSRLLVGTGK T0284 31 :PMSARIAADLGFECGILG 1wv2A 1033 :DETRRAIEASGAEIVTVA T0284 62 :FALI 1wv2A 1051 :VRRT T0284 81 :A 1wv2A 1070 :P T0284 82 :RLPVIADA 1wv2A 1073 :RYTILPNT T0284 91 :HGYGNALNVMRTVVELERAG 1wv2A 1081 :AGCYDAVEAVRTCRLARELL T0284 111 :IAALTIEDTLLPAQFGR 1wv2A 1103 :HNLVKLEVLADQKTLFP T0284 137 :EGVGKIRAALEARVD 1wv2A 1120 :NVVETLKAAEQLVKD T0284 153 :ALTIIARTNAELI 1wv2A 1135 :GFDVMVYTSDDPI T0284 173 :RTLAYQEAGADGICLVGV 1wv2A 1148 :IARQLAEIGCIAVMPLAG T0284 191 :RDFAHLEAIAEHLHIPLM 1wv2A 1174 :CNPYNLRIILEEAKVPVL T0284 210 :VTYGNPQLRDDARLARLGVRVVVNGHAAYFA 1wv2A 1192 :VDAGVGTASDAAIAMELGCEAVLMNTAIAHA T0284 245 :TYDCLREERGAVASDLTASELSKKYT 1wv2A 1225 :PVMMAEAMKHAIVAGRLAYLAGRMPR Number of specific fragments extracted= 13 number of extra gaps= 1 total=677 Number of alignments=46 # 1wv2A read from 1wv2A/merged-good-all-a2m # found chain 1wv2A in template set T0284 21 :RCYHTASVFDP 1wv2A 1019 :GSRLLVGTGKY T0284 32 :MSARIAADLGFECGILG 1wv2A 1034 :ETRRAIEASGAEIVTVA T0284 59 :APDFALI 1wv2A 1070 :PPDRYTI T0284 66 :TLSEFVEQATRIGR 1wv2A 1085 :DAVEAVRTCRLARE T0284 80 :VARL 1wv2A 1100 :LDGH T0284 84 :PVIADADH 1wv2A 1105 :LVKLEVLA T0284 93 :YGNALNVMRTVVELERAGIAALTIEDT 1wv2A 1118 :FPNVVETLKAAEQLVKDGFDVMVYTSD T0284 161 :NAE 1wv2A 1145 :DPI T0284 173 :RTLAYQEAGADGICLVGVR 1wv2A 1148 :IARQLAEIGCIAVMPLAGL T0284 192 :DFAHLEAIAEHLHIPLM 1wv2A 1175 :NPYNLRIILEEAKVPVL T0284 210 :VTYGNPQLRDDARLARLGVRVVVNGHAA 1wv2A 1192 :VDAGVGTASDAAIAMELGCEAVLMNTAI T0284 238 :YFAAIKATYDCLREERGAVAS 1wv2A 1229 :AEAMKHAIVAGRLAYLAGRMP Number of specific fragments extracted= 12 number of extra gaps= 0 total=689 Number of alignments=47 # 1wv2A read from 1wv2A/merged-good-all-a2m # found chain 1wv2A in template set Warning: unaligning (T0284)T66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wv2A)I1069 Warning: unaligning (T0284)L67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wv2A)I1069 T0284 21 :RCYHTASVFD 1wv2A 1019 :GSRLLVGTGK T0284 32 :MSARIAADLGFECGILG 1wv2A 1034 :ETRRAIEASGAEIVTVA T0284 62 :FALI 1wv2A 1051 :VRRT T0284 84 :PVIADADHGYGNALNVMRTVVELERA 1wv2A 1074 :YTILPNTAGCYDAVEAVRTCRLAREL T0284 110 :GIAALTIEDTLLPA 1wv2A 1102 :GHNLVKLEVLADQK T0284 130 :TDLICVEEGVGKIRAAL 1wv2A 1116 :TLFPNVVETLKAAEQLV T0284 152 :PALTIIARTNAE 1wv2A 1134 :DGFDVMVYTSDD T0284 171 :IQRTLAYQEAGADGICLVGVRD 1wv2A 1146 :PIIARQLAEIGCIAVMPLAGLI T0284 193 :FAHLEAIAEHLHIPLMLVTYG 1wv2A 1176 :PYNLRIILEEAKVPVLVDAGV T0284 218 :RDDARLA 1wv2A 1197 :GTASDAA T0284 225 :RLGVRVVVNGHAA 1wv2A 1207 :ELGCEAVLMNTAI T0284 238 :YFAAIKATYDCLREERGAV 1wv2A 1229 :AEAMKHAIVAGRLAYLAGR Number of specific fragments extracted= 12 number of extra gaps= 1 total=701 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rvkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1rvkA/merged-good-all-a2m # 1rvkA read from 1rvkA/merged-good-all-a2m # found chain 1rvkA in training set T0284 7 :HELRAMFRALLDS 1rvkA 79 :ERLWQDLAHWQRG T0284 20 :S 1rvkA 94 :A T0284 27 :SVFDPMSARIAADL 1rvkA 95 :QLTDRTLAVVDCAL T0284 50 :SVASLQVLAAP 1rvkA 109 :WDLAGRSLGQP T0284 73 :QATRIGRVA 1rvkA 120 :VYKLIGGYR T0284 82 :RLPVIADADH 1rvkA 130 :KVLAYGSIMC T0284 92 :GYGNALNVMRTVVELERAGIAALTIED 1rvkA 146 :GLATPEDYGRFAETLVKRGYKGIKLHT T0284 125 :FGRKSTDLICVEEGVGKIRAALEAR 1rvkA 173 :WMPPVSWAPDVKMDLKACAAVREAV T0284 151 :DPALTIIART 1rvkA 198 :GPDIRLMIDA T0284 162 :AELIDVDAVIQRTLAYQEAGADGICLVG 1rvkA 208 :FHWYSRTDALALGRGLEKLGFDWIEEPM T0284 190 :VRDFAHLEAIAEHLHIPL 1rvkA 237 :EQSLSSYKWLSDNLDIPV T0284 210 :VTYGNPQLRDD 1rvkA 255 :VGPESAAGKHW T0284 221 :ARLARLGVRVVVNGHAAYFAA 1rvkA 297 :HLAEAFGMECEVHGNTAMNLH Number of specific fragments extracted= 13 number of extra gaps= 0 total=714 Number of alignments=49 # 1rvkA read from 1rvkA/merged-good-all-a2m # found chain 1rvkA in training set T0284 5 :SHHELRAMFRALLDS 1rvkA 77 :DRERLWQDLAHWQRG T0284 20 :SR 1rvkA 94 :AQ T0284 28 :VFDPMSARIAADL 1rvkA 96 :LTDRTLAVVDCAL T0284 50 :SVASLQVLAAP 1rvkA 109 :WDLAGRSLGQP T0284 73 :QATRIGRVAR 1rvkA 120 :VYKLIGGYRD T0284 83 :LPVIADADH 1rvkA 131 :VLAYGSIMC T0284 92 :GYGNALNVMRTVVELERAGIAALTIED 1rvkA 146 :GLATPEDYGRFAETLVKRGYKGIKLHT T0284 125 :FGRKSTDLICVEEGVGKIRAALEAR 1rvkA 173 :WMPPVSWAPDVKMDLKACAAVREAV T0284 151 :DPALTIIAR 1rvkA 198 :GPDIRLMID T0284 161 :NAELIDVDAVIQRTLAYQEAGADGICLVG 1rvkA 207 :AFHWYSRTDALALGRGLEKLGFDWIEEPM T0284 190 :VRDFAHLEAIAEHLHIPLMLVTYGNPQLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVAS 1rvkA 237 :EQSLSSYKWLSDNLDIPVVGPESAAGKHWHRAEWIKAGACDILRTGVNDVGGITPALKTMHLAEAFGME Number of specific fragments extracted= 11 number of extra gaps= 0 total=725 Number of alignments=50 # 1rvkA read from 1rvkA/merged-good-all-a2m # found chain 1rvkA in training set T0284 4 :ASHHELRAMFRALLDSSR 1rvkA 76 :RDRERLWQDLAHWQRGSA T0284 27 :SVFDPMSARIAADL 1rvkA 95 :QLTDRTLAVVDCAL T0284 50 :SVASLQVLAAP 1rvkA 109 :WDLAGRSLGQP T0284 77 :IGRVARL 1rvkA 120 :VYKLIGG T0284 84 :PVIADA 1rvkA 132 :LAYGSI T0284 90 :DHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1rvkA 144 :EGGLATPEDYGRFAETLVKRGYKGIKLHTWMPP T0284 123 :A 1rvkA 178 :S T0284 132 :LICVEEGVGKIRAALEAR 1rvkA 180 :APDVKMDLKACAAVREAV T0284 151 :DPALTIIA 1rvkA 198 :GPDIRLMI T0284 161 :NAELI 1rvkA 206 :DAFHW T0284 166 :DVDAVIQRTLAYQEAGADGICLVG 1rvkA 212 :SRTDALALGRGLEKLGFDWIEEPM T0284 190 :VRDFAHLEAIAEHLHIPLMLVTYG 1rvkA 237 :EQSLSSYKWLSDNLDIPVVGPESA T0284 216 :Q 1rvkA 261 :A T0284 218 :R 1rvkA 262 :G T0284 220 :DARLARL 1rvkA 264 :HWHRAEW T0284 227 :GVRVVVNGHAAY 1rvkA 275 :ACDILRTGVNDV T0284 239 :FAAIKATYDCLREE 1rvkA 289 :ITPALKTMHLAEAF Number of specific fragments extracted= 17 number of extra gaps= 0 total=742 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m3uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m3uA expands to /projects/compbio/data/pdb/1m3u.pdb.gz 1m3uA:Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 1m3uA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 1m3uA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 1m3uA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 1m3uA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 1m3uA Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 1m3uA Skipped atom 785, because occupancy 0.500 <= existing 0.500 in 1m3uA Skipped atom 787, because occupancy 0.500 <= existing 0.500 in 1m3uA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 1m3uA Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 1m3uA Skipped atom 1829, because occupancy 0.500 <= existing 0.500 in 1m3uA Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 1m3uA Skipped atom 1833, because occupancy 0.500 <= existing 0.500 in 1m3uA # T0284 read from 1m3uA/merged-good-all-a2m # 1m3uA read from 1m3uA/merged-good-all-a2m # adding 1m3uA to template set # found chain 1m3uA in template set Warning: unaligning (T0284)H7 because first residue in template chain is (1m3uA)P3 Warning: unaligning (T0284)F42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1m3uA)N39 Warning: unaligning (T0284)E43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m3uA)N39 Warning: unaligning (T0284)D88 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1m3uA)L85 Warning: unaligning (T0284)A89 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m3uA)L85 T0284 8 :ELRAMFRALLDSSRCYHTASVFDPMSARIAADLG 1m3uA 4 :TTISLLQKYKQEKKRFATITAYDYSFAKLFADEG T0284 44 :CGIL 1m3uA 40 :VMLV T0284 49 :GSVASLQVLAAPDFALITLSEFVEQATRIGRVA 1m3uA 44 :GDSLGMTVQGHDSTLPVTVADIAYHTAAVRRGA T0284 82 :RLPVIA 1m3uA 78 :NCLLLA T0284 90 :DH 1m3uA 86 :PF T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTL 1m3uA 89 :AYATPEQAFENAATVMRAGANMVKIEGGE T0284 137 :EGVGKIRAALEA 1m3uA 118 :WLVETVQMLTER T0284 153 :ALTIIART 1m3uA 130 :AVPVCGHL T0284 161 :NAEL 1m3uA 140 :TPQS T0284 166 :D 1m3uA 156 :G T0284 167 :VDAVIQRTLAYQEAGADGICLVGVR 1m3uA 160 :GDQLLSDALALEAAGAQLLVLECVP T0284 193 :FAHLEAIAEHLHIPL 1m3uA 185 :VELAKRITEALAIPV T0284 210 :VTYGNPQLRD 1m3uA 200 :IGIGAGNVTD T0284 230 :VVVNG 1m3uA 210 :GQILV T0284 249 :LREERG 1m3uA 215 :MHDAFG T0284 255 :AVASDLTASELSKKYTFPEE 1m3uA 243 :AVRQYMAEVESGVYPGEEHS Number of specific fragments extracted= 16 number of extra gaps= 2 total=758 Number of alignments=52 # 1m3uA read from 1m3uA/merged-good-all-a2m # found chain 1m3uA in template set Warning: unaligning (T0284)F42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1m3uA)N39 Warning: unaligning (T0284)E43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m3uA)N39 Warning: unaligning (T0284)D88 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1m3uA)L85 Warning: unaligning (T0284)A89 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m3uA)L85 T0284 10 :RAMFRALLDSSRCYHTASVFDPMSARIAADLG 1m3uA 6 :ISLLQKYKQEKKRFATITAYDYSFAKLFADEG T0284 44 :CGIL 1m3uA 40 :VMLV T0284 49 :GSVASLQVLAAPDFALITLSEFVEQATRIGR 1m3uA 44 :GDSLGMTVQGHDSTLPVTVADIAYHTAAVRR T0284 80 :VARLPVIA 1m3uA 76 :APNCLLLA T0284 90 :DH 1m3uA 86 :PF T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTL 1m3uA 89 :AYATPEQAFENAATVMRAGANMVKIEGGE T0284 137 :EGVGKIRAALE 1m3uA 118 :WLVETVQMLTE T0284 152 :PALTIIAR 1m3uA 129 :RAVPVCGH T0284 160 :TNAELIDV 1m3uA 139 :LTPQSVNI T0284 168 :DAVIQRTLAYQEAGADGICLVGVR 1m3uA 161 :DQLLSDALALEAAGAQLLVLECVP T0284 193 :FAHLEAIAEHLHIPLMLVTYGNPQLRDDARLARL 1m3uA 185 :VELAKRITEALAIPVIGIGAGNVTDGQILVMHDA T0284 227 :GVRVVVNGHA 1m3uA 220 :GITGGHIPKF T0284 246 :YDCLREERGAVAS 1m3uA 241 :RAAVRQYMAEVES T0284 259 :DLTAS 1m3uA 256 :YPGEE Number of specific fragments extracted= 14 number of extra gaps= 2 total=772 Number of alignments=53 # 1m3uA read from 1m3uA/merged-good-all-a2m # found chain 1m3uA in template set Warning: unaligning (T0284)F42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1m3uA)N39 Warning: unaligning (T0284)E43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m3uA)N39 Warning: unaligning (T0284)D88 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1m3uA)L85 Warning: unaligning (T0284)A89 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m3uA)L85 T0284 10 :RAMFRALLDSSRCYHTASVFDPMSARIAADLG 1m3uA 6 :ISLLQKYKQEKKRFATITAYDYSFAKLFADEG T0284 44 :CGILGGSVASLQ 1m3uA 40 :VMLVGDSLGMTV T0284 57 :LAAPDFALITLSEFVEQATRIGRVA 1m3uA 52 :QGHDSTLPVTVADIAYHTAAVRRGA T0284 82 :RLPVIA 1m3uA 78 :NCLLLA T0284 90 :DH 1m3uA 86 :PF T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDT 1m3uA 89 :AYATPEQAFENAATVMRAGANMVKIEGG T0284 136 :EEGVGKIRAALEARVD 1m3uA 117 :EWLVETVQMLTERAVP T0284 154 :LTIIARTNAE 1m3uA 134 :CGHLGLTPQS T0284 167 :VDAVIQRTLAYQEAGADGICLVGVR 1m3uA 160 :GDQLLSDALALEAAGAQLLVLECVP T0284 193 :FAHLEAIAEHLHIPLMLVTYG 1m3uA 185 :VELAKRITEALAIPVIGIGAG T0284 226 :LGVRVVVNGHAAY 1m3uA 206 :NVTDGQILVMHDA T0284 239 :FAAIKATYDCLRE 1m3uA 241 :RAAVRQYMAEVES Number of specific fragments extracted= 12 number of extra gaps= 2 total=784 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qwgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1qwgA/merged-good-all-a2m # 1qwgA read from 1qwgA/merged-good-all-a2m # found chain 1qwgA in training set Warning: unaligning (T0284)L154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0284)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0284 22 :CYHTASVFDPMSA 1qwgA 16 :TVVLDKGLPPKFV T0284 35 :RIAADL 1qwgA 30 :DYLKVC T0284 42 :FECGIL 1qwgA 39 :IDFVKF T0284 49 :GS 1qwgA 45 :GW T0284 60 :PDFALITLSEFVEQATRIGRVA 1qwgA 47 :GTSAVIDRDVVKEKINYYKDWG T0284 82 :RL 1qwgA 70 :KV T0284 101 :RTVVELERAGIAALTIEDTLLPA 1qwgA 89 :EFLNECEKLGFEAVEISDGSSDI T0284 134 :CVEEGVGKIRAALEA 1qwgA 112 :SLEERNNAIKRAKDN T0284 153 :A 1qwgA 127 :G T0284 156 :IIART 1qwgA 130 :VLTEV T0284 161 :NAELIDVDAVIQRTLAYQEAGADGICLVGV 1qwgA 141 :KDKQLTIDDRIKLINFDLDAGADYVIIEGR T0284 192 :DFAHLEAIAEHLHIPLMLVTYG 1qwgA 186 :KENELDVLAKNVDINKVIFEAP T0284 219 :DDARLAR 1qwgA 208 :QKSQQVA T0284 226 :LGVRVVVNGHAAY 1qwgA 221 :SSVNLANIAFDEV T0284 243 :KATYDCLR 1qwgA 234 :ISLETLRR Number of specific fragments extracted= 15 number of extra gaps= 1 total=799 Number of alignments=55 # 1qwgA read from 1qwgA/merged-good-all-a2m # found chain 1qwgA in training set Warning: unaligning (T0284)I111 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0284)A112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0284 4 :ASHHELRAMFRAL 1qwgA 23 :LPPKFVEDYLKVC T0284 42 :FECGIL 1qwgA 39 :IDFVKF T0284 49 :GS 1qwgA 45 :GW T0284 60 :PDFALITLSEFVEQATRIGR 1qwgA 47 :GTSAVIDRDVVKEKINYYKD T0284 80 :VAR 1qwgA 68 :GIK T0284 83 :LPVIADADHGYG 1qwgA 99 :FEAVEISDGSSD T0284 95 :NALNVMRTVVELERAG 1qwgA 112 :SLEERNNAIKRAKDNG T0284 113 :ALTIEDTLLPAQ 1qwgA 130 :VLTEVGKKMPDK T0284 162 :AELIDVDAVIQRTLAYQEAGADGICLVGVR 1qwgA 142 :DKQLTIDDRIKLINFDLDAGADYVIIEGRE T0284 192 :DFAHLEAIAEHLH 1qwgA 186 :KENELDVLAKNVD T0284 208 :MLVTY 1qwgA 202 :VIFEA T0284 214 :NPQLRDDARLARL 1qwgA 207 :PQKSQQVAFILKF T0284 227 :GVRVVVNG 1qwgA 222 :SVNLANIA Number of specific fragments extracted= 13 number of extra gaps= 1 total=812 Number of alignments=56 # 1qwgA read from 1qwgA/merged-good-all-a2m # found chain 1qwgA in training set Warning: unaligning (T0284)L154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0284)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0284 22 :CYHTASVFDPMSARIAADL 1qwgA 16 :TVVLDKGLPPKFVEDYLKV T0284 41 :GFECGILG 1qwgA 38 :YIDFVKFG T0284 59 :APDFALITLSEFVEQATRIGRV 1qwgA 46 :WGTSAVIDRDVVKEKINYYKDW T0284 82 :RLPVIA 1qwgA 68 :GIKVYP T0284 92 :G 1qwgA 74 :G T0284 94 :GNALN 1qwgA 75 :GTLFE T0284 99 :VMRTVVELERAGIAALTIEDTLLP 1qwgA 87 :FDEFLNECEKLGFEAVEISDGSSD T0284 133 :ICVEEGVGKIRAALEA 1qwgA 111 :ISLEERNNAIKRAKDN T0284 153 :A 1qwgA 127 :G T0284 156 :IIARTNAELI 1qwgA 130 :VLTEVGKKMP T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRD 1qwgA 146 :TIDDRIKLINFDLDAGADYVIIEGRES T0284 193 :FAHLEAIAEHLHIPLMLVTYG 1qwgA 187 :ENELDVLAKNVDINKVIFEAP T0284 234 :GHAAYFAAIKAT 1qwgA 208 :QKSQQVAFILKF Number of specific fragments extracted= 13 number of extra gaps= 1 total=825 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gvfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1gvfA/merged-good-all-a2m # 1gvfA read from 1gvfA/merged-good-all-a2m # found chain 1gvfA in training set T0284 10 :RAMFRALLDSSRCYHTASVFDPMSA 1gvfA 7 :KYLLQDAQANGYAVPAFNIHNAETI T0284 35 :RIAADLGFECGILG 1gvfA 36 :EVCSEMRSPVILAG T0284 50 :SVASLQ 1gvfA 50 :TPGTFK T0284 64 :LITLSEFVEQATRIGRVARLPVIADADH 1gvfA 56 :HIALEEIYALCSAYSTTYNMPLALHLDH T0284 93 :YGNALNVMRTV 1gvfA 84 :HESLDDIRRKV T0284 108 :RAGIAALTIEDTLLPA 1gvfA 95 :HAGVRSAMIDGSHFPF T0284 136 :EEGVGKIRAALEARVDPALTIIART 1gvfA 111 :AENVKLVKSVVDFCHSQDCSVEAEL T0284 166 :DVDA 1gvfA 156 :DPQE T0284 174 :TLAYQE 1gvfA 160 :AKRFVE T0284 180 :AGADGICLV 1gvfA 167 :TGVDSLAVA T0284 189 :G 1gvfA 177 :G T0284 192 :DFAHLEAIAEHLHIPL 1gvfA 190 :DFQRLAEIREVVDVPL T0284 210 :VTYGNPQLRDD 1gvfA 206 :VLHGASDVPDE T0284 221 :ARLARLGVRVVVNGHAAY 1gvfA 219 :RRTIELGVTKVNVATELK T0284 243 :KATYDCLREERG 1gvfA 237 :IAFAGAVKAWFA T0284 255 :AVASDLTASE 1gvfA 263 :GMDAMKEVVR Number of specific fragments extracted= 16 number of extra gaps= 0 total=841 Number of alignments=58 # 1gvfA read from 1gvfA/merged-good-all-a2m # found chain 1gvfA in training set T0284 10 :RAMFRALLDSSRCYHTASVFDPMSARIAADL 1gvfA 7 :KYLLQDAQANGYAVPAFNIHNAETIQAILEV T0284 41 :GFECGILG 1gvfA 42 :RSPVILAG T0284 57 :LA 1gvfA 51 :PG T0284 64 :LITLSEFVEQATRIGRVARL 1gvfA 56 :HIALEEIYALCSAYSTTYNM T0284 84 :PVIADA 1gvfA 78 :ALHLDH T0284 93 :YGNALNVMRTV 1gvfA 84 :HESLDDIRRKV T0284 108 :RAGIAALTIEDTLL 1gvfA 95 :HAGVRSAMIDGSHF T0284 134 :CVEEGVGKIRAALEARVDPALTIIART 1gvfA 109 :PFAENVKLVKSVVDFCHSQDCSVEAEL T0284 168 :DAVIQRTLA 1gvfA 158 :QEAKRFVEL T0284 181 :GADGICLVGVR 1gvfA 168 :GVDSLAVAIGT T0284 192 :DFAHLEAIAEHLHIPLMLVTYGNPQLRDDARLARLGVRVVVNGHAAYFA 1gvfA 190 :DFQRLAEIREVVDVPLVLHGASDVPDEFVRRTIELGVTKVNVATELKIA T0284 245 :TYDCLREERGAVASDLTASELSKK 1gvfA 239 :FAGAVKAWFAENPQGNDPRYYMRV T0284 274 :EYQAWARDYME 1gvfA 263 :GMDAMKEVVRN Number of specific fragments extracted= 13 number of extra gaps= 0 total=854 Number of alignments=59 # 1gvfA read from 1gvfA/merged-good-all-a2m # found chain 1gvfA in training set T0284 10 :RAMFRALLDSSRCYHTASVFDPMSARIAADL 1gvfA 7 :KYLLQDAQANGYAVPAFNIHNAETIQAILEV T0284 41 :GFECGILGGSVASL 1gvfA 42 :RSPVILAGTPGTFK T0284 64 :LITLSEFVEQATRIGRVARLPVIADADHG 1gvfA 56 :HIALEEIYALCSAYSTTYNMPLALHLDHH T0284 94 :GNALNVMRTV 1gvfA 85 :ESLDDIRRKV T0284 108 :RAGIAALTIEDTLLP 1gvfA 95 :HAGVRSAMIDGSHFP T0284 135 :VEEGVGKIRAALEARVDPALTIIART 1gvfA 110 :FAENVKLVKSVVDFCHSQDCSVEAEL T0284 167 :VDA 1gvfA 157 :PQE T0284 174 :TLAYQE 1gvfA 160 :AKRFVE T0284 180 :AGADGICLVGVRD 1gvfA 167 :TGVDSLAVAIGTA T0284 193 :FAHLEAIAEHLHIPLMLVT 1gvfA 191 :FQRLAEIREVVDVPLVLHG T0284 215 :PQLRDDARLA 1gvfA 210 :ASDVPDEFVR T0284 225 :RLGVRVVVNGHAAYFAAIKATYDCLREERGAVASDLTASELSKK 1gvfA 223 :ELGVTKVNVATELKIAFAGAVKAWFAENPQGNDPRYYMRVGMDA T0284 271 :FPEEYQ 1gvfA 267 :MKEVVR Number of specific fragments extracted= 13 number of extra gaps= 0 total=867 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f8mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1f8mA/merged-good-all-a2m # 1f8mA read from 1f8mA/merged-good-all-a2m # found chain 1f8mA in training set T0284 7 :HELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQ 1f8mA 50 :RRGAEVLWEQLHDLEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGD T0284 56 :VLA 1f8mA 101 :LSG T0284 59 :APDFALITLSEFVEQATRIGRVA 1f8mA 106 :YPDQSLYPANSVPQVVRRINNAL T0284 84 :PVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1f8mA 149 :PIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLAS T0284 123 :AQFGR 1f8mA 189 :KKCGH T0284 128 :KSTDLICVEEGVGKIRAALEAR 1f8mA 195 :GGKVLIPTQQHIRTLTSARLAA T0284 150 :VDPALTIIARTNAELI 1f8mA 219 :ADVPTVVIARTDAEAA T0284 166 :DVDAVIQRTLAYQEA 1f8mA 264 :GIEPCIARAKAYAPF T0284 182 :ADGICLV 1f8mA 279 :ADLIWME T0284 189 :GVRDFAHLEAIAEHL 1f8mA 287 :GTPDLEAARQFSEAV T0284 204 :HIPLMLVTYGNPQLRDD 1f8mA 304 :EYPDQMLAYNCSPSFNW T0284 221 :ARLARLGVRVVVNGHAAYFAAIKATYDCLREERG 1f8mA 334 :KELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQ T0284 257 :ASDLTASELSK 1f8mA 368 :NQMSAYVELQE T0284 268 :KYTFPEEY 1f8mA 381 :FAAEERGY Number of specific fragments extracted= 14 number of extra gaps= 0 total=881 Number of alignments=61 # 1f8mA read from 1f8mA/merged-good-all-a2m # found chain 1f8mA in training set T0284 2 :HRASHHELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASL 1f8mA 45 :EHTLARRGAEVLWEQLHDLEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAG T0284 55 :QVLA 1f8mA 100 :NLSG T0284 59 :APDFALITLSEFVEQATRIGRVAR 1f8mA 106 :YPDQSLYPANSVPQVVRRINNALQ T0284 83 :LPVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1f8mA 148 :APIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLAS T0284 123 :AQFGR 1f8mA 189 :KKCGH T0284 128 :KSTDLICVEEGVGKIRAALEA 1f8mA 195 :GGKVLIPTQQHIRTLTSARLA T0284 149 :RVDPALTIIARTNAELIDV 1f8mA 218 :VADVPTVVIARTDAEAATL T0284 168 :DAVIQRTLAYQEA 1f8mA 266 :EPCIARAKAYAPF T0284 182 :ADGICLVG 1f8mA 279 :ADLIWMET T0284 190 :VRDFAHLEAIAEHL 1f8mA 288 :TPDLEAARQFSEAV T0284 205 :IPLMLVTYGNPQLRDDA 1f8mA 305 :YPDQMLAYNCSPSFNWK T0284 222 :RLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVAS 1f8mA 335 :ELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQMS T0284 271 :FPEEYQAWARDYME 1f8mA 372 :AYVELQEREFAAEE Number of specific fragments extracted= 13 number of extra gaps= 0 total=894 Number of alignments=62 # 1f8mA read from 1f8mA/merged-good-all-a2m # found chain 1f8mA in training set T0284 1 :MHRASHHELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQ 1f8mA 44 :EEHTLARRGAEVLWEQLHDLEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGD T0284 57 :LAAPDFALITLSEFVEQATRIGRVARL 1f8mA 104 :HTYPDQSLYPANSVPQVVRRINNALQR T0284 84 :PVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1f8mA 149 :PIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLAS T0284 123 :AQFGRKSTD 1f8mA 189 :KKCGHLGGK T0284 132 :LICVEEGVGKIRAAL 1f8mA 199 :LIPTQQHIRTLTSAR T0284 147 :EARVDPALTIIARTNAELI 1f8mA 216 :ADVADVPTVVIARTDAEAA T0284 167 :VDAVIQRTLAYQEA 1f8mA 265 :IEPCIARAKAYAPF T0284 182 :ADGICLVGVRD 1f8mA 279 :ADLIWMETGTP T0284 193 :FAHLEAIAEHL 1f8mA 291 :LEAARQFSEAV T0284 204 :HIPLMLVTYGNPQLRDD 1f8mA 304 :EYPDQMLAYNCSPSFNW T0284 221 :ARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVAS 1f8mA 334 :KELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQMS T0284 271 :FPEEYQAWARDYME 1f8mA 372 :AYVELQEREFAAEE Number of specific fragments extracted= 12 number of extra gaps= 0 total=906 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tx2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tx2A expands to /projects/compbio/data/pdb/1tx2.pdb.gz 1tx2A:# T0284 read from 1tx2A/merged-good-all-a2m # 1tx2A read from 1tx2A/merged-good-all-a2m # adding 1tx2A to template set # found chain 1tx2A in template set Warning: unaligning (T0284)R3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tx2A)G36 Warning: unaligning (T0284)A4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tx2A)G36 Warning: unaligning (T0284)V51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tx2A)F71 Warning: unaligning (T0284)F62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tx2A)F71 T0284 5 :SHHELRAMFRA 1tx2A 37 :GSYNEVDAAVR T0284 33 :SARIAADLGFECGILGGS 1tx2A 48 :HAKEMRDEGAHIIDIGGE T0284 63 :ALITLSE 1tx2A 72 :AKVSVEE T0284 70 :FVEQATRIGRVARLPVIADAD 1tx2A 83 :VVPMIQAVSKEVKLPISIDTY T0284 100 :MRTVVELERAGIAALTIEDTL 1tx2A 105 :AEVAKQAIEAGAHIINDIWGA T0284 136 :EEGVGKIRAALEA 1tx2A 126 :KAEPKIAEVAAHY T0284 153 :ALTIIARTNAELID 1tx2A 139 :DVPIILMHNRDNMN T0284 167 :VDAVIQRTLAYQE 1tx2A 157 :MADMIADLYDSIK T0284 180 :AGAD 1tx2A 174 :AGVR T0284 184 :GICLV 1tx2A 181 :IILDP T0284 189 :GVRDFAHLEAIAEHLH 1tx2A 189 :FAKTPEQNLEAMRNLE T0284 205 :IPLM 1tx2A 211 :YPVL T0284 211 :TYG 1tx2A 215 :LGT T0284 216 :QLRDD 1tx2A 218 :SRKSF T0284 221 :ARLARLGVRVVVNGH 1tx2A 243 :CLGIEKGCEFVRVHD T0284 242 :IKATYDCLREERGAV 1tx2A 258 :VKEMSRMAKMMDAMI Number of specific fragments extracted= 16 number of extra gaps= 1 total=922 Number of alignments=64 # 1tx2A read from 1tx2A/merged-good-all-a2m # found chain 1tx2A in template set Warning: unaligning (T0284)L57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tx2A)F71 Warning: unaligning (T0284)F62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tx2A)F71 T0284 6 :HHELRAMFRALLDSS 1tx2A 42 :VDAAVRHAKEMRDEG T0284 42 :FECGILGGS 1tx2A 57 :AHIIDIGGE T0284 63 :ALITLSE 1tx2A 72 :AKVSVEE T0284 70 :FVEQATRIGRVARLPVIADAD 1tx2A 83 :VVPMIQAVSKEVKLPISIDTY T0284 95 :NA 1tx2A 104 :KA T0284 101 :RTVVELERAGIAALTIEDTLLP 1tx2A 106 :EVAKQAIEAGAHIINDIWGAKA T0284 138 :GVGKIRAALEA 1tx2A 128 :EPKIAEVAAHY T0284 153 :ALTIIARTNAELID 1tx2A 139 :DVPIILMHNRDNMN T0284 167 :VDAVIQRT 1tx2A 157 :MADMIADL T0284 175 :LAYQEAGA 1tx2A 169 :KIAKDAGV T0284 184 :GICLVG 1tx2A 181 :IILDPG T0284 190 :VRDFAHLEAIAEHLH 1tx2A 190 :AKTPEQNLEAMRNLE T0284 205 :IPLMLVTYGNPQLRDDA 1tx2A 211 :YPVLLGTSRKSFIGHVL T0284 222 :RLARLGVRVVVNGH 1tx2A 244 :LGIEKGCEFVRVHD T0284 242 :IKATYDCLREERGA 1tx2A 258 :VKEMSRMAKMMDAM Number of specific fragments extracted= 15 number of extra gaps= 0 total=937 Number of alignments=65 # 1tx2A read from 1tx2A/merged-good-all-a2m # found chain 1tx2A in template set Warning: unaligning (T0284)L57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tx2A)F71 Warning: unaligning (T0284)F62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tx2A)F71 T0284 6 :HHELRAMFRAL 1tx2A 38 :SYNEVDAAVRH T0284 34 :ARIAADLGFECGILGGS 1tx2A 49 :AKEMRDEGAHIIDIGGE T0284 63 :ALITLSE 1tx2A 72 :AKVSVEE T0284 70 :FVEQATRIGRVARLPVIADADH 1tx2A 83 :VVPMIQAVSKEVKLPISIDTYK T0284 100 :MRTVVELERAGIAALT 1tx2A 105 :AEVAKQAIEAGAHIIN T0284 118 :DTLLPAQFG 1tx2A 121 :DIWGAKAEP T0284 140 :GKIRAALEA 1tx2A 130 :KIAEVAAHY T0284 153 :ALTIIARTNA 1tx2A 139 :DVPIILMHNR T0284 167 :VDAVIQRTLAYQEAGAD 1tx2A 161 :IADLYDSIKIAKDAGVR T0284 184 :GICLVGV 1tx2A 181 :IILDPGI T0284 191 :RDFAHLEAIAEHL 1tx2A 191 :KTPEQNLEAMRNL T0284 204 :HIPLMLVTY 1tx2A 210 :GYPVLLGTS T0284 213 :GNPQLRDDARLA 1tx2A 228 :DLPVEERLEGTG T0284 225 :RLGVRVVVNGH 1tx2A 247 :EKGCEFVRVHD T0284 242 :IKATYDCLREERG 1tx2A 258 :VKEMSRMAKMMDA Number of specific fragments extracted= 15 number of extra gaps= 0 total=952 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2mnr/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2mnr expands to /projects/compbio/data/pdb/2mnr.pdb.gz 2mnr:Warning: there is no chain 2mnr will retry with 2mnrA # T0284 read from 2mnr/merged-good-all-a2m # 2mnr read from 2mnr/merged-good-all-a2m # adding 2mnr to template set # found chain 2mnr in template set T0284 7 :HELRAMFRALLD 2mnr 60 :KSLKQLLDDMAA T0284 19 :SS 2mnr 74 :VN T0284 63 :ALITLSEFVEQATRIGRVARL 2mnr 76 :EPLAPVSLEAMLAKRFCLAGY T0284 84 :PVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 2mnr 133 :PVQAYDSHSLDGVKLATERAVTAAELGFRAVKTKIGYPA T0284 135 :VEEGVGKIRAALEAR 2mnr 172 :LDQDLAVVRSIRQAV T0284 151 :DPALTIIART 2mnr 187 :GDDFGIMVDY T0284 162 :AELIDVDAVIQRTLAYQEAGADGICLVGV 2mnr 197 :NQSLDVPAAIKRSQALQQEGVTWIEEPTL T0284 191 :RDFAHLEAIAEHLHIPLML 2mnr 227 :HDYEGHQRIQSKLNVPVQM T0284 214 :NPQLRDDARLARL 2mnr 246 :GENWLGPEEMFKA T0284 227 :GVRVVVNG 2mnr 262 :GACRLAMP T0284 237 :AYFAAIKATYDCLREE 2mnr 275 :GGVTGWIRASALAQQF Number of specific fragments extracted= 11 number of extra gaps= 0 total=963 Number of alignments=67 # 2mnr read from 2mnr/merged-good-all-a2m # found chain 2mnr in template set T0284 5 :SHHELRAMFRALLDSSRC 2mnr 79 :APVSLEAMLAKRFCLAGY T0284 31 :PMSARIAADL 2mnr 103 :AAAGIDMAAW T0284 50 :SVASLQ 2mnr 113 :DALGKV T0284 56 :VLA 2mnr 126 :LLG T0284 87 :ADADHGYGNALNVMRTVVELERAGIAALTIEDTLL 2mnr 136 :AYDSHSLDGVKLATERAVTAAELGFRAVKTKIGYP T0284 134 :CVEEGVGKIRAALEA 2mnr 171 :ALDQDLAVVRSIRQA T0284 150 :VDPALTIIART 2mnr 186 :VGDDFGIMVDY T0284 162 :AELIDVDAVIQRTLAYQEAGADGICLVG 2mnr 197 :NQSLDVPAAIKRSQALQQEGVTWIEEPT T0284 190 :VRDFAHLEAIAEHLHIPLMLV 2mnr 226 :QHDYEGHQRIQSKLNVPVQMG T0284 215 :PQLRDDARLARL 2mnr 247 :ENWLGPEEMFKA T0284 227 :GVRVVVNGHA 2mnr 262 :GACRLAMPDA T0284 241 :AIKATYDCLREERGAVAS 2mnr 276 :GVTGWIRASALAQQFGIP Number of specific fragments extracted= 12 number of extra gaps= 0 total=975 Number of alignments=68 # 2mnr read from 2mnr/merged-good-all-a2m # found chain 2mnr in template set T0284 5 :SHHELRAMFRALLDSSRC 2mnr 79 :APVSLEAMLAKRFCLAGY T0284 30 :DPMSARIA 2mnr 97 :TGLIRMAA T0284 48 :GGSVASLQ 2mnr 105 :AGIDMAAW T0284 56 :VLAAP 2mnr 118 :VHETP T0284 77 :IGRVARL 2mnr 123 :LVKLLGA T0284 84 :PVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 2mnr 133 :PVQAYDSHSLDGVKLATERAVTAAELGFRAVKTKIGYPA T0284 135 :VEEGVGKIRAALEAR 2mnr 172 :LDQDLAVVRSIRQAV T0284 151 :DPALTIIARTN 2mnr 187 :GDDFGIMVDYN T0284 163 :ELIDVDAVIQRTLAYQEAGADGICLVGV 2mnr 198 :QSLDVPAAIKRSQALQQEGVTWIEEPTL T0284 191 :RDFAHLEAIAEHLHIPLMLVT 2mnr 227 :HDYEGHQRIQSKLNVPVQMGE T0284 216 :QLRDDARLARL 2mnr 248 :NWLGPEEMFKA T0284 227 :GVRVVVN 2mnr 263 :ACRLAMP T0284 234 :GHAAYFAAIKATY 2mnr 276 :GVTGWIRASALAQ T0284 251 :EE 2mnr 289 :QF Number of specific fragments extracted= 14 number of extra gaps= 0 total=989 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xg4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1xg4A/merged-good-all-a2m # 1xg4A read from 1xg4A/merged-good-all-a2m # found chain 1xg4A in training set Warning: unaligning (T0284)R280 because last residue in template chain is (1xg4A)N288 T0284 9 :LRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQVLAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1xg4A 6 :PGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFG T0284 95 :NALNVMRTVVELERAGIAALTIEDTLLPAQFGR 1xg4A 93 :SAFNVARTVKSMIKAGAAGLHIEDQVGAKRSGH T0284 128 :KSTDLICVEEGVGKIRAALEARVDPALTIIARTNAEL 1xg4A 127 :PNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALA T0284 165 :IDVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTY 1xg4A 165 :EGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANIT T0284 213 :GNPQLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERG 1xg4A 215 :GATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQ T0284 255 :AVASDLTASELSKKYTFPEEYQAWA 1xg4A 263 :VIDTMQTRNELYESINYYQYEEKLD Number of specific fragments extracted= 6 number of extra gaps= 0 total=995 Number of alignments=70 # 1xg4A read from 1xg4A/merged-good-all-a2m # found chain 1xg4A in training set Warning: unaligning (T0284)R280 because last residue in template chain is (1xg4A)N288 T0284 8 :ELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQVLAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1xg4A 5 :SPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFG T0284 95 :NALNVMRTVVELERAGIAALTIEDTLLPAQFGR 1xg4A 93 :SAFNVARTVKSMIKAGAAGLHIEDQVGAKRSGH T0284 128 :KSTDLICVEEGVGKIRAALEARVDPALTIIARTNAELI 1xg4A 127 :PNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAV T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTY 1xg4A 166 :GLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANIT T0284 213 :GNPQLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVAS 1xg4A 215 :GATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQ T0284 259 :DLTASELSKKYTFPEEYQAWA 1xg4A 267 :MQTRNELYESINYYQYEEKLD Number of specific fragments extracted= 6 number of extra gaps= 0 total=1001 Number of alignments=71 # 1xg4A read from 1xg4A/merged-good-all-a2m # found chain 1xg4A in training set Warning: unaligning (T0284)K286 because last residue in template chain is (1xg4A)N288 T0284 9 :LRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQVLAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1xg4A 6 :PGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFG T0284 95 :NALNVMRTVVELERAGIAALTIEDTLLPAQFGRKSTD 1xg4A 93 :SAFNVARTVKSMIKAGAAGLHIEDQVGAKRSGHRPNK T0284 132 :LICVEEGVGKIRAALEARVDPALTIIARTNAELI 1xg4A 131 :IVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAV T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTY 1xg4A 166 :GLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANIT T0284 213 :GNPQLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVASDLTASELSKKYTFPEEYQAWARDYMEV 1xg4A 215 :GATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLD Number of specific fragments extracted= 5 number of extra gaps= 0 total=1006 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ojxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ojxA expands to /projects/compbio/data/pdb/1ojx.pdb.gz 1ojxA:# T0284 read from 1ojxA/merged-good-all-a2m # 1ojxA read from 1ojxA/merged-good-all-a2m # adding 1ojxA to template set # found chain 1ojxA in template set T0284 9 :LRAMFRALLDSSRCYHTASVFDPM 1ojxA 4 :LTEKFLRIFARRGKSIILAYDHGI T0284 33 :SARIAADLGFECGILG 1ojxA 46 :ILRLARDAGFDGVVFQ T0284 67 :LSEFVE 1ojxA 62 :RGIAEK T0284 80 :VA 1ojxA 68 :YY T0284 82 :RLPVIADAD 1ojxA 72 :SVPLILKLN T0284 91 :H 1ojxA 84 :T T0284 93 :YGN 1ojxA 86 :YNG T0284 103 :VVELERAGIAALTIE 1ojxA 98 :VEEAVSLGASAVGYT T0284 120 :L 1ojxA 115 :P T0284 126 :GRKS 1ojxA 116 :GSGF T0284 135 :VEEGVGKIRAALEAR 1ojxA 120 :EWKMFEELARIKRDA T0284 150 :VDPALTIIARTNAELID 1ojxA 137 :FDLPLVVWSYPRGGKVV T0284 167 :VDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLH 1ojxA 158 :PEIVAYAARIALELGADAMKIKYTGDPKTFSWAVKVAG T0284 205 :IPLMLVTYGNPQ 1ojxA 197 :VPVLMSGGPKTK T0284 219 :DD 1ojxA 209 :TE T0284 221 :ARLARLGVRVVVNGHAAY 1ojxA 218 :EGVLEAGALGIAVGRNVW T0284 245 :TYDCLREERGAV 1ojxA 240 :ALKFARALAELV Number of specific fragments extracted= 17 number of extra gaps= 0 total=1023 Number of alignments=73 # 1ojxA read from 1ojxA/merged-good-all-a2m # found chain 1ojxA in template set Warning: unaligning (T0284)E8 because first residue in template chain is (1ojxA)N3 Warning: unaligning (T0284)A257 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ojxA)G253 Warning: unaligning (T0284)S258 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ojxA)G253 T0284 9 :LRAMFRALLDSSRCYHTASVFDP 1ojxA 4 :LTEKFLRIFARRGKSIILAYDHG T0284 32 :MSARIAADLGFECGIL 1ojxA 45 :YILRLARDAGFDGVVF T0284 49 :GSVASLQ 1ojxA 61 :QRGIAEK T0284 80 :VARLPVIADA 1ojxA 70 :DGSVPLILKL T0284 90 :DHG 1ojxA 90 :PVS T0284 93 :YGNALNV 1ojxA 95 :NCSVEEA T0284 107 :ERAGIAALTIEDTLL 1ojxA 102 :VSLGASAVGYTIYPG T0284 125 :FGR 1ojxA 117 :SGF T0284 135 :VEEGVGKIRAALEA 1ojxA 120 :EWKMFEELARIKRD T0284 149 :RVDPALTIIARTNAELID 1ojxA 136 :KFDLPLVVWSYPRGGKVV T0284 167 :VDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLH 1ojxA 158 :PEIVAYAARIALELGADAMKIKYTGDPKTFSWAVKVAG T0284 205 :IPLMLVTYGNPQLR 1ojxA 197 :VPVLMSGGPKTKTE T0284 219 :DDARLARLGVRVVVNGHAAY 1ojxA 216 :QVEGVLEAGALGIAVGRNVW T0284 245 :TYDCLREERGAV 1ojxA 240 :ALKFARALAELV Number of specific fragments extracted= 14 number of extra gaps= 1 total=1037 Number of alignments=74 # 1ojxA read from 1ojxA/merged-good-all-a2m # found chain 1ojxA in template set T0284 9 :LRAMFRALLDSSRCYHTASVFDPM 1ojxA 4 :LTEKFLRIFARRGKSIILAYDHGI T0284 33 :SARIAADLGFECGILGGSVASLQ 1ojxA 46 :ILRLARDAGFDGVVFQRGIAEKY T0284 82 :RLPVIADA 1ojxA 72 :SVPLILKL T0284 94 :GN 1ojxA 88 :GE T0284 103 :VVELERAGIAALTIEDT 1ojxA 98 :VEEAVSLGASAVGYTIY T0284 123 :AQFGR 1ojxA 115 :PGSGF T0284 135 :VEEGVGKIRAALEAR 1ojxA 120 :EWKMFEELARIKRDA T0284 150 :VDPALTIIARTNAELI 1ojxA 137 :FDLPLVVWSYPRGGKV T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHL 1ojxA 157 :APEIVAYAARIALELGADAMKIKYTGDPKTFSWAVKVA T0284 204 :HIPLMLVTYGNPQ 1ojxA 196 :KVPVLMSGGPKTK T0284 219 :DDARLAR 1ojxA 209 :TEEDFLK T0284 226 :LGVRVVVNGHAAY 1ojxA 223 :AGALGIAVGRNVW T0284 239 :FAAIKATYDCL 1ojxA 241 :LKFARALAELV Number of specific fragments extracted= 13 number of extra gaps= 0 total=1050 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aj2/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aj2 expands to /projects/compbio/data/pdb/1aj2.pdb.gz 1aj2:Warning: there is no chain 1aj2 will retry with 1aj2A # T0284 read from 1aj2/merged-good-all-a2m # 1aj2 read from 1aj2/merged-good-all-a2m # adding 1aj2 to template set # found chain 1aj2 in template set Warning: unaligning (T0284)V80 because of BadResidue code BAD_PEPTIDE in next template residue (1aj2)F89 Warning: unaligning (T0284)A81 because of BadResidue code BAD_PEPTIDE at template residue (1aj2)F89 T0284 21 :RCYHTASVFD 1aj2 16 :HVMGILNVTP T0284 31 :PMSARIAADLGFECGILGGSVA 1aj2 41 :VKHANLMINAGATIIDVGGEST T0284 59 :APDFALITLSE 1aj2 63 :RPGAAEVSVEE T0284 70 :FVEQATRIGR 1aj2 78 :VIPVVEAIAQ T0284 82 :RLPVIADAD 1aj2 90 :EVWISVDTS T0284 100 :MRTVVELERAGIAALTI 1aj2 100 :PEVIRESAKVGAHIIND T0284 135 :VEEGV 1aj2 117 :IRSLS T0284 140 :GKIRAALEA 1aj2 124 :GALEAAAET T0284 153 :ALTIIART 1aj2 133 :GLPVCLMH T0284 164 :L 1aj2 141 :M T0284 167 :VDAVIQRTLAYQEAGAD 1aj2 162 :NRYFIEQIARCEQAGIA T0284 184 :GICLV 1aj2 182 :LLLDP T0284 189 :GVRDFAHLEAIAEHLH 1aj2 190 :FGKNLSHNYSLLARLA T0284 205 :IPLMLVTY 1aj2 212 :LPLLVGMS T0284 213 :GNPQLRDD 1aj2 229 :NVGPSERL T0284 221 :ARLARLGVRVVVNGH 1aj2 244 :VIAAMQGAHIIRVHD T0284 242 :IKATYDCLREERGAVAS 1aj2 259 :VKETVEAMRVVEATLSA Number of specific fragments extracted= 17 number of extra gaps= 1 total=1067 Number of alignments=76 # 1aj2 read from 1aj2/merged-good-all-a2m # found chain 1aj2 in template set Warning: unaligning (T0284)V80 because of BadResidue code BAD_PEPTIDE in next template residue (1aj2)F89 Warning: unaligning (T0284)A81 because of BadResidue code BAD_PEPTIDE at template residue (1aj2)F89 T0284 22 :CYHTASVF 1aj2 17 :VMGILNVT T0284 30 :DPMSARIAADLGFECGILGGS 1aj2 40 :AVKHANLMINAGATIIDVGGE T0284 57 :LAAPDFALITLSE 1aj2 61 :STRPGAAEVSVEE T0284 70 :FVEQATRIGR 1aj2 78 :VIPVVEAIAQ T0284 82 :RLPVIADADH 1aj2 90 :EVWISVDTSK T0284 101 :RTVVELERAGIAAL 1aj2 101 :EVIRESAKVGAHII T0284 133 :ICVEEGV 1aj2 115 :NDIRSLS T0284 140 :GKIRAALEA 1aj2 124 :GALEAAAET T0284 153 :A 1aj2 133 :G T0284 154 :LTIIARTNAELID 1aj2 135 :PVCLMHMQGNPKT T0284 167 :VDAVIQRTLAYQEAGAD 1aj2 162 :NRYFIEQIARCEQAGIA T0284 184 :GICLVG 1aj2 182 :LLLDPG T0284 190 :VRDFAHLEAIAEHLH 1aj2 191 :GKNLSHNYSLLARLA T0284 205 :IPLMLVTY 1aj2 212 :LPLLVGMS T0284 213 :GNPQLRDDA 1aj2 229 :NVGPSERLS T0284 222 :RLARLGVRVVVNGH 1aj2 245 :IAAMQGAHIIRVHD T0284 242 :IKATYDCLREERGAVA 1aj2 259 :VKETVEAMRVVEATLS Number of specific fragments extracted= 17 number of extra gaps= 1 total=1084 Number of alignments=77 # 1aj2 read from 1aj2/merged-good-all-a2m # found chain 1aj2 in template set Warning: unaligning (T0284)V80 because of BadResidue code BAD_PEPTIDE in next template residue (1aj2)F89 Warning: unaligning (T0284)A81 because of BadResidue code BAD_PEPTIDE at template residue (1aj2)F89 T0284 18 :DSSRCYHTASVF 1aj2 13 :SHPHVMGILNVT T0284 30 :DPMSARIAADLGFECGILGGS 1aj2 40 :AVKHANLMINAGATIIDVGGE T0284 57 :LAAPDFALITLSE 1aj2 61 :STRPGAAEVSVEE T0284 70 :FVEQATRIGR 1aj2 78 :VIPVVEAIAQ T0284 82 :RLPVIADADH 1aj2 90 :EVWISVDTSK T0284 100 :MRTVVELERAGIAALT 1aj2 100 :PEVIRESAKVGAHIIN T0284 118 :DT 1aj2 116 :DI T0284 125 :FGRKSTD 1aj2 118 :RSLSEPG T0284 138 :GVGKIRAA 1aj2 125 :ALEAAAET T0284 149 :R 1aj2 133 :G T0284 152 :P 1aj2 134 :L T0284 154 :LTIIARTNAELI 1aj2 135 :PVCLMHMQGNPK T0284 167 :VDAVIQRTLAYQEAGAD 1aj2 162 :NRYFIEQIARCEQAGIA T0284 184 :GICLVGVRD 1aj2 182 :LLLDPGFGF T0284 193 :FAHLEAIAEHL 1aj2 194 :LSHNYSLLARL T0284 204 :HIPL 1aj2 211 :NLPL T0284 208 :MLVTYGNPQLRDDARLAR 1aj2 224 :IGQLLNVGPSERLSGSLA T0284 226 :LGVRVVVNGHA 1aj2 249 :QGAHIIRVHDV T0284 239 :FAAIKATYDCLREERGAV 1aj2 260 :KETVEAMRVVEATLSAKE Number of specific fragments extracted= 19 number of extra gaps= 1 total=1103 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1twdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1twdA/merged-good-all-a2m # 1twdA read from 1twdA/merged-good-all-a2m # found chain 1twdA in training set Warning: unaligning (T0284)C22 because first residue in template chain is (1twdA)A2 T0284 23 :YHTASVFDPMSARIAADLGFECGIL 1twdA 3 :LLEICCYSMECALTAQQNGADRVEL T0284 57 :LAA 1twdA 28 :CAA T0284 60 :PDFALITLS 1twdA 33 :EGGLTPSLG T0284 73 :QATRIGRVARLPVIADAD 1twdA 42 :VLKSVRQRVTIPVHPIIR T0284 91 :HGYG 1twdA 65 :FCYS T0284 95 :NALNVMRTVVELERAGIAALTIE 1twdA 71 :EFAAILEDVRTVRELGFPGLVTG T0284 125 :FGRKSTDL 1twdA 94 :VLDVDGNV T0284 138 :GVGKIRAALEAR 1twdA 102 :DMPRMEKIMAAA T0284 153 :ALTIIARTNAEL 1twdA 115 :PLAVTFHRAFDM T0284 165 :IDVDAVIQR 1twdA 128 :ANPLYTLNN T0284 177 :YQEAGADGICLVGVRD 1twdA 137 :LAELGIARVLTSGQKS T0284 193 :FAHLEAIAEHLHIPLMLVTYGNPQ 1twdA 158 :LSKIMELIAHRDAPIIMAGAGVRA T0284 218 :RDDARLARLGVRVVVNG 1twdA 182 :ENLHHFLDAGVLEVHSS Number of specific fragments extracted= 13 number of extra gaps= 0 total=1116 Number of alignments=79 # 1twdA read from 1twdA/merged-good-all-a2m # found chain 1twdA in training set T0284 23 :YHTASVFDPMSARIAADLGFECGILG 1twdA 3 :LLEICCYSMECALTAQQNGADRVELC T0284 57 :LAAPDFALITLS 1twdA 30 :APKEGGLTPSLG T0284 73 :QATRIGRVARLPVIADADH 1twdA 42 :VLKSVRQRVTIPVHPIIRP T0284 92 :G 1twdA 62 :G T0284 93 :YG 1twdA 67 :YS T0284 95 :NALNVMRTVVELERAGIAALTIE 1twdA 71 :EFAAILEDVRTVRELGFPGLVTG T0284 125 :FGRKSTDLI 1twdA 94 :VLDVDGNVD T0284 139 :VGKIRAALEAR 1twdA 103 :MPRMEKIMAAA T0284 152 :PALTIIARTNAELI 1twdA 114 :GPLAVTFHRAFDMC T0284 166 :DVDAVIQR 1twdA 129 :NPLYTLNN T0284 177 :YQEAGADGICLVGVRD 1twdA 137 :LAELGIARVLTSGQKS T0284 193 :FAHLEAIAEHLHIPLMLVTYGNPQL 1twdA 158 :LSKIMELIAHRDAPIIMAGAGVRAE T0284 219 :DDARLARLGVRVVVNG 1twdA 183 :NLHHFLDAGVLEVHSS Number of specific fragments extracted= 13 number of extra gaps= 0 total=1129 Number of alignments=80 # 1twdA read from 1twdA/merged-good-all-a2m # found chain 1twdA in training set Warning: unaligning (T0284)C22 because first residue in template chain is (1twdA)A2 T0284 23 :YHTASVFDPMSARIAADLGFECGIL 1twdA 3 :LLEICCYSMECALTAQQNGADRVEL T0284 57 :LAAPDFALIT 1twdA 28 :CAAPKEGGLT T0284 71 :VEQATRIGRVARLPVIADA 1twdA 40 :LGVLKSVRQRVTIPVHPII T0284 90 :DHGYG 1twdA 64 :DFCYS T0284 95 :NALNVMRTVVELERAGIAALTIE 1twdA 71 :EFAAILEDVRTVRELGFPGLVTG T0284 120 :LLP 1twdA 94 :VLD T0284 128 :KSTDLI 1twdA 97 :VDGNVD T0284 139 :VGKIRAALEARV 1twdA 103 :MPRMEKIMAAAG T0284 152 :PALTIIARTNAELIDVDAVIQR 1twdA 115 :PLAVTFHRAFDMCANPLYTLNN T0284 177 :YQEAGADGICLVGVRD 1twdA 137 :LAELGIARVLTSGQKS T0284 193 :FAHLEAIAEHLHIPLMLVTYG 1twdA 158 :LSKIMELIAHRDAPIIMAGAG T0284 215 :PQLRDDARLARLGVRVVVNG 1twdA 179 :VRAENLHHFLDAGVLEVHSS Number of specific fragments extracted= 12 number of extra gaps= 0 total=1141 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pe1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1pe1A/merged-good-all-a2m # 1pe1A read from 1pe1A/merged-good-all-a2m # found chain 1pe1A in training set T0284 21 :RCYHTASVFD 1pe1A 1003 :KFLVIAGPCA T0284 31 :PMSARIAADL 1pe1A 1020 :LKVGEEIKRL T0284 41 :GFECGILGGSVASLQ 1pe1A 1035 :EVEFVFKSSFDKANR T0284 57 :LAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1pe1A 1050 :SSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQ T0284 103 :VVELERA 1pe1A 1088 :AEPVAEV T0284 111 :IAALTIEDTL 1pe1A 1095 :ADIIQIPAFL T0284 125 :FGR 1pe1A 1105 :CRQ T0284 140 :GKIRAALEA 1pe1A 1109 :DLLLAAAKT T0284 153 :ALTIIARTNAELI 1pe1A 1118 :GRAVNVKKGQFLA T0284 167 :VDAVIQRTLAYQEAGADGICLVGVRDFA 1pe1A 1201 :REFIFPLIRAAVAVGCDGVFMETHPEPE T0284 211 :TYGNPQLR 1pe1A 1229 :KALSDAST T0284 232 :VNGHAAYFAAIKATYDCLREERG 1pe1A 1237 :QLPLSQLEGIIEAILEIREVASK Number of specific fragments extracted= 12 number of extra gaps= 0 total=1153 Number of alignments=82 # 1pe1A read from 1pe1A/merged-good-all-a2m # found chain 1pe1A in training set T0284 21 :RCYHTASVFD 1pe1A 1003 :KFLVIAGPCA T0284 31 :PMSARIAADL 1pe1A 1017 :ELLLKVGEEI T0284 41 :GFECGILGGSVASLQ 1pe1A 1035 :EVEFVFKSSFDKANR T0284 57 :LAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1pe1A 1050 :SSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQ T0284 103 :VVELERA 1pe1A 1088 :AEPVAEV T0284 111 :IAALTIEDTL 1pe1A 1095 :ADIIQIPAFL T0284 125 :FG 1pe1A 1105 :CR T0284 140 :GKIRAALE 1pe1A 1109 :DLLLAAAK T0284 152 :PALTIIARTNAELI 1pe1A 1117 :TGRAVNVKKGQFLA T0284 166 :DVDAVIQRTLA 1pe1A 1133 :DTKNVVEKLKF T0284 180 :AGA 1pe1A 1144 :GGA T0284 183 :DGICLVG 1pe1A 1148 :EIYLTER T0284 190 :VR 1pe1A 1156 :TT T0284 192 :DFAHLEAIAEHLH 1pe1A 1166 :DFRSLPIMKQWAK T0284 207 :LMLVTY 1pe1A 1179 :VIYDAT T0284 214 :NPQLRDDARLARL 1pe1A 1199 :GMREFIFPLIRAA T0284 227 :GVRVVVN 1pe1A 1215 :GCDGVFM T0284 234 :GHAAYFAAIKATYDCLREERGAVAS 1pe1A 1239 :PLSQLEGIIEAILEIREVASKYYET Number of specific fragments extracted= 18 number of extra gaps= 0 total=1171 Number of alignments=83 # 1pe1A read from 1pe1A/merged-good-all-a2m # found chain 1pe1A in training set Warning: unaligning (T0284)R218 because last residue in template chain is (1pe1A)I1264 T0284 21 :RCYHTASVFD 1pe1A 1003 :KFLVIAGPCA T0284 31 :PMSARIAADL 1pe1A 1020 :LKVGEEIKRL T0284 41 :GFECGILGGSVASLQ 1pe1A 1035 :EVEFVFKSSFDKANR T0284 57 :LAAPDFALITLSEFVEQATRIGRVARLPVIADADHG 1pe1A 1050 :SSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHES T0284 95 :NALNVM 1pe1A 1087 :QAEPVA T0284 101 :RTVVELERAGIAALTIEDTLLPAQF 1pe1A 1109 :DLLLAAAKTGRAVNVKKGQFLAPWD T0284 135 :VEEGVGKIRA 1pe1A 1134 :TKNVVEKLKF T0284 149 :RVDPALTIIAR 1pe1A 1144 :GGAKEIYLTER T0284 167 :VDAVIQRTLAYQEAGADGICLVGVRD 1pe1A 1201 :REFIFPLIRAAVAVGCDGVFMETHPE T0284 193 :FAHLEAIAEHL 1pe1A 1244 :EGIIEAILEIR T0284 211 :TYGNPQL 1pe1A 1257 :ASKYYET Number of specific fragments extracted= 11 number of extra gaps= 0 total=1182 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eyeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1eyeA/merged-good-all-a2m # 1eyeA read from 1eyeA/merged-good-all-a2m # found chain 1eyeA in training set Warning: unaligning (T0284)G49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1eyeA)E65 Warning: unaligning (T0284)S50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1eyeA)E65 T0284 21 :RCYHTASVFD 1eyeA 7 :QVMGVLNVTD T0284 31 :PMSARIAADLGFECGILG 1eyeA 32 :VKHGLAMAAAGAGIVDVG T0284 67 :LSEFVEQATRIGR 1eyeA 66 :TSRVIPVVKELAA T0284 81 :ARLPVIADAD 1eyeA 79 :QGITVSIDTM T0284 100 :MRTVVELERAGIAALTIEDTLLP 1eyeA 90 :ADVARAALQNGAQMVNDVSGGRA T0284 135 :VEEGVGKIRAA 1eyeA 113 :DPAMGPLLAEA T0284 153 :ALTIIAR 1eyeA 124 :DVPWVLM T0284 160 :TNAELI 1eyeA 132 :WRAVSA T0284 167 :VDAVIQRTLAYQE 1eyeA 150 :VAEVRADLLASVA T0284 180 :AGAD 1eyeA 167 :AGVD T0284 184 :GICLV 1eyeA 174 :LVLDP T0284 189 :GVRDFAHLEAIAEHLH 1eyeA 182 :FAKTAQHNWAILHALP T0284 205 :IPLMLVTYGN 1eyeA 204 :IPVLVGASRK T0284 220 :D 1eyeA 214 :R T0284 221 :ARLARLGVRVVVNGH 1eyeA 242 :ALAALHGAWGVRVHD T0284 242 :IKATYDCLREERGAVA 1eyeA 257 :VRASVDAIKVVEAWMG Number of specific fragments extracted= 16 number of extra gaps= 1 total=1198 Number of alignments=85 # 1eyeA read from 1eyeA/merged-good-all-a2m # found chain 1eyeA in training set Warning: unaligning (T0284)G49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1eyeA)E65 Warning: unaligning (T0284)S50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1eyeA)E65 T0284 22 :CYHTASVFD 1eyeA 8 :VMGVLNVTD T0284 31 :PMSARIAADLGFECGILG 1eyeA 32 :VKHGLAMAAAGAGIVDVG T0284 67 :LSEFVEQATRIGR 1eyeA 66 :TSRVIPVVKELAA T0284 81 :ARLPVIADADH 1eyeA 79 :QGITVSIDTMR T0284 100 :MRTVVELERAGIAALTIEDTLLP 1eyeA 90 :ADVARAALQNGAQMVNDVSGGRA T0284 135 :VEEGVGKIRAA 1eyeA 113 :DPAMGPLLAEA T0284 153 :A 1eyeA 124 :D T0284 154 :LTIIARTNAELI 1eyeA 126 :PWVLMHWRAVSA T0284 167 :VDAVIQRTLA 1eyeA 150 :VAEVRADLLA T0284 177 :YQEAGAD 1eyeA 164 :AVAAGVD T0284 184 :GICLVG 1eyeA 174 :LVLDPG T0284 190 :VRDFAHLEAIAEHLH 1eyeA 183 :AKTAQHNWAILHALP T0284 205 :IPLMLVTYGN 1eyeA 204 :IPVLVGASRK T0284 222 :RLARLGVRVVVNGH 1eyeA 243 :LAALHGAWGVRVHD T0284 242 :IKATYDCLREERGAVAS 1eyeA 257 :VRASVDAIKVVEAWMGA Number of specific fragments extracted= 15 number of extra gaps= 1 total=1213 Number of alignments=86 # 1eyeA read from 1eyeA/merged-good-all-a2m # found chain 1eyeA in training set Warning: unaligning (T0284)G49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1eyeA)E65 Warning: unaligning (T0284)S50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1eyeA)E65 Warning: unaligning (T0284)D259 because last residue in template chain is (1eyeA)E274 T0284 22 :CYHTASVFD 1eyeA 8 :VMGVLNVTD T0284 31 :PMSARIAADLGFECGILG 1eyeA 32 :VKHGLAMAAAGAGIVDVG T0284 67 :LSEFVEQATRIGRV 1eyeA 66 :TSRVIPVVKELAAQ T0284 82 :RL 1eyeA 80 :GI T0284 84 :PVIADADHGYGN 1eyeA 102 :QMVNDVSGGRAD T0284 102 :TVVELERAGIAALTIEDTLLPAQFGRKSTD 1eyeA 116 :MGPLLAEADVPWVLMHWRAVSADTPHVPVR T0284 132 :LICVEEGVGKIRAAL 1eyeA 147 :GNVVAEVRADLLASV T0284 147 :EARVDPALTIIARTNAELI 1eyeA 166 :AAGVDPARLVLDPGLGFAK T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRD 1eyeA 188 :HNWAILHALPELVATGIPVLVGASRKR T0284 193 :FAHLEAIAE 1eyeA 234 :DTATAVISA T0284 222 :RLARLGVRVVVNGH 1eyeA 243 :LAALHGAWGVRVHD T0284 242 :IKATYDCLREERGAVAS 1eyeA 257 :VRASVDAIKVVEAWMGA Number of specific fragments extracted= 12 number of extra gaps= 1 total=1225 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a53/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a53 expands to /projects/compbio/data/pdb/1a53.pdb.gz 1a53:Warning: there is no chain 1a53 will retry with 1a53A # T0284 read from 1a53/merged-good-all-a2m # 1a53 read from 1a53/merged-good-all-a2m # adding 1a53 to template set # found chain 1a53 in template set T0284 8 :ELRAMFRALLDSSRCYHTASVFD 1a53 32 :SLNERILEFNKRNITAIIAEYKR T0284 31 :PMSARIAADL 1a53 67 :IEYSKFMERY T0284 42 :FECGIL 1a53 77 :AVGLSI T0284 57 :LAAPDFALITLSEF 1a53 83 :LTEEKYFNGSYETL T0284 75 :TRIGRVARLPVIADADH 1a53 97 :RKIASSVSIPILMKDFI T0284 100 :MRTVVELERAGIAALTIEDTLLPA 1a53 116 :ESQIDDAYNLGADTVLLIVKILTE T0284 136 :EEGVGKIRAALEARV 1a53 140 :RELESLLEYARSYGM T0284 153 :ALTIIART 1a53 155 :EPLIEIND T0284 168 :DAVIQRTLA 1a53 163 :ENDLDIALR T0284 180 :AGADGICLVGV 1a53 172 :IGARFIGINSR T0284 191 :RDFAHLEAIAEHLH 1a53 189 :INKENQRKLISMIP T0284 205 :I 1a53 205 :V T0284 207 :LMLVTYGNPQLRDDARLARLGVRVVVNGHAAYF 1a53 206 :VKVAESGISERNEIEELRKLGVNAFLIGSSLMR Number of specific fragments extracted= 13 number of extra gaps= 0 total=1238 Number of alignments=88 # 1a53 read from 1a53/merged-good-all-a2m # found chain 1a53 in template set T0284 3 :RASHHELRAMFRALLDSSRCYHTASVFD 1a53 27 :QRPIISLNERILEFNKRNITAIIAEYKR T0284 31 :PMSARIAADL 1a53 67 :IEYSKFMERY T0284 42 :FECGIL 1a53 77 :AVGLSI T0284 57 :LAAPDFALITLSE 1a53 83 :LTEEKYFNGSYET T0284 74 :ATRIGRVARLPVIADADH 1a53 96 :LRKIASSVSIPILMKDFI T0284 100 :MRTVVELERAGIAALTIEDTLLPA 1a53 116 :ESQIDDAYNLGADTVLLIVKILTE T0284 140 :GKIRAALEARVDPA 1a53 140 :RELESLLEYARSYG T0284 154 :LTIIART 1a53 156 :PLIEIND T0284 168 :DAVIQRTL 1a53 163 :ENDLDIAL T0284 179 :EAGADGICLVGVR 1a53 171 :RIGARFIGINSRD T0284 192 :DFAHLEAIAEHLH 1a53 190 :NKENQRKLISMIP T0284 205 :I 1a53 205 :V T0284 207 :LMLVTYGNPQLRDDARLARLGVRVVVNGHAAYF 1a53 206 :VKVAESGISERNEIEELRKLGVNAFLIGSSLMR Number of specific fragments extracted= 13 number of extra gaps= 0 total=1251 Number of alignments=89 # 1a53 read from 1a53/merged-good-all-a2m # found chain 1a53 in template set T0284 9 :LRAMFRALLDSSRCYHTASVFD 1a53 33 :LNERILEFNKRNITAIIAEYKR T0284 31 :PMSARIAADL 1a53 67 :IEYSKFMERY T0284 42 :FECGIL 1a53 77 :AVGLSI T0284 57 :LAAPDFALITL 1a53 83 :LTEEKYFNGSY T0284 72 :EQATRIGRVARLPVIADA 1a53 94 :ETLRKIASSVSIPILMKD T0284 100 :MRTVVELERAGIAALTIEDTLLP 1a53 116 :ESQIDDAYNLGADTVLLIVKILT T0284 135 :VEEGVGKIRAALEARV 1a53 139 :ERELESLLEYARSYGM T0284 153 :ALTIIAR 1a53 155 :EPLIEIN T0284 167 :VDAVIQ 1a53 162 :DENDLD T0284 176 :AYQEAGADGICLVGVRD 1a53 168 :IALRIGARFIGINSRDL T0284 193 :FAHLEAIAEHLHI 1a53 191 :KENQRKLISMIPS T0284 206 :PLMLVTYG 1a53 205 :VVKVAESG T0284 217 :LRDDARLAR 1a53 213 :ISERNEIEE T0284 226 :LGVRVVVNGHAAYF 1a53 225 :LGVNAFLIGSSLMR Number of specific fragments extracted= 14 number of extra gaps= 0 total=1265 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w5nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1w5nA/merged-good-all-a2m # 1w5nA read from 1w5nA/merged-good-all-a2m # found chain 1w5nA in training set Warning: unaligning (T0284)E117 because of BadResidue code BAD_PEPTIDE in next template residue (1w5nA)D176 Warning: unaligning (T0284)D118 because of BadResidue code BAD_PEPTIDE at template residue (1w5nA)D176 T0284 31 :PMSARIAADLGFECGILG 1w5nA 69 :LIEAEEWVALGIPALALF T0284 56 :VLAAPDFALIT 1w5nA 93 :KKSLDAAEAYN T0284 69 :EFVEQATRIGRVA 1w5nA 107 :IAQRATRALRERF T0284 82 :RLPVIADADHG 1w5nA 121 :ELGIITDVALC T0284 93 :YGN 1w5nA 133 :FTT T0284 96 :ALNVMRTVVELERAGIAALTI 1w5nA 154 :IDVLVRQALSHAEAGAQVVAP T0284 119 :TL 1w5nA 177 :MM T0284 140 :GKIRAALEAR 1w5nA 180 :GRIGAIREAL T0284 150 :VDPALTIIA 1w5nA 193 :GHTNVRVMA T0284 159 :RTNAELI 1w5nA 205 :KYASAYY T0284 166 :DVDAVIQRTLAYQEAGADGICLV 1w5nA 238 :NSDEALHEVAADLAEGADMVMVK T0284 189 :GVRDFAHLEAIAEHLHIPLMLVTY 1w5nA 262 :GMPYLDIVRRVKDEFRAPTFVYQV T0284 219 :DD 1w5nA 286 :SG T0284 221 :ARLARLGVRVVVNGHA 1w5nA 311 :TAFKRAGADGILTYFA T0284 243 :KATYDCLR 1w5nA 327 :KQAAEQLR Number of specific fragments extracted= 15 number of extra gaps= 1 total=1280 Number of alignments=91 # 1w5nA read from 1w5nA/merged-good-all-a2m # found chain 1w5nA in training set Warning: unaligning (T0284)E117 because of BadResidue code BAD_PEPTIDE in next template residue (1w5nA)D176 Warning: unaligning (T0284)D118 because of BadResidue code BAD_PEPTIDE at template residue (1w5nA)D176 T0284 10 :RAMFRALLDS 1w5nA 65 :IDQLLIEAEE T0284 37 :AADLGFECGILG 1w5nA 75 :WVALGIPALALF T0284 56 :VLAAPDF 1w5nA 100 :EAYNPEG T0284 69 :EFVEQATRIGR 1w5nA 107 :IAQRATRALRE T0284 80 :VARLPVIADADHG 1w5nA 119 :FPELGIITDVALC T0284 93 :YGN 1w5nA 133 :FTT T0284 96 :ALNVMRTVVELERAGIAALTI 1w5nA 154 :IDVLVRQALSHAEAGAQVVAP T0284 119 :TL 1w5nA 177 :MM T0284 136 :EEGVGKIRAALEARVDPALTIIA 1w5nA 179 :DGRIGAIREALESAGHTNVRVMA T0284 159 :RTNAELIDV 1w5nA 205 :KYASAYYGP T0284 168 :DAVIQRTLAYQEAGADGICLVG 1w5nA 240 :DEALHEVAADLAEGADMVMVKP T0284 190 :VRDFAHLEAIAEHLHIPLMLVTY 1w5nA 263 :MPYLDIVRRVKDEFRAPTFVYQV T0284 217 :LRDDA 1w5nA 286 :SGEYA T0284 222 :RLARLGVRVVVNGH 1w5nA 312 :AFKRAGADGILTYF T0284 245 :TYDCLREER 1w5nA 326 :AKQAAEQLR Number of specific fragments extracted= 15 number of extra gaps= 1 total=1295 Number of alignments=92 # 1w5nA read from 1w5nA/merged-good-all-a2m # found chain 1w5nA in training set Warning: unaligning (T0284)E117 because of BadResidue code BAD_PEPTIDE in next template residue (1w5nA)D176 Warning: unaligning (T0284)D118 because of BadResidue code BAD_PEPTIDE at template residue (1w5nA)D176 T0284 31 :PMSARIAADLGFECGILGGSV 1w5nA 69 :LIEAEEWVALGIPALALFPVT T0284 56 :VLAAPDFALITLS 1w5nA 93 :KKSLDAAEAYNPE T0284 69 :EFVEQATRIGRVA 1w5nA 107 :IAQRATRALRERF T0284 82 :RLPVIADA 1w5nA 121 :ELGIITDV T0284 90 :DHGYG 1w5nA 144 :DDGYV T0284 95 :NALNVMRTVVELERAGIAALTI 1w5nA 153 :SIDVLVRQALSHAEAGAQVVAP T0284 119 :TLLP 1w5nA 177 :MMDG T0284 138 :GVGKIRAALEARVDPALTIIARTNAELI 1w5nA 181 :RIGAIREALESAGHTNVRVMAYSAKYAS T0284 167 :VDAVIQRTLAYQEAGADGICLVGVRD 1w5nA 239 :SDEALHEVAADLAEGADMVMVKPGMP T0284 193 :FAHLEAIAEHLHIPLMLVTY 1w5nA 266 :LDIVRRVKDEFRAPTFVYQV T0284 213 :GNPQLR 1w5nA 299 :GWLAES T0284 220 :DARLARLGVRVVVNGHAAYFA 1w5nA 310 :LTAFKRAGADGILTYFAKQAA Number of specific fragments extracted= 12 number of extra gaps= 1 total=1307 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ps9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ps9A expands to /projects/compbio/data/pdb/1ps9.pdb.gz 1ps9A:# T0284 read from 1ps9A/merged-good-all-a2m # 1ps9A read from 1ps9A/merged-good-all-a2m # adding 1ps9A to template set # found chain 1ps9A in template set T0284 24 :HTASVFD 1ps9A 20 :VLMGSMH T0284 31 :PMSARIAADLGFECGILGGSVASLQVLAAPDFALIT 1ps9A 40 :AAFYAERARHGVALIVSGGIAPDLTGVGMEGGAMLN T0284 67 :LSEFVEQATRIGRVARLPVIADADHG 1ps9A 80 :IPHHRTITEAVHQEGGKIALQILHTG T0284 93 :YG 1ps9A 109 :YQ T0284 96 :ALNVMRTVVELERAGIAALTIEDTL 1ps9A 140 :IDNFARCAQLAREAGYDGVEVMGSE T0284 121 :LPAQFG 1ps9A 179 :RSDQWG T0284 136 :EEGVGKIRAALEAR 1ps9A 185 :GDYRNRMRFAVEVV T0284 150 :VDPALTIIAR 1ps9A 205 :VGNDFIIIYR T0284 160 :TNAELIDVDAVIQRTLAYQEAGADGICLV 1ps9A 220 :LVEDGGTFAETVELAQAIEAAGATIINTG T0284 189 :GV 1ps9A 250 :GW T0284 193 :FAHLEAIAEHLHIPL 1ps9A 269 :SWVTRKLKGHVSLPL T0284 210 :VTYGNP 1ps9A 284 :VTTNRI T0284 218 :RDDARLARL 1ps9A 290 :NDPQVADDI T0284 227 :GVRVVVNGHAAYFA 1ps9A 303 :DADMVSMARPFLAD T0284 246 :YDCLREER 1ps9A 317 :AELLSKAQ Number of specific fragments extracted= 15 number of extra gaps= 0 total=1322 Number of alignments=94 # 1ps9A read from 1ps9A/merged-good-all-a2m # found chain 1ps9A in template set T0284 22 :CYHTASVFD 1ps9A 19 :RVLMGSMHT T0284 31 :PMSARIAADLGFECGILGGSVASLQVLAAPDFALIT 1ps9A 40 :AAFYAERARHGVALIVSGGIAPDLTGVGMEGGAMLN T0284 67 :LSEFVEQATRIGRVARLPVIADADHG 1ps9A 80 :IPHHRTITEAVHQEGGKIALQILHTG T0284 93 :YG 1ps9A 107 :YS T0284 96 :ALNVMRTVVELERAGIAALTIEDTLL 1ps9A 140 :IDNFARCAQLAREAGYDGVEVMGSEG T0284 122 :PAQFG 1ps9A 180 :SDQWG T0284 136 :EEGVGKIRAALEA 1ps9A 185 :GDYRNRMRFAVEV T0284 149 :RVDPALTIIAR 1ps9A 204 :RVGNDFIIIYR T0284 160 :TNAELIDVDAVIQRTLAYQEAGADGICLVGVR 1ps9A 220 :LVEDGGTFAETVELAQAIEAAGATIINTGIGW T0284 194 :AHLEAIAEHLHIPLMLV 1ps9A 270 :WVTRKLKGHVSLPLVTT T0284 215 :PQLRDDARLARL 1ps9A 287 :NRINDPQVADDI T0284 227 :G 1ps9A 302 :G T0284 228 :VRVVVNGHAAYF 1ps9A 304 :ADMVSMARPFLA T0284 247 :DCLREERGAVAS 1ps9A 318 :ELLSKAQSGRAD Number of specific fragments extracted= 14 number of extra gaps= 0 total=1336 Number of alignments=95 # 1ps9A read from 1ps9A/merged-good-all-a2m # found chain 1ps9A in template set T0284 23 :YHTASVFD 1ps9A 20 :VLMGSMHT T0284 31 :PMSARIAADLGFECGILGGSVASLQVLAAPDFALITLSEFVEQATRIGRVA 1ps9A 40 :AAFYAERARHGVALIVSGGIAPDLTGVGMEGGAMLNDASQIPHHRTITEAV T0284 96 :ALNVMRTVVELERAGIAALTIEDTL 1ps9A 140 :IDNFARCAQLAREAGYDGVEVMGSE T0284 121 :LPAQFGRKST 1ps9A 177 :NQRSDQWGGD T0284 135 :VEEGVGKIRAALEAR 1ps9A 191 :MRFAVEVVRAVRERV T0284 151 :DPALTIIARTNAELI 1ps9A 206 :GNDFIIIYRLSMLDL T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRD 1ps9A 226 :TFAETVELAQAIEAAGATIINTGIGWH T0284 193 :FAHLEAIAEHLHIPLMLVTYG 1ps9A 269 :SWVTRKLKGHVSLPLVTTNRI T0284 218 :RDDARLARL 1ps9A 290 :NDPQVADDI T0284 227 :GVRVVVNGHAAYF 1ps9A 303 :DADMVSMARPFLA T0284 247 :DCLREERGA 1ps9A 318 :ELLSKAQSG Number of specific fragments extracted= 11 number of extra gaps= 0 total=1347 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v93A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v93A expands to /projects/compbio/data/pdb/1v93.pdb.gz 1v93A:# T0284 read from 1v93A/merged-good-all-a2m # 1v93A read from 1v93A/merged-good-all-a2m # adding 1v93A to template set # found chain 1v93A in template set T0284 13 :FRALLDS 1v93A 3 :IRDLLKA T0284 20 :SRCYHTASVFD 1v93A 11 :RGPLFSFEFFP T0284 31 :PMSARIAADLGFECGILGGSVASLQ 1v93A 32 :FRTLEELKAFRPAFVSITYGAMGST T0284 67 :LSEFVEQATRIGR 1v93A 57 :RERSVAWAQRIQS T0284 81 :ARLPVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLPAQ 1v93A 70 :LGLNPLAHLTVAGQSRKEVAEVLHRFVESGVENLLALRGDPPRG T0284 126 :GR 1v93A 118 :RP T0284 128 :KST 1v93A 121 :PEG T0284 135 :VEEGVGKIRAALEARV 1v93A 124 :FRYAAELVALIRERYG T0284 152 :PALTIIARTNAELID 1v93A 140 :DRVSVGGAAYPEGHP T0284 167 :VDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLH 1v93A 159 :LEADLRHFKAKVEAGLDFAITQLFFNNAHYFGFLERAR T0284 205 :IPLMLVTY 1v93A 202 :IPILPGIM T0284 216 :QLRDD 1v93A 210 :PVTSY T0284 221 :ARLARLGVRVVVN 1v93A 259 :AELLEAGVEGVHF T0284 234 :GHAAYFAAIKA 1v93A 276 :KSPATRMVLER Number of specific fragments extracted= 14 number of extra gaps= 0 total=1361 Number of alignments=97 # 1v93A read from 1v93A/merged-good-all-a2m # found chain 1v93A in template set T0284 13 :FRALLDS 1v93A 3 :IRDLLKA T0284 20 :SRCYHTASVFD 1v93A 11 :RGPLFSFEFFP T0284 31 :PMSARIAADLGFECGILGGSVASLQ 1v93A 32 :FRTLEELKAFRPAFVSITYGAMGST T0284 67 :LSEFVEQATRIGRV 1v93A 57 :RERSVAWAQRIQSL T0284 82 :RLPVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLPA 1v93A 71 :GLNPLAHLTVAGQSRKEVAEVLHRFVESGVENLLALRGDPPR T0284 126 :GRKSTDLI 1v93A 113 :GERVFRPH T0284 135 :VEEGVGKIRAALEAR 1v93A 124 :FRYAAELVALIRERY T0284 151 :DPALTIIARTNAELI 1v93A 139 :GDRVSVGGAAYPEGH T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHL 1v93A 158 :SLEADLRHFKAKVEAGLDFAITQLFFNNAHYFGFLERA T0284 204 :HIPLMLVTYGNPQLRDDA 1v93A 201 :GIPILPGIMPVTSYRQLR T0284 222 :RLARLGVRVVVN 1v93A 260 :ELLEAGVEGVHF T0284 234 :GH 1v93A 273 :TL T0284 243 :KATYDCLR 1v93A 278 :PATRMVLE Number of specific fragments extracted= 13 number of extra gaps= 0 total=1374 Number of alignments=98 # 1v93A read from 1v93A/merged-good-all-a2m # found chain 1v93A in template set T0284 13 :FRALLDS 1v93A 3 :IRDLLKA T0284 20 :SRCYHTASVFD 1v93A 11 :RGPLFSFEFFP T0284 31 :PMSARIAADLGFECGILGGS 1v93A 32 :FRTLEELKAFRPAFVSITYG T0284 60 :PDFAL 1v93A 52 :AMGST T0284 67 :LSEFVEQATRIGRVARLPVIADADHG 1v93A 57 :RERSVAWAQRIQSLGLNPLAHLTVAG T0284 94 :GNALNVMRTVVELERAGIAALTIEDTLLP 1v93A 83 :QSRKEVAEVLHRFVESGVENLLALRGDPP T0284 123 :AQFGRKSTDLICVEEGVGKIR 1v93A 115 :RVFRPHPEGFRYAAELVALIR T0284 147 :E 1v93A 136 :E T0284 149 :RVDPALTIIARTNAELI 1v93A 137 :RYGDRVSVGGAAYPEGH T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHL 1v93A 158 :SLEADLRHFKAKVEAGLDFAITQLFFNNAHYFGFLERA T0284 204 :HIPLMLVTYG 1v93A 201 :GIPILPGIMP T0284 217 :LRDDARLARL 1v93A 211 :VTSYRQLRRF T0284 250 :REERGAVASDLTASELSKKYTFPEEYQAWARDY 1v93A 221 :TEVCGASIPGPLLAKLERHQDDPKAVLEIGVEH Number of specific fragments extracted= 13 number of extra gaps= 0 total=1387 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nvmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1nvmA/merged-good-all-a2m # 1nvmA read from 1nvmA/merged-good-all-a2m # found chain 1nvmA in training set T0284 22 :CYHTASVFDPMSA 1nvmA 10 :YISDVTLRDGSHA T0284 35 :RIAADLGFECGILG 1nvmA 37 :RALDKAKVDSIEVA T0284 49 :GSVASLQ 1nvmA 52 :GDGLQGS T0284 56 :VLAAPDF 1nvmA 61 :NYGFGRH T0284 69 :EFVEQATRIGRVA 1nvmA 68 :TDLEYIEAVAGEI T0284 82 :RLPVIADADHGYGNALNV 1nvmA 82 :HAQIATLLLPGIGSVHDL T0284 104 :VELERAGIAALTIEDT 1nvmA 100 :KNAYQAGARVVRVATH T0284 132 :LICVEEGVGKIRAALEA 1nvmA 116 :CTEADVSKQHIEYARNL T0284 153 :ALTIIA 1nvmA 133 :GMDTVG T0284 159 :RTNAELIDVDAVIQRTLAYQEAGADGICLV 1nvmA 140 :LMMSHMIPAEKLAEQGKLMESYGATCIYMA T0284 189 :GVRDFAHLEAIAEHLH 1nvmA 173 :GAMSMNDIRDRMRAFK T0284 205 :IPL 1nvmA 195 :TQV T0284 210 :VTYGNPQLRDD 1nvmA 198 :GMHAHHNLSLG T0284 221 :ARLARLGVRVVVNG 1nvmA 213 :IVAVEEGCDRVDAS T0284 235 :HAAYFAAIKATYDC 1nvmA 236 :NAPLEVFIAVAERL T0284 249 :LREERGAVASDL 1nvmA 257 :LYTLMDAADDIV Number of specific fragments extracted= 16 number of extra gaps= 0 total=1403 Number of alignments=100 # 1nvmA read from 1nvmA/merged-good-all-a2m # found chain 1nvmA in training set T0284 22 :CYHTASVFDPMSA 1nvmA 10 :YISDVTLRDGSHA T0284 35 :RIAADLGFECGILG 1nvmA 37 :RALDKAKVDSIEVA T0284 49 :GSVA 1nvmA 52 :GDGL T0284 57 :LAAPDFALITLSEFVEQATRIGR 1nvmA 56 :QGSSFNYGFGRHTDLEYIEAVAG T0284 80 :VARLPVIADADHGYGNALN 1nvmA 80 :ISHAQIATLLLPGIGSVHD T0284 103 :VVELERAGIAALTIEDTL 1nvmA 99 :LKNAYQAGARVVRVATHC T0284 133 :ICVEEGVGKIRAALEA 1nvmA 117 :TEADVSKQHIEYARNL T0284 153 :ALTIIA 1nvmA 133 :GMDTVG T0284 159 :RTNAELIDVDAVIQRTLAYQEAGADGICLVG 1nvmA 140 :LMMSHMIPAEKLAEQGKLMESYGATCIYMAD T0284 190 :VRDFAHLEAIAEHLH 1nvmA 174 :AMSMNDIRDRMRAFK T0284 205 :IP 1nvmA 195 :TQ T0284 208 :MLVTYGNPQLRDDA 1nvmA 197 :VGMHAHHNLSLGVA T0284 222 :RLARLGVRVVVNGHAA 1nvmA 214 :VAVEEGCDRVDASLAG T0284 245 :TYDCLREERGAVAS 1nvmA 239 :LEVFIAVAERLGWN T0284 259 :DLTASELSKKYT 1nvmA 254 :GTDLYTLMDAAD Number of specific fragments extracted= 15 number of extra gaps= 0 total=1418 Number of alignments=101 # 1nvmA read from 1nvmA/merged-good-all-a2m # found chain 1nvmA in training set T0284 4 :ASHHELRAMFRALLDSSRCYHTA 1nvmA 67 :HTDLEYIEAVAGEISHAQIATLL T0284 27 :SVFDPMSARIAADLGFECGILGG 1nvmA 92 :GIGSVHDLKNAYQAGARVVRVAT T0284 63 :ALITLSEFVEQATRIGRVARLPVIADADHGYGNALNVMRTVVELERAGIAALTIEDT 1nvmA 115 :HCTEADVSKQHIEYARNLGMDTVGFLMMSHMIPAEKLAEQGKLMESYGATCIYMADS T0284 130 :TDLICVEEGVGKIRAALEARVDPALTIIARTNAELI 1nvmA 172 :GGAMSMNDIRDRMRAFKAVLKPETQVGMHAHHNLSL T0284 171 :IQRTLAYQEAGADGICLVGVRD 1nvmA 209 :VANSIVAVEEGCDRVDASLAGM T0284 193 :FAHLEAIAEHL 1nvmA 257 :LYTLMDAADDI T0284 214 :NPQLRDDARLARLGVR 1nvmA 273 :DRPVRVDRETLGLGYA T0284 232 :VNGHAAYFAAIKATYDC 1nvmA 289 :GVYSSFLRHAEIAAAKY T0284 255 :AVASDLTASELSKKYTFPEEYQAWARDYMEV 1nvmA 306 :NLKTLDILVELGHRRMVGGQEDMIVDVALDL Number of specific fragments extracted= 9 number of extra gaps= 0 total=1427 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1igwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1igwA expands to /projects/compbio/data/pdb/1igw.pdb.gz 1igwA:# T0284 read from 1igwA/merged-good-all-a2m # 1igwA read from 1igwA/merged-good-all-a2m # adding 1igwA to template set # found chain 1igwA in template set Warning: unaligning (T0284)F125 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1igwA)G200 Warning: unaligning (T0284)G126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1igwA)G200 Warning: unaligning (T0284)N214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1igwA)S335 Warning: unaligning (T0284)P215 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1igwA)S335 T0284 7 :HELRAMFRALLDSS 1igwA 47 :QLGAAKMWRLLHGE T0284 21 :RCYHTASVFDPMSARIAADLGFECGILGGSVASLQ 1igwA 64 :GYINSLGALTGGQALQQAKAGIEAVYLSGWQVAAD T0284 57 :LA 1igwA 101 :LA T0284 59 :APDFALITLSEFVEQATRIGR 1igwA 106 :YPDQSLYPANSVPAVVERINN T0284 84 :PVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLL 1igwA 153 :PIVADAEAGFGGVLNAFELMKAMIEAGAAAVHFEDQLA T0284 122 :PAQ 1igwA 192 :VKK T0284 130 :TDLICVEEGVGKIRAALEAR 1igwA 201 :KVLVPTQEAIQKLVAARLCA T0284 150 :VDPALTIIARTNAELI 1igwA 223 :TGVPTLLVARTDADAA T0284 166 :DVDAVIQRTLAYQEA 1igwA 268 :GIEQAISRGLAYAPY T0284 182 :ADGICLV 1igwA 283 :ADLVWCE T0284 189 :GVRDFAHLEAIAEHLH 1igwA 291 :STPDLELARRFAQAIH T0284 205 :IPLMLVTYG 1igwA 309 :YPGKLLAYN T0284 221 :ARLARLGVRVVVNGHAAYFAAIKATYDCLREERG 1igwA 338 :QQLSDMGYKFQFITLAGIHSMWFNMFDLANAYAQ T0284 255 :AVASDLTASELSKKYTFPEE 1igwA 383 :QQPEFAAAKDGYTFVSHQQE T0284 275 :YQAWARDYMEVKE 1igwA 405 :TGYFDKVTTIIQG Number of specific fragments extracted= 15 number of extra gaps= 2 total=1442 Number of alignments=103 # 1igwA read from 1igwA/merged-good-all-a2m # found chain 1igwA in template set Warning: unaligning (T0284)F125 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1igwA)G200 Warning: unaligning (T0284)G126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1igwA)G200 Warning: unaligning (T0284)N214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1igwA)S335 Warning: unaligning (T0284)P215 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1igwA)S335 T0284 1 :MHRASHHELRAMFRALLDSS 1igwA 41 :PECTLAQLGAAKMWRLLHGE T0284 21 :RCYHTASVFDPMSARIAADLGFECGILGGSVASL 1igwA 64 :GYINSLGALTGGQALQQAKAGIEAVYLSGWQVAA T0284 55 :QVLA 1igwA 99 :ANLA T0284 59 :APDFALITLSEFVEQATRIGRVAR 1igwA 106 :YPDQSLYPANSVPAVVERINNTFR T0284 83 :LPVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1igwA 152 :LPIVADAEAGFGGVLNAFELMKAMIEAGAAAVHFEDQLAS T0284 123 :AQ 1igwA 193 :KK T0284 130 :TDLICVEEGVGKIRAALEA 1igwA 201 :KVLVPTQEAIQKLVAARLC T0284 149 :RVDPALTIIARTNAELIDV 1igwA 222 :VTGVPTLLVARTDADAADL T0284 168 :DAVIQRTLAYQEA 1igwA 270 :EQAISRGLAYAPY T0284 182 :ADGICLVG 1igwA 283 :ADLVWCET T0284 190 :VRDFAHLEAIAEHL 1igwA 292 :TPDLELARRFAQAI T0284 204 :H 1igwA 311 :G T0284 208 :MLVTYG 1igwA 312 :KLLAYN T0284 222 :RLARLGVRVVVNGHAAYFAAIKATYDCLREERG 1igwA 339 :QLSDMGYKFQFITLAGIHSMWFNMFDLANAYAQ T0284 260 :LTASELSKKY 1igwA 372 :GEGMKHYVEK T0284 274 :EYQAWARDYME 1igwA 382 :VQQPEFAAAKD Number of specific fragments extracted= 16 number of extra gaps= 2 total=1458 Number of alignments=104 # 1igwA read from 1igwA/merged-good-all-a2m # found chain 1igwA in template set Warning: unaligning (T0284)F125 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1igwA)G200 Warning: unaligning (T0284)G126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1igwA)G200 Warning: unaligning (T0284)T211 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1igwA)S335 Warning: unaligning (T0284)Y212 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1igwA)S335 T0284 2 :HRASHHELRAMFRALLDSS 1igwA 42 :ECTLAQLGAAKMWRLLHGE T0284 21 :RCYHTASVFDPMSARIAADLGFECGILGGSVASLQV 1igwA 64 :GYINSLGALTGGQALQQAKAGIEAVYLSGWQVAADA T0284 57 :LAAPDFALITLSEFVEQATRIGRVARL 1igwA 104 :SMYPDQSLYPANSVPAVVERINNTFRR T0284 84 :PVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1igwA 153 :PIVADAEAGFGGVLNAFELMKAMIEAGAAAVHFEDQLAS T0284 123 :AQ 1igwA 193 :KK T0284 131 :D 1igwA 201 :K T0284 132 :LICVEEGVGKIRAAL 1igwA 203 :LVPTQEAIQKLVAAR T0284 147 :EARVDPALTIIARTNAELI 1igwA 220 :ADVTGVPTLLVARTDADAA T0284 167 :VDAVIQRTLAYQE 1igwA 269 :IEQAISRGLAYAP T0284 182 :ADGICLVGVRD 1igwA 283 :ADLVWCETSTP T0284 193 :FAHLEAIAEHL 1igwA 295 :LELARRFAQAI T0284 204 :HIPLMLV 1igwA 311 :GKLLAYN T0284 219 :DDARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVASDLTASELSKKYT 1igwA 336 :FQQQLSDMGYKFQFITLAGIHSMWFNMFDLANAYAQGEGMKHYVEKVQQPEF T0284 281 :DY 1igwA 388 :AA Number of specific fragments extracted= 14 number of extra gaps= 2 total=1472 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xi3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1xi3A/merged-good-all-a2m # 1xi3A read from 1xi3A/merged-good-all-a2m # found chain 1xi3A in training set Warning: unaligning (T0284)G94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xi3A)R70 Warning: unaligning (T0284)N95 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xi3A)R70 Warning: unaligning (T0284)V188 because of BadResidue code BAD_PEPTIDE in next template residue (1xi3A)S128 Warning: unaligning (T0284)D192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xi3A)D137 T0284 21 :RCYHTAS 1xi3A 8 :KLYVITD T0284 29 :FDPMSARIAADLGFECGILG 1xi3A 19 :PEVESVREALEGGATAIQMR T0284 62 :FALITLSEFVEQATRIGRVA 1xi3A 39 :IKNAPTREMYEIGKTLRQLT T0284 82 :RLPVIAD 1xi3A 62 :DALFFVD T0284 103 :VVELERAGIAALTIEDTLLP 1xi3A 71 :VDVALAVDADGVQLGPEDMP T0284 142 :IRAALEAR 1xi3A 91 :IEVAKEIA T0284 152 :PALTIIARTNAE 1xi3A 99 :PNLIIGASVYSL T0284 168 :D 1xi3A 111 :E T0284 173 :RTLAYQEAGADGICL 1xi3A 112 :EALEAEKKGADYLGA T0284 189 :GVR 1xi3A 129 :VFP T0284 193 :FAHLEAIAEHLHIPL 1xi3A 143 :LEGLRKIVESVKIPV T0284 210 :VTYGNPQLRDDARLARLGVRVVVNGHAAY 1xi3A 158 :VAIGGINKDNAREVLKTGVDGIAVISAVM T0284 241 :AIKATYDCLREERGAV 1xi3A 191 :VRKATEELRKIVEEVL Number of specific fragments extracted= 13 number of extra gaps= 2 total=1485 Number of alignments=106 # 1xi3A read from 1xi3A/merged-good-all-a2m # found chain 1xi3A in training set Warning: unaligning (T0284)G94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xi3A)R70 Warning: unaligning (T0284)N95 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xi3A)R70 Warning: unaligning (T0284)V188 because of BadResidue code BAD_PEPTIDE in next template residue (1xi3A)S128 Warning: unaligning (T0284)G189 because of BadResidue code BAD_PEPTIDE at template residue (1xi3A)S128 T0284 22 :CYHTASV 1xi3A 8 :KLYVITD T0284 30 :DPMSARIAADLGFECGIL 1xi3A 20 :EVESVREALEGGATAIQM T0284 61 :DFALITLSEFVEQATRIGR 1xi3A 38 :RIKNAPTREMYEIGKTLRQ T0284 80 :VARLPVIAD 1xi3A 60 :EYDALFFVD T0284 96 :ALNV 1xi3A 71 :VDVA T0284 107 :ERAGIAALTIEDTLLP 1xi3A 75 :LAVDADGVQLGPEDMP T0284 142 :IRAALEA 1xi3A 91 :IEVAKEI T0284 151 :DPALTIIART 1xi3A 98 :APNLIIGASV T0284 165 :IDVD 1xi3A 108 :YSLE T0284 173 :RTLAYQEAGADGICL 1xi3A 112 :EALEAEKKGADYLGA T0284 190 :VR 1xi3A 129 :VF T0284 192 :DFAHLEAIAEHLHIPLMLVT 1xi3A 142 :GLEGLRKIVESVKIPVVAIG T0284 213 :GNPQL 1xi3A 162 :GINKD T0284 219 :DDARLARLGVRVVVNGHAAY 1xi3A 167 :NAREVLKTGVDGIAVISAVM T0284 245 :TYDCLREERGAV 1xi3A 191 :VRKATEELRKIV T0284 279 :A 1xi3A 203 :E Number of specific fragments extracted= 16 number of extra gaps= 2 total=1501 Number of alignments=107 # 1xi3A read from 1xi3A/merged-good-all-a2m # found chain 1xi3A in training set Warning: unaligning (T0284)V188 because of BadResidue code BAD_PEPTIDE in next template residue (1xi3A)S128 Warning: unaligning (T0284)G189 because of BadResidue code BAD_PEPTIDE at template residue (1xi3A)S128 T0284 21 :RCYHTASV 1xi3A 8 :KLYVITDR T0284 29 :FDPMSARIAADLGFECGILG 1xi3A 19 :PEVESVREALEGGATAIQMR T0284 62 :FALITLSEFVEQATRIGRVA 1xi3A 39 :IKNAPTREMYEIGKTLRQLT T0284 82 :RLPVIAD 1xi3A 62 :DALFFVD T0284 103 :VVELERAGIAALTIEDTLLP 1xi3A 71 :VDVALAVDADGVQLGPEDMP T0284 142 :IRAALEAR 1xi3A 91 :IEVAKEIA T0284 152 :PALTIIARTNA 1xi3A 99 :PNLIIGASVYS T0284 171 :IQRTLAYQEAGADGICL 1xi3A 110 :LEEALEAEKKGADYLGA T0284 190 :VRD 1xi3A 129 :VFP T0284 193 :FAHLEAIAEHLHIPLMLVTYGNPQ 1xi3A 143 :LEGLRKIVESVKIPVVAIGGINKD T0284 219 :DDARLARLGVRVVVNGHAAY 1xi3A 167 :NAREVLKTGVDGIAVISAVM T0284 239 :FAAIKATYDCLREER 1xi3A 192 :RKATEELRKIVEEVL Number of specific fragments extracted= 12 number of extra gaps= 1 total=1513 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o66A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1o66A/merged-good-all-a2m # 1o66A read from 1o66A/merged-good-all-a2m # found chain 1o66A in training set Warning: unaligning (T0284)E274 because last residue in template chain is (1o66A)I260 T0284 9 :LRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGIL 1o66A 3 :TVNTLQKMKAAGEKIAMLTAYESSFAALMDDAGVEMLLV T0284 49 :GSVASLQVLAAPDFALITLSEFVEQATRIGRVA 1o66A 42 :GDSLGMAVQGRKSTLPVSLRDMCYHTECVARGA T0284 82 :RLPVIADADHG 1o66A 76 :NAMIVSDLPFG T0284 93 :YG 1o66A 88 :YQ T0284 95 :NALNVMRTVVELERAGIAALTIEDTL 1o66A 91 :SKEQAFAAAAELMAAGAHMVKLEGGV T0284 137 :EGVGKIRAALEA 1o66A 117 :WMAETTEFLQMR T0284 153 :ALTIIAR 1o66A 129 :GIPVCAH T0284 160 :TNAELI 1o66A 139 :TPQSVF T0284 167 :VDAVIQRTLAYQEAGADGICLVGVR 1o66A 158 :AQALLNDAKAHDDAGAAVVLMECVL T0284 193 :FAHLEAIAEHLHIPL 1o66A 183 :AELAKKVTETVSCPT T0284 210 :VTYGNPQLRD 1o66A 198 :IGIGAGADCD T0284 230 :VVVNG 1o66A 208 :GQVLV T0284 249 :LREERG 1o66A 213 :MHDMLG T0284 255 :AVASDLTASELSKKYTFPE 1o66A 241 :AVRAYVAEVKAKTFPAAEH Number of specific fragments extracted= 14 number of extra gaps= 0 total=1527 Number of alignments=109 # 1o66A read from 1o66A/merged-good-all-a2m # found chain 1o66A in training set Warning: unaligning (T0284)D166 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o66A)K157 T0284 10 :RAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGIL 1o66A 4 :VNTLQKMKAAGEKIAMLTAYESSFAALMDDAGVEMLLV T0284 49 :GSVASLQVLAAPDFALITLSEFVEQATRIGR 1o66A 42 :GDSLGMAVQGRKSTLPVSLRDMCYHTECVAR T0284 80 :VARLPVIADADHG 1o66A 74 :AKNAMIVSDLPFG T0284 93 :YG 1o66A 88 :YQ T0284 95 :NALNVMRTVVELERAGIAALTIEDTL 1o66A 91 :SKEQAFAAAAELMAAGAHMVKLEGGV T0284 137 :EGVGKIRAALE 1o66A 117 :WMAETTEFLQM T0284 152 :PALTIIAR 1o66A 128 :RGIPVCAH T0284 160 :TNAELI 1o66A 139 :TPQSVF T0284 168 :DAVIQRTLAYQEAGADGICLVGVR 1o66A 159 :QALLNDAKAHDDAGAAVVLMECVL T0284 193 :FAHLEAIAEHLHIPLMLVTYGNPQLRDDARLARL 1o66A 183 :AELAKKVTETVSCPTIGIGAGADCDGQVLVMHDM T0284 227 :GVR 1o66A 218 :GIF T0284 246 :YDCLREERGAVAS 1o66A 239 :QAAVRAYVAEVKA T0284 259 :DLTASEL 1o66A 253 :TFPAAEH Number of specific fragments extracted= 13 number of extra gaps= 0 total=1540 Number of alignments=110 # 1o66A read from 1o66A/merged-good-all-a2m # found chain 1o66A in training set Warning: unaligning (T0284)D166 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o66A)K157 T0284 10 :RAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQ 1o66A 4 :VNTLQKMKAAGEKIAMLTAYESSFAALMDDAGVEMLLVGDSLGMAV T0284 57 :LAAPDFALITLSEFVEQATRIGRVA 1o66A 50 :QGRKSTLPVSLRDMCYHTECVARGA T0284 82 :RLPVIADADHGYG 1o66A 76 :NAMIVSDLPFGAY T0284 95 :NALNVMRTVVELERAGIAALTIEDTLL 1o66A 91 :SKEQAFAAAAELMAAGAHMVKLEGGVW T0284 138 :GVGKIRAALEAR 1o66A 118 :MAETTEFLQMRG T0284 154 :LTIIART 1o66A 130 :IPVCAHI T0284 161 :NAELI 1o66A 140 :PQSVF T0284 167 :VDAVIQRTLAYQEAGADGICLVGVR 1o66A 158 :AQALLNDAKAHDDAGAAVVLMECVL T0284 193 :FAHLEAIAEHLHIPLMLVTYGNP 1o66A 183 :AELAKKVTETVSCPTIGIGAGAD T0284 228 :VRVVVNGHAAY 1o66A 206 :CDGQVLVMHDM T0284 239 :FAAIKATYDCLRE 1o66A 239 :QAAVRAYVAEVKA Number of specific fragments extracted= 11 number of extra gaps= 0 total=1551 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rd5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rd5A expands to /projects/compbio/data/pdb/1rd5.pdb.gz 1rd5A:Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 862, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 864, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 866, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1030, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1032, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1742, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1744, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1746, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 1rd5A # T0284 read from 1rd5A/merged-good-all-a2m # 1rd5A read from 1rd5A/merged-good-all-a2m # adding 1rd5A to template set # found chain 1rd5A in template set Warning: unaligning (T0284)V104 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)F108 Warning: unaligning (T0284)R159 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)T150 Warning: unaligning (T0284)T160 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rd5A)T150 T0284 9 :LRAMFRALLDSSRCYHTASV 1rd5A 5 :VSDTMAALMAKGKTAFIPYI T0284 29 :FD 1rd5A 27 :GD T0284 31 :PMSARIAADLGFECGILG 1rd5A 35 :AEALRLLDGCGADVIELG T0284 51 :VASLQ 1rd5A 68 :SVARA T0284 57 :LA 1rd5A 73 :LA T0284 63 :ALITLSEFVEQATRIGRVARLPVIADAD 1rd5A 75 :SGTTMDAVLEMLREVTPELSCPVVLLSY T0284 94 :GNA 1rd5A 103 :YKP T0284 103 :V 1rd5A 106 :I T0284 105 :ELERAGIAALTIEDTL 1rd5A 113 :KMKEAGVHGLIVPDLP T0284 136 :EEGV 1rd5A 129 :YVAA T0284 140 :GKIRAALEA 1rd5A 134 :SLWSEAKNN T0284 153 :ALTIIA 1rd5A 143 :NLELVL T0284 161 :NAEL 1rd5A 151 :TPAI T0284 166 :DVDAVI 1rd5A 155 :PEDRMK T0284 176 :AYQEAGADGICLVGVRD 1rd5A 161 :EITKASEGFVYLVSVNG T0284 193 :FAHLEAIAEHLHIPL 1rd5A 190 :ESLIQEVKKVTNKPV T0284 209 :LVTYGNPQLRDDARLARLGVRVVVNGHAAYFAA 1rd5A 205 :AVGFGISKPEHVKQIAQWGADGVIIGSAMVRQL T0284 242 :IKATYDCLREERGAV 1rd5A 247 :LRRLEEYARGMKNAL Number of specific fragments extracted= 18 number of extra gaps= 2 total=1569 Number of alignments=112 # 1rd5A read from 1rd5A/merged-good-all-a2m # found chain 1rd5A in template set Warning: unaligning (T0284)Y93 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rd5A)F108 Warning: unaligning (T0284)G94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)S110 Warning: unaligning (T0284)N95 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rd5A)S110 Warning: unaligning (T0284)R159 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)T150 Warning: unaligning (T0284)T160 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rd5A)T150 Warning: unaligning (T0284)R191 because of BadResidue code BAD_PEPTIDE in next template residue (1rd5A)G180 T0284 9 :LRAMFRALLDSSRCYHTASVF 1rd5A 5 :VSDTMAALMAKGKTAFIPYIT T0284 30 :D 1rd5A 28 :D T0284 31 :PMSARIAADLGFECGILG 1rd5A 35 :AEALRLLDGCGADVIELG T0284 51 :VASLQ 1rd5A 68 :SVARA T0284 57 :LA 1rd5A 73 :LA T0284 63 :ALITLSEFVEQATRIGRVARLPVIADADH 1rd5A 75 :SGTTMDAVLEMLREVTPELSCPVVLLSYY T0284 96 :AL 1rd5A 111 :LA T0284 105 :ELERAGIAALTIEDTL 1rd5A 113 :KMKEAGVHGLIVPDLP T0284 128 :K 1rd5A 129 :Y T0284 137 :EGVGKIRAALEA 1rd5A 130 :VAAHSLWSEAKN T0284 152 :PALTIIA 1rd5A 142 :NNLELVL T0284 161 :NAE 1rd5A 151 :TPA T0284 165 :IDVDAVIQRTLA 1rd5A 154 :IPEDRMKEITKA T0284 182 :ADGICLVG 1rd5A 168 :GFVYLVSV T0284 190 :V 1rd5A 178 :V T0284 193 :FAHLEAIAEHLHIPL 1rd5A 190 :ESLIQEVKKVTNKPV T0284 209 :LVTYGNPQLRDDARLARLGVRVVVNGHAAYFAA 1rd5A 205 :AVGFGISKPEHVKQIAQWGADGVIIGSAMVRQL T0284 242 :IKATYDCLREERGA 1rd5A 247 :LRRLEEYARGMKNA Number of specific fragments extracted= 18 number of extra gaps= 3 total=1587 Number of alignments=113 # 1rd5A read from 1rd5A/merged-good-all-a2m # found chain 1rd5A in template set Warning: unaligning (T0284)M100 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)F108 Warning: unaligning (T0284)R159 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)T150 Warning: unaligning (T0284)T160 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rd5A)T150 T0284 9 :LRAMFRALLDSSRCYHTASVF 1rd5A 5 :VSDTMAALMAKGKTAFIPYIT T0284 31 :PMSARIAADLGFECGILG 1rd5A 35 :AEALRLLDGCGADVIELG T0284 49 :GSVASLQ 1rd5A 68 :SVARALA T0284 63 :ALITLSEFVEQATRIGRVARLPVIADAD 1rd5A 75 :SGTTMDAVLEMLREVTPELSCPVVLLSY T0284 94 :G 1rd5A 103 :Y T0284 97 :LNV 1rd5A 104 :KPI T0284 105 :ELERAGIAALTIEDTLLPA 1rd5A 113 :KMKEAGVHGLIVPDLPYVA T0284 135 :VEEGVGKIRA 1rd5A 132 :AHSLWSEAKN T0284 152 :PALTIIA 1rd5A 142 :NNLELVL T0284 161 :NAELI 1rd5A 151 :TPAIP T0284 172 :QRTLAYQEAGADGICLVGVRD 1rd5A 157 :DRMKEITKASEGFVYLVSVNG T0284 193 :FAHLEAIAEHLHIPLMLVTYG 1rd5A 190 :ESLIQEVKKVTNKPVAVGFGI T0284 218 :RDDARLA 1rd5A 211 :SKPEHVK T0284 225 :RLGVRVVVNGHAAYFAA 1rd5A 221 :QWGADGVIIGSAMVRQL T0284 242 :IKATYDCLREERG 1rd5A 247 :LRRLEEYARGMKN Number of specific fragments extracted= 15 number of extra gaps= 2 total=1602 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f6kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f6kA expands to /projects/compbio/data/pdb/1f6k.pdb.gz 1f6kA:Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1346, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1348, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1350, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 2143, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 2145, because occupancy 0.500 <= existing 0.500 in 1f6kA # T0284 read from 1f6kA/merged-good-all-a2m # 1f6kA read from 1f6kA/merged-good-all-a2m # adding 1f6kA to template set # found chain 1f6kA in template set T0284 22 :CYHTASV 1f6kA 7 :IFSALLV T0284 29 :FDPMSARIAADL 1f6kA 21 :INEKGLRQIIRH T0284 41 :GFECGILGGSVASLQ 1f6kA 38 :KVDGLYVGGSTGENF T0284 64 :LITLSEFVEQATRIGR 1f6kA 53 :MLSTEEKKEIFRIAKD T0284 80 :VA 1f6kA 70 :AK T0284 82 :RLPVIADAD 1f6kA 73 :QIALIAQVG T0284 93 :YGNALNVMRTVVELERAGIAALTIEDTLLPA 1f6kA 82 :SVNLKEAVELGKYATELGYDCLSAVTPFYYK T0284 133 :ICVEEGVGKIRAALEAR 1f6kA 113 :FSFPEIKHYYDTIIAET T0284 153 :ALTIIARTNAELID 1f6kA 130 :GSNMIVYSIPFLTG T0284 167 :VDA 1f6kA 148 :IEQ T0284 174 :TLAYQEA 1f6kA 151 :FGELYKN T0284 181 :GADGICLVGVR 1f6kA 159 :KVLGVKFTAGD T0284 193 :FAHLEAIAEHLH 1f6kA 170 :FYLLERLKKAYP T0284 205 :IP 1f6kA 183 :HL T0284 210 :VTYGNPQL 1f6kA 185 :IWAGFDEM T0284 220 :DARLARLGVRVVVNGHAAYFA 1f6kA 193 :MLPAASLGVDGAIGSTFNVNG T0284 243 :KATYDCLREERG 1f6kA 214 :VRARQIFELTKA T0284 275 :YQAWAR 1f6kA 239 :NDLIEG Number of specific fragments extracted= 18 number of extra gaps= 0 total=1620 Number of alignments=115 # 1f6kA read from 1f6kA/merged-good-all-a2m # found chain 1f6kA in template set T0284 21 :RCYHTASV 1f6kA 6 :GIFSALLV T0284 29 :FDPMSARIAADL 1f6kA 21 :INEKGLRQIIRH T0284 41 :GFECGILGGSVASLQ 1f6kA 38 :KVDGLYVGGSTGENF T0284 64 :LITLSEFVEQATRIGR 1f6kA 53 :MLSTEEKKEIFRIAKD T0284 80 :VARLPVIADADH 1f6kA 71 :KDQIALIAQVGS T0284 95 :NALNVMRTVVELERAGIAALTIEDTLLPA 1f6kA 84 :NLKEAVELGKYATELGYDCLSAVTPFYYK T0284 133 :ICVEEGVGKIRAALEA 1f6kA 113 :FSFPEIKHYYDTIIAE T0284 150 :VDPALTIIAR 1f6kA 129 :TGSNMIVYSI T0284 161 :NAELI 1f6kA 139 :PFLTG T0284 166 :DVDAV 1f6kA 147 :GIEQF T0284 175 :LAYQEAG 1f6kA 152 :GELYKNP T0284 182 :ADGICLVGVR 1f6kA 160 :VLGVKFTAGD T0284 193 :FAHLEAIAEHLH 1f6kA 170 :FYLLERLKKAYP T0284 205 :I 1f6kA 183 :H T0284 207 :LMLVTY 1f6kA 184 :LIWAGF T0284 217 :LRDDARLARLGVRVVVNGHAAYFA 1f6kA 190 :DEMMLPAASLGVDGAIGSTFNVNG T0284 243 :KATYDCLREERGA 1f6kA 214 :VRARQIFELTKAG T0284 261 :TASELSKKY 1f6kA 227 :KLKEALEIQ T0284 272 :PEEYQAWARDY 1f6kA 236 :HVTNDLIEGIL Number of specific fragments extracted= 19 number of extra gaps= 0 total=1639 Number of alignments=116 # 1f6kA read from 1f6kA/merged-good-all-a2m # found chain 1f6kA in template set T0284 21 :RCYHTASV 1f6kA 6 :GIFSALLV T0284 29 :FDPMSARIAADL 1f6kA 21 :INEKGLRQIIRH T0284 41 :GFECGILGGSVASLQ 1f6kA 38 :KVDGLYVGGSTGENF T0284 64 :LITLSEFVEQATRIGRVA 1f6kA 53 :MLSTEEKKEIFRIAKDEA T0284 82 :RLPVIADA 1f6kA 73 :QIALIAQV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLLPA 1f6kA 81 :GSVNLKEAVELGKYATELGYDCLSAVTPFYYK T0284 133 :ICVEEGVGKIRAALEAR 1f6kA 113 :FSFPEIKHYYDTIIAET T0284 151 :DPA 1f6kA 130 :GSN T0284 155 :TIIARTNAELI 1f6kA 133 :MIVYSIPFLTG T0284 166 :DVD 1f6kA 147 :GIE T0284 173 :RTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTYGNP 1f6kA 150 :QFGELYKNPKVLGVKFTAGDFYLLERLKKAYPNHLIWAGFDEM T0284 222 :RLARLGVRVVVNGHAA 1f6kA 195 :PAASLGVDGAIGSTFN T0284 240 :AAIKATYDCLREERGA 1f6kA 211 :VNGVRARQIFELTKAG T0284 257 :ASDLTASELSKKYTFPEEYQAWARD 1f6kA 227 :KLKEALEIQHVTNDLIEGILANGLY Number of specific fragments extracted= 14 number of extra gaps= 0 total=1653 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nal1/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nal1 expands to /projects/compbio/data/pdb/1nal.pdb.gz 1nal1:# T0284 read from 1nal1/merged-good-all-a2m # 1nal1 read from 1nal1/merged-good-all-a2m # adding 1nal1 to template set # found chain 1nal1 in template set Warning: unaligning (T0284)A81 because of BadResidue code BAD_PEPTIDE in next template residue (1nal1)G72 T0284 24 :HTASVFD 1nal1 11 :ALLTPFD T0284 31 :PMSARIAADLGFECGILGGSVASLQ 1nal1 28 :RRLVQFNIQQGIDGLYVGGSTGEAF T0284 64 :LITLSEFVEQATRIGR 1nal1 53 :VQSLSEREQVLEIVAE T0284 80 :V 1nal1 70 :G T0284 82 :RLPVIADA 1nal1 73 :KIKLIAHV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLLP 1nal1 81 :GCVTTAESQQLAASAKRYGFDAVSAVTPFYY T0284 128 :KS 1nal1 112 :PF T0284 134 :CVEEGVGKIRAALEAR 1nal1 114 :SFEEHCDHYRAIIDSA T0284 152 :PALTIIARTNAELID 1nal1 130 :DGLPMVVYNIPALSG T0284 167 :VDAV 1nal1 149 :LDQI T0284 175 :LAYQEA 1nal1 153 :NTLVTL T0284 181 :GADGICLVGVR 1nal1 160 :GVGALKQTSGD T0284 193 :FAHLEAIAEHLH 1nal1 171 :LYQMEQIRREHP T0284 205 :I 1nal1 184 :L T0284 207 :L 1nal1 185 :V T0284 210 :VTYGNPQLR 1nal1 186 :LYNGYDEIF T0284 221 :ARLARLGVRVVVNGHAAYFA 1nal1 195 :ASGLLAGADGGIGSTYNIMG T0284 243 :KATYDCLREERG 1nal1 215 :WRYQGIVKALKE Number of specific fragments extracted= 18 number of extra gaps= 1 total=1671 Number of alignments=118 # 1nal1 read from 1nal1/merged-good-all-a2m # found chain 1nal1 in template set Warning: unaligning (T0284)V80 because of BadResidue code BAD_PEPTIDE in next template residue (1nal1)G72 Warning: unaligning (T0284)A81 because of BadResidue code BAD_PEPTIDE at template residue (1nal1)G72 T0284 10 :RAMFRA 1nal1 24 :KASLRR T0284 33 :SARIAADLGFECGILGGSVASL 1nal1 30 :LVQFNIQQGIDGLYVGGSTGEA T0284 63 :ALITLSEFVEQATRIGR 1nal1 52 :FVQSLSEREQVLEIVAE T0284 82 :RLPVIADA 1nal1 73 :KIKLIAHV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLL 1nal1 81 :GCVTTAESQQLAASAKRYGFDAVSAVTPFY T0284 127 :RK 1nal1 111 :YP T0284 133 :ICVEEGVGKIRAALEAR 1nal1 113 :FSFEEHCDHYRAIIDSA T0284 152 :PA 1nal1 130 :DG T0284 154 :LTIIARTNAELI 1nal1 133 :PMVVYNIPALSG T0284 166 :DVDAV 1nal1 148 :TLDQI T0284 175 :LAYQEA 1nal1 153 :NTLVTL T0284 181 :GADGICLVGV 1nal1 160 :GVGALKQTSG T0284 192 :DFAHLEAIAEHLH 1nal1 170 :DLYQMEQIRREHP T0284 205 :IPLML 1nal1 184 :LVLYN T0284 213 :GNPQL 1nal1 189 :GYDEI T0284 223 :LARL 1nal1 194 :FASG T0284 227 :GVRVVVNGHAAYFA 1nal1 201 :GADGGIGSTYNIMG T0284 243 :KATYDCLREERGA 1nal1 215 :WRYQGIVKALKEG T0284 261 :TASELSKKY 1nal1 228 :DIQTAQKLQ T0284 272 :PEEYQAWARDY 1nal1 237 :TECNKVIDLLI Number of specific fragments extracted= 20 number of extra gaps= 1 total=1691 Number of alignments=119 # 1nal1 read from 1nal1/merged-good-all-a2m # found chain 1nal1 in template set T0284 30 :D 1nal1 23 :D T0284 31 :PMSARIAADLGFECGILGGSVASLQ 1nal1 28 :RRLVQFNIQQGIDGLYVGGSTGEAF T0284 64 :LITLSEFVEQATRIGRVA 1nal1 53 :VQSLSEREQVLEIVAEEG T0284 82 :RLPVIADA 1nal1 73 :KIKLIAHV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLLPA 1nal1 81 :GCVTTAESQQLAASAKRYGFDAVSAVTPFYYP T0284 133 :ICVEEGVGKIRAALEARVDPALTII 1nal1 113 :FSFEEHCDHYRAIIDSADGLPMVVY T0284 159 :RTNAELI 1nal1 138 :NIPALSG T0284 166 :DVD 1nal1 148 :TLD T0284 173 :RTLAYQEA 1nal1 151 :QINTLVTL T0284 181 :GADGI 1nal1 160 :GVGAL T0284 187 :LVGVRDFAHLEAIAEHLHIPLMLVTYGNP 1nal1 165 :KQTSGDLYQMEQIRREHPDLVLYNGYDEI T0284 220 :DARLARLGVRVVVNGHAAYFAAIKATYDC 1nal1 195 :ASGLLAGADGGIGSTYNIMGWRYQGIVKA T0284 252 :E 1nal1 224 :L T0284 254 :GAVASDLTASELSKKYTFPEEYQAWARD 1nal1 225 :KEGDIQTAQKLQTECNKVIDLLIKTGVF Number of specific fragments extracted= 14 number of extra gaps= 0 total=1705 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oy0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0284/1oy0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0284/1oy0A/merged-good-all-a2m.gz for input Trying 1oy0A/merged-good-all-a2m Error: Couldn't open file 1oy0A/merged-good-all-a2m or 1oy0A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nal3/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nal3 expands to /projects/compbio/data/pdb/1nal.pdb.gz 1nal3:# T0284 read from 1nal3/merged-good-all-a2m # 1nal3 read from 1nal3/merged-good-all-a2m # adding 1nal3 to template set # found chain 1nal3 in template set T0284 4 :ASHHELRAMF 1nal3 21 :ALDKASLRRL T0284 34 :ARIAADLGFECGILGGSVASLQ 1nal3 31 :VQFNIQQGIDGLYVGGSTGEAF T0284 64 :LITLSEFVEQATRIGR 1nal3 53 :VQSLSEREQVLEIVAE T0284 80 :VA 1nal3 70 :GK T0284 82 :RLPVIADA 1nal3 73 :KIKLIAHV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLL 1nal3 81 :GCVTTAESQQLAASAKRYGFDAVSAVTPFY T0284 127 :RKS 1nal3 111 :YPF T0284 134 :CVEEGVGKIRAALEAR 1nal3 114 :SFEEHCDHYRAIIDSA T0284 153 :ALTIIA 1nal3 131 :GLPMVV T0284 159 :RTNAEL 1nal3 138 :NIPALS T0284 165 :IDVDAV 1nal3 147 :LTLDQI T0284 175 :LAYQEA 1nal3 153 :NTLVTL T0284 181 :GADGICLVGVR 1nal3 160 :GVGALKQTSGD T0284 193 :FAHLEAIAEHLH 1nal3 171 :LYQMEQIRREHP T0284 205 :I 1nal3 184 :L T0284 207 :L 1nal3 185 :V T0284 210 :VTYGNPQLR 1nal3 186 :LYNGYDEIF T0284 221 :ARLARLGVRVVVNGHAAYFA 1nal3 195 :ASGLLAGADGGIGSTYNIMG T0284 243 :KATYDCLREERG 1nal3 215 :WRYQGIVKALKE T0284 257 :ASDLTASEL 1nal3 233 :QKLQTECNK Number of specific fragments extracted= 20 number of extra gaps= 0 total=1725 Number of alignments=121 # 1nal3 read from 1nal3/merged-good-all-a2m # found chain 1nal3 in template set T0284 11 :AMFRALL 1nal3 25 :ASLRRLV T0284 35 :RIAADLGFECGILGGSVASLQ 1nal3 32 :QFNIQQGIDGLYVGGSTGEAF T0284 64 :LITLSEFVEQATRIGR 1nal3 53 :VQSLSEREQVLEIVAE T0284 80 :VARLPVIADA 1nal3 71 :KGKIKLIAHV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLL 1nal3 81 :GCVTTAESQQLAASAKRYGFDAVSAVTPFY T0284 127 :RK 1nal3 111 :YP T0284 133 :ICVEEGVGKIRAALEAR 1nal3 113 :FSFEEHCDHYRAIIDSA T0284 152 :PA 1nal3 130 :DG T0284 154 :LTIIARTNAELI 1nal3 133 :PMVVYNIPALSG T0284 166 :DVDAVI 1nal3 148 :TLDQIN T0284 176 :AYQEA 1nal3 154 :TLVTL T0284 181 :GADGICLVGV 1nal3 160 :GVGALKQTSG T0284 192 :DFAHLEAIAEHLH 1nal3 170 :DLYQMEQIRREHP T0284 205 :IPLML 1nal3 184 :LVLYN T0284 213 :GNPQLR 1nal3 189 :GYDEIF T0284 221 :ARLARLGVRVVVNGHAAYF 1nal3 195 :ASGLLAGADGGIGSTYNIM T0284 242 :IKATYDCLREERGA 1nal3 214 :GWRYQGIVKALKEG T0284 261 :TASELSKKY 1nal3 228 :DIQTAQKLQ T0284 272 :PEEYQAWARD 1nal3 237 :TECNKVIDLL Number of specific fragments extracted= 19 number of extra gaps= 0 total=1744 Number of alignments=122 # 1nal3 read from 1nal3/merged-good-all-a2m # found chain 1nal3 in template set T0284 5 :SHHELRAMFRA 1nal3 22 :LDKASLRRLVQ T0284 36 :IAADLGFECGILGGSVASLQ 1nal3 33 :FNIQQGIDGLYVGGSTGEAF T0284 64 :LITLSEFVEQATRIGRVA 1nal3 53 :VQSLSEREQVLEIVAEEG T0284 82 :RLPVIADA 1nal3 73 :KIKLIAHV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLLPA 1nal3 81 :GCVTTAESQQLAASAKRYGFDAVSAVTPFYYP T0284 133 :ICVEEGVGKIRAALEARVDPALTII 1nal3 113 :FSFEEHCDHYRAIIDSADGLPMVVY T0284 159 :RTNAELI 1nal3 138 :NIPALSG T0284 166 :DVD 1nal3 148 :TLD T0284 173 :RTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTYGNP 1nal3 151 :QINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEI T0284 220 :DARLARLGVRVVVNGHAAYFAAIKATYDCLREE 1nal3 195 :ASGLLAGADGGIGSTYNIMGWRYQGIVKALKEG T0284 254 :GAVASDLTASELSKKYTFPEEYQAWA 1nal3 228 :DIQTAQKLQTECNKVIDLLIKTGVFR Number of specific fragments extracted= 11 number of extra gaps= 0 total=1755 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p0kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1p0kA expands to /projects/compbio/data/pdb/1p0k.pdb.gz 1p0kA:# T0284 read from 1p0kA/merged-good-all-a2m # 1p0kA read from 1p0kA/merged-good-all-a2m # adding 1p0kA to template set # found chain 1p0kA in template set Warning: unaligning (T0284)Q124 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0kA)F163 Warning: unaligning (T0284)V135 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p0kA)F163 Warning: unaligning (T0284)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0kA)R226 T0284 22 :CYHTASVFD 1p0kA 56 :SPIFINAMT T0284 31 :PMSARIAADLGFECG 1p0kA 76 :KSLARAASQAGIPLA T0284 47 :L 1p0kA 91 :V T0284 49 :GSVASLQ 1p0kA 92 :GSQMSAL T0284 60 :PD 1p0kA 99 :KD T0284 68 :SEFVEQATRIGR 1p0kA 101 :PSERLSYEIVRK T0284 80 :VARLPVIADADHG 1p0kA 114 :NPNGLIFANLGSE T0284 94 :GNALNVMRTVVE 1p0kA 127 :ATAAQAKEAVEM T0284 109 :AGIAALTIEDTLLPA 1p0kA 139 :IGANALQIHLNVIQE T0284 136 :EEGVGKIRAALEAR 1p0kA 164 :SGALKRIEQICSRV T0284 153 :ALTIIARTNAELIDVDA 1p0kA 178 :SVPVIVKEVGFGMSKAS T0284 174 :TLAYQEAGADGICLV 1p0kA 195 :AGKLYEAGAAAVDIG T0284 199 :IAEHLHIPLMLVTYGNPQLRDDARLARLGVRVVVNGHAAYFAAIKA 1p0kA 245 :IRSEFPASTMIASGGLQDALDVAKAIALGASCTGMAGHFLKALTDS T0284 245 :TYDCLREERGAVASDLTA 1p0kA 295 :LLEEIQLILEELKLIMTV Number of specific fragments extracted= 14 number of extra gaps= 0 total=1769 Number of alignments=124 # 1p0kA read from 1p0kA/merged-good-all-a2m # found chain 1p0kA in template set Warning: unaligning (T0284)Q124 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0kA)F163 Warning: unaligning (T0284)V135 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p0kA)F163 Warning: unaligning (T0284)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0kA)R226 T0284 1 :MHRASHHELRAMF 1p0kA 63 :MTGGGGKLTYEIN T0284 31 :PMSARIAADLGFECG 1p0kA 76 :KSLARAASQAGIPLA T0284 47 :L 1p0kA 91 :V T0284 49 :GSVA 1p0kA 92 :GSQM T0284 57 :LAAPD 1p0kA 96 :SALKD T0284 68 :SEFVEQATRIGR 1p0kA 101 :PSERLSYEIVRK T0284 80 :VARLPVIADADHG 1p0kA 114 :NPNGLIFANLGSE T0284 94 :GNALNVMRTVVE 1p0kA 127 :ATAAQAKEAVEM T0284 109 :AGIAALTIEDTLLPA 1p0kA 139 :IGANALQIHLNVIQE T0284 136 :EEGVGKIRAALEAR 1p0kA 164 :SGALKRIEQICSRV T0284 153 :ALTIIARTNAELIDVD 1p0kA 178 :SVPVIVKEVGFGMSKA T0284 173 :RTLAYQEAGADGICLV 1p0kA 194 :SAGKLYEAGAAAVDIG T0284 199 :IAEHLHIPLMLVTYGNPQLRDDARLARLGVRVVVNGHAAYFAAIK 1p0kA 245 :IRSEFPASTMIASGGLQDALDVAKAIALGASCTGMAGHFLKALTD T0284 244 :ATYDCLREERGAVAS 1p0kA 294 :GLLEEIQLILEELKL T0284 259 :DLTASELSK 1p0kA 315 :ARTIADLQK T0284 271 :FPEEYQAWAR 1p0kA 329 :KGETHHWLTE Number of specific fragments extracted= 16 number of extra gaps= 0 total=1785 Number of alignments=125 # 1p0kA read from 1p0kA/merged-good-all-a2m # found chain 1p0kA in template set Warning: unaligning (T0284)L57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0kA)F163 Warning: unaligning (T0284)L67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p0kA)F163 Warning: unaligning (T0284)A123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p0kA)R226 T0284 3 :RASHHELRAMFRALLDSSRCYHTASV 1p0kA 100 :DPSERLSYEIVRKENPNGLIFANLGS T0284 29 :FDPMSARIAADL 1p0kA 127 :ATAAQAKEAVEM T0284 41 :GFECGIL 1p0kA 140 :GANALQI T0284 55 :QV 1p0kA 152 :QE T0284 68 :SEFVEQATRIGRVARLPVIA 1p0kA 164 :SGALKRIEQICSRVSVPVIV T0284 89 :ADHGYG 1p0kA 184 :KEVGFG T0284 95 :NAL 1p0kA 191 :SKA T0284 102 :TVVELERAGIAALTI 1p0kA 194 :SAGKLYEAGAAAVDI T0284 124 :QFGRKSTDLICVEEGVGKIRA 1p0kA 227 :QISFFNSWGISTAASLAEIRS T0284 149 :RVDPALTIIA 1p0kA 248 :EFPASTMIAS T0284 164 :LI 1p0kA 259 :GL T0284 166 :D 1p0kA 262 :D T0284 171 :IQRTLAYQEAGADGICLV 1p0kA 263 :ALDVAKAIALGASCTGMA T0284 197 :EAIAEHL 1p0kA 281 :GHFLKAL T0284 219 :DDARLAR 1p0kA 291 :GEEGLLE T0284 237 :AYFAAIKATYDCLREE 1p0kA 298 :EIQLILEELKLIMTVL T0284 257 :AS 1p0kA 314 :GA T0284 260 :LTASELSK 1p0kA 316 :RTIADLQK Number of specific fragments extracted= 18 number of extra gaps= 0 total=1803 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fiqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fiqA expands to /projects/compbio/data/pdb/2fiq.pdb.gz 2fiqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1190, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1192, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1194, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1196, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1200, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1739, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 2fiqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2442, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 2444, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 2446, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 2448, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 2450, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 2452, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 2454, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 2456, because occupancy 0.500 <= existing 0.500 in 2fiqA Skipped atom 2458, because occupancy 0.500 <= existing 0.500 in 2fiqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0284 read from 2fiqA/merged-good-all-a2m # 2fiqA read from 2fiqA/merged-good-all-a2m # adding 2fiqA to template set # found chain 2fiqA in template set Warning: unaligning (T0284)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fiqA)V185 Warning: unaligning (T0284)Y282 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fiqA)Y343 Warning: unaligning (T0284)M283 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fiqA)Y343 T0284 10 :RAMFRALLDSSRC 2fiqA 2 :KTLIARHKAGEHI T0284 23 :YHTASVFDPMSARIAADLG 2fiqA 16 :ICSVCSAHPLVIEAALAFD T0284 42 :FECGILG 2fiqA 39 :RKVLIEA T0284 49 :GS 2fiqA 47 :SN T0284 55 :QVLAAPDFALITLSEFVEQATRIGR 2fiqA 49 :QVNQFGGYTGMTPADFREFVFAIAD T0284 82 :RLPVIAD 2fiqA 81 :RIILGGD T0284 89 :ADHGYG 2fiqA 90 :GPNCWQ T0284 95 :N 2fiqA 98 :N T0284 96 :ALNVMRTVVELERAGIAALTIEDTL 2fiqA 103 :MEKSVELVKAYVRAGFSKIHLDASM T0284 124 :QFGR 2fiqA 128 :SCAG T0284 128 :KSTD 2fiqA 133 :PIPL T0284 134 :CVEEGVGKIRAALEAR 2fiqA 137 :APETVAERAAVLCFAA T0284 150 :VD 2fiqA 156 :AT T0284 154 :LTIIARTNAE 2fiqA 164 :LSYVIGTEVP T0284 166 :DVDAVIQRTLAYQEA 2fiqA 189 :HVEDAANTLRTHQKA T0284 182 :ADGICLV 2fiqA 216 :VIAIVVQ T0284 189 :GV 2fiqA 224 :GV T0284 192 :DFAHLEAIAEHLH 2fiqA 236 :QPQEAQALAQWIE T0284 205 :IPL 2fiqA 251 :RMV T0284 210 :VTYGNPQLRDD 2fiqA 254 :YEAHSTDYQTR T0284 221 :ARLARLGVRVVVNGHAAYFAAIKATYDCLREERG 2fiqA 268 :WELVRDHFAILKVGPALTFALREAIFALAQIEQE T0284 255 :AVASDLTASELSKKYTFPEEYQAWARD 2fiqA 315 :IEEVMLDEPQYWKKYYRTGFNDSLLDI Number of specific fragments extracted= 22 number of extra gaps= 1 total=1825 Number of alignments=127 # 2fiqA read from 2fiqA/merged-good-all-a2m # found chain 2fiqA in template set Warning: unaligning (T0284)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fiqA)V185 T0284 10 :RAMFRALLDSSRC 2fiqA 2 :KTLIARHKAGEHI T0284 23 :YHTASVFDPMSARIAADL 2fiqA 16 :ICSVCSAHPLVIEAALAF T0284 41 :GFECGILG 2fiqA 38 :TRKVLIEA T0284 54 :LQVLAAPDFALITLSEFVEQATRIGR 2fiqA 48 :NQVNQFGGYTGMTPADFREFVFAIAD T0284 80 :VARLPVIAD 2fiqA 79 :RERIILGGD T0284 89 :ADHGYG 2fiqA 90 :GPNCWQ T0284 95 :N 2fiqA 98 :N T0284 96 :ALNVMRTVVELERAGIAALTIEDTLL 2fiqA 103 :MEKSVELVKAYVRAGFSKIHLDASMS T0284 126 :GRKSTDLICVEEGVGKIRAALEA 2fiqA 129 :CAGDPIPLAPETVAERAAVLCFA T0284 149 :RVDP 2fiqA 155 :VATD T0284 154 :LTIIARTNAE 2fiqA 164 :LSYVIGTEVP T0284 167 :VDAVIQRTLAYQEA 2fiqA 190 :VEDAANTLRTHQKA T0284 182 :ADGICLVGVR 2fiqA 216 :VIAIVVQPGV T0284 192 :DFAHLEAIAEHLH 2fiqA 236 :QPQEAQALAQWIE T0284 205 :IPLMLVT 2fiqA 250 :TRMVYEA T0284 213 :GNPQLRDDARLARL 2fiqA 257 :HSTDYQTRTAYWEL T0284 227 :GVRVVVNGHAAYFAAIKATYDCLREERGAVAS 2fiqA 274 :HFAILKVGPALTFALREAIFALAQIEQELIAP T0284 259 :DLTASELSKKY 2fiqA 331 :RTGFNDSLLDI Number of specific fragments extracted= 18 number of extra gaps= 0 total=1843 Number of alignments=128 # 2fiqA read from 2fiqA/merged-good-all-a2m # found chain 2fiqA in template set T0284 11 :AMFRALLDSSR 2fiqA 3 :TLIARHKAGEH T0284 22 :CYHTASVFDPMSARIAADL 2fiqA 15 :GICSVCSAHPLVIEAALAF T0284 41 :GFECGILGGSVAS 2fiqA 38 :TRKVLIEATSNQV T0284 57 :LAAPDFALITLSEFVEQATRIGRVARL 2fiqA 51 :NQFGGYTGMTPADFREFVFAIADKVGF T0284 84 :PVIADADHGYG 2fiqA 82 :IILGGDHLGPN T0284 95 :N 2fiqA 98 :N T0284 96 :ALNVMRTVVELERAGIAALTIEDTLLPAQFG 2fiqA 103 :MEKSVELVKAYVRAGFSKIHLDASMSCAGDP T0284 132 :LICVEEGVGKIRAALEARVD 2fiqA 135 :PLAPETVAERAAVLCFAAES T0284 154 :LTIIA 2fiqA 165 :SYVIG T0284 160 :TNA 2fiqA 170 :TEV T0284 167 :VDAVIQRTLAYQEA 2fiqA 193 :AANTLRTHQKAFIA T0284 181 :GA 2fiqA 208 :GL T0284 183 :DGICLVGVRD 2fiqA 217 :IAIVVQPGVE T0284 193 :FAHLEAIAEHLHIPLMLVTYGNPQLRDDARLA 2fiqA 237 :PQEAQALAQWIENTRMVYEAHSTDYQTRTAYW T0284 225 :RLGVRVVVNGHAAYFAAIKATYDCLR 2fiqA 272 :RDHFAILKVGPALTFALREAIFALAQ T0284 261 :TASELSKKYTFPEEYQAWARDYMEV 2fiqA 298 :IEQELIAPENRSGCLAVIEEVMLDE Number of specific fragments extracted= 16 number of extra gaps= 0 total=1859 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hl2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1hl2A/merged-good-all-a2m # 1hl2A read from 1hl2A/merged-good-all-a2m # found chain 1hl2A in training set T0284 25 :TASVFD 1hl2A 12 :LLTPFD T0284 31 :PMSARIAADLGFECGILGGSVASLQ 1hl2A 28 :RRLVQFNIQQGIDGLYVGGSTGEAF T0284 64 :LITLSEFVEQATRIGR 1hl2A 53 :VQSLSEREQVLEIVAE T0284 80 :VA 1hl2A 70 :AK T0284 82 :RLPVIADA 1hl2A 73 :KIKLIAHV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTL 1hl2A 81 :GCVSTAESQQLAASAKRYGFDAVSAVTPF T0284 126 :GRKS 1hl2A 110 :YYPF T0284 134 :CVEEGVGKIRAALEAR 1hl2A 114 :SFEEHCDHYRAIIDSA T0284 152 :PALTIIA 1hl2A 130 :DGLPMVV T0284 159 :RTNAEL 1hl2A 138 :NIPARS T0284 167 :VDAV 1hl2A 149 :LDQI T0284 175 :LAYQEA 1hl2A 153 :NTLVTL T0284 181 :GADGICLVGVR 1hl2A 160 :GVGALKQTSGD T0284 193 :FAHLEAIAEHLH 1hl2A 171 :LYQMEQIRREHP T0284 205 :I 1hl2A 184 :L T0284 207 :L 1hl2A 185 :V T0284 210 :VTYGNPQLR 1hl2A 186 :LYNGYDEIF T0284 221 :ARLARLGVRVVVNGHAAYFA 1hl2A 195 :ASGLLAGADGGIGSTYNIMG T0284 243 :KATYDCLREERG 1hl2A 215 :WRYQGIVKALKE T0284 255 :AVASDLTASEL 1hl2A 231 :TAQKLQTECNK Number of specific fragments extracted= 20 number of extra gaps= 0 total=1879 Number of alignments=130 # 1hl2A read from 1hl2A/merged-good-all-a2m # found chain 1hl2A in training set T0284 11 :AMFRA 1hl2A 25 :ASLRR T0284 33 :SARIAADLGFECGILGGSVASL 1hl2A 30 :LVQFNIQQGIDGLYVGGSTGEA T0284 63 :ALITLSEFVEQATRIGR 1hl2A 52 :FVQSLSEREQVLEIVAE T0284 80 :VARLPVIADA 1hl2A 71 :KGKIKLIAHV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLL 1hl2A 81 :GCVSTAESQQLAASAKRYGFDAVSAVTPFY T0284 127 :RK 1hl2A 111 :YP T0284 133 :ICVEEGVGKIRAALEAR 1hl2A 113 :FSFEEHCDHYRAIIDSA T0284 152 :PA 1hl2A 130 :DG T0284 154 :LTIIARTNAELI 1hl2A 133 :PMVVYNIPARSG T0284 166 :DVDAV 1hl2A 148 :TLDQI T0284 175 :LAYQEA 1hl2A 153 :NTLVTL T0284 181 :GADGICLVGV 1hl2A 160 :GVGALKQTSG T0284 192 :DFAHLEAIAEHLH 1hl2A 170 :DLYQMEQIRREHP T0284 205 :IPL 1hl2A 184 :LVL T0284 209 :LV 1hl2A 187 :YN T0284 213 :GNPQL 1hl2A 189 :GYDEI T0284 223 :LARL 1hl2A 194 :FASG T0284 227 :GVRVVVNGHAAYFA 1hl2A 201 :GADGGIGSTYNIMG T0284 243 :KATYDCLREERGA 1hl2A 215 :WRYQGIVKALKEG T0284 261 :TASELSKKYT 1hl2A 228 :DIQTAQKLQT T0284 273 :EEYQAWA 1hl2A 238 :ECNKVID Number of specific fragments extracted= 21 number of extra gaps= 0 total=1900 Number of alignments=131 # 1hl2A read from 1hl2A/merged-good-all-a2m # found chain 1hl2A in training set T0284 5 :SHHELRAM 1hl2A 22 :LDKASLRR T0284 33 :SARIAADLGFECGILGGSVASLQ 1hl2A 30 :LVQFNIQQGIDGLYVGGSTGEAF T0284 64 :LITLSEFVEQATRIGRVA 1hl2A 53 :VQSLSEREQVLEIVAEEA T0284 82 :RLPVIADA 1hl2A 73 :KIKLIAHV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLLPA 1hl2A 81 :GCVSTAESQQLAASAKRYGFDAVSAVTPFYYP T0284 133 :ICVEEGVGKIRAALEARVDPALTIIA 1hl2A 113 :FSFEEHCDHYRAIIDSADGLPMVVYN T0284 160 :TNAELI 1hl2A 139 :IPARSG T0284 166 :DVD 1hl2A 148 :TLD T0284 173 :RTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTYGNP 1hl2A 151 :QINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEI T0284 220 :DARLARLGVRVVVNGHAAYFAAIKATYDCL 1hl2A 195 :ASGLLAGADGGIGSTYNIMGWRYQGIVKAL T0284 253 :RGA 1hl2A 225 :KEG T0284 256 :VASDLTASELSKKYTFPEEYQAWA 1hl2A 230 :QTAQKLQTECNKVIDLLIKTGVFR Number of specific fragments extracted= 12 number of extra gaps= 0 total=1912 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p4cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1p4cA/merged-good-all-a2m # 1p4cA read from 1p4cA/merged-good-all-a2m # found chain 1p4cA in training set Warning: unaligning (T0284)F125 because of BadResidue code BAD_PEPTIDE at template residue (1p4cA)L189 Warning: unaligning (T0284)T130 because of BadResidue code BAD_PEPTIDE in next template residue (1p4cA)A195 T0284 22 :CYHTASV 1p4cA 74 :PLLIGPT T0284 30 :DPMSARIAADLGFECGIL 1p4cA 91 :DLALARAATKAGIPFVLS T0284 50 :SV 1p4cA 109 :TA T0284 63 :ALIT 1p4cA 111 :SNMS T0284 74 :ATRIGRVARLPVIADADHG 1p4cA 115 :IEDLARQCDGDLWFQLYVI T0284 95 :NALNVMRTVVELERAGIAALTIEDTLLPA 1p4cA 134 :HREIAQGMVLKALHTGYTTLVLTTDVAVN T0284 126 :GRKS 1p4cA 190 :GKMD T0284 131 :DLICVEEGVGKIRAALEARVD 1p4cA 206 :RQMDASFNWEALRWLRDLWPH T0284 153 :ALTIIART 1p4cA 227 :KLLVKGLL T0284 166 :DVDA 1p4cA 235 :SAED T0284 174 :TLAYQEAGADGICLVG 1p4cA 239 :ADRCIAEGADGVILSN T0284 191 :RD 1p4cA 264 :IS T0284 193 :FAHLEAIAEHLHIPL 1p4cA 267 :MEVLAQSVAKTGKPV T0284 209 :LVTYGNPQLRDDARLARLGVRVVVNGHAAYFAAIKA 1p4cA 282 :LIDSGFRRGSDIVKALALGAEAVLLGRATLYGLAAR T0284 245 :TYDCLREERGAVASDLTASELSKK 1p4cA 322 :VDEVLTLLKADIDRTLAQIGCPDI Number of specific fragments extracted= 15 number of extra gaps= 2 total=1927 Number of alignments=133 # 1p4cA read from 1p4cA/merged-good-all-a2m # found chain 1p4cA in training set T0284 22 :CYHTASV 1p4cA 74 :PLLIGPT T0284 30 :DPMSARIAADLGFECGIL 1p4cA 91 :DLALARAATKAGIPFVLS T0284 61 :DFALIT 1p4cA 109 :TASNMS T0284 74 :ATRIGRVARLPVIADADHG 1p4cA 115 :IEDLARQCDGDLWFQLYVI T0284 95 :NALNVMRTVVELERAGIAALTIED 1p4cA 134 :HREIAQGMVLKALHTGYTTLVLTT T0284 122 :P 1p4cA 177 :P T0284 123 :AQFGRKS 1p4cA 181 :LKNFEGI T0284 131 :DLICVEEGVGKIRAALEAR 1p4cA 206 :RQMDASFNWEALRWLRDLW T0284 151 :DPALTIIART 1p4cA 225 :PHKLLVKGLL T0284 166 :DVD 1p4cA 235 :SAE T0284 173 :RTLAYQEAGADGICLV 1p4cA 238 :DADRCIAEGADGVILS T0284 189 :GVRDFAHLEAIAEHLHIPL 1p4cA 263 :AISPMEVLAQSVAKTGKPV T0284 209 :LVTYGNPQLRDDARLARLGVRVVVNGHAAYFAAI 1p4cA 282 :LIDSGFRRGSDIVKALALGAEAVLLGRATLYGLA T0284 244 :ATYDCLREERGAVA 1p4cA 321 :GVDEVLTLLKADID T0284 264 :ELSKK 1p4cA 335 :RTLAQ Number of specific fragments extracted= 15 number of extra gaps= 0 total=1942 Number of alignments=134 # 1p4cA read from 1p4cA/merged-good-all-a2m # found chain 1p4cA in training set Warning: unaligning (T0284)Q124 because of BadResidue code BAD_PEPTIDE in next template residue (1p4cA)L189 Warning: unaligning (T0284)F125 because of BadResidue code BAD_PEPTIDE at template residue (1p4cA)L189 Warning: unaligning (T0284)T130 because of BadResidue code BAD_PEPTIDE in next template residue (1p4cA)A195 Warning: unaligning (T0284)D131 because of BadResidue code BAD_PEPTIDE at template residue (1p4cA)A195 T0284 22 :CYHTASVF 1p4cA 74 :PLLIGPTG T0284 30 :DPMSARIAADLGFECGILG 1p4cA 91 :DLALARAATKAGIPFVLST T0284 59 :APDFA 1p4cA 110 :ASNMS T0284 74 :ATRIGRVARLPVIADADHG 1p4cA 115 :IEDLARQCDGDLWFQLYVI T0284 95 :NALNVMRTVVELERAGIAALTIEDTLLPA 1p4cA 134 :HREIAQGMVLKALHTGYTTLVLTTDVAVN T0284 126 :GRKS 1p4cA 190 :GKMD T0284 135 :VEEG 1p4cA 199 :MQAA T0284 139 :VGKIRAALE 1p4cA 214 :WEALRWLRD T0284 149 :RVDPALTIIARTNA 1p4cA 223 :LWPHKLLVKGLLSA T0284 172 :QRTLAYQEAGADGICLVGVRD 1p4cA 237 :EDADRCIAEGADGVILSNHGG T0284 193 :FAHLEAIAEHLHIPLMLVT 1p4cA 267 :MEVLAQSVAKTGKPVLIDS T0284 216 :QLRDDARLAR 1p4cA 286 :GFRRGSDIVK T0284 226 :LGVRVVVNGHAAYFAA 1p4cA 299 :LGAEAVLLGRATLYGL T0284 242 :IKATYDCLREERGAVASDLTAS 1p4cA 326 :LTLLKADIDRTLAQIGCPDITS Number of specific fragments extracted= 14 number of extra gaps= 2 total=1956 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gqnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1gqnA/merged-good-all-a2m # 1gqnA read from 1gqnA/merged-good-all-a2m # found chain 1gqnA in training set Warning: unaligning (T0284)P206 because of BadResidue code BAD_PEPTIDE in next template residue (1gqnA)V200 Warning: unaligning (T0284)L207 because of BadResidue code BAD_PEPTIDE at template residue (1gqnA)V200 T0284 19 :SSRCYHTASVFD 1gqnA 13 :EGMPKIIVSLMG T0284 31 :PMSARIAADLGFECGILGGSV 1gqnA 31 :KAEALAYREATFDILEWRVDH T0284 59 :APDFA 1gqnA 52 :FMDIA T0284 66 :TLSEFVEQATRIGRVA 1gqnA 57 :STQSVLTAARVIRDAM T0284 82 :RLPVIADADH 1gqnA 74 :DIPLLFTFRS T0284 92 :GYG 1gqnA 87 :GGE T0284 95 :NALNVMRTVVELERAG 1gqnA 93 :TTQHYLTLNRAAIDSG T0284 111 :IAALTIE 1gqnA 110 :VDMIDLE T0284 137 :EGV 1gqnA 117 :LFT T0284 140 :GKIRAALEAR 1gqnA 122 :ADVKATVDYA T0284 150 :VDPALTIIARTNAELID 1gqnA 133 :AHNVYVVMSNHDFHQTP T0284 167 :VDAVIQRTLAYQEAGADGICLV 1gqnA 151 :AEEMVSRLRKMQALGADIPKIA T0284 189 :GVRDFAHLEAIAEHL 1gqnA 174 :MPQSKHDVLTLLTAT T0284 204 :HI 1gqnA 197 :DR T0284 208 :MLVTYGNP 1gqnA 201 :ITMSMAKE T0284 219 :DD 1gqnA 209 :GV T0284 221 :ARLARLGVRVVVNGHA 1gqnA 214 :LAGEVFGSAATFGAVK T0284 239 :FA 1gqnA 238 :AV T0284 243 :KATYDCLREERG 1gqnA 240 :NDLRSVLMILHN Number of specific fragments extracted= 19 number of extra gaps= 1 total=1975 Number of alignments=136 # 1gqnA read from 1gqnA/merged-good-all-a2m # found chain 1gqnA in training set Warning: unaligning (T0284)P206 because of BadResidue code BAD_PEPTIDE in next template residue (1gqnA)V200 Warning: unaligning (T0284)L207 because of BadResidue code BAD_PEPTIDE at template residue (1gqnA)V200 T0284 19 :SSRCYHTASVFD 1gqnA 13 :EGMPKIIVSLMG T0284 31 :PMSARIAADLGFECGILGGS 1gqnA 31 :KAEALAYREATFDILEWRVD T0284 58 :AAPDFA 1gqnA 51 :HFMDIA T0284 66 :TLSEFVEQATRIGR 1gqnA 57 :STQSVLTAARVIRD T0284 80 :VARLPVIADADH 1gqnA 72 :MPDIPLLFTFRS T0284 92 :GYG 1gqnA 87 :GGE T0284 95 :NALNVMRTVVELERAG 1gqnA 93 :TTQHYLTLNRAAIDSG T0284 111 :IAALTIED 1gqnA 110 :VDMIDLEL T0284 138 :GV 1gqnA 118 :FT T0284 140 :GKIRAALEARVDPA 1gqnA 122 :ADVKATVDYAHAHN T0284 154 :LTIIARTNAELI 1gqnA 137 :YVVMSNHDFHQT T0284 166 :DVDAVIQRTLAYQEAGADGICLVG 1gqnA 150 :SAEEMVSRLRKMQALGADIPKIAV T0284 190 :VRDFAHLEAIAEHL 1gqnA 175 :PQSKHDVLTLLTAT T0284 204 :HI 1gqnA 197 :DR T0284 208 :MLVTYGNPQLRDDARLARLGVRVVVNG 1gqnA 201 :ITMSMAKEGVISRLAGEVFGSAATFGA T0284 256 :VAS 1gqnA 228 :VKQ T0284 259 :DLTASELSKKY 1gqnA 236 :QIAVNDLRSVL Number of specific fragments extracted= 17 number of extra gaps= 1 total=1992 Number of alignments=137 # 1gqnA read from 1gqnA/merged-good-all-a2m # found chain 1gqnA in training set Warning: unaligning (T0284)P206 because of BadResidue code BAD_PEPTIDE in next template residue (1gqnA)V200 Warning: unaligning (T0284)L207 because of BadResidue code BAD_PEPTIDE at template residue (1gqnA)V200 T0284 19 :SSRCYHTASVFD 1gqnA 13 :EGMPKIIVSLMG T0284 31 :PMSARIAADLGFECGILG 1gqnA 31 :KAEALAYREATFDILEWR T0284 56 :VLAAPDF 1gqnA 49 :VDHFMDI T0284 65 :ITLSEFVEQATRIGRVA 1gqnA 56 :ASTQSVLTAARVIRDAM T0284 82 :RLPVIADA 1gqnA 74 :DIPLLFTF T0284 92 :G 1gqnA 87 :G T0284 94 :G 1gqnA 88 :G T0284 95 :NALNVMRTVVELERAG 1gqnA 93 :TTQHYLTLNRAAIDSG T0284 111 :IAALTIEDTLL 1gqnA 110 :VDMIDLELFTG T0284 135 :VEEGVGKIRAALEARV 1gqnA 121 :DADVKATVDYAHAHNV T0284 154 :LTIIARTNAELI 1gqnA 137 :YVVMSNHDFHQT T0284 166 :DVDAVIQRTLAYQEAGADGICL 1gqnA 150 :SAEEMVSRLRKMQALGADIPKI T0284 188 :VGVRDFAHLEAIAEHL 1gqnA 173 :VMPQSKHDVLTLLTAT T0284 204 :HI 1gqnA 197 :DR T0284 208 :MLVTYGN 1gqnA 201 :ITMSMAK T0284 223 :LARLGVRVVVNGH 1gqnA 216 :GEVFGSAATFGAV T0284 242 :IKATYDCLREERG 1gqnA 239 :VNDLRSVLMILHN Number of specific fragments extracted= 17 number of extra gaps= 1 total=2009 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mdl/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mdl expands to /projects/compbio/data/pdb/1mdl.pdb.gz 1mdl:Warning: there is no chain 1mdl will retry with 1mdlA # T0284 read from 1mdl/merged-good-all-a2m # 1mdl read from 1mdl/merged-good-all-a2m # adding 1mdl to template set # found chain 1mdl in template set Warning: unaligning (T0284)A153 because of BadResidue code BAD_PEPTIDE in next template residue (1mdl)F190 Warning: unaligning (T0284)L154 because of BadResidue code BAD_PEPTIDE at template residue (1mdl)F190 T0284 7 :HELRAMFRALLD 1mdl 60 :KSLKQLLDDMAA T0284 19 :SSRCY 1mdl 74 :VNEPL T0284 31 :PMSARIAADLG 1mdl 82 :SLEAMLAKRFC T0284 49 :GSVASLQ 1mdl 106 :GIDMAAW T0284 84 :PVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1mdl 133 :PVQAYDSHSLDGVKLATERAVTAAELGFRAVKTRIGYPA T0284 135 :VEEGVGKIRAALEARVD 1mdl 172 :LDQDLAVVRSIRQAVGD T0284 155 :TIIART 1mdl 191 :GIMVDY T0284 162 :AELIDVDAVIQRTLAYQEAGADGICLVGV 1mdl 197 :NQSLDVPAAIKRSQALQQEGVTWIEEPTL T0284 191 :RDFAHLEAIAEHLHIPLML 1mdl 227 :HDYEGHQRIQSKLNVPVQM T0284 214 :NPQLRDDARLARL 1mdl 246 :GENWLGPEEMFKA T0284 227 :GVRVVVNG 1mdl 262 :GACRLAMP T0284 237 :AYFAAIKATYDCLREE 1mdl 275 :GGVTGWIRASALAQQF Number of specific fragments extracted= 12 number of extra gaps= 1 total=2021 Number of alignments=139 # 1mdl read from 1mdl/merged-good-all-a2m # found chain 1mdl in template set Warning: unaligning (T0284)V80 because of BadResidue code BAD_PEPTIDE in next template residue (1mdl)A94 Warning: unaligning (T0284)A81 because of BadResidue code BAD_PEPTIDE at template residue (1mdl)A94 Warning: unaligning (T0284)A153 because of BadResidue code BAD_PEPTIDE in next template residue (1mdl)F190 Warning: unaligning (T0284)L154 because of BadResidue code BAD_PEPTIDE at template residue (1mdl)F190 T0284 5 :SHHELRAMFRALLDS 1mdl 58 :ALKSLKQLLDDMAAM T0284 20 :S 1mdl 75 :N T0284 63 :ALITLSEFVEQATRIGR 1mdl 76 :EPLAPVSLEAMLAKRFC T0284 82 :R 1mdl 95 :G T0284 87 :ADADHGYGNALNVMRTVVELERAGIAALTIEDTLL 1mdl 136 :AYDSHSLDGVKLATERAVTAAELGFRAVKTRIGYP T0284 134 :CVEEGVGKIRAALEAR 1mdl 171 :ALDQDLAVVRSIRQAV T0284 151 :DP 1mdl 187 :GD T0284 155 :TIIART 1mdl 191 :GIMVDY T0284 162 :AELIDVDAVIQRTLAYQEAGADGICLVG 1mdl 197 :NQSLDVPAAIKRSQALQQEGVTWIEEPT T0284 190 :VRDFAHLEAIAEHLHIPLMLV 1mdl 226 :QHDYEGHQRIQSKLNVPVQMG T0284 215 :PQLRDDARLARL 1mdl 247 :ENWLGPEEMFKA T0284 227 :GVRVVVNGHA 1mdl 262 :GACRLAMPDA T0284 241 :AIKATYDCLREERGAVAS 1mdl 276 :GVTGWIRASALAQQFGIP Number of specific fragments extracted= 13 number of extra gaps= 2 total=2034 Number of alignments=140 # 1mdl read from 1mdl/merged-good-all-a2m # found chain 1mdl in template set Warning: unaligning (T0284)S19 because of BadResidue code BAD_PEPTIDE in next template residue (1mdl)A94 Warning: unaligning (T0284)S20 because of BadResidue code BAD_PEPTIDE at template residue (1mdl)A94 Warning: unaligning (T0284)A153 because of BadResidue code BAD_PEPTIDE in next template residue (1mdl)F190 Warning: unaligning (T0284)L154 because of BadResidue code BAD_PEPTIDE at template residue (1mdl)F190 T0284 4 :ASHHELRAMFRALLD 1mdl 78 :LAPVSLEAMLAKRFC T0284 21 :RC 1mdl 95 :GY T0284 30 :DPMSARIA 1mdl 97 :TGLIRMAA T0284 48 :GGSVASLQ 1mdl 105 :AGIDMAAW T0284 56 :VLAAP 1mdl 118 :VHETP T0284 77 :IGRVARL 1mdl 123 :LVKLLGA T0284 84 :PVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1mdl 133 :PVQAYDSHSLDGVKLATERAVTAAELGFRAVKTRIGYPA T0284 135 :VEEGVGKIRAALEAR 1mdl 172 :LDQDLAVVRSIRQAV T0284 151 :DP 1mdl 187 :GD T0284 155 :TIIAR 1mdl 191 :GIMVD T0284 162 :AELI 1mdl 196 :YNQS T0284 166 :DVDAVIQRTLAYQEAGADGICLVGV 1mdl 201 :DVPAAIKRSQALQQEGVTWIEEPTL T0284 191 :RDFAHLEAIAEHLHIPLMLVT 1mdl 227 :HDYEGHQRIQSKLNVPVQMGE T0284 216 :QLRDDARLARL 1mdl 248 :NWLGPEEMFKA T0284 227 :GVRVVVN 1mdl 263 :ACRLAMP T0284 238 :YFAAIKATYDCLRE 1mdl 276 :GVTGWIRASALAQQ Number of specific fragments extracted= 16 number of extra gaps= 2 total=2050 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ad1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ad1A expands to /projects/compbio/data/pdb/1ad1.pdb.gz 1ad1A:# T0284 read from 1ad1A/merged-good-all-a2m # 1ad1A read from 1ad1A/merged-good-all-a2m # adding 1ad1A to template set # found chain 1ad1A in template set T0284 4 :ASHHELRAMFRALLDSS 1ad1A 24 :NNVESAVTRVKAMMDEG T0284 42 :FECGILGGS 1ad1A 41 :ADIIDVGGV T0284 57 :LAAPDFALITLSEFVEQATRIGR 1ad1A 50 :STRPGHEMITVEEELNRVLPVVE T0284 81 :A 1ad1A 75 :V T0284 82 :RLPVIADADH 1ad1A 78 :DVKISVDTFR T0284 100 :MRTVVELERAGIAALTIEDTLL 1ad1A 88 :SEVAEACLKLGVDIINDQWAGL T0284 126 :GR 1ad1A 110 :YD T0284 140 :GKIRAALE 1ad1A 113 :RMFQVVAK T0284 152 :PALTIIARTNAEL 1ad1A 121 :YDAEIVLMHNGNG T0284 167 :VDAVIQRTLAYQEAGAD 1ad1A 144 :LTSLLAQAHQAKIAGIP T0284 184 :GICLV 1ad1A 165 :WLDPG T0284 189 :GVRDFAHLEAIAEHLH 1ad1A 172 :FAKTRNEEAEVMARLD T0284 205 :IPLML 1ad1A 194 :YPVLL T0284 214 :NPQLRDD 1ad1A 199 :ATSRKRF T0284 221 :ARLARLGVRVVVNGHA 1ad1A 228 :AYGIMKGVRAVRVHNV T0284 243 :KATYDCLREERGAVASD 1ad1A 244 :ELNAKLAKGIDFLKENE T0284 263 :SE 1ad1A 261 :NA Number of specific fragments extracted= 17 number of extra gaps= 0 total=2067 Number of alignments=142 # 1ad1A read from 1ad1A/merged-good-all-a2m # found chain 1ad1A in template set Warning: unaligning (T0284)K286 because last residue in template chain is (1ad1A)N265 T0284 5 :SHHELRAMFRALLDSS 1ad1A 25 :NVESAVTRVKAMMDEG T0284 42 :FECGILGGS 1ad1A 41 :ADIIDVGGV T0284 57 :LAAPDFALITLSEFVEQATRIGR 1ad1A 50 :STRPGHEMITVEEELNRVLPVVE T0284 80 :VARLPVIADADHG 1ad1A 76 :GFDVKISVDTFRS T0284 101 :RTVVELERAGIAALTIEDTLL 1ad1A 89 :EVAEACLKLGVDIINDQWAGL T0284 125 :FG 1ad1A 110 :YD T0284 136 :EEGVGKIRA 1ad1A 112 :HRMFQVVAK T0284 152 :PA 1ad1A 121 :YD T0284 154 :LTIIARTNAELID 1ad1A 124 :EIVLMHNGNGNRD T0284 167 :VDAVIQRTLAYQEAGA 1ad1A 144 :LTSLLAQAHQAKIAGI T0284 184 :GICLVG 1ad1A 164 :IWLDPG T0284 190 :VRDFAHLEAIAE 1ad1A 173 :AKTRNEEAEVMA T0284 202 :HLHIPLMLVT 1ad1A 191 :ATEYPVLLAT T0284 212 :YGNPQLRDDARLARL 1ad1A 212 :YDTTPVERDEVTAAT T0284 227 :GVRVVVNGHA 1ad1A 234 :GVRAVRVHNV T0284 243 :KATYDCLREE 1ad1A 244 :ELNAKLAKGI T0284 275 :YQAWARDYMEV 1ad1A 254 :DFLKENENARH Number of specific fragments extracted= 17 number of extra gaps= 0 total=2084 Number of alignments=143 # 1ad1A read from 1ad1A/merged-good-all-a2m # found chain 1ad1A in template set Warning: unaligning (T0284)A257 because last residue in template chain is (1ad1A)N265 T0284 3 :RASHHELRAMFRALL 1ad1A 23 :FNNVESAVTRVKAMM T0284 39 :DLGFECGILGGS 1ad1A 38 :DEGADIIDVGGV T0284 57 :LAAPDFALITLSEFVEQATRIGRVA 1ad1A 50 :STRPGHEMITVEEELNRVLPVVEAI T0284 82 :RLPVIADADH 1ad1A 78 :DVKISVDTFR T0284 100 :MRTVVELERAGIAALT 1ad1A 88 :SEVAEACLKLGVDIIN T0284 118 :DT 1ad1A 104 :DQ T0284 124 :QFGRKST 1ad1A 106 :WAGLYDH T0284 137 :EGVGKIRA 1ad1A 113 :RMFQVVAK T0284 152 :PALTIIARTNAEL 1ad1A 121 :YDAEIVLMHNGNG T0284 167 :VDAVIQRTLAYQEAGAD 1ad1A 144 :LTSLLAQAHQAKIAGIP T0284 184 :GICLVGVRD 1ad1A 164 :IWLDPGIGF T0284 193 :FAHLEAIAE 1ad1A 176 :RNEEAEVMA T0284 202 :HLHIPLMLVTY 1ad1A 191 :ATEYPVLLATS T0284 213 :GNPQLRDDARLA 1ad1A 213 :DTTPVERDEVTA T0284 225 :RLGVRVVVNG 1ad1A 232 :MKGVRAVRVH T0284 235 :HAAYFAAIKATYDCLREERGAV 1ad1A 243 :VELNAKLAKGIDFLKENENARH Number of specific fragments extracted= 16 number of extra gaps= 0 total=2100 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yxyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yxyA expands to /projects/compbio/data/pdb/1yxy.pdb.gz 1yxyA:# T0284 read from 1yxyA/merged-good-all-a2m # 1yxyA read from 1yxyA/merged-good-all-a2m # adding 1yxyA to template set # found chain 1yxyA in template set Warning: unaligning (T0284)R3 because first residue in template chain is (1yxyA)K4 T0284 4 :ASHHELRAMF 1yxyA 5 :PTKEKLMEQL T0284 19 :SSRCYHTASV 1yxyA 15 :KGGIIVSCQA T0284 31 :PMSARIAADLGFECGILGG 1yxyA 39 :PLMAKAAQEAGAVGIRANS T0284 71 :VEQATRIGRVARLPVIADADHGYG 1yxyA 58 :VRDIKEIQAITDLPIIGIIKKDYP T0284 95 :N 1yxyA 84 :E T0284 100 :MRTVVELERAGIAALTIEDTLLPAQ 1yxyA 91 :MTEVDQLAALNIAVIAMDCTKRDRH T0284 127 :RKS 1yxyA 116 :DGL T0284 137 :EGVGKIRAALEAR 1yxyA 119 :DIASFIRQVKEKY T0284 152 :PALTIIARTNAE 1yxyA 132 :PNQLLMADISTF T0284 168 :D 1yxyA 144 :D T0284 173 :RTLAYQEAGADGICLV 1yxyA 145 :EGLVAHQAGIDFVGTT T0284 191 :RDFAHLEAIAEH 1yxyA 174 :PDVALIEALCKA T0284 204 :HIPL 1yxyA 186 :GIAV T0284 210 :VTYGN 1yxyA 190 :IAEGK T0284 217 :LRDDARLAR 1yxyA 195 :IHSPEEAKK T0284 226 :LGVRVVVNGHAAYFA 1yxyA 207 :LGVAGIVVGGAITRP T0284 243 :KATYDCLRE 1yxyA 222 :KEIAERFIE Number of specific fragments extracted= 17 number of extra gaps= 0 total=2117 Number of alignments=145 # 1yxyA read from 1yxyA/merged-good-all-a2m # found chain 1yxyA in template set Warning: unaligning (T0284)R3 because first residue in template chain is (1yxyA)K4 Warning: unaligning (T0284)E284 because last residue in template chain is (1yxyA)K233 T0284 4 :ASHHELRAMF 1yxyA 5 :PTKEKLMEQL T0284 19 :SSRCYHTASV 1yxyA 15 :KGGIIVSCQA T0284 29 :FDPMSARIAADLGFECGILGG 1yxyA 37 :IMPLMAKAAQEAGAVGIRANS T0284 71 :VEQATRIGRVARLPVIADADHGY 1yxyA 58 :VRDIKEIQAITDLPIIGIIKKDY T0284 94 :GNALN 1yxyA 89 :ATMTE T0284 103 :VVELERAGIAALTIEDTLLP 1yxyA 94 :VDQLAALNIAVIAMDCTKRD T0284 126 :GRKST 1yxyA 114 :RHDGL T0284 137 :EGVGKIRAALEA 1yxyA 119 :DIASFIRQVKEK T0284 151 :DPALTIIARTNAE 1yxyA 131 :YPNQLLMADISTF T0284 172 :QRTLAYQEAGADGICL 1yxyA 144 :DEGLVAHQAGIDFVGT T0284 192 :DFAHLEAIAEH 1yxyA 175 :DVALIEALCKA T0284 204 :HIPL 1yxyA 186 :GIAV T0284 209 :LVTYGNPQLRDDARLARLGVRVVVNGHAAY 1yxyA 190 :IAEGKIHSPEEAKKINDLGVAGIVVGGAIT T0284 271 :FPEEYQAWARDYM 1yxyA 220 :RPKEIAERFIEAL Number of specific fragments extracted= 14 number of extra gaps= 0 total=2131 Number of alignments=146 # 1yxyA read from 1yxyA/merged-good-all-a2m # found chain 1yxyA in template set Warning: unaligning (T0284)R3 because first residue in template chain is (1yxyA)K4 T0284 4 :ASHHELRAMF 1yxyA 5 :PTKEKLMEQL T0284 19 :SSRCYHTASVF 1yxyA 15 :KGGIIVSCQAL T0284 31 :PMSARIAADLGFECGILGG 1yxyA 39 :PLMAKAAQEAGAVGIRANS T0284 71 :VEQATRIGRVARLPVIADADHGYG 1yxyA 58 :VRDIKEIQAITDLPIIGIIKKDYP T0284 95 :N 1yxyA 84 :E T0284 100 :MRTVVELERAGIAALTIEDTLLPAQFGR 1yxyA 91 :MTEVDQLAALNIAVIAMDCTKRDRHDGL T0284 134 :C 1yxyA 119 :D T0284 138 :GVGKIRAALEAR 1yxyA 120 :IASFIRQVKEKY T0284 152 :PALTIIARTNAE 1yxyA 132 :PNQLLMADISTF T0284 172 :QRTLAYQEAGADGICLVGVRD 1yxyA 144 :DEGLVAHQAGIDFVGTTLSGY T0284 193 :FAHLEAIAEH 1yxyA 176 :VALIEALCKA T0284 204 :HIPLMLV 1yxyA 186 :GIAVIAE T0284 213 :G 1yxyA 193 :G T0284 216 :QLRDDAR 1yxyA 194 :KIHSPEE T0284 223 :LARLGVRVVVNGHAAYFAAIKATYD 1yxyA 204 :INDLGVAGIVVGGAITRPKEIAERF Number of specific fragments extracted= 15 number of extra gaps= 0 total=2146 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dquA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dquA expands to /projects/compbio/data/pdb/1dqu.pdb.gz 1dquA:# T0284 read from 1dquA/merged-good-all-a2m # 1dquA read from 1dquA/merged-good-all-a2m # adding 1dquA to template set # found chain 1dquA in template set Warning: unaligning (T0284)A123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dquA)G211 Warning: unaligning (T0284)S129 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dquA)G211 T0284 7 :HELRAMFRALLDSSRCYHTASVFDPMSARIAADL 1dquA 57 :KKLWGILERNFKNKEASFTYGCLDPTMVTQMAKY T0284 42 :FECGILGGSVASLQVLA 1dquA 91 :LDTVYVSGWQSSSTASS T0284 59 :APDFALITLSEFVEQATRIGRV 1dquA 112 :SPDLADYPMNTVPNKVNHLWMA T0284 84 :PVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1dquA 164 :PIIADADTGHGGLTAVMKLTKLFVERGAAGIHIEDQAPG T0284 130 :TDLICVEEGVGKIRAALEAR 1dquA 212 :KVLVPISEHINRLVAIRAQA T0284 150 :VDPALTIIARTNAELI 1dquA 234 :MGTDLLAIARTDSEAA T0284 166 :DVDAVIQRTLAYQEA 1dquA 374 :GTQCAINRAVAYAPF T0284 182 :ADGICLV 1dquA 389 :ADLIWME T0284 189 :GVRDFAHLEAIAEHLH 1dquA 397 :KLPDYKQAKEFADGVH T0284 205 :IPLMLVTYGNPQLRDD 1dquA 415 :WPEQKLAYNLSPSFNW T0284 221 :ARLARLGVRVVVNGHAAYFAAIKATYDCLREERG 1dquA 444 :KRLGALGYAWQFITLAGLHTTALISDTFAKAYAK T0284 255 :AVASDLTASELSKKYTF 1dquA 482 :AYGELVQEPEMANGVDV T0284 278 :WARDYME 1dquA 499 :VTHQKWS Number of specific fragments extracted= 13 number of extra gaps= 0 total=2159 Number of alignments=148 # 1dquA read from 1dquA/merged-good-all-a2m # found chain 1dquA in template set Warning: unaligning (T0284)A123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dquA)G211 Warning: unaligning (T0284)S129 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dquA)G211 T0284 7 :HELRAMFRALLDSSRCYHTASVFDPMSARIAAD 1dquA 57 :KKLWGILERNFKNKEASFTYGCLDPTMVTQMAK T0284 41 :GFECGILGGSVASLQVLA 1dquA 90 :YLDTVYVSGWQSSSTASS T0284 59 :APDFALITLSEFVEQATRIGRVA 1dquA 112 :SPDLADYPMNTVPNKVNHLWMAQ T0284 83 :LPVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1dquA 163 :RPIIADADTGHGGLTAVMKLTKLFVERGAAGIHIEDQAPG T0284 130 :TDLICVEEGVGKIRAALEA 1dquA 212 :KVLVPISEHINRLVAIRAQ T0284 149 :RVDPALTIIARTNAELIDV 1dquA 233 :IMGTDLLAIARTDSEAATL T0284 168 :DAVIQRTLAYQEA 1dquA 376 :QCAINRAVAYAPF T0284 182 :ADGICLVG 1dquA 389 :ADLIWMES T0284 190 :VRDFAHLEAIAEHL 1dquA 398 :LPDYKQAKEFADGV T0284 204 :HI 1dquA 417 :EQ T0284 209 :LVTYGNPQLRDDA 1dquA 419 :KLAYNLSPSFNWK T0284 222 :RLARLGVRVVVNGHAAYFAAIK 1dquA 445 :RLGALGYAWQFITLAGLHTTAL T0284 253 :RGA 1dquA 467 :ISD T0284 261 :TASELSKKYTFPEEYQAWARDYMEVK 1dquA 470 :TFAKAYAKQGMRAYGELVQEPEMANG Number of specific fragments extracted= 14 number of extra gaps= 0 total=2173 Number of alignments=149 # 1dquA read from 1dquA/merged-good-all-a2m # found chain 1dquA in template set Warning: unaligning (T0284)A123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dquA)G211 Warning: unaligning (T0284)T130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dquA)G211 T0284 4 :ASHHELRAMFRALLDSSRCYHTASVFDPMSARIAADL 1dquA 54 :VQAKKLWGILERNFKNKEASFTYGCLDPTMVTQMAKY T0284 42 :FECGILGGSVASLQV 1dquA 91 :LDTVYVSGWQSSSTA T0284 57 :LAAPDFALITLSEFVEQATRIGRVA 1dquA 110 :EPSPDLADYPMNTVPNKVNHLWMAQ T0284 84 :PVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1dquA 164 :PIIADADTGHGGLTAVMKLTKLFVERGAAGIHIEDQAPG T0284 131 :D 1dquA 212 :K T0284 132 :LICVEEGVGKIRAAL 1dquA 214 :LVPISEHINRLVAIR T0284 147 :EARVDPALTIIARTNAELI 1dquA 231 :ADIMGTDLLAIARTDSEAA T0284 167 :VDAVIQRTLAYQ 1dquA 375 :TQCAINRAVAYA T0284 182 :ADGICLVGVRD 1dquA 389 :ADLIWMESKLP T0284 193 :FAHLEAIAEHL 1dquA 401 :YKQAKEFADGV T0284 204 :HIPLMLVTYGN 1dquA 417 :EQKLAYNLSPS T0284 215 :PQLRDDAR 1dquA 431 :KKAMPRDE T0284 223 :LARLGVRVVVNGHAAYFAAIKATYDCLREERGAV 1dquA 446 :LGALGYAWQFITLAGLHTTALISDTFAKAYAKQG T0284 259 :DLTASELSKKYTFP 1dquA 480 :MRAYGELVQEPEMA Number of specific fragments extracted= 14 number of extra gaps= 0 total=2187 Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vhnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1vhnA/merged-good-all-a2m # 1vhnA read from 1vhnA/merged-good-all-a2m # found chain 1vhnA in training set Warning: unaligning (T0284)K286 because last residue in template chain is (1vhnA)E309 T0284 20 :SRCYHTASVFDP 1vhnA 59 :RNVAVQIFGSEP T0284 32 :MSARIAADL 1vhnA 72 :ELSEAARIL T0284 41 :GFECGILG 1vhnA 83 :KYKWIDLN T0284 49 :GSVAS 1vhnA 92 :GCPVR T0284 54 :LQVLAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1vhnA 98 :VVKEGAGGALLKDLRHFRYIVRELRKSVSGKFSVKTRLGWE T0284 95 :N 1vhnA 141 :E T0284 99 :VMRTVVELERAGIAALTIEDTLLPAQFGRKST 1vhnA 142 :VEEIYRILVEEGVDEVFIHTRTVVQSFTGRAE T0284 135 :VEE 1vhnA 174 :WKA T0284 147 :EARVDPALTIIARTNAEL 1vhnA 177 :LSVLEKRIPTFVSGDIFT T0284 167 :VDAVIQ 1vhnA 195 :PEDAKR T0284 176 :AYQEAGADGICLV 1vhnA 201 :ALEESGCDGLLVA T0284 189 :GVRD 1vhnA 218 :GRPW T0284 195 :HLEAIAEHLH 1vhnA 222 :IFKQIKDFLR T0284 213 :GNPQLRDDARLA 1vhnA 233 :GKYSEPSREEIL T0284 243 :KATYDCLREERG 1vhnA 245 :RTFERHLELLIK T0284 257 :ASDLT 1vhnA 279 :KGARR T0284 262 :ASELSKKYTFPEEYQAWARDYMEV 1vhnA 285 :REKVMKIEEVQILKEMFYNFIKEV Number of specific fragments extracted= 17 number of extra gaps= 0 total=2204 Number of alignments=151 # 1vhnA read from 1vhnA/merged-good-all-a2m # found chain 1vhnA in training set Warning: unaligning (T0284)K286 because last residue in template chain is (1vhnA)E309 T0284 20 :SRCYHTASVFDPMSARIAADL 1vhnA 59 :RNVAVQIFGSEPNELSEAARI T0284 41 :GFE 1vhnA 83 :KYK T0284 44 :CGILGGSV 1vhnA 87 :IDLNAGCP T0284 54 :LQVLAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1vhnA 98 :VVKEGAGGALLKDLRHFRYIVRELRKSVSGKFSVKTRLGWE T0284 95 :NALNVMR 1vhnA 141 :EVEEIYR T0284 105 :ELERAGIAALTIEDTLL 1vhnA 148 :ILVEEGVDEVFIHTRTV T0284 124 :QFGRKSTD 1vhnA 165 :VQSFTGRA T0284 134 :CVEEG 1vhnA 173 :EWKAL T0284 146 :LEARVDPALTIIA 1vhnA 178 :SVLEKRIPTFVSG T0284 161 :NA 1vhnA 191 :DI T0284 165 :IDVDAVIQRTL 1vhnA 193 :FTPEDAKRALE T0284 179 :EAGADGICLV 1vhnA 204 :ESGCDGLLVA T0284 190 :VR 1vhnA 219 :RP T0284 195 :HLEAIAEHL 1vhnA 222 :IFKQIKDFL T0284 213 :GNPQLRDDARLAR 1vhnA 233 :GKYSEPSREEILR T0284 244 :ATYDCLREERGAVAS 1vhnA 246 :TFERHLELLIKTKGE T0284 259 :DL 1vhnA 277 :DL T0284 261 :TASELSKKY 1vhnA 280 :GARRFREKV T0284 270 :TFPEEYQAWARDYMEV 1vhnA 293 :EVQILKEMFYNFIKEV Number of specific fragments extracted= 19 number of extra gaps= 0 total=2223 Number of alignments=152 # 1vhnA read from 1vhnA/merged-good-all-a2m # found chain 1vhnA in training set T0284 18 :DSSRCYHTASVFDPMSARIAADL 1vhnA 57 :HERNVAVQIFGSEPNELSEAARI T0284 41 :GFECGILGGSV 1vhnA 83 :KYKWIDLNAGC T0284 53 :SLQ 1vhnA 98 :VVK T0284 57 :LAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1vhnA 101 :EGAGGALLKDLRHFRYIVRELRKSVSGKFSVKTRLGWE T0284 98 :NVMRTVVELERAGIAALTIEDTLLPA 1vhnA 141 :EVEEIYRILVEEGVDEVFIHTRTVVQ T0284 126 :GRKSTD 1vhnA 167 :SFTGRA T0284 147 :EARVDPALTIIA 1vhnA 179 :VLEKRIPTFVSG T0284 163 :ELIDVDAVIQRT 1vhnA 191 :DIFTPEDAKRAL T0284 178 :QEAGADGICLV 1vhnA 203 :EESGCDGLLVA T0284 189 :GVRDFAHLEAIAEHL 1vhnA 216 :AIGRPWIFKQIKDFL T0284 213 :GNPQLRDDARLAR 1vhnA 233 :GKYSEPSREEILR T0284 241 :AIKATYDCLREERGA 1vhnA 246 :TFERHLELLIKTKGE T0284 256 :VASDLTASELSKKYTFPEEYQAWARDYME 1vhnA 279 :KGARRFREKVMKIEEVQILKEMFYNFIKE Number of specific fragments extracted= 13 number of extra gaps= 0 total=2236 Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fdyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fdyA expands to /projects/compbio/data/pdb/1fdy.pdb.gz 1fdyA:# T0284 read from 1fdyA/merged-good-all-a2m # 1fdyA read from 1fdyA/merged-good-all-a2m # adding 1fdyA to template set # found chain 1fdyA in template set T0284 31 :PMSARIAADLGFECGILGGSVASLQ 1fdyA 28 :RRLVQFNIQQGIDGLYVGGSTGEAF T0284 64 :LITLSEFVEQATRIGRVA 1fdyA 53 :VQSLSEREQVLEIVAEEG T0284 82 :RLPVIADA 1fdyA 73 :KIKLIAHV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTL 1fdyA 81 :GCVTTAESQQLAASAKRYGFDAVSAVTPF T0284 126 :GRKS 1fdyA 110 :YYPF T0284 134 :CVEEGVGKIRAALEAR 1fdyA 114 :SFEEHCDHYRAIIDSA T0284 152 :PALTIIARTNAELID 1fdyA 130 :DGLPMVVYNIPALSG T0284 167 :VDAV 1fdyA 149 :LDQI T0284 175 :LAYQEA 1fdyA 153 :NTLVTL T0284 181 :GADGICLVGVR 1fdyA 160 :GVGALKQTSGD T0284 193 :FAHLEAIAEHLH 1fdyA 171 :LYQMEQIRREHP T0284 205 :I 1fdyA 184 :L T0284 207 :L 1fdyA 185 :V T0284 210 :VTYGNPQLR 1fdyA 186 :LYNGYDEIF T0284 221 :ARLARLGVRVVVNGHAAYFA 1fdyA 195 :ASGLLAGADGGIGSTYNIMG T0284 243 :KATYDCLREERG 1fdyA 215 :WRYQGIVKALKE T0284 255 :AVASDLTASEL 1fdyA 231 :TAQKLQTECNK Number of specific fragments extracted= 17 number of extra gaps= 0 total=2253 Number of alignments=154 # 1fdyA read from 1fdyA/merged-good-all-a2m # found chain 1fdyA in template set T0284 10 :RAMFRAL 1fdyA 24 :KASLRRL T0284 34 :ARIAADLGFECGILGGSVASL 1fdyA 31 :VQFNIQQGIDGLYVGGSTGEA T0284 63 :ALITLSEFVEQATRIGR 1fdyA 52 :FVQSLSEREQVLEIVAE T0284 80 :VARLPVIADA 1fdyA 71 :KGKIKLIAHV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLL 1fdyA 81 :GCVTTAESQQLAASAKRYGFDAVSAVTPFY T0284 127 :RK 1fdyA 111 :YP T0284 133 :ICVEEGVGKIRAALEAR 1fdyA 113 :FSFEEHCDHYRAIIDSA T0284 152 :PA 1fdyA 130 :DG T0284 154 :LTIIARTNAELI 1fdyA 133 :PMVVYNIPALSG T0284 166 :DVDAV 1fdyA 148 :TLDQI T0284 175 :LAYQEA 1fdyA 153 :NTLVTL T0284 181 :GADGICLVGV 1fdyA 160 :GVGALKQTSG T0284 192 :DFAHLEAIAEHLH 1fdyA 170 :DLYQMEQIRREHP T0284 205 :IPLM 1fdyA 184 :LVLY T0284 210 :V 1fdyA 188 :N T0284 213 :GNPQL 1fdyA 189 :GYDEI T0284 223 :LARL 1fdyA 194 :FASG T0284 227 :GVRVVVNGHAAYFA 1fdyA 201 :GADGGIGSTYNIMG T0284 243 :KATYDCLREERGA 1fdyA 215 :WRYQGIVKALKEG T0284 261 :TASELSKKY 1fdyA 228 :DIQTAQKLQ T0284 272 :PEEYQAWARDY 1fdyA 237 :TECNKVIDLLI Number of specific fragments extracted= 21 number of extra gaps= 0 total=2274 Number of alignments=155 # 1fdyA read from 1fdyA/merged-good-all-a2m # found chain 1fdyA in template set T0284 5 :SHHELRAMFRA 1fdyA 22 :LDKASLRRLVQ T0284 36 :IAADLGFECGILGGSVASLQ 1fdyA 33 :FNIQQGIDGLYVGGSTGEAF T0284 64 :LITLSEFVEQATRIGRVA 1fdyA 53 :VQSLSEREQVLEIVAEEG T0284 82 :RLPVIADA 1fdyA 73 :KIKLIAHV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLLPA 1fdyA 81 :GCVTTAESQQLAASAKRYGFDAVSAVTPFYYP T0284 133 :ICVEEGVGKIRAALEARVDPALTII 1fdyA 113 :FSFEEHCDHYRAIIDSADGLPMVVY T0284 159 :RTNAELI 1fdyA 138 :NIPALSG T0284 166 :DVD 1fdyA 148 :TLD T0284 173 :RTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTYGNP 1fdyA 151 :QINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEI T0284 220 :DARLARLGVRVVVNGHAAYFAAIKATYDCLR 1fdyA 195 :ASGLLAGADGGIGSTYNIMGWRYQGIVKALK T0284 255 :AVASDLTASELSKKYTFPEEYQAWARD 1fdyA 226 :EGDIQTAQKLQTECNKVIDLLIKTGVF Number of specific fragments extracted= 11 number of extra gaps= 0 total=2285 Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f74A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1f74A/merged-good-all-a2m # 1f74A read from 1f74A/merged-good-all-a2m # found chain 1f74A in training set T0284 22 :CYHTASV 1f74A 7 :IFSALLV T0284 29 :FDPMSARIAADL 1f74A 21 :INEKGLRQIIRH T0284 41 :GFECGILGGSVASLQ 1f74A 38 :KVDGLYVGGSTGENF T0284 64 :LITLSEFVEQATRIGR 1f74A 53 :MLSTEEKKEIFRIAKD T0284 80 :VA 1f74A 70 :AK T0284 82 :RLPVIADAD 1f74A 73 :QIALIAQVG T0284 93 :YGNALNVMRTVVELERAGIAALTIEDTLLPA 1f74A 82 :SVNLKEAVELGKYATELGYDCLSAVTPFYYK T0284 133 :ICVEEGVGKIRAALEAR 1f74A 113 :FSFPEIKHYYDTIIAET T0284 153 :ALTIIARTNAELIDVDAVIQRTLAYQEA 1f74A 130 :GSNMIVYSIPFLTGVNMGIEQFGELYKN T0284 181 :GADGICLVGVR 1f74A 159 :KVLGVKFTAGD T0284 193 :FAHLEAIAEHLH 1f74A 170 :FYLLERLKKAYP T0284 205 :IP 1f74A 183 :HL T0284 210 :VTYGNPQLR 1f74A 185 :IWAGFDEMM T0284 221 :ARLARLGVRVVVNGHAAYFA 1f74A 194 :LPAASLGVDGAIGSTFNVNG T0284 243 :KATYDCLREERG 1f74A 214 :VRARQIFELTKA T0284 262 :ASEL 1f74A 234 :IQHV T0284 274 :EYQAWARD 1f74A 238 :TNDLIEGI Number of specific fragments extracted= 17 number of extra gaps= 0 total=2302 Number of alignments=157 # 1f74A read from 1f74A/merged-good-all-a2m # found chain 1f74A in training set T0284 21 :RCYHTASV 1f74A 6 :GIFSALLV T0284 29 :FDPMSARIAADL 1f74A 21 :INEKGLRQIIRH T0284 41 :GFECGILGGS 1f74A 38 :KVDGLYVGGS T0284 52 :ASLQ 1f74A 48 :TGEN T0284 63 :ALITLSEFVEQATRIGR 1f74A 52 :FMLSTEEKKEIFRIAKD T0284 80 :VARLPVIADADH 1f74A 71 :KDQIALIAQVGS T0284 95 :NALNVMRTVVELERAGIAALTIEDT 1f74A 84 :NLKEAVELGKYATELGYDCLSAVTP T0284 127 :RKST 1f74A 109 :FYYK T0284 133 :ICVEEGVGKIRAALEAR 1f74A 113 :FSFPEIKHYYDTIIAET T0284 153 :ALTIIARTNAELIDVDAVIQRTLAYQEAG 1f74A 130 :GSNMIVYSIPFLTGVNMGIEQFGELYKNP T0284 182 :ADGICLVGVR 1f74A 160 :VLGVKFTAGD T0284 193 :FAHLEAIAEHLH 1f74A 170 :FYLLERLKKAYP T0284 205 :IP 1f74A 183 :HL T0284 208 :MLVT 1f74A 185 :IWAG T0284 214 :NPQ 1f74A 189 :FDE T0284 219 :DDARLARLGVRVVVNGHAAYFA 1f74A 192 :MMLPAASLGVDGAIGSTFNVNG T0284 243 :KATYDCLREERGA 1f74A 214 :VRARQIFELTKAG T0284 261 :TASELSKKY 1f74A 227 :KLKEALEIQ T0284 272 :PEEYQAWARDYM 1f74A 236 :HVTNDLIEGILA Number of specific fragments extracted= 19 number of extra gaps= 0 total=2321 Number of alignments=158 # 1f74A read from 1f74A/merged-good-all-a2m # found chain 1f74A in training set T0284 21 :RCYHTASV 1f74A 6 :GIFSALLV T0284 29 :FDPMSARIAADL 1f74A 21 :INEKGLRQIIRH T0284 41 :GFECGILGGSVASLQ 1f74A 38 :KVDGLYVGGSTGENF T0284 64 :LITLSEFVEQATRIGRVA 1f74A 53 :MLSTEEKKEIFRIAKDEA T0284 82 :RLPVIADA 1f74A 73 :QIALIAQV T0284 92 :GYGNALNVMRTVVELERAGIAALTIEDTLLPA 1f74A 81 :GSVNLKEAVELGKYATELGYDCLSAVTPFYYK T0284 133 :ICVEEGVGKIRAALEAR 1f74A 113 :FSFPEIKHYYDTIIAET T0284 151 :DPALTIIA 1f74A 130 :GSNMIVYS T0284 161 :NAELIDVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTYGNP 1f74A 138 :IPFLTGVNMGIEQFGELYKNPKVLGVKFTAGDFYLLERLKKAYPNHLIWAGFDEM T0284 222 :RLARLGVRVVVNGHAA 1f74A 195 :PAASLGVDGAIGSTFN T0284 240 :AAIKATYDCLREERGA 1f74A 211 :VNGVRARQIFELTKAG T0284 257 :ASDLTASELSKKYTFPEEYQAWARD 1f74A 227 :KLKEALEIQHVTNDLIEGILANGLY Number of specific fragments extracted= 12 number of extra gaps= 0 total=2333 Number of alignments=159 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xm3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0284 read from 1xm3A/merged-good-all-a2m # 1xm3A read from 1xm3A/merged-good-all-a2m # found chain 1xm3A in training set Warning: unaligning (T0284)F62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xm3A)L58 T0284 21 :RCYHTASVFD 1xm3A 12 :QSRLLLGTGK T0284 31 :PMSARIAADLGFECGILG 1xm3A 26 :DIQKEAVAVSESDILTFA T0284 56 :VLAAPD 1xm3A 44 :VRRMNI T0284 84 :PVIADA 1xm3A 67 :TLLPNT T0284 91 :HGYGNALNVMRTVVELERAG 1xm3A 73 :AGASTAEEAVRIARLAKASG T0284 111 :IAALTIED 1xm3A 94 :CDMIKVEV T0284 125 :FGRKSTDLI 1xm3A 102 :IGCSRSLLP T0284 137 :EGVGKIRAALEAR 1xm3A 111 :DPVETLKASEQLL T0284 152 :PALTIIARTNAELI 1xm3A 125 :EGFIVLPYTSDDVV T0284 173 :RTLAYQEAGADGICLVGVR 1xm3A 139 :LARKLEELGVHAIMPGASP T0284 192 :DFAHLEAIAEHLHIPLM 1xm3A 166 :NPLNLSFIIEQAKVPVI T0284 210 :VTYGNPQLRDDARLARLGVRVVVNG 1xm3A 183 :VDAGIGSPKDAAYAMELGADGVLLN T0284 245 :TYDCLREERGAVASDLTASELSKKYTFP 1xm3A 216 :PVKMARAMKLAVEAGRLSYEAGRIPLKQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=2346 Number of alignments=160 # 1xm3A read from 1xm3A/merged-good-all-a2m # found chain 1xm3A in training set Warning: unaligning (T0284)F62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xm3A)L58 T0284 21 :RCYHTASVFDP 1xm3A 12 :QSRLLLGTGKY T0284 32 :MSARIAADLGFECGILG 1xm3A 27 :IQKEAVAVSESDILTFA T0284 56 :VLAAPD 1xm3A 44 :VRRMNI T0284 83 :LPVIADA 1xm3A 66 :YTLLPNT T0284 91 :HGYGNALNVMRTVVELERAG 1xm3A 73 :AGASTAEEAVRIARLAKASG T0284 111 :IAALTIED 1xm3A 94 :CDMIKVEV T0284 125 :FGRKSTDLICVEEGVGKIRAALE 1xm3A 102 :IGCSRSLLPDPVETLKASEQLLE T0284 152 :PALTIIARTNAEL 1xm3A 125 :EGFIVLPYTSDDV T0284 172 :QRTLAYQEAGADGICLVGVR 1xm3A 138 :VLARKLEELGVHAIMPGASP T0284 192 :DFAHLEAIAEHLHIPLMLVT 1xm3A 166 :NPLNLSFIIEQAKVPVIVDA T0284 213 :GNPQLRDDARLARLGVRVVVNGHAA 1xm3A 186 :GIGSPKDAAYAMELGADGVLLNTAV T0284 238 :YFAAIKATYDCLREERGAVAS 1xm3A 220 :ARAMKLAVEAGRLSYEAGRIP Number of specific fragments extracted= 12 number of extra gaps= 0 total=2358 Number of alignments=161 # 1xm3A read from 1xm3A/merged-good-all-a2m # found chain 1xm3A in training set Warning: unaligning (T0284)L57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xm3A)L58 T0284 22 :CYHTASVFD 1xm3A 13 :SRLLLGTGK T0284 32 :MSARIAADLGFECGILG 1xm3A 27 :IQKEAVAVSESDILTFA T0284 58 :AAPDFALI 1xm3A 59 :EQLDLSKY T0284 85 :VIADADHGYGNALNVMRTVVELERAG 1xm3A 67 :TLLPNTAGASTAEEAVRIARLAKASG T0284 111 :IAALTIEDTLLP 1xm3A 94 :CDMIKVEVIGCS T0284 129 :STDLICVEEGVGKIRAALE 1xm3A 106 :RSLLPDPVETLKASEQLLE T0284 152 :PALTIIARTNAE 1xm3A 125 :EGFIVLPYTSDD T0284 171 :IQRTLAYQEAGADGICL 1xm3A 137 :VVLARKLEELGVHAIMP T0284 188 :VGVRDFAHLEAIAEHLHIPLMLVTYG 1xm3A 162 :QGILNPLNLSFIIEQAKVPVIVDAGI T0284 218 :RDDARLA 1xm3A 188 :GSPKDAA T0284 225 :RLGVRVVVN 1xm3A 198 :ELGADGVLL T0284 234 :GHAAYFAAIKATYDCLREERGAV 1xm3A 216 :PVKMARAMKLAVEAGRLSYEAGR Number of specific fragments extracted= 12 number of extra gaps= 0 total=2370 Number of alignments=162 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ep3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ep3A expands to /projects/compbio/data/pdb/1ep3.pdb.gz 1ep3A:# T0284 read from 1ep3A/merged-good-all-a2m # 1ep3A read from 1ep3A/merged-good-all-a2m # adding 1ep3A to template set # found chain 1ep3A in template set Warning: unaligning (T0284)I116 because of BadResidue code BAD_PEPTIDE in next template residue (1ep3A)I196 Warning: unaligning (T0284)E117 because of BadResidue code BAD_PEPTIDE at template residue (1ep3A)I196 T0284 7 :HELRA 1ep3A 82 :EVIMT T0284 12 :MFRALLD 1ep3A 88 :KLPWLNE T0284 19 :SSRCYHTASVFD 1ep3A 97 :PELPIIANVAGS T0284 31 :PMSARIAADLG 1ep3A 111 :ADYVAVCAKIG T0284 42 :FECGIL 1ep3A 126 :VKAIEL T0284 49 :GSVASLQVLA 1ep3A 132 :NISCPNVKHG T0284 60 :PDFALITLSEFVEQATRIGRVARLPVIADADHGYGNA 1ep3A 142 :GQAFGTDPEVAAALVKACKAVSKVPLYVKLSPNVTDI T0284 100 :MRTVVELERAGIAALT 1ep3A 179 :VPIAKAVEAAGADGLT T0284 118 :DTLL 1ep3A 197 :NTLM T0284 123 :AQFGR 1ep3A 201 :GVRFD T0284 128 :KSTD 1ep3A 208 :TRQP T0284 148 :A 1ep3A 213 :L T0284 153 :ALTIIARTNAELI 1ep3A 214 :ANITGGLSGPAIK T0284 168 :DAVI 1ep3A 227 :PVAL T0284 194 :AHLEAIAEHLHIPL 1ep3A 231 :KLIHQVAQDVDIPI T0284 210 :VTYG 1ep3A 245 :IGMG T0284 216 :QLRDDARLARL 1ep3A 249 :GVANAQDVLEM T0284 227 :GVRVVVNGHAAYF 1ep3A 263 :GASAVAVGTANFA T0284 243 :KATYDCLREERGAVASD 1ep3A 278 :FVCPKIIDKLPELMDQY T0284 270 :TFPEEYQAWARDYM 1ep3A 295 :RIESLESLIQEVKE Number of specific fragments extracted= 20 number of extra gaps= 1 total=2390 Number of alignments=163 # 1ep3A read from 1ep3A/merged-good-all-a2m # found chain 1ep3A in template set Warning: unaligning (T0284)L187 because of BadResidue code BAD_PEPTIDE in next template residue (1ep3A)I196 Warning: unaligning (T0284)V188 because of BadResidue code BAD_PEPTIDE at template residue (1ep3A)I196 T0284 63 :ALITLSEFVE 1ep3A 77 :QNPGLEVIMT T0284 73 :QATRIGR 1ep3A 88 :KLPWLNE T0284 80 :VARLPVIADADH 1ep3A 96 :FPELPIIANVAG T0284 94 :GNALNVMRTVVELERAG 1ep3A 108 :SEEADYVAVCAKIGDAA T0284 111 :IAALTIEDTLLPAQFGR 1ep3A 126 :VKAIELNISCPNVKHGG T0284 129 :S 1ep3A 144 :A T0284 134 :CVEEGVGKIRAALEA 1ep3A 148 :DPEVAAALVKACKAV T0284 150 :VDPALTIIARTNAELI 1ep3A 163 :SKVPLYVKLSPNVTDI T0284 171 :IQRTLAYQEAGADGIC 1ep3A 179 :VPIAKAVEAAGADGLT T0284 189 :GVR 1ep3A 197 :NTL T0284 193 :FAHLEAIAEHLHIPLMLVT 1ep3A 230 :LKLIHQVAQDVDIPIIGMG T0284 213 :GNPQLRDDARLARLGVRVVVNGHAAYF 1ep3A 249 :GVANAQDVLEMYMAGASAVAVGTANFA T0284 244 :ATYDCLREE 1ep3A 279 :VCPKIIDKL T0284 263 :SELSKKYTFPEEYQAWARDYMEV 1ep3A 288 :PELMDQYRIESLESLIQEVKEGK Number of specific fragments extracted= 14 number of extra gaps= 1 total=2404 Number of alignments=164 # 1ep3A read from 1ep3A/merged-good-all-a2m # found chain 1ep3A in template set Warning: unaligning (T0284)L187 because of BadResidue code BAD_PEPTIDE in next template residue (1ep3A)I196 Warning: unaligning (T0284)V188 because of BadResidue code BAD_PEPTIDE at template residue (1ep3A)I196 T0284 66 :TLSEFVE 1ep3A 80 :GLEVIMT T0284 73 :QATRIGRVA 1ep3A 88 :KLPWLNENF T0284 82 :RLPVIADADH 1ep3A 98 :ELPIIANVAG T0284 94 :GNALNVMRTVVELERA 1ep3A 108 :SEEADYVAVCAKIGDA T0284 110 :GIAALTIEDTLLPAQFG 1ep3A 125 :NVKAIELNISCPNVKHG T0284 130 :TD 1ep3A 142 :GQ T0284 132 :LICVEEGVGKIRAALEA 1ep3A 146 :GTDPEVAAALVKACKAV T0284 150 :VDPALTIIARTNAELI 1ep3A 163 :SKVPLYVKLSPNVTDI T0284 171 :IQRTLAYQEAGADGIC 1ep3A 179 :VPIAKAVEAAGADGLT T0284 189 :GVRD 1ep3A 197 :NTLM T0284 193 :FAHLEAIAEHLHIPLMLVTY 1ep3A 230 :LKLIHQVAQDVDIPIIGMGG T0284 217 :LRDDARLARL 1ep3A 250 :VANAQDVLEM T0284 227 :GVRVVVNGHAAYF 1ep3A 263 :GASAVAVGTANFA T0284 241 :AIKATYDCLREERGAVASDLTASELSKKYT 1ep3A 279 :VCPKIIDKLPELMDQYRIESLESLIQEVKE Number of specific fragments extracted= 14 number of extra gaps= 1 total=2418 Number of alignments=165 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zfjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zfjA expands to /projects/compbio/data/pdb/1zfj.pdb.gz 1zfjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0284 read from 1zfjA/merged-good-all-a2m # 1zfjA read from 1zfjA/merged-good-all-a2m # adding 1zfjA to template set # found chain 1zfjA in template set T0284 22 :CYHTA 1zfjA 47 :PIITA T0284 27 :SVFDPMSARIAADLGFECGILG 1zfjA 55 :TVTGSKMAIAIARAGGLGVIHK T0284 64 :LITLSEFVEQATRIGRVARL 1zfjA 77 :NMSITEQAEEVRKVKRSENG T0284 94 :G 1zfjA 170 :G T0284 95 :NALNVMRTV 1zfjA 172 :DLETAERIL T0284 107 :ERAGIAALTIEDTL 1zfjA 181 :HEHRIEKLPLVDNS T0284 127 :RKSTDLIC 1zfjA 195 :GRLSGLIT T0284 139 :VGKIRAALEAR 1zfjA 203 :IKDIEKVIEFP T0284 150 :VD 1zfjA 220 :FG T0284 153 :ALTIIARTNAE 1zfjA 222 :RLLVAAAVGVT T0284 168 :DAVIQRTLAYQEAGADGICLVGVR 1zfjA 233 :SDTFERAEALFEAGADAIVIDTAH T0284 192 :D 1zfjA 259 :S T0284 193 :FAHLEAIAEHLH 1zfjA 263 :LRKIAEIRAHFP T0284 205 :IPL 1zfjA 276 :RTL T0284 210 :VTYGNPQLRDDARLARLGVRVVVNGHAA 1zfjA 279 :IAGNIATAEGARALYDAGVDVVKVGIGP T0284 238 :YFA 1zfjA 313 :RVV T0284 241 :AIKATYDCLREERG 1zfjA 322 :QVTAIYDAAAVARE Number of specific fragments extracted= 17 number of extra gaps= 0 total=2435 Number of alignments=166 # 1zfjA read from 1zfjA/merged-good-all-a2m # found chain 1zfjA in template set T0284 22 :CYHTA 1zfjA 47 :PIITA T0284 27 :SVFDPMSARIAADLGFECGIL 1zfjA 55 :TVTGSKMAIAIARAGGLGVIH T0284 63 :ALITLSEFVEQATRIGRVAR 1zfjA 76 :KNMSITEQAEEVRKVKRSEN T0284 83 :LPVIADADH 1zfjA 223 :LLVAAAVGV T0284 92 :G 1zfjA 233 :S T0284 98 :NVMRTVVELERAGIAALTIEDTL 1zfjA 234 :DTFERAEALFEAGADAIVIDTAH T0284 126 :GR 1zfjA 257 :GH T0284 135 :VEEGVGKIRAALEAR 1zfjA 259 :SAGVLRKIAEIRAHF T0284 152 :PALTIIARTNAEL 1zfjA 274 :PNRTLIAGNIATA T0284 172 :QRTLAYQEAGADGICLVGVR 1zfjA 287 :EGARALYDAGVDVVKVGIGP T0284 193 :FAHLEAIAEH 1zfjA 327 :YDAAAVAREY T0284 206 :PLMLVTYGNPQLRDDARLARLGVRVVVNG 1zfjA 338 :KTIIADGGIKYSGDIVKALAAGGNAVMLG Number of specific fragments extracted= 12 number of extra gaps= 0 total=2447 Number of alignments=167 # 1zfjA read from 1zfjA/merged-good-all-a2m # found chain 1zfjA in template set T0284 22 :CYHTA 1zfjA 47 :PIITA T0284 27 :SVFDPMSARIAADLGFECGILG 1zfjA 55 :TVTGSKMAIAIARAGGLGVIHK T0284 64 :LITLSEFVEQATRIGRVARL 1zfjA 77 :NMSITEQAEEVRKVKRSENG T0284 84 :PVIADADHG 1zfjA 224 :LVAAAVGVT T0284 97 :LNVMRTVVELERAGIAALTIEDTLLPA 1zfjA 233 :SDTFERAEALFEAGADAIVIDTAHGHS T0284 136 :EEGVGKIRAALEARVDPALTIIARTN 1zfjA 260 :AGVLRKIAEIRAHFPNRTLIAGNIAT T0284 171 :IQRTLAYQEAGADGICLVGVRD 1zfjA 286 :AEGARALYDAGVDVVKVGIGPG T0284 193 :FAHLEAIAEHLHIPLMLVTYGNP 1zfjA 326 :IYDAAAVAREYGKTIIADGGIKY T0284 220 :DARLA 1zfjA 349 :SGDIV T0284 226 :LGVRVVVNG 1zfjA 358 :AGGNAVMLG Number of specific fragments extracted= 10 number of extra gaps= 0 total=2457 Number of alignments=168 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ujqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ujqA expands to /projects/compbio/data/pdb/1ujq.pdb.gz 1ujqA:Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 1ujqA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 1ujqA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 1ujqA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 1ujqA Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 1ujqA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 1ujqA Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 1ujqA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 1ujqA # T0284 read from 1ujqA/merged-good-all-a2m # 1ujqA read from 1ujqA/merged-good-all-a2m # adding 1ujqA to template set # found chain 1ujqA in template set Warning: unaligning (T0284)L120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ujqA)A130 Warning: unaligning (T0284)D131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ujqA)A130 Warning: unaligning (T0284)W278 because last residue in template chain is (1ujqA)L286 T0284 8 :ELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQVLAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1ujqA 5 :SPGQAFRAALAKENPLQIVGAINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCPLPLLVDADIGFG T0284 95 :NALNVMRTVVELERAGIAALTIEDT 1ujqA 93 :SAFNVARTVKSIAKAGAAALHIEDQ T0284 132 :LICVEEGVGKIRAALEARVDPALTIIARTNAEL 1ujqA 131 :IVSKEEMVDRIRAAVDARTDPNFVIMARTDALA T0284 165 :IDVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTY 1ujqA 165 :EGLEAALDRAQAYVDAGADMLFPEAITELSMYRRFADVAQVPILANIT T0284 213 :GNPQLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERG 1ujqA 215 :GATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEKVYTVLRQ T0284 255 :AVASDLTASELSKKYTFPEEYQA 1ujqA 263 :VIDIMQTRNELYESINYYQFEEK Number of specific fragments extracted= 6 number of extra gaps= 0 total=2463 Number of alignments=169 # 1ujqA read from 1ujqA/merged-good-all-a2m # found chain 1ujqA in template set Warning: unaligning (T0284)H7 because first residue in template chain is (1ujqA)H4 Warning: unaligning (T0284)L120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ujqA)A130 Warning: unaligning (T0284)D131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ujqA)A130 Warning: unaligning (T0284)W278 because last residue in template chain is (1ujqA)L286 T0284 8 :ELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQVLAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1ujqA 5 :SPGQAFRAALAKENPLQIVGAINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCPLPLLVDADIGFG T0284 95 :NALNVMRTVVELERAGIAALTIEDT 1ujqA 93 :SAFNVARTVKSIAKAGAAALHIEDQ T0284 132 :LICVEEGVGKIRAALEARVDPALTIIARTNAELI 1ujqA 131 :IVSKEEMVDRIRAAVDARTDPNFVIMARTDALAV T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTY 1ujqA 166 :GLEAALDRAQAYVDAGADMLFPEAITELSMYRRFADVAQVPILANIT T0284 213 :GNPQLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVAS 1ujqA 215 :GATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEKVYTVLRQEGTQ T0284 259 :DLTASELSKKYTFPEEYQA 1ujqA 267 :MQTRNELYESINYYQFEEK Number of specific fragments extracted= 6 number of extra gaps= 0 total=2469 Number of alignments=170 # 1ujqA read from 1ujqA/merged-good-all-a2m # found chain 1ujqA in template set Warning: unaligning (T0284)L120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ujqA)A130 T0284 9 :LRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQVLAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1ujqA 6 :PGQAFRAALAKENPLQIVGAINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCPLPLLVDADIGFG T0284 95 :NALNVMRTVVELERAGIAALTIEDT 1ujqA 93 :SAFNVARTVKSIAKAGAAALHIEDQ T0284 132 :LICVEEGVGKIRAALEARVDPALTIIARTNAELI 1ujqA 131 :IVSKEEMVDRIRAAVDARTDPNFVIMARTDALAV T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTY 1ujqA 166 :GLEAALDRAQAYVDAGADMLFPEAITELSMYRRFADVAQVPILANIT T0284 213 :GNPQLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVASDLTASELSKKYTFPEEYQAWARDYM 1ujqA 215 :GATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEKVYTVLRQEGTQKNVIDIMQTRNELYESINYYQFEEK Number of specific fragments extracted= 5 number of extra gaps= 0 total=2474 Number of alignments=171 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mumA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mumA expands to /projects/compbio/data/pdb/1mum.pdb.gz 1mumA:# T0284 read from 1mumA/merged-good-all-a2m # 1mumA read from 1mumA/merged-good-all-a2m # adding 1mumA to template set # found chain 1mumA in template set T0284 9 :LRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQVLAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1mumA 6 :PGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFG T0284 95 :NALNVMRTVVELERAGIAALTIEDTLLPAQFGR 1mumA 93 :SAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGH T0284 128 :KSTDLICVEEGVGKIRAALEARVDPALTIIARTNAEL 1mumA 127 :PNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALA T0284 165 :IDVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTY 1mumA 165 :EGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANIT T0284 213 :GNPQLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERG 1mumA 215 :GATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQ T0284 255 :AVASDLTASELSKKYTFPEEYQAWARDY 1mumA 263 :VIDTMQTRNELYESINYYQYEEKLDNLF Number of specific fragments extracted= 6 number of extra gaps= 0 total=2480 Number of alignments=172 # 1mumA read from 1mumA/merged-good-all-a2m # found chain 1mumA in template set Warning: unaligning (T0284)M283 because last residue in template chain is (1mumA)A291 T0284 8 :ELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQVLAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1mumA 5 :SPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFG T0284 95 :NALNVMRTVVELERAGIAALTIEDTLLPAQFGR 1mumA 93 :SAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGH T0284 128 :KSTDLICVEEGVGKIRAALEARVDPALTIIARTNAELI 1mumA 127 :PNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAV T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTY 1mumA 166 :GLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANIT T0284 213 :GNPQLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVAS 1mumA 215 :GATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQ T0284 259 :DLTASELSKKYTFPEEYQAWARDY 1mumA 267 :MQTRNELYESINYYQYEEKLDNLF Number of specific fragments extracted= 6 number of extra gaps= 0 total=2486 Number of alignments=173 # 1mumA read from 1mumA/merged-good-all-a2m # found chain 1mumA in template set T0284 9 :LRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQVLAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYG 1mumA 6 :PGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFG T0284 95 :NALNVMRTVVELERAGIAALTIEDTLLPAQFGRKSTD 1mumA 93 :SAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNK T0284 132 :LICVEEGVGKIRAALEARVDPALTIIARTNAELI 1mumA 131 :IVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAV T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRDFAHLEAIAEHLHIPLMLVTY 1mumA 166 :GLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANIT T0284 213 :GNPQLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVASDLTASELSKKYTFPEEYQAWARDYMEV 1mumA 215 :GATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLD Number of specific fragments extracted= 5 number of extra gaps= 0 total=2491 Number of alignments=174 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pymA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pymA expands to /projects/compbio/data/pdb/1pym.pdb.gz 1pymA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 419, because occupancy 0.500 <= existing 0.500 in 1pymA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 550, because occupancy 0.500 <= existing 0.500 in 1pymA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1776, because occupancy 0.500 <= existing 0.500 in 1pymA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0284 read from 1pymA/merged-good-all-a2m # 1pymA read from 1pymA/merged-good-all-a2m # adding 1pymA to template set # found chain 1pymA in template set T0284 8 :ELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQ 1pymA 6 :KKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQ T0284 57 :LAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLPAQ 1pymA 54 :LGVRDSNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKT T0284 125 :FGR 1pymA 123 :SLH T0284 128 :KSTDLICVEEGVGKIRAALEARVDPALTIIARTNAELID 1pymA 128 :RAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAG T0284 167 :VDAVIQRTLAYQEAGADGICLV 1pymA 169 :LDEALKRAEAYRNAGADAILMH T0284 189 :GVRDFAHLEAIAEHLH 1pymA 192 :KKADPSDIEAFMKAWN T0284 205 :IPLMLVTYGN 1pymA 210 :GPVVIVPTKY T0284 216 :QLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERG 1pymA 220 :YKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYD T0284 255 :AVASDLTASELSKKYTFPEEYQAWARDY 1pymA 265 :VEDKIVSVKEIFRLQRDDELVQAEDKYL Number of specific fragments extracted= 9 number of extra gaps= 0 total=2500 Number of alignments=175 # 1pymA read from 1pymA/merged-good-all-a2m # found chain 1pymA in template set T0284 8 :ELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQ 1pymA 6 :KKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQ T0284 57 :LAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLPAQFGR 1pymA 54 :LGVRDSNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTNSL T0284 128 :KSTD 1pymA 126 :DGRA T0284 132 :LICVEEGVGKIRAALEARVDPALTIIARTNAELI 1pymA 132 :LADIEEFALKIKACKDSQTDPDFCIVARVEAFIA T0284 166 :DVDAVIQRTLAYQEAGADGICLVG 1pymA 168 :GLDEALKRAEAYRNAGADAILMHS T0284 190 :VRDFAHLEAIAEHLH 1pymA 193 :KADPSDIEAFMKAWN T0284 205 :IPLMLVTYGNPQL 1pymA 210 :GPVVIVPTKYYKT T0284 219 :DDARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVAS 1pymA 223 :PTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSL T0284 259 :DLTASELSKKYTFPEEYQAWARDY 1pymA 269 :IVSVKEIFRLQRDDELVQAEDKYL Number of specific fragments extracted= 9 number of extra gaps= 0 total=2509 Number of alignments=176 # 1pymA read from 1pymA/merged-good-all-a2m # found chain 1pymA in template set T0284 9 :LRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQ 1pymA 7 :KTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQ T0284 57 :LAAPDFALITLSEFVEQATRIGRVARLPVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLPAQFGRKSTD 1pymA 54 :LGVRDSNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTNSLHDGR T0284 132 :LICVEEGVGKIRAALEARVDPALTIIARTNAELI 1pymA 132 :LADIEEFALKIKACKDSQTDPDFCIVARVEAFIA T0284 166 :DVDAVIQRTLAYQEAGADGICLVGVRD 1pymA 168 :GLDEALKRAEAYRNAGADAILMHSKKA T0284 193 :FAHLEAIAEHL 1pymA 196 :PSDIEAFMKAW T0284 204 :HIPLMLVTYGNPQLRDDARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVASDLTASELSKKYTFPEEYQAWARDYMEV 1pymA 208 :NQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAED Number of specific fragments extracted= 6 number of extra gaps= 0 total=2515 Number of alignments=177 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f61A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f61A expands to /projects/compbio/data/pdb/1f61.pdb.gz 1f61A:# T0284 read from 1f61A/merged-good-all-a2m # 1f61A read from 1f61A/merged-good-all-a2m # adding 1f61A to template set # found chain 1f61A in template set T0284 7 :HELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQ 1f61A 50 :RRGAEVLWEQLHDLEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGD T0284 56 :VLA 1f61A 101 :LSG T0284 59 :APDFALITLSEFVEQATRIGRVA 1f61A 106 :YPDQSLYPANSVPQVVRRINNAL T0284 84 :PVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLL 1f61A 149 :PIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLA T0284 122 :PAQFGR 1f61A 188 :EKKCGH T0284 128 :KSTDLICVEEGVGKIRAALEAR 1f61A 195 :GGKVLIPTQQHIRTLTSARLAA T0284 150 :VDPALTIIARTNAELI 1f61A 219 :ADVPTVVIARTDAEAA T0284 166 :DVDAVIQRTLAYQEA 1f61A 264 :GIEPCIARAKAYAPF T0284 182 :ADGICLV 1f61A 279 :ADLIWME T0284 189 :GVRDFAHLEAIAEHL 1f61A 287 :GTPDLEAARQFSEAV T0284 204 :HIPLMLVTYGNPQLRDD 1f61A 304 :EYPDQMLAYNCSPSFNW T0284 221 :ARLARLGVRVVVNGHAAYFAAIKATYDCLREERG 1f61A 334 :KELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQ T0284 255 :AVASDLTASELSKKYTFPEEYQAWARDY 1f61A 375 :ELQEREFAAEERGYTATKHQREVGAGYF Number of specific fragments extracted= 13 number of extra gaps= 0 total=2528 Number of alignments=178 # 1f61A read from 1f61A/merged-good-all-a2m # found chain 1f61A in template set T0284 2 :HRASHHELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVAS 1f61A 45 :EHTLARRGAEVLWEQLHDLEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVA T0284 54 :LQVLA 1f61A 99 :ANLSG T0284 59 :APDFALITLSEFVEQATRIGRVAR 1f61A 106 :YPDQSLYPANSVPQVVRRINNALQ T0284 83 :LPVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1f61A 148 :APIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLAS T0284 123 :AQFGR 1f61A 189 :KKCGH T0284 128 :KSTDLICVEEGVGKIRAALEA 1f61A 195 :GGKVLIPTQQHIRTLTSARLA T0284 149 :RVDPALTIIARTNAELIDV 1f61A 218 :VADVPTVVIARTDAEAATL T0284 168 :DAVIQRTLAYQEA 1f61A 266 :EPCIARAKAYAPF T0284 182 :ADGICLVG 1f61A 279 :ADLIWMET T0284 190 :VRDFAHLEAIAEHL 1f61A 288 :TPDLEAARQFSEAV T0284 206 :PLMLVTYGNPQLRDDA 1f61A 306 :PDQMLAYNCSPSFNWK T0284 222 :RLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVAS 1f61A 335 :ELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQMS T0284 271 :FPEEYQAWARDYME 1f61A 372 :AYVELQEREFAAEE Number of specific fragments extracted= 13 number of extra gaps= 0 total=2541 Number of alignments=179 # 1f61A read from 1f61A/merged-good-all-a2m # found chain 1f61A in template set T0284 1 :MHRASHHELRAMFRALLDSSRCYHTASVFDPMSARIAADLGFECGILGGSVASLQ 1f61A 44 :EEHTLARRGAEVLWEQLHDLEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGD T0284 57 :LAAPDFALITLSEFVEQATRIGRVARL 1f61A 104 :HTYPDQSLYPANSVPQVVRRINNALQR T0284 84 :PVIADADHGYGNALNVMRTVVELERAGIAALTIEDTLLP 1f61A 149 :PIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLAS T0284 123 :AQFGRKSTD 1f61A 189 :KKCGHLGGK T0284 132 :LICVEEGVGKIRAAL 1f61A 199 :LIPTQQHIRTLTSAR T0284 147 :EARVDPALTIIARTNAELI 1f61A 216 :ADVADVPTVVIARTDAEAA T0284 167 :VDAVIQRTLAYQEA 1f61A 265 :IEPCIARAKAYAPF T0284 182 :ADGICLVGVRD 1f61A 279 :ADLIWMETGTP T0284 193 :FAHLEAIAEHL 1f61A 291 :LEAARQFSEAV T0284 204 :HIPLMLVTY 1f61A 307 :DQMLAYNCS T0284 216 :QLRDD 1f61A 316 :PSFNW T0284 221 :ARLARLGVRVVVNGHAAYFAAIKATYDCLREERGAVA 1f61A 334 :KELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQNQM T0284 260 :LTASELSKKYT 1f61A 371 :SAYVELQEREF T0284 281 :DYM 1f61A 382 :AAE Number of specific fragments extracted= 14 number of extra gaps= 0 total=2555 Number of alignments=180 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w5qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w5qA expands to /projects/compbio/data/pdb/1w5q.pdb.gz 1w5qA:Skipped atom 260, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 262, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 264, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 266, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 268, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 270, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 272, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 479, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 481, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 483, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 485, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 487, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 489, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 491, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 493, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 495, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 497, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 499, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 578, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 580, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 582, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 584, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 586, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 881, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 883, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 885, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 887, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 889, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 891, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 893, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 895, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 897, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 899, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 901, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 915, because occupancy 0.750 <= existing 0.750 in 1w5qA Skipped atom 917, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 919, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 921, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 923, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 925, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 927, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 929, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 931, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 933, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 935, because occupancy 0.250 <= existing 0.750 in 1w5qA Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1094, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1131, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1133, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1135, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1272, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1274, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1276, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1278, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1280, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1282, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1284, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1286, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1310, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1312, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1314, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1316, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1318, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1320, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1322, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1324, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1326, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1328, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1330, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1375, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1389, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1391, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 1531, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1533, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1535, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1537, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1539, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1541, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1543, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1545, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1547, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1571, because occupancy 0.200 <= existing 0.800 in 1w5qA Skipped atom 1573, because occupancy 0.200 <= existing 0.800 in 1w5qA Skipped atom 1575, because occupancy 0.200 <= existing 0.800 in 1w5qA Skipped atom 1577, because occupancy 0.200 <= existing 0.800 in 1w5qA Skipped atom 1579, because occupancy 0.200 <= existing 0.800 in 1w5qA Skipped atom 1581, because occupancy 0.200 <= existing 0.800 in 1w5qA Skipped atom 1992, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1994, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1996, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 1998, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2000, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2002, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2004, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2006, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2015, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2017, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2019, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2021, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2023, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2025, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2027, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2029, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2058, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2062, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2064, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2066, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2068, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2070, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2072, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2124, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2126, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2128, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2130, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2132, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2134, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2136, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2138, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2140, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2142, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2144, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2181, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2183, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2185, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2187, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2189, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2191, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2193, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2195, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2197, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2210, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2212, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2214, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2216, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2218, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2220, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2222, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2224, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2226, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2228, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2230, because occupancy 0.500 <= existing 0.500 in 1w5qA Skipped atom 2333, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2335, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2337, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2339, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2341, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2343, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2345, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2347, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2359, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2361, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2363, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2365, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2367, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2369, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2371, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2373, because occupancy 0.300 <= existing 0.700 in 1w5qA Skipped atom 2470, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2472, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2474, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2476, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2478, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2480, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2482, because occupancy 0.400 <= existing 0.600 in 1w5qA Skipped atom 2484, because occupancy 0.400 <= existing 0.600 in 1w5qA # T0284 read from 1w5qA/merged-good-all-a2m # 1w5qA read from 1w5qA/merged-good-all-a2m # adding 1w5qA to template set # found chain 1w5qA in template set Warning: unaligning (T0284)A158 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w5qA)Y202 Warning: unaligning (T0284)N161 because of BadResidue code BAD_PEPTIDE in next template residue (1w5qA)S208 Warning: unaligning (T0284)A162 because of BadResidue code BAD_PEPTIDE at template residue (1w5qA)S208 Warning: unaligning (T0284)G189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w5qA)G262 T0284 10 :RAMFR 1w5qA 65 :IDQLL T0284 32 :MSARIAADLGFECGILG 1w5qA 70 :IEAEEWVALGIPALALF T0284 56 :VLAAPDFALIT 1w5qA 93 :KKSLDAAEAYN T0284 69 :EFVEQATRIGRVA 1w5qA 107 :IAQRATRALRERF T0284 82 :RLPVIADADHG 1w5qA 121 :ELGIITDVCLC T0284 93 :YG 1w5qA 133 :FT T0284 95 :N 1w5qA 137 :G T0284 96 :ALNVMRTVVELERAGIAALTIEDTL 1w5qA 154 :IDVLVRQALSHAEAGAQVVAPSDMM T0284 140 :GKIRAALEAR 1w5qA 180 :GRIGAIREAL T0284 150 :VDPALTII 1w5qA 193 :GHTNVRVM T0284 159 :RT 1w5qA 205 :KY T0284 163 :ELI 1w5qA 209 :AYY T0284 166 :DVDAVIQRTLAYQEAGADGICLV 1w5qA 238 :NSDEALHEVAADLAEGADMVMVK T0284 190 :VRDFAHLEAIAEHLHIPLMLVTY 1w5qA 263 :MPYLDIVRRVKDEFRAPTFVYQV T0284 219 :DD 1w5qA 286 :SG T0284 221 :ARLARLGVRVVVNGHAAYFA 1w5qA 311 :TAFKRAGADGILTYFAKQAA T0284 243 :KATY 1w5qA 331 :EQLR Number of specific fragments extracted= 17 number of extra gaps= 3 total=2572 Number of alignments=181 # 1w5qA read from 1w5qA/merged-good-all-a2m # found chain 1w5qA in template set Warning: unaligning (T0284)A158 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w5qA)Y202 Warning: unaligning (T0284)N161 because of BadResidue code BAD_PEPTIDE in next template residue (1w5qA)S208 Warning: unaligning (T0284)A162 because of BadResidue code BAD_PEPTIDE at template residue (1w5qA)S208 Warning: unaligning (T0284)G189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w5qA)G262 T0284 10 :RAMFRALLDS 1w5qA 65 :IDQLLIEAEE T0284 37 :AADLGFECGILG 1w5qA 75 :WVALGIPALALF T0284 57 :LA 1w5qA 96 :LD T0284 59 :APDF 1w5qA 103 :NPEG T0284 69 :EFVEQATRIGR 1w5qA 107 :IAQRATRALRE T0284 80 :VARLPVIADADHG 1w5qA 119 :FPELGIITDVCLC T0284 93 :YG 1w5qA 133 :FT T0284 95 :N 1w5qA 137 :G T0284 96 :ALNVMRTVVELERAGIAALTIEDTL 1w5qA 154 :IDVLVRQALSHAEAGAQVVAPSDMM T0284 136 :EEGVGKIRAALEARVDPALTII 1w5qA 179 :DGRIGAIREALESAGHTNVRVM T0284 159 :RT 1w5qA 205 :KY T0284 163 :ELIDV 1w5qA 209 :AYYGP T0284 168 :DAVIQRTLAYQEAGADGICLV 1w5qA 240 :DEALHEVAADLAEGADMVMVK T0284 190 :VRDFAHLEAIAEHLHIPLMLVTY 1w5qA 263 :MPYLDIVRRVKDEFRAPTFVYQV T0284 218 :RDDA 1w5qA 287 :GEYA T0284 222 :RLARLGVRVVVNGH 1w5qA 312 :AFKRAGADGILTYF T0284 245 :TYDCLREER 1w5qA 326 :AKQAAEQLR Number of specific fragments extracted= 17 number of extra gaps= 3 total=2589 Number of alignments=182 # 1w5qA read from 1w5qA/merged-good-all-a2m # found chain 1w5qA in template set Warning: unaligning (T0284)A158 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w5qA)Y202 Warning: unaligning (T0284)R159 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1w5qA)Y202 Warning: unaligning (T0284)L164 because of BadResidue code BAD_PEPTIDE in next template residue (1w5qA)S208 Warning: unaligning (T0284)I165 because of BadResidue code BAD_PEPTIDE at template residue (1w5qA)S208 Warning: unaligning (T0284)G189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w5qA)G262 Warning: unaligning (T0284)V190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w5qA)G262 T0284 10 :RAMFRALLD 1w5qA 65 :IDQLLIEAE T0284 36 :IAADLGFECGILGGS 1w5qA 74 :EWVALGIPALALFPV T0284 56 :VLAAPDFALITLS 1w5qA 93 :KKSLDAAEAYNPE T0284 69 :EFVEQATRIGRVA 1w5qA 107 :IAQRATRALRERF T0284 82 :RLPVIADA 1w5qA 121 :ELGIITDV T0284 90 :DHGYG 1w5qA 144 :DDGYV T0284 95 :NALNVMRTVVELERAGIAALTIEDTLLP 1w5qA 153 :SIDVLVRQALSHAEAGAQVVAPSDMMDG T0284 138 :GVGKIRAALEARVDPALTII 1w5qA 181 :RIGAIREALESAGHTNVRVM T0284 160 :TNAE 1w5qA 203 :SAKY T0284 167 :VDAVIQRTLAYQEAGADGICLV 1w5qA 239 :SDEALHEVAADLAEGADMVMVK T0284 191 :RD 1w5qA 263 :MP T0284 193 :FAHLEAIAEHLHIPLMLVTY 1w5qA 266 :LDIVRRVKDEFRAPTFVYQV T0284 249 :LREERGAVASDLTASE 1w5qA 293 :MGAIQNGWLAESVILE T0284 274 :EYQA 1w5qA 309 :SLTA Number of specific fragments extracted= 14 number of extra gaps= 3 total=2603 Number of alignments=183 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 183 Adding 6200 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: -505.8054, CN propb: -505.8054 weights: 0.2286 constraints: 1245 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 1245 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 1245 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 4955 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 4955 # 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 6200 # command: