parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0301/ # command:# Making conformation for sequence T0301 numbered 1 through 395 Created new target T0301 from T0301.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0301/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0301//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0301/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0301//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0301/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0301/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0301/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wc3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wc3A expands to /projects/compbio/data/pdb/1wc3.pdb.gz 1wc3A:# T0301 read from 1wc3A/merged-good-all-a2m # 1wc3A read from 1wc3A/merged-good-all-a2m # adding 1wc3A to template set # found chain 1wc3A in template set Warning: unaligning (T0301)N196 because first residue in template chain is (1wc3A)S1002 T0301 197 :LV 1wc3A 1003 :HM # choosing archetypes in rotamer library T0301 205 :GVGTFKATM 1wc3A 1005 :RPEPRLITI T0301 221 :VFVNAEEI 1wc3A 1014 :LFSDIVGF T0301 233 :TELREEING 1wc3A 1022 :TRMSNALQS T0301 243 :PQQLARFERIRVAGALRM 1wc3A 1031 :QGVAELLNEYLGEMTRAV T0301 288 :RTASGKLVAAGDIDLLVRALSMGKLHHAMMGTAAVAIGTAAA 1wc3A 1049 :FENQGTVDKFVGDAIMALYGAPEEMSPSEQVRRAIATARQML T0301 338 :A 1wc3A 1096 :L T0301 340 :GGGERSA 1wc3A 1107 :GRNEVPP T0301 347 :VRFGHPSGTLRVGAEASQANGEWTVTKAIMSRSA 1wc3A 1116 :FRCGIHQGMAVVGLFGSQERSDFTAIGPSVNIAA T0301 382 :ILME 1wc3A 1150 :RLQE Number of specific fragments extracted= 10 number of extra gaps= 0 total=10 Number of alignments=1 # 1wc3A read from 1wc3A/merged-good-all-a2m # found chain 1wc3A in template set T0301 211 :AT 1wc3A 1011 :IT T0301 220 :TVFVNAEEI 1wc3A 1013 :ILFSDIVGF T0301 233 :TELREEING 1wc3A 1022 :TRMSNALQS T0301 243 :PQQLARFERIRVAGALR 1wc3A 1031 :QGVAELLNEYLGEMTRA T0301 269 :AA 1wc3A 1048 :VF T0301 289 :TASGKLVAAGDIDLLVRALSMGKLHHAMMGTAAVAIGTAAA 1wc3A 1050 :ENQGTVDKFVGDAIMALYGAPEEMSPSEQVRRAIATARQML T0301 336 :NLA 1wc3A 1094 :EKL T0301 340 :GGG 1wc3A 1107 :GRN T0301 343 :ERSAVRFGHPSGTLRVGAEASQANGEWTVTKAIMSR 1wc3A 1112 :PPVRFRCGIHQGMAVVGLFGSQERSDFTAIGPSVNI T0301 380 :ARILME 1wc3A 1148 :AARLQE Number of specific fragments extracted= 10 number of extra gaps= 0 total=20 Number of alignments=2 # 1wc3A read from 1wc3A/merged-good-all-a2m # found chain 1wc3A in template set T0301 220 :TVFVNAEEI 1wc3A 1013 :ILFSDIVGF T0301 233 :TELREEING 1wc3A 1022 :TRMSNALQS T0301 243 :PQQLARFERIRVAGA 1wc3A 1031 :QGVAELLNEYLGEMT T0301 267 :EEAATR 1wc3A 1046 :RAVFEN T0301 291 :SGKLVAAGDIDLLVRALSMGKLHHAMMGTAAVAIGTA 1wc3A 1052 :QGTVDKFVGDAIMALYGAPEEMSPSEQVRRAIATARQ T0301 338 :AA 1wc3A 1089 :ML T0301 340 :GGGERSAVRFGHPSGTLRVGAEASQANGEWTVTKAIMSRSAR 1wc3A 1109 :NEVPPVRFRCGIHQGMAVVGLFGSQERSDFTAIGPSVNIAAR T0301 383 :LME 1wc3A 1151 :LQE Number of specific fragments extracted= 8 number of extra gaps= 0 total=28 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sdjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sdjA expands to /projects/compbio/data/pdb/1sdj.pdb.gz 1sdjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0301 read from 1sdjA/merged-good-all-a2m # 1sdjA read from 1sdjA/merged-good-all-a2m # adding 1sdjA to template set # found chain 1sdjA in template set T0301 17 :GTSKGVFFRLEDLP 1sdjA 18 :GNSAGVVFPADNLS T0301 37 :GEARDRLFMRV 1sdjA 32 :EAQMQLIAREL T0301 67 :STSKCVILSKSSQPGHDVDYL 1sdjA 43 :GHSETAFLLHSDDSDVRIRYF T0301 93 :IDKPFV 1sdjA 64 :TPTVEV T0301 102 :GNCGNLSTGAGAF 1sdjA 70 :PICGHATVAAHYV T0301 115 :ALHAGL 1sdjA 84 :AKVLGL T0301 128 :EDGIC 1sdjA 90 :GNCTI T0301 137 :WQANIGKTIIAHVPVSGGQVQETGDFELD 1sdjA 95 :WQTSLAGKHRVTIEKHNDDYRISLEQGTP T0301 177 :EFLDPSDD 1sdjA 124 :GFEPPLEG T0301 186 :E 1sdjA 132 :E T0301 187 :DGGAI 1sdjA 144 :TEDDI T0301 203 :VPGV 1sdjA 149 :LPGL T0301 210 :KATMINAGIPTVFVNAE 1sdjA 153 :PIQVATTGHSKVMIPLK T0301 227 :EIGYRGTEL 1sdjA 171 :EVDIDALSP T0301 246 :LARFERIR 1sdjA 181 :LNALTAIS T0301 258 :LRMGL 1sdjA 189 :KKIGC T0301 275 :TPKIAFVAPP 1sdjA 194 :NGFFPFQIRP T0301 298 :GDIDLLVRALSMGKLHHA 1sdjA 204 :GKNETDGRMFSPAIGIVE T0301 316 :MMGTAAVAIGTAA 1sdjA 224 :VTGNANGPMGAWL T0301 335 :VNLAAG 1sdjA 237 :VHHNVL T0301 341 :GGERSAVRFGHPS 1sdjA 245 :DGNVLRVKGHQGR T0301 354 :GTLRVGAEAS 1sdjA 263 :GMIEVTVTIR T0301 366 :NG 1sdjA 273 :DN T0301 370 :TVTKA 1sdjA 275 :QPEKV Number of specific fragments extracted= 24 number of extra gaps= 0 total=52 Number of alignments=4 # 1sdjA read from 1sdjA/merged-good-all-a2m # found chain 1sdjA in template set T0301 17 :GTSKGVFFRLEDLP 1sdjA 18 :GNSAGVVFPADNLS T0301 37 :GEARDRLFMRV 1sdjA 32 :EAQMQLIAREL T0301 67 :STSKCVILSKSSQPGHDVDYL 1sdjA 43 :GHSETAFLLHSDDSDVRIRYF T0301 93 :IDKPFV 1sdjA 64 :TPTVEV T0301 102 :GNCGNLSTGAGAFALH 1sdjA 70 :PICGHATVAAHYVRAK T0301 118 :AGL 1sdjA 87 :LGL T0301 129 :DGIC 1sdjA 90 :GNCT T0301 136 :IWQANIGKTIIAHVPVSGGQVQETGDFEL 1sdjA 94 :IWQTSLAGKHRVTIEKHNDDYRISLEQGT T0301 176 :LEFLDPSDD 1sdjA 123 :PGFEPPLEG T0301 186 :E 1sdjA 132 :E T0301 187 :DGGAIFP 1sdjA 144 :TEDDILP T0301 208 :TFKATMINAGIPTVFVNAE 1sdjA 151 :GLPIQVATTGHSKVMIPLK T0301 227 :EIGYRGTEL 1sdjA 171 :EVDIDALSP T0301 242 :D 1sdjA 180 :D T0301 246 :LARFERIRV 1sdjA 181 :LNALTAISK T0301 259 :RMGL 1sdjA 190 :KIGC T0301 275 :TPKIAFVAPP 1sdjA 194 :NGFFPFQIRP T0301 298 :GDIDLLVRALSMGKLHHA 1sdjA 204 :GKNETDGRMFSPAIGIVE T0301 316 :MMGTAAVAIGTAAA 1sdjA 224 :VTGNANGPMGAWLV T0301 336 :NLAAG 1sdjA 238 :HHNVL T0301 341 :GGERSAVRFGHPS 1sdjA 245 :DGNVLRVKGHQGR T0301 354 :GTLRVGAEASQA 1sdjA 263 :GMIEVTVTIRDN T0301 370 :TVTKA 1sdjA 275 :QPEKV Number of specific fragments extracted= 23 number of extra gaps= 0 total=75 Number of alignments=5 # 1sdjA read from 1sdjA/merged-good-all-a2m # found chain 1sdjA in template set T0301 17 :GTSKGVFFRLEDLP 1sdjA 18 :GNSAGVVFPADNLS T0301 37 :GEARDRLFMRV 1sdjA 32 :EAQMQLIAREL T0301 67 :STSKCVILSKSSQPGHDVDYL 1sdjA 43 :GHSETAFLLHSDDSDVRIRYF T0301 93 :IDKPFV 1sdjA 64 :TPTVEV T0301 102 :GNCGNLSTGAGAFALH 1sdjA 70 :PICGHATVAAHYVRAK T0301 118 :AGL 1sdjA 87 :LGL T0301 128 :EDGICEVR 1sdjA 90 :GNCTIWQT T0301 140 :NIGKTIIAHVPVSGGQVQETGDFEL 1sdjA 98 :SLAGKHRVTIEKHNDDYRISLEQGT T0301 176 :LEFLDPSD 1sdjA 123 :PGFEPPLE T0301 185 :GEDGGAIFP 1sdjA 142 :HLTEDDILP T0301 195 :GNLVDDLE 1sdjA 151 :GLPIQVAT T0301 216 :AGIPTVFVNAE 1sdjA 159 :TGHSKVMIPLK T0301 227 :EIGYRGTEL 1sdjA 171 :EVDIDALSP T0301 246 :LARFERIRVAG 1sdjA 181 :LNALTAISKKI T0301 273 :QHTPKIAFVAPPRDY 1sdjA 192 :GCNGFFPFQIRPGKN T0301 301 :DLLVRALSMGKLHH 1sdjA 207 :ETDGRMFSPAIGIV T0301 315 :AMMGTAAVAIGTAAA 1sdjA 223 :PVTGNANGPMGAWLV T0301 336 :NLAAG 1sdjA 238 :HHNVL T0301 341 :GGERSAVRFGH 1sdjA 245 :DGNVLRVKGHQ T0301 352 :PSGTLRVGAEASQA 1sdjA 261 :RDGMIEVTVTIRDN T0301 370 :TVTKA 1sdjA 275 :QPEKV Number of specific fragments extracted= 21 number of extra gaps= 0 total=96 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gkeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gkeA expands to /projects/compbio/data/pdb/2gke.pdb.gz 2gkeA:Skipped atom 758, because occupancy 0.5 <= existing 0.500 in 2gkeA Skipped atom 760, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 788, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 790, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 792, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 794, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1266, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1310, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1312, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1314, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1316, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1428, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1430, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1927, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1929, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1931, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1933, because occupancy 0.500 <= existing 0.500 in 2gkeA # T0301 read from 2gkeA/merged-good-all-a2m # 2gkeA read from 2gkeA/merged-good-all-a2m # adding 2gkeA to template set # found chain 2gkeA in template set Warning: unaligning (T0301)G21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gkeA)V14 Warning: unaligning (T0301)V22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gkeA)V14 Warning: unaligning (T0301)A211 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gkeA)G151 Warning: unaligning (T0301)T212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gkeA)G151 T0301 10 :PATYLRGGTSK 2gkeA 2 :QFSKMHGLGND T0301 23 :FFR 2gkeA 15 :VVD T0301 28 :DLPESCRVPGEARDRLF 2gkeA 18 :GVTQNVFFTPETIRRLA T0301 51 :PDPYAAH 2gkeA 35 :NRHCGIG T0301 68 :TSKCVILSKSSQPGHDVDYLYGQ 2gkeA 42 :FDQLLIVEAPYDPELDFHYRIFN T0301 93 :IDKPFV 2gkeA 65 :ADGSEV T0301 102 :GNCGNLSTGAGAFALHAGLVDPA 2gkeA 71 :SQCGNGARCFARFVTLKGLTNKK T0301 131 :ICEVR 2gkeA 94 :DISVS T0301 140 :NIGKTIIAH 2gkeA 99 :TQKGNMVLT T0301 168 :TFPAAEIVLEFLDPSDDGEDGGAIFPTGNLVDDLEV 2gkeA 108 :VKDDNQIRVNMGEPIWEPAKIPFTANKFEKNYILRT T0301 205 :GVGTFK 2gkeA 144 :DIQTVL T0301 213 :MINAGIPTVFVNAEEIGYRG 2gkeA 152 :AVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 2gkeA 173 :EQLGPLLE T0301 261 :GL 2gkeA 181 :SH T0301 268 :EAA 2gkeA 183 :ERF T0301 273 :QHTPKIAFV 2gkeA 186 :PERVNAGFM T0301 293 :KLVAAG 2gkeA 195 :QIINKE T0301 301 :DLLVRALSMGK 2gkeA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAA 2gkeA 213 :ETQACGSGACAAVAVGI T0301 339 :AGGGERSAVRFGHPSGTLRV 2gkeA 230 :MQGLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 2gkeA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 21 number of extra gaps= 2 total=117 Number of alignments=7 # 2gkeA read from 2gkeA/merged-good-all-a2m # found chain 2gkeA in template set Warning: unaligning (T0301)G21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gkeA)V14 Warning: unaligning (T0301)V22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gkeA)V14 Warning: unaligning (T0301)A211 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gkeA)G151 Warning: unaligning (T0301)T212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gkeA)G151 T0301 10 :PATYLRGGTSK 2gkeA 2 :QFSKMHGLGND T0301 23 :FFR 2gkeA 15 :VVD T0301 28 :DLPESCRVPGEARDRLF 2gkeA 18 :GVTQNVFFTPETIRRLA T0301 51 :PDPYAAH 2gkeA 35 :NRHCGIG T0301 68 :TSKCVILSKSSQPGHDVDYLYGQ 2gkeA 42 :FDQLLIVEAPYDPELDFHYRIFN T0301 93 :IDKPFV 2gkeA 65 :ADGSEV T0301 102 :GNCGNLSTGAGAFALHAGLVDPA 2gkeA 71 :SQCGNGARCFARFVTLKGLTNKK T0301 131 :ICEVR 2gkeA 94 :DISVS T0301 151 :VSGGQVQET 2gkeA 99 :TQKGNMVLT T0301 168 :TFPAAEIVLEFLDPSDDGEDGGA 2gkeA 108 :VKDDNQIRVNMGEPIWEPAKIPF T0301 193 :PTGNLVDDLEVP 2gkeA 131 :TANKFEKNYILR T0301 205 :GVGTFK 2gkeA 144 :DIQTVL T0301 213 :MINAGIPTVFVNAEEIGYRG 2gkeA 152 :AVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 2gkeA 173 :EQLGPLLE T0301 261 :GL 2gkeA 184 :RF T0301 273 :QHTPKIAFVA 2gkeA 186 :PERVNAGFMQ T0301 294 :LVAAG 2gkeA 196 :IINKE T0301 301 :DLLVRALSMG 2gkeA 201 :HIKLRVYERG T0301 311 :KLHHAMMGTAAVAIGTAAA 2gkeA 212 :GETQACGSGACAAVAVGIM T0301 340 :GGGERSAVRFGHPSGTLRV 2gkeA 231 :QGLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 2gkeA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 21 number of extra gaps= 2 total=138 Number of alignments=8 # 2gkeA read from 2gkeA/merged-good-all-a2m # found chain 2gkeA in template set Warning: unaligning (T0301)F23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gkeA)V14 Warning: unaligning (T0301)F24 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gkeA)V14 Warning: unaligning (T0301)A211 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gkeA)G151 Warning: unaligning (T0301)T212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gkeA)G151 T0301 10 :PATYLRGGTS 2gkeA 2 :QFSKMHGLGN T0301 22 :V 2gkeA 12 :D T0301 25 :RLEDLPESCRVPGEARDRLF 2gkeA 15 :VVDGVTQNVFFTPETIRRLA T0301 51 :PDPYAAHI 2gkeA 35 :NRHCGIGF T0301 69 :SKCVILSKSSQPGHDVDYLYGQ 2gkeA 43 :DQLLIVEAPYDPELDFHYRIFN T0301 93 :IDKPFV 2gkeA 65 :ADGSEV T0301 102 :GNCGNLSTGAGAFALHAGLVDP 2gkeA 71 :SQCGNGARCFARFVTLKGLTNK T0301 130 :GICEVR 2gkeA 93 :KDISVS T0301 140 :NIGKTIIAHV 2gkeA 99 :TQKGNMVLTV T0301 169 :FPAAEIVLEFLDPSDDGEDGG 2gkeA 109 :KDDNQIRVNMGEPIWEPAKIP T0301 192 :FPTGNLVDDLEVP 2gkeA 130 :FTANKFEKNYILR T0301 205 :GVGTFK 2gkeA 144 :DIQTVL T0301 213 :MINAGIPTVFVNAEEIGYRG 2gkeA 152 :AVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 2gkeA 173 :EQLGPLLE T0301 272 :RQHTPKIAFV 2gkeA 185 :FPERVNAGFM T0301 293 :KLVAAGDIDLLVRALSMGKL 2gkeA 195 :QIINKEHIKLRVYERGAGET T0301 314 :HAMMGTAAVAIGTAA 2gkeA 215 :QACGSGACAAVAVGI T0301 339 :AGGGERSAVRFGHPSGTLRV 2gkeA 230 :MQGLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 2gkeA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 19 number of extra gaps= 2 total=157 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ym5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ym5A expands to /projects/compbio/data/pdb/1ym5.pdb.gz 1ym5A:# T0301 read from 1ym5A/merged-good-all-a2m # 1ym5A read from 1ym5A/merged-good-all-a2m # adding 1ym5A to template set # found chain 1ym5A in template set Warning: unaligning (T0301)A225 because of BadResidue code BAD_PEPTIDE in next template residue (1ym5A)E168 Warning: unaligning (T0301)E226 because of BadResidue code BAD_PEPTIDE at template residue (1ym5A)E168 Warning: unaligning (T0301)L302 because of BadResidue code BAD_PEPTIDE in next template residue (1ym5A)E211 Warning: unaligning (T0301)L303 because of BadResidue code BAD_PEPTIDE at template residue (1ym5A)E211 Warning: unaligning (T0301)H351 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ym5A)G255 Warning: unaligning (T0301)P352 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ym5A)G255 T0301 19 :SKGVFFRLEDLPES 1ym5A 21 :NPVAVINFLEIDEN T0301 34 :RVPGEARDRLFMRV 1ym5A 35 :EVSQEELQAIANWT T0301 67 :STSKCVILSKSSQPGHDVDYL 1ym5A 49 :NLSETTFLFKPSDKKYDYKLR T0301 91 :VSIDKPFVDW 1ym5A 70 :IFTPRSELPF T0301 104 :CGNLSTGAGAFALH 1ym5A 80 :AGHPTIGSCKAFLE T0301 118 :AGL 1ym5A 95 :TKN T0301 127 :PEDGICEVRI 1ym5A 98 :TTATSLVQEC T0301 140 :NI 1ym5A 108 :KI T0301 143 :KTI 1ym5A 110 :GAV T0301 148 :HVPVSGGQVQET 1ym5A 113 :PITINEGLISFK T0301 160 :GDFELD 1ym5A 126 :PMADYE T0301 166 :GVT 1ym5A 146 :GLK T0301 178 :FLD 1ym5A 149 :FIK T0301 210 :KATMINAGIPTVFVN 1ym5A 152 :PPALLHTGPEWIVAL T0301 227 :EI 1ym5A 169 :DA T0301 236 :REEINGD 1ym5A 171 :ETCFNAN T0301 243 :PQQLARFERI 1ym5A 181 :AMLAHQTKQN T0301 274 :HTPKIAFVAPPRDYR 1ym5A 191 :DHVGIILAGPKKEAA T0301 298 :GDID 1ym5A 206 :IKNS T0301 304 :VRALSMGK 1ym5A 212 :MRAFAPVI T0301 313 :HHAMMGTAAVAIGTAA 1ym5A 223 :EDPVCGSGSVALARYL T0301 336 :NLAAGGGERSAVRFG 1ym5A 239 :QEVYKFEKTTDITIS T0301 353 :SGTLRVGAE 1ym5A 261 :NGLMLASIK T0301 363 :SQANGEWTVT 1ym5A 270 :KEADNSTSYY Number of specific fragments extracted= 24 number of extra gaps= 3 total=181 Number of alignments=10 # 1ym5A read from 1ym5A/merged-good-all-a2m # found chain 1ym5A in template set Warning: unaligning (T0301)A225 because of BadResidue code BAD_PEPTIDE in next template residue (1ym5A)E168 Warning: unaligning (T0301)E226 because of BadResidue code BAD_PEPTIDE at template residue (1ym5A)E168 Warning: unaligning (T0301)L302 because of BadResidue code BAD_PEPTIDE in next template residue (1ym5A)E211 Warning: unaligning (T0301)L303 because of BadResidue code BAD_PEPTIDE at template residue (1ym5A)E211 Warning: unaligning (T0301)H351 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ym5A)G255 Warning: unaligning (T0301)P352 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ym5A)G255 T0301 19 :SKGVFFRLEDLPES 1ym5A 21 :NPVAVINFLEIDEN T0301 34 :RVPGEARDRLFMRV 1ym5A 35 :EVSQEELQAIANWT T0301 67 :STSKCVILSKSSQPGHDVDYLY 1ym5A 49 :NLSETTFLFKPSDKKYDYKLRI T0301 92 :SIDKPFVDW 1ym5A 71 :FTPRSELPF T0301 104 :CGNLSTGAGAFALHAG 1ym5A 80 :AGHPTIGSCKAFLEFT T0301 125 :RIPEDGICEVRI 1ym5A 96 :KNTTATSLVQEC T0301 140 :NI 1ym5A 108 :KI T0301 143 :KTIIAH 1ym5A 110 :GAVPIT T0301 151 :VSGGQVQET 1ym5A 116 :INEGLISFK T0301 160 :GDFELDGVT 1ym5A 126 :PMADYESIS T0301 176 :LEFLDPS 1ym5A 147 :LKFIKPP T0301 199 :DDLE 1ym5A 154 :ALLH T0301 216 :AGIPTVFVN 1ym5A 158 :TGPEWIVAL T0301 227 :EI 1ym5A 169 :DA T0301 234 :ELREEINGDPQQ 1ym5A 171 :ETCFNANPNFAM T0301 249 :FER 1ym5A 183 :LAH T0301 268 :EAATRQH 1ym5A 186 :QTKQNDH T0301 276 :PKIAFVAPPRDY 1ym5A 193 :VGIILAGPKKEA T0301 297 :AGDID 1ym5A 205 :AIKNS T0301 304 :VRALSM 1ym5A 212 :MRAFAP T0301 310 :GKLHHAMMGTAAVAIGTAA 1ym5A 220 :NVYEDPVCGSGSVALARYL T0301 336 :NLAAGGGERSAVRFG 1ym5A 239 :QEVYKFEKTTDITIS T0301 353 :SGTLRVGAE 1ym5A 261 :NGLMLASIK T0301 363 :SQANGEWTVT 1ym5A 270 :KEADNSTSYY Number of specific fragments extracted= 24 number of extra gaps= 3 total=205 Number of alignments=11 # 1ym5A read from 1ym5A/merged-good-all-a2m # found chain 1ym5A in template set Warning: unaligning (T0301)A225 because of BadResidue code BAD_PEPTIDE in next template residue (1ym5A)E168 Warning: unaligning (T0301)E226 because of BadResidue code BAD_PEPTIDE at template residue (1ym5A)E168 Warning: unaligning (T0301)L302 because of BadResidue code BAD_PEPTIDE in next template residue (1ym5A)E211 Warning: unaligning (T0301)L303 because of BadResidue code BAD_PEPTIDE at template residue (1ym5A)E211 Warning: unaligning (T0301)H351 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ym5A)G255 Warning: unaligning (T0301)P352 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ym5A)G255 T0301 7 :IRIPATYLRGGTSK 1ym5A 3 :LMVPFKQVDVFTEK T0301 21 :GVFFRLEDLPES 1ym5A 23 :VAVINFLEIDEN T0301 34 :RVPGEARDRLFMRV 1ym5A 35 :EVSQEELQAIANWT T0301 67 :STSKCVILSKSSQPGHDVDYLY 1ym5A 49 :NLSETTFLFKPSDKKYDYKLRI T0301 92 :SIDKPFVDWS 1ym5A 71 :FTPRSELPFA T0301 105 :GNLSTGAGAFALHA 1ym5A 81 :GHPTIGSCKAFLEF T0301 124 :ARIPEDGICEVRI 1ym5A 95 :TKNTTATSLVQEC T0301 143 :KTII 1ym5A 110 :GAVP T0301 149 :VPVSGGQVQET 1ym5A 114 :ITINEGLISFK T0301 160 :GDFELD 1ym5A 126 :PMADYE T0301 166 :GVT 1ym5A 146 :GLK T0301 178 :FLDPS 1ym5A 149 :FIKPP T0301 199 :DDLE 1ym5A 154 :ALLH T0301 216 :AGIPTVFVN 1ym5A 158 :TGPEWIVAL T0301 227 :E 1ym5A 169 :D T0301 235 :LREEINGD 1ym5A 170 :AETCFNAN T0301 243 :P 1ym5A 180 :F T0301 247 :ARFER 1ym5A 181 :AMLAH T0301 268 :EAATRQHT 1ym5A 186 :QTKQNDHV T0301 277 :KIAFVAPPRDYRT 1ym5A 194 :GIILAGPKKEAAI T0301 299 :DID 1ym5A 207 :KNS T0301 304 :VRALSMGK 1ym5A 212 :MRAFAPVI T0301 314 :HAMMGTAAVAIGTAA 1ym5A 224 :DPVCGSGSVALARYL T0301 336 :NLAAGGGERSAVRFG 1ym5A 239 :QEVYKFEKTTDITIS T0301 353 :SGTLRVGAE 1ym5A 261 :NGLMLASIK T0301 363 :SQANGEWTVT 1ym5A 270 :KEADNSTSYY Number of specific fragments extracted= 26 number of extra gaps= 3 total=231 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xubA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0301 read from 1xubA/merged-good-all-a2m # 1xubA read from 1xubA/merged-good-all-a2m # found chain 1xubA in training set Warning: unaligning (T0301)R8 because first residue in template chain is (1xubA)M1 Warning: unaligning (T0301)K70 because of BadResidue code BAD_PEPTIDE in next template residue (1xubA)S46 Warning: unaligning (T0301)C71 because of BadResidue code BAD_PEPTIDE at template residue (1xubA)S46 Warning: unaligning (T0301)S92 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1xubA)T64 Warning: unaligning (T0301)I93 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1xubA)T64 Warning: unaligning (T0301)A147 because of BadResidue code BAD_PEPTIDE in next template residue (1xubA)E104 Warning: unaligning (T0301)H148 because of BadResidue code BAD_PEPTIDE at template residue (1xubA)E104 Warning: unaligning (T0301)S353 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xubA)R244 Warning: unaligning (T0301)G354 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xubA)R244 T0301 9 :IPATYLRG 1xubA 2 :HNYVIIDA T0301 17 :GTSKGVFFRLEDLP 1xubA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1xubA 31 :PAQMQRIAREM T0301 67 :STS 1xubA 42 :NLS T0301 72 :VILSKSSQPGH 1xubA 47 :TFVLKPRNGGD T0301 87 :LYGQV 1xubA 58 :ALIRI T0301 94 :DKPFVDW 1xubA 65 :PVNELPF T0301 104 :CGNLSTGAGAFALHAG 1xubA 72 :AGAPLLGTAIALGAHT T0301 128 :EDGICEVRI 1xubA 88 :DNHRLYLET T0301 141 :IGKTII 1xubA 97 :QMGTIA T0301 149 :VPVSGGQVQE 1xubA 105 :LERQNGSVIA T0301 162 :FELDGVTFPAAEI 1xubA 115 :ASMDQPIPTWTAL T0301 185 :GE 1xubA 128 :GR T0301 201 :LEVPGV 1xubA 137 :LGISDS T0301 208 :TFKATMINAGIPTVFVNAEEI 1xubA 143 :TFPIEIYHNGPRHVFVGLPSI T0301 234 :ELREE 1xubA 164 :DALSA T0301 263 :IKTPEEAATRQHTPKIAFVAPP 1xubA 169 :LHPDHRALSNFHDMAINCFAGA T0301 291 :SG 1xubA 191 :GR T0301 301 :DLLVRALSM 1xubA 193 :RWRSRMFSP T0301 310 :GKLHHAMMGTAAVAIGTAAAIPGTL 1xubA 204 :GVVEDAATGSAAGPLAIHLARHGQI T0301 342 :GERSAVRFGHP 1xubA 229 :EFGQPVEILQG T0301 355 :TLRVGAEASQANGEWT 1xubA 245 :PSLMFAKAEGRAEQLT T0301 373 :K 1xubA 261 :R Number of specific fragments extracted= 23 number of extra gaps= 4 total=254 Number of alignments=13 # 1xubA read from 1xubA/merged-good-all-a2m # found chain 1xubA in training set Warning: unaligning (T0301)R8 because first residue in template chain is (1xubA)M1 Warning: unaligning (T0301)K70 because of BadResidue code BAD_PEPTIDE in next template residue (1xubA)S46 Warning: unaligning (T0301)C71 because of BadResidue code BAD_PEPTIDE at template residue (1xubA)S46 Warning: unaligning (T0301)S92 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1xubA)T64 Warning: unaligning (T0301)I93 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1xubA)T64 Warning: unaligning (T0301)A147 because of BadResidue code BAD_PEPTIDE in next template residue (1xubA)E104 Warning: unaligning (T0301)H148 because of BadResidue code BAD_PEPTIDE at template residue (1xubA)E104 Warning: unaligning (T0301)S353 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xubA)R244 Warning: unaligning (T0301)G354 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xubA)R244 T0301 9 :IPATYLRG 1xubA 2 :HNYVIIDA T0301 17 :GTSKGVFFRLEDLP 1xubA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1xubA 31 :PAQMQRIAREM T0301 67 :STS 1xubA 42 :NLS T0301 72 :VILSKSSQPGHD 1xubA 47 :TFVLKPRNGGDA T0301 88 :YGQV 1xubA 59 :LIRI T0301 94 :DKPFVDW 1xubA 65 :PVNELPF T0301 104 :CGNLSTGAGAFALHAG 1xubA 72 :AGAPLLGTAIALGAHT T0301 128 :EDGICEVRI 1xubA 88 :DNHRLYLET T0301 141 :IGKTII 1xubA 97 :QMGTIA T0301 149 :VPVSGGQVQE 1xubA 105 :LERQNGSVIA T0301 162 :FELDGVTFPAAEI 1xubA 115 :ASMDQPIPTWTAL T0301 185 :GE 1xubA 128 :GR T0301 205 :GVG 1xubA 138 :GIS T0301 208 :TFKATMINAGIPTVFVNAEEI 1xubA 143 :TFPIEIYHNGPRHVFVGLPSI T0301 247 :ARFER 1xubA 164 :DALSA T0301 262 :LIKTPEEAATRQHT 1xubA 169 :LHPDHRALSNFHDM T0301 277 :KIAFVAP 1xubA 183 :AINCFAG T0301 290 :ASG 1xubA 190 :AGR T0301 301 :DLLVRALSM 1xubA 193 :RWRSRMFSP T0301 310 :GKLHHAMMGTAAVAIGTAAAIPGTL 1xubA 204 :GVVEDAATGSAAGPLAIHLARHGQI T0301 342 :GERSAVRFGHP 1xubA 229 :EFGQPVEILQG T0301 355 :TLRVGAEASQANGEWT 1xubA 245 :PSLMFAKAEGRAEQLT Number of specific fragments extracted= 23 number of extra gaps= 4 total=277 Number of alignments=14 # 1xubA read from 1xubA/merged-good-all-a2m # found chain 1xubA in training set Warning: unaligning (T0301)R8 because first residue in template chain is (1xubA)M1 Warning: unaligning (T0301)K70 because of BadResidue code BAD_PEPTIDE in next template residue (1xubA)S46 Warning: unaligning (T0301)C71 because of BadResidue code BAD_PEPTIDE at template residue (1xubA)S46 Warning: unaligning (T0301)S92 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1xubA)T64 Warning: unaligning (T0301)I93 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1xubA)T64 Warning: unaligning (T0301)A147 because of BadResidue code BAD_PEPTIDE in next template residue (1xubA)E104 Warning: unaligning (T0301)H148 because of BadResidue code BAD_PEPTIDE at template residue (1xubA)E104 Warning: unaligning (T0301)S353 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xubA)R244 Warning: unaligning (T0301)G354 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xubA)R244 T0301 9 :IPATYLRG 1xubA 2 :HNYVIIDA T0301 17 :GTSKGVFFRLEDLP 1xubA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1xubA 31 :PAQMQRIAREM T0301 67 :STS 1xubA 42 :NLS T0301 72 :VILSKSSQPGHD 1xubA 47 :TFVLKPRNGGDA T0301 88 :YGQV 1xubA 59 :LIRI T0301 94 :DKPFVDWS 1xubA 65 :PVNELPFA T0301 105 :GNLSTGAGA 1xubA 73 :GAPLLGTAI T0301 115 :ALHAGL 1xubA 82 :ALGAHT T0301 128 :EDGICEVRI 1xubA 88 :DNHRLYLET T0301 141 :IGKTII 1xubA 97 :QMGTIA T0301 149 :VPVSGGQVQE 1xubA 105 :LERQNGSVIA T0301 162 :FELDGVTFPAAEI 1xubA 115 :ASMDQPIPTWTAL T0301 205 :GVGTFKATMINAGIPTVFVNAEEI 1xubA 140 :SDSTFPIEIYHNGPRHVFVGLPSI T0301 237 :E 1xubA 164 :D T0301 248 :RFER 1xubA 165 :ALSA T0301 262 :LIKTPEEAATRQHTPKIAFVA 1xubA 169 :LHPDHRALSNFHDMAINCFAG T0301 298 :GDIDLLVRALSM 1xubA 190 :AGRRWRSRMFSP T0301 310 :GKLHHAMMGTAAVAIGTAAAIPGTL 1xubA 204 :GVVEDAATGSAAGPLAIHLARHGQI T0301 342 :GERSAVRFGHP 1xubA 229 :EFGQPVEILQG T0301 355 :TLRVGAEASQANGEWTV 1xubA 245 :PSLMFAKAEGRAEQLTR Number of specific fragments extracted= 21 number of extra gaps= 4 total=298 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u1wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u1wA expands to /projects/compbio/data/pdb/1u1w.pdb.gz 1u1wA:Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 99, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 101, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 103, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 105, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 107, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 109, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 315, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 616, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 618, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 620, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 622, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 624, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 626, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 628, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 630, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 632, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 634, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 636, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 638, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 640, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 642, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 644, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 646, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 677, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 679, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 681, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 683, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 685, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 687, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 689, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 691, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 729, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 733, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 764, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 766, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 768, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 770, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 772, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 774, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 776, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 778, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 816, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 818, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 820, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 822, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 824, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 826, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 828, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 830, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 832, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 935, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 937, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 939, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 941, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 943, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 945, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1046, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1048, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1050, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1052, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1054, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1056, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1058, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1455, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1457, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1459, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1461, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1463, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1465, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1467, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1469, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1471, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1473, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1475, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1477, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1479, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1481, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1525, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1527, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1529, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1531, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1533, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1535, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1537, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1539, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1631, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1633, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1635, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1637, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1639, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1641, because occupancy 0.300 <= existing 0.700 in 1u1wA # T0301 read from 1u1wA/merged-good-all-a2m # 1u1wA read from 1u1wA/merged-good-all-a2m # adding 1u1wA to template set # found chain 1u1wA in template set Warning: unaligning (T0301)P4 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1u1wA)V13 Warning: unaligning (T0301)G205 because of BadResidue code BAD_PEPTIDE in next template residue (1u1wA)S142 Warning: unaligning (T0301)V206 because of BadResidue code BAD_PEPTIDE at template residue (1u1wA)S142 T0301 5 :PQIRIPA 1u1wA 14 :PLEGNPV T0301 21 :GVFFRLEDLP 1u1wA 21 :AVFFDADDLP T0301 37 :GEARDRLFMRV 1u1wA 31 :PAQMQRIAREM T0301 67 :STSKCVILSKSSQPGH 1u1wA 42 :NLSESTFVLKPRNGGD T0301 87 :LYGQVSIDKPFVDW 1u1wA 58 :ALIRIFTPVNELPF T0301 104 :CGNLSTGAGAFALHA 1u1wA 72 :AGHPLLGTAIALGAH T0301 127 :PEDGICEVRI 1u1wA 87 :TDNHRLYLET T0301 141 :IGKTIIAHVPVSGGQVQE 1u1wA 97 :QMGTIAFELERQNGSVIA T0301 162 :FELDGVTFPAAEI 1u1wA 115 :ASMDQPIPTWTAL T0301 185 :GE 1u1wA 128 :GR T0301 201 :LEVP 1u1wA 137 :LGIS T0301 208 :TFKATMINAGIPTVFVNAEEI 1u1wA 143 :TFPIEIYHNGPRHVFVGLPSI T0301 234 :ELREEINGDPQQL 1u1wA 164 :DALSALHPDHRAL T0301 260 :MGL 1u1wA 177 :SNF T0301 274 :HTPKIAFVAPP 1u1wA 180 :HDMAINCFAGA T0301 291 :SG 1u1wA 191 :GR T0301 301 :DLLVRALSMGKL 1u1wA 193 :RWRSRMFSPAYG T0301 315 :AMMGTAAVAIGTAAAIPGTL 1u1wA 209 :AATGSAAGPLAIHLARHGQI T0301 340 :GGGERSAVRFGHPSG 1u1wA 229 :EFGQPVEILQGVEIG T0301 355 :TLRVGAEASQANGEWT 1u1wA 245 :PSLMFAKAEGRAEQLT T0301 373 :K 1u1wA 261 :R Number of specific fragments extracted= 21 number of extra gaps= 2 total=319 Number of alignments=16 # 1u1wA read from 1u1wA/merged-good-all-a2m # found chain 1u1wA in template set T0301 7 :I 1u1wA 16 :E T0301 17 :GTSKGVFFRLEDLP 1u1wA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1u1wA 31 :PAQMQRIAREM T0301 67 :STSKCVILSKSSQPGH 1u1wA 42 :NLSESTFVLKPRNGGD T0301 87 :LYGQVSIDKPFVDW 1u1wA 58 :ALIRIFTPVNELPF T0301 104 :CGNLSTGAGAFALHA 1u1wA 72 :AGHPLLGTAIALGAH T0301 127 :PEDGICEVRI 1u1wA 87 :TDNHRLYLET T0301 141 :IGKTIIAHVPVSGGQVQE 1u1wA 97 :QMGTIAFELERQNGSVIA T0301 162 :FELDGVTFPAAEI 1u1wA 115 :ASMDQPIPTWTAL T0301 204 :P 1u1wA 128 :G T0301 205 :GVG 1u1wA 138 :GIS T0301 208 :TFKATMINAGIPTVFVNAEE 1u1wA 143 :TFPIEIYHNGPRHVFVGLPS T0301 236 :R 1u1wA 163 :I T0301 247 :ARFER 1u1wA 164 :DALSA T0301 262 :LIKTPEEAATRQHTPKIAF 1u1wA 169 :LHPDHRALSNFHDMAINCF T0301 282 :AP 1u1wA 188 :AG T0301 290 :ASG 1u1wA 190 :AGR T0301 301 :DLLVRALSMGKL 1u1wA 193 :RWRSRMFSPAYG T0301 313 :HHAMMGTAAVAIGTAAAIPGTL 1u1wA 207 :EDAATGSAAGPLAIHLARHGQI T0301 342 :GERSAVRFGHP 1u1wA 229 :EFGQPVEILQG T0301 353 :SG 1u1wA 242 :IG T0301 355 :TLRVGAEASQANGEWT 1u1wA 245 :PSLMFAKAEGRAEQLT Number of specific fragments extracted= 22 number of extra gaps= 0 total=341 Number of alignments=17 # 1u1wA read from 1u1wA/merged-good-all-a2m # found chain 1u1wA in template set Warning: unaligning (T0301)R8 because first residue in template chain is (1u1wA)M1 Warning: unaligning (T0301)S19 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1u1wA)V13 Warning: unaligning (T0301)K20 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1u1wA)V13 Warning: unaligning (T0301)V206 because of BadResidue code BAD_PEPTIDE in next template residue (1u1wA)S142 Warning: unaligning (T0301)G207 because of BadResidue code BAD_PEPTIDE at template residue (1u1wA)S142 T0301 9 :IPATYLRGGT 1u1wA 2 :HNYVIIDAFA T0301 21 :GVFFRLEDLP 1u1wA 21 :AVFFDADDLP T0301 37 :GEARDRLFMRV 1u1wA 31 :PAQMQRIAREM T0301 67 :STSKCVILSKSSQPGHD 1u1wA 42 :NLSESTFVLKPRNGGDA T0301 88 :YGQVSIDKPFVDWS 1u1wA 59 :LIRIFTPVNELPFA T0301 105 :GNLSTGAGAFALHA 1u1wA 73 :GHPLLGTAIALGAH T0301 127 :PEDGICEVRI 1u1wA 87 :TDNHRLYLET T0301 141 :IGKTIIAHVPVSGGQVQE 1u1wA 97 :QMGTIAFELERQNGSVIA T0301 162 :FELDGVTFPAAEI 1u1wA 115 :ASMDQPIPTWTAL T0301 204 :P 1u1wA 128 :G T0301 205 :G 1u1wA 140 :S T0301 208 :TFKATMINAGIPTVFVNAEE 1u1wA 143 :TFPIEIYHNGPRHVFVGLPS T0301 236 :REE 1u1wA 163 :IDA T0301 249 :FER 1u1wA 166 :LSA T0301 262 :LIKTPEEAATRQHTPKIAFVA 1u1wA 169 :LHPDHRALSNFHDMAINCFAG T0301 298 :GDIDLLVRALSMGKL 1u1wA 190 :AGRRWRSRMFSPAYG T0301 315 :AMMGTAAVAIGTAAAIPGTL 1u1wA 209 :AATGSAAGPLAIHLARHGQI T0301 342 :GERSAVRFGHP 1u1wA 229 :EFGQPVEILQG T0301 353 :SGTLRVGAEASQANGEWTV 1u1wA 243 :GRPSLMFAKAEGRAEQLTR Number of specific fragments extracted= 19 number of extra gaps= 2 total=360 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u0kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0301 read from 1u0kA/merged-good-all-a2m # 1u0kA read from 1u0kA/merged-good-all-a2m # found chain 1u0kA in training set Warning: unaligning (T0301)S92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u0kA)T65 Warning: unaligning (T0301)I93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u0kA)T65 T0301 4 :PPQIRIPATYLRG 1u0kA 14 :RPLTGNGLAVFDD T0301 26 :LE 1u0kA 27 :AS T0301 34 :RVPGEARDRLFMRV 1u0kA 29 :ALDDAAMQAWTREL T0301 67 :STSKCVILSKSSQPGH 1u0kA 43 :RQFESIFLLPGDDPRA T0301 87 :LYGQV 1u0kA 59 :FRARI T0301 94 :DKPFVDWSGN 1u0kA 66 :LEEELPFAGH T0301 106 :NLSTGAGAFALHAGL 1u0kA 76 :PLLGAAALLHHLRGG T0301 123 :PARI 1u0kA 91 :DNEQ T0301 128 :EDGICEVRIWQANIGKTIIAHV 1u0kA 101 :ASKSVALRSVRAGSGFYAEMDQ T0301 160 :GD 1u0kA 123 :GR T0301 176 :LEFLDPSDDG 1u0kA 125 :AEFGATPDAG T0301 200 :DLEVPGVGTFKATMINAGIPTVFVNAE 1u0kA 144 :SLSANDLSGHPPRVVSTGLPYLLLPVT T0301 236 :REEING 1u0kA 171 :AEALGR T0301 243 :PQQLARF 1u0kA 184 :QEALDKL T0301 261 :G 1u0kA 191 :G T0301 275 :TPKIAFVA 1u0kA 192 :AAFVYLLD T0301 290 :ASG 1u0kA 200 :VDG T0301 302 :LLVRALSMGKLHHAMMGTAAVAIGTAAAI 1u0kA 203 :REGRTWDNLGLVEDVATGSAAGPVAAYLV T0301 331 :PGT 1u0kA 233 :YGL T0301 339 :AGGGER 1u0kA 236 :AARGEP T0301 347 :VRFGH 1u0kA 256 :LDVQV T0301 352 :PSGTLRVGAEASQ 1u0kA 262 :TDGSVRVGGHVQL Number of specific fragments extracted= 22 number of extra gaps= 1 total=382 Number of alignments=19 # 1u0kA read from 1u0kA/merged-good-all-a2m # found chain 1u0kA in training set Warning: unaligning (T0301)S92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u0kA)T65 Warning: unaligning (T0301)I93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u0kA)T65 T0301 7 :IRIPATYLR 1u0kA 17 :TGNGLAVFD T0301 25 :RLE 1u0kA 26 :DAS T0301 34 :RVPGEARDRLFMRV 1u0kA 29 :ALDDAAMQAWTREL T0301 67 :STSKCVILSKSSQPGH 1u0kA 43 :RQFESIFLLPGDDPRA T0301 87 :LYGQV 1u0kA 59 :FRARI T0301 94 :DKPFVDWSG 1u0kA 66 :LEEELPFAG T0301 105 :GNLSTGAGAFALHAG 1u0kA 75 :HPLLGAAALLHHLRG T0301 122 :D 1u0kA 90 :G T0301 127 :PEDGIC 1u0kA 91 :DNEQHW T0301 133 :EVRIWQANIGKTIIAHVPV 1u0kA 104 :SVALRSVRAGSGFYAEMDQ T0301 160 :G 1u0kA 123 :G T0301 175 :VLEFLDPSDDG 1u0kA 124 :RAEFGATPDAG T0301 200 :DLEVPGVGTFKATMINAGIPTVFVNAE 1u0kA 144 :SLSANDLSGHPPRVVSTGLPYLLLPVT T0301 236 :REEINGD 1u0kA 171 :AEALGRA T0301 261 :GLIKTPEEAATRQHTPKIAFVA 1u0kA 178 :RQVNDLQEALDKLGAAFVYLLD T0301 290 :ASG 1u0kA 200 :VDG T0301 302 :LLVRALSMGKLHHAMMGTAAVAIGTAAAIPG 1u0kA 203 :REGRTWDNLGLVEDVATGSAAGPVAAYLVEY T0301 333 :TLVNLAAGGGERSAVRFGH 1u0kA 242 :FVLHQGRFLERPSRLDVQV T0301 352 :PSGTLRVGAEASQ 1u0kA 262 :TDGSVRVGGHVQL Number of specific fragments extracted= 19 number of extra gaps= 1 total=401 Number of alignments=20 # 1u0kA read from 1u0kA/merged-good-all-a2m # found chain 1u0kA in training set Warning: unaligning (T0301)S92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u0kA)T65 Warning: unaligning (T0301)I93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u0kA)T65 T0301 7 :IRIPATYLR 1u0kA 17 :TGNGLAVFD T0301 31 :ESCRVPGEARDRLFMRV 1u0kA 26 :DASALDDAAMQAWTREL T0301 56 :A 1u0kA 43 :R T0301 68 :TSKCVILSKSSQPGH 1u0kA 44 :QFESIFLLPGDDPRA T0301 87 :LYGQV 1u0kA 59 :FRARI T0301 94 :DKPFVDWSGN 1u0kA 66 :LEEELPFAGH T0301 106 :NLSTGAGAFALHAGL 1u0kA 76 :PLLGAAALLHHLRGG T0301 127 :PEDGICE 1u0kA 91 :DNEQHWT T0301 134 :VRIWQANIGKTIIAHVPV 1u0kA 105 :VALRSVRAGSGFYAEMDQ T0301 160 :GDFE 1u0kA 123 :GRAE T0301 178 :FLDPSDDG 1u0kA 127 :FGATPDAG T0301 186 :EDGGAI 1u0kA 145 :LSANDL T0301 194 :TGNLVDDLE 1u0kA 151 :SGHPPRVVS T0301 216 :AGIPTVFVNAE 1u0kA 160 :TGLPYLLLPVT T0301 236 :REEINGD 1u0kA 171 :AEALGRA T0301 261 :GLIKTPEEAATRQHTPKIAFVAP 1u0kA 178 :RQVNDLQEALDKLGAAFVYLLDV T0301 298 :GD 1u0kA 201 :DG T0301 302 :LLVRALSMGKLHHAMM 1u0kA 203 :REGRTWDNLGLVEDVA T0301 318 :GTAAVAIGTAAAIPG 1u0kA 220 :GSAAGPVAAYLVEYG T0301 333 :TLVNLAAGGGERSAVRFGH 1u0kA 242 :FVLHQGRFLERPSRLDVQV T0301 352 :PSGTLRVGAEASQ 1u0kA 262 :TDGSVRVGGHVQL Number of specific fragments extracted= 21 number of extra gaps= 1 total=422 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sr8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sr8A expands to /projects/compbio/data/pdb/1sr8.pdb.gz 1sr8A:# T0301 read from 1sr8A/merged-good-all-a2m # 1sr8A read from 1sr8A/merged-good-all-a2m # adding 1sr8A to template set # found chain 1sr8A in template set T0301 29 :LPESCRVPGEARDRL 1sr8A 11 :YPEKWIKDRDAEKKV T0301 55 :A 1sr8A 28 :G T0301 89 :GQVSIDKPFVDWSGNCGNLSTGAGAFALHAG 1sr8A 29 :LYILTEDGYLRRGITTGTTASAAAVAAIASL T0301 128 :EDGICEVRI 1sr8A 60 :KEKVEKVKV T0301 139 :ANIGKTIIAHVPVSGGQVQET 1sr8A 70 :TPAGVDVEVEVEAEKGFARVR T0301 178 :FLDPS 1sr8A 91 :KFSGD T0301 189 :GAIFPTGNLVDDLEVPGVGTFKA 1sr8A 96 :HEFDVTNGIIFEAEVCETSGIFF T0301 215 :NAG 1sr8A 121 :GVG T0301 230 :YRGTEL 1sr8A 125 :KAGEKA T0301 242 :DPQQLARFERIRVAGALRMGL 1sr8A 132 :SRSAKLQILENFIKASREFNF T0301 291 :SG 1sr8A 153 :SG T0301 301 :DLLVR 1sr8A 155 :GVRIS T0301 308 :SMG 1sr8A 160 :VPD T0301 315 :AMM 1sr8A 163 :GEE T0301 326 :TAAAIP 1sr8A 166 :VAKKTG T0301 338 :AAGGGERSAVRFGHPSGTL 1sr8A 172 :NEKVGIKGGISILGTTGFV T0301 372 :TKAIMSRSARILM 1sr8A 193 :WCKKLVETKLKIA Number of specific fragments extracted= 17 number of extra gaps= 0 total=439 Number of alignments=22 # 1sr8A read from 1sr8A/merged-good-all-a2m # found chain 1sr8A in template set T0301 29 :LPESCRVPGEARDRL 1sr8A 11 :YPEKWIKDRDAEKKV T0301 54 :YA 1sr8A 27 :SG T0301 89 :GQVSIDKPFVDWSGNCGNLSTGAGAFALHA 1sr8A 29 :LYILTEDGYLRRGITTGTTASAAAVAAIAS T0301 123 :PA 1sr8A 59 :LK T0301 129 :DGICEVRI 1sr8A 61 :EKVEKVKV T0301 139 :ANIGKTIIAHVPVSGGQV 1sr8A 70 :TPAGVDVEVEVEAEKGFA T0301 175 :VLEFLD 1sr8A 88 :RVRKFS T0301 185 :GE 1sr8A 94 :GD T0301 189 :GAIFPTGNLVDDLEVPGVGTFKA 1sr8A 96 :HEFDVTNGIIFEAEVCETSGIFF T0301 215 :N 1sr8A 121 :G T0301 228 :IG 1sr8A 122 :VG T0301 230 :YRGTEL 1sr8A 125 :KAGEKA T0301 242 :DPQQLARFERIRVAGALRMGLIK 1sr8A 132 :SRSAKLQILENFIKASREFNFSG T0301 303 :LVRALSMG 1sr8A 155 :GVRISVPD T0301 326 :TAAAIP 1sr8A 166 :VAKKTG T0301 338 :AAGGGERSAVRFGHPSGTL 1sr8A 172 :NEKVGIKGGISILGTTGFV T0301 372 :TKAIMSRSARILM 1sr8A 193 :WCKKLVETKLKIA Number of specific fragments extracted= 17 number of extra gaps= 0 total=456 Number of alignments=23 # 1sr8A read from 1sr8A/merged-good-all-a2m # found chain 1sr8A in template set T0301 29 :LPESCRVPGEARDRLF 1sr8A 11 :YPEKWIKDRDAEKKVR T0301 54 :YA 1sr8A 27 :SG T0301 89 :GQVSIDKPFVDWSGNCGNLSTGAGAFALHAG 1sr8A 29 :LYILTEDGYLRRGITTGTTASAAAVAAIASL T0301 128 :EDGICEVRI 1sr8A 60 :KEKVEKVKV T0301 139 :ANIGKTIIAHVPVSGGQVQET 1sr8A 70 :TPAGVDVEVEVEAEKGFARVR T0301 178 :F 1sr8A 91 :K T0301 185 :GEDGGAIFPTGNLVDDLEVPGVGTFKA 1sr8A 92 :FSGDHEFDVTNGIIFEAEVCETSGIFF T0301 215 :NAG 1sr8A 121 :GVG T0301 230 :YRGTEL 1sr8A 125 :KAGEKA T0301 242 :DPQQLARFERIRVAGALRMGLIK 1sr8A 132 :SRSAKLQILENFIKASREFNFSG T0301 303 :LVRALSMG 1sr8A 155 :GVRISVPD T0301 335 :VNLAA 1sr8A 163 :GEEVA T0301 340 :GGGERSAVRFGHPSGTL 1sr8A 174 :KVGIKGGISILGTTGFV T0301 372 :TKAIMSRSARIL 1sr8A 193 :WCKKLVETKLKI Number of specific fragments extracted= 14 number of extra gaps= 0 total=470 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mr1A/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/T0301/1mr1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0301/1mr1A/merged-good-all-a2m.gz for input Trying 1mr1A/merged-good-all-a2m Error: Couldn't open file 1mr1A/merged-good-all-a2m or 1mr1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tm0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tm0A expands to /projects/compbio/data/pdb/1tm0.pdb.gz 1tm0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0301 read from 1tm0A/merged-good-all-a2m # 1tm0A read from 1tm0A/merged-good-all-a2m # adding 1tm0A to template set # found chain 1tm0A in template set Warning: unaligning (T0301)H3 because first residue in template chain is (1tm0A)M1 Warning: unaligning (T0301)G229 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tm0A)E187 Warning: unaligning (T0301)T233 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)E187 Warning: unaligning (T0301)L262 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)F211 Warning: unaligning (T0301)M316 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)P254 Warning: unaligning (T0301)P352 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tm0A)T286 Warning: unaligning (T0301)T355 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)T286 T0301 4 :PPQIRIPATYLRGGTSKGVFFR 1tm0A 2 :RSTKVIHIVGCHAEGEVGDVIV T0301 27 :EDL 1tm0A 24 :GGV T0301 33 :CRVPGEARDRLFMRVI 1tm0A 27 :APPPGETVWEQSRFIA T0301 51 :PDPY 1tm0A 53 :NKPR T0301 65 :TSSTSKCVILSKSSQPGHDVDYLYGQ 1tm0A 57 :GGVFRHVNLLVPPKDPRAQMGFIIME T0301 97 :FVDWSGNCGNLSTGAGAFALHAGLVDP 1tm0A 83 :PADTPPMSGSNSICVSTVLLDSGIIAM T0301 128 :EDGICEVRIW 1tm0A 110 :QEPVTHMVLE T0301 140 :NIGKTIIAHVPVSGGQVQE 1tm0A 120 :APGGIIEVEAECRNGKAER T0301 174 :IVLEFLDPS 1tm0A 139 :ISVRNVPSF T0301 194 :TGNLVDDLEVPGVGTFKATMINAGIPTVFVNAEEI 1tm0A 148 :ADRLDAPLDVTGLGTIMVDTAYGGDSFVIVDAAQI T0301 242 :DPQQLARFERIRVA 1tm0A 188 :PGQARELAEIGVKI T0301 263 :I 1tm0A 212 :R T0301 267 :EEAATRQHTPKIAFVAPPRD 1tm0A 213 :HPERDWRHISFCQITEPVTR T0301 291 :SG 1tm0A 233 :EG T0301 301 :DLLVR 1tm0A 235 :DVLTG T0301 317 :MGTAAVAIGTAAAIPGT 1tm0A 255 :TGTGCSARMAVLHAKGQ T0301 341 :GGERSAVRFGH 1tm0A 272 :MKAGERFIGKS T0301 356 :LRVGA 1tm0A 288 :FHCRL T0301 361 :EASQANGEWTVT 1tm0A 294 :KVLELGGKPAIS Number of specific fragments extracted= 19 number of extra gaps= 0 total=489 Number of alignments=25 # 1tm0A read from 1tm0A/merged-good-all-a2m # found chain 1tm0A in template set Warning: unaligning (T0301)H3 because first residue in template chain is (1tm0A)M1 Warning: unaligning (T0301)G229 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tm0A)E187 Warning: unaligning (T0301)T233 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)E187 Warning: unaligning (T0301)L262 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)F211 Warning: unaligning (T0301)M316 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)P254 Warning: unaligning (T0301)P352 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tm0A)T286 Warning: unaligning (T0301)T355 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)T286 T0301 4 :PPQIRIPATYLRGGTSKGVFFRLEDL 1tm0A 2 :RSTKVIHIVGCHAEGEVGDVIVGGVA T0301 34 :RVPGEARDRLFMRVI 1tm0A 28 :PPPGETVWEQSRFIA T0301 51 :PDPY 1tm0A 53 :NKPR T0301 65 :TSSTSKCVILSKSSQPGHDVDYLYGQ 1tm0A 57 :GGVFRHVNLLVPPKDPRAQMGFIIME T0301 97 :FVDWSGNCGNLSTGAGAFALHAGLVDPA 1tm0A 83 :PADTPPMSGSNSICVSTVLLDSGIIAMQ T0301 129 :DGICEVRIW 1tm0A 111 :EPVTHMVLE T0301 140 :NIGKTIIAHVPVSGGQVQE 1tm0A 120 :APGGIIEVEAECRNGKAER T0301 174 :IVLEFLDPS 1tm0A 139 :ISVRNVPSF T0301 194 :TGNLVDDLEVPGVGTFKATMINAGIPTVFVNAEEI 1tm0A 148 :ADRLDAPLDVTGLGTIMVDTAYGGDSFVIVDAAQI T0301 242 :DPQQLARFER 1tm0A 188 :PGQARELAEI T0301 252 :IRVA 1tm0A 199 :VKIT T0301 265 :TPEEA 1tm0A 212 :RHPER T0301 271 :TRQHTPKIAFVAPPRD 1tm0A 217 :DWRHISFCQITEPVTR T0301 291 :SGK 1tm0A 233 :EGD T0301 302 :LLVR 1tm0A 236 :VLTG T0301 317 :MGTAAVAIGTAAAIPGT 1tm0A 255 :TGTGCSARMAVLHAKGQ T0301 341 :GGERSAVRFGH 1tm0A 272 :MKAGERFIGKS T0301 356 :LRVGA 1tm0A 288 :FHCRL T0301 361 :EASQANGEWTVT 1tm0A 294 :KVLELGGKPAIS Number of specific fragments extracted= 19 number of extra gaps= 0 total=508 Number of alignments=26 # 1tm0A read from 1tm0A/merged-good-all-a2m # found chain 1tm0A in template set Warning: unaligning (T0301)H3 because first residue in template chain is (1tm0A)M1 Warning: unaligning (T0301)G229 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tm0A)E187 Warning: unaligning (T0301)T233 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)E187 Warning: unaligning (T0301)L262 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)F211 Warning: unaligning (T0301)M316 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)P254 Warning: unaligning (T0301)P352 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tm0A)T286 Warning: unaligning (T0301)T355 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)T286 T0301 4 :PPQIRIPATYLRGGTSKGVFFRLEDLPESCRVPGEARDRL 1tm0A 2 :RSTKVIHIVGCHAEGEVGDVIVGGVAPPPGETVWEQSRFI T0301 44 :FMRVIGSPDP 1tm0A 48 :RNFVLNKPRG T0301 66 :SSTSKCVILSKSSQPGHDVDYLYGQ 1tm0A 58 :GVFRHVNLLVPPKDPRAQMGFIIME T0301 97 :FVDWSGNCGNLSTGAGAFALHAGLVDP 1tm0A 83 :PADTPPMSGSNSICVSTVLLDSGIIAM T0301 128 :EDGICEVRIW 1tm0A 110 :QEPVTHMVLE T0301 140 :NIGKTIIAHVPVSGGQVQ 1tm0A 120 :APGGIIEVEAECRNGKAE T0301 173 :EIVLEFLDPS 1tm0A 138 :RISVRNVPSF T0301 194 :TGNLVDDLEVPGVGTFKATMINAGIPTVFVNAEEI 1tm0A 148 :ADRLDAPLDVTGLGTIMVDTAYGGDSFVIVDAAQI T0301 234 :E 1tm0A 188 :P T0301 243 :PQQLARFERIRVA 1tm0A 189 :GQARELAEIGVKI T0301 263 :I 1tm0A 212 :R T0301 272 :RQHTPKIAFVAPPRDYRT 1tm0A 218 :WRHISFCQITEPVTREGD T0301 301 :DLLV 1tm0A 236 :VLTG T0301 317 :MGTAAVAIGTAAAIPG 1tm0A 255 :TGTGCSARMAVLHAKG T0301 340 :GGGERSAVRFGH 1tm0A 271 :QMKAGERFIGKS T0301 356 :LRVGA 1tm0A 288 :FHCRL T0301 361 :EASQANGEWTVT 1tm0A 294 :KVLELGGKPAIS Number of specific fragments extracted= 17 number of extra gaps= 0 total=525 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gqzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0301 read from 1gqzA/merged-good-all-a2m # 1gqzA read from 1gqzA/merged-good-all-a2m # found chain 1gqzA in training set T0301 10 :PATYLRGGTSKGVFFR 1gqzA 2 :QFSKMHGLGNDFVVVD T0301 28 :DLPESCRVPGEARDRLF 1gqzA 18 :GVTQNVFFTPETIRRLA T0301 51 :PDPYAAHI 1gqzA 35 :NRHCGIGF T0301 69 :SKCVILSKSSQPGHDVDYLYGQ 1gqzA 43 :DQLLIVEAPYDPELDFHYRIFN T0301 93 :IDKPFVD 1gqzA 65 :ADGSEVS T0301 103 :NCGNLSTGAGAFALHAGLVDPA 1gqzA 72 :QCGNGARCFARFVTLKGLTNKK T0301 131 :ICEVR 1gqzA 94 :DISVS T0301 140 :NIGKTIIAH 1gqzA 99 :TQKGNMVLT T0301 168 :TFPAAEIVLEFLDPSDDGEDGGAIFPTGNLVDDLEV 1gqzA 108 :VKDDNQIRVNMGEPIWEPAKIPFTANKFEKNYILRT T0301 205 :GVGTFKATMINAGIPTVFVNAEEIGYRG 1gqzA 144 :DIQTVLCGAVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 1gqzA 173 :EQLGPLLE T0301 261 :GL 1gqzA 181 :SH T0301 268 :EAA 1gqzA 183 :ERF T0301 273 :QHTPKIAFV 1gqzA 186 :PERVNAGFM T0301 293 :KLVAAG 1gqzA 195 :QIINKE T0301 301 :DLLVRALSMGK 1gqzA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAAAI 1gqzA 213 :ETQACGSGACAAVAVGIMQ T0301 341 :GGERSAVRFGHPSGTLRV 1gqzA 232 :GLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 1gqzA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 19 number of extra gaps= 0 total=544 Number of alignments=28 # 1gqzA read from 1gqzA/merged-good-all-a2m # found chain 1gqzA in training set T0301 10 :PATYLRGGTSKGVFFR 1gqzA 2 :QFSKMHGLGNDFVVVD T0301 28 :DLPESCRVPGEARDRLF 1gqzA 18 :GVTQNVFFTPETIRRLA T0301 51 :PDPYAAHI 1gqzA 35 :NRHCGIGF T0301 69 :SKCVILSKSSQPGHDVDYLYGQ 1gqzA 43 :DQLLIVEAPYDPELDFHYRIFN T0301 93 :IDKPFV 1gqzA 65 :ADGSEV T0301 102 :GNCGNLSTGAGAFALHAGLVDPA 1gqzA 71 :SQCGNGARCFARFVTLKGLTNKK T0301 131 :ICEVR 1gqzA 94 :DISVS T0301 151 :VSGGQVQET 1gqzA 99 :TQKGNMVLT T0301 168 :TFPAAEIVLEFLDPSDDGEDGGAIFPTGNLVDDLEV 1gqzA 108 :VKDDNQIRVNMGEPIWEPAKIPFTANKFEKNYILRT T0301 205 :GVGTFKATMINAGIPTVFVNAEEIGYRG 1gqzA 144 :DIQTVLCGAVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 1gqzA 173 :EQLGPLLE T0301 261 :GL 1gqzA 184 :RF T0301 273 :QHTPKIAFVA 1gqzA 186 :PERVNAGFMQ T0301 294 :LVAAG 1gqzA 196 :IINKE T0301 301 :DLLVRALSMGK 1gqzA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAAAI 1gqzA 213 :ETQACGSGACAAVAVGIMQ T0301 341 :GGERSAVRFGHPSGTLRV 1gqzA 232 :GLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 1gqzA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 18 number of extra gaps= 0 total=562 Number of alignments=29 # 1gqzA read from 1gqzA/merged-good-all-a2m # found chain 1gqzA in training set T0301 10 :PATYLRGG 1gqzA 2 :QFSKMHGL T0301 20 :KGVFFRLEDLPESCRVPGEARDRLF 1gqzA 10 :GNDFVVVDGVTQNVFFTPETIRRLA T0301 51 :PDPYAAHI 1gqzA 35 :NRHCGIGF T0301 69 :SKCVILSKSSQPGHDVDYLYGQ 1gqzA 43 :DQLLIVEAPYDPELDFHYRIFN T0301 93 :IDKPFV 1gqzA 65 :ADGSEV T0301 102 :GNCGNLSTGAGAFALHAGLVDP 1gqzA 71 :SQCGNGARCFARFVTLKGLTNK T0301 130 :GICEVR 1gqzA 93 :KDISVS T0301 140 :NIGKTIIAHV 1gqzA 99 :TQKGNMVLTV T0301 169 :FPAAEIVLEFLDPSDDGEDGG 1gqzA 109 :KDDNQIRVNMGEPIWEPAKIP T0301 192 :FPTGNLVDDLEVP 1gqzA 130 :FTANKFEKNYILR T0301 205 :GVGTFKATMINAGIPTVFVNAEEIGYRG 1gqzA 144 :DIQTVLCGAVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 1gqzA 173 :EQLGPLLE T0301 272 :RQHTPKIAFVA 1gqzA 185 :FPERVNAGFMQ T0301 294 :LVAAG 1gqzA 196 :IINKE T0301 301 :DLLVRALSMGK 1gqzA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAAAIP 1gqzA 213 :ETQACGSGACAAVAVGIMQG T0301 342 :GERSAVRFGHPSGTLRV 1gqzA 233 :LLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 1gqzA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 18 number of extra gaps= 0 total=580 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w61A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w61A expands to /projects/compbio/data/pdb/1w61.pdb.gz 1w61A:# T0301 read from 1w61A/merged-good-all-a2m # 1w61A read from 1w61A/merged-good-all-a2m # adding 1w61A to template set # found chain 1w61A in template set Warning: unaligning (T0301)P5 because first residue in template chain is (1w61A)F42 Warning: unaligning (T0301)A11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)I49 Warning: unaligning (T0301)T12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)I49 Warning: unaligning (T0301)L14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)H52 Warning: unaligning (T0301)R15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)H52 Warning: unaligning (T0301)S182 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w61A)L193 Warning: unaligning (T0301)I191 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1w61A)L193 Warning: unaligning (T0301)G217 because of BadResidue code BAD_PEPTIDE in next template residue (1w61A)N218 Warning: unaligning (T0301)I218 because of BadResidue code BAD_PEPTIDE at template residue (1w61A)N218 Warning: unaligning (T0301)T220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)A221 Warning: unaligning (T0301)V221 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)A221 Warning: unaligning (T0301)L258 because of BadResidue code BAD_PEPTIDE in next template residue (1w61A)S254 Warning: unaligning (T0301)R259 because of BadResidue code BAD_PEPTIDE at template residue (1w61A)S254 T0301 6 :QIRIP 1w61A 43 :KKSFT T0301 13 :Y 1w61A 50 :D T0301 16 :GGTSKGV 1w61A 53 :TEGEAAR T0301 24 :FRLEDLPE 1w61A 60 :IVTSGLPH T0301 33 :CRVPG 1w61A 68 :IPGSN T0301 38 :EARDRLFMRVIGSPDPYAA 1w61A 82 :ENMDYLRRGIMLEPRGHDD T0301 69 :SKCVILSKSSQPGHDVDYLYGQV 1w61A 101 :MFGAFLFDPIEEGADLGIVFMDT T0301 98 :VDWSGNCGNLSTGAGAFALHAGLVDPA 1w61A 124 :GGYLNMCGHNSIAAVTAAVETGIVSVP T0301 127 :PEDGICEVRIWQ 1w61A 151 :AKATNVPVVLDT T0301 141 :IGKTIIAHVPVSGGQV 1w61A 163 :PAGLVRGTAHLQSGTE T0301 169 :FPAAEIVLEFLDP 1w61A 179 :SEVSNASIINVPS T0301 192 :F 1w61A 194 :Y T0301 196 :NLVDDLEV 1w61A 195 :QQDVVVVL T0301 204 :PGVGTFKATMINA 1w61A 204 :KPYGEVRVDIAFG T0301 219 :P 1w61A 219 :F T0301 222 :FVNAEEIGYRGTE 1w61A 222 :IVPAEQLGIDISV T0301 240 :NGDPQQLARFERIRVAGA 1w61A 235 :QNLSRLQEAGELLRTEIN T0301 260 :MGL 1w61A 255 :VKV T0301 268 :EAATRQHT 1w61A 258 :QHPQLPHI T0301 276 :PKIAFVAPPRD 1w61A 269 :DCVEIYGPPTN T0301 298 :GDIDLLVRALSMGK 1w61A 280 :PEANYKNVVIFGNR T0301 312 :LHHAMMGTAAVAIGTAAAIPGTL 1w61A 295 :ADRSPCGTGTSAKMATLYAKGQL T0301 342 :GERSAVRFGHPSG 1w61A 318 :RIGETFVYESILG T0301 355 :TLRVGAEA 1w61A 332 :LFQGRVLG T0301 363 :SQ 1w61A 341 :ER Number of specific fragments extracted= 25 number of extra gaps= 6 total=605 Number of alignments=31 # 1w61A read from 1w61A/merged-good-all-a2m # found chain 1w61A in template set Warning: unaligning (T0301)P5 because first residue in template chain is (1w61A)F42 Warning: unaligning (T0301)A11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)I49 Warning: unaligning (T0301)T12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)I49 Warning: unaligning (T0301)L14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)H52 Warning: unaligning (T0301)R15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)H52 Warning: unaligning (T0301)S182 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w61A)L193 Warning: unaligning (T0301)I191 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1w61A)L193 Warning: unaligning (T0301)G217 because of BadResidue code BAD_PEPTIDE in next template residue (1w61A)N218 Warning: unaligning (T0301)I218 because of BadResidue code BAD_PEPTIDE at template residue (1w61A)N218 Warning: unaligning (T0301)T220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)A221 Warning: unaligning (T0301)V221 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)A221 Warning: unaligning (T0301)L258 because of BadResidue code BAD_PEPTIDE in next template residue (1w61A)S254 Warning: unaligning (T0301)R259 because of BadResidue code BAD_PEPTIDE at template residue (1w61A)S254 T0301 6 :QIRIP 1w61A 43 :KKSFT T0301 13 :Y 1w61A 50 :D T0301 16 :GGTSKGVFF 1w61A 53 :TEGEAARIV T0301 26 :LEDLPE 1w61A 62 :TSGLPH T0301 33 :CRVPG 1w61A 68 :IPGSN T0301 38 :EARDRLFMRVIGSPDPYAAH 1w61A 82 :ENMDYLRRGIMLEPRGHDDM T0301 70 :KCVILSKSSQPGHDVDYLYGQV 1w61A 102 :FGAFLFDPIEEGADLGIVFMDT T0301 98 :VDWSGNCGNLSTGAGAFALHAGLVDPA 1w61A 124 :GGYLNMCGHNSIAAVTAAVETGIVSVP T0301 127 :PEDGICEVRIWQ 1w61A 151 :AKATNVPVVLDT T0301 141 :IGKTIIAHVPVSGGQVQET 1w61A 163 :PAGLVRGTAHLQSGTESEV T0301 172 :AEIVLEFLDP 1w61A 182 :SNASIINVPS T0301 195 :GNLVDDLEV 1w61A 194 :YQQDVVVVL T0301 204 :PGVGTFKATMINA 1w61A 204 :KPYGEVRVDIAFG T0301 219 :P 1w61A 219 :F T0301 222 :FVNAEEIGYRGTE 1w61A 222 :IVPAEQLGIDISV T0301 240 :NGDPQQLARFERIRVAGA 1w61A 235 :QNLSRLQEAGELLRTEIN T0301 260 :MGL 1w61A 255 :VKV T0301 264 :KT 1w61A 258 :QH T0301 272 :RQHTPKIAFVAPPRD 1w61A 265 :INTVDCVEIYGPPTN T0301 291 :SGK 1w61A 280 :PEA T0301 300 :IDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTL 1w61A 283 :NYKNVVIFGNRQADRSPCGTGTSAKMATLYAKGQL T0301 342 :GERSAVRFGHPSG 1w61A 318 :RIGETFVYESILG T0301 355 :TLRVGA 1w61A 332 :LFQGRV T0301 361 :EASQANG 1w61A 339 :GEERIPG Number of specific fragments extracted= 24 number of extra gaps= 6 total=629 Number of alignments=32 # 1w61A read from 1w61A/merged-good-all-a2m # found chain 1w61A in template set Warning: unaligning (T0301)P5 because first residue in template chain is (1w61A)F42 Warning: unaligning (T0301)A11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)I49 Warning: unaligning (T0301)T12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)I49 Warning: unaligning (T0301)L14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)H52 Warning: unaligning (T0301)R15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)H52 Warning: unaligning (T0301)S182 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w61A)L193 Warning: unaligning (T0301)I191 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1w61A)L193 Warning: unaligning (T0301)G217 because of BadResidue code BAD_PEPTIDE in next template residue (1w61A)N218 Warning: unaligning (T0301)I218 because of BadResidue code BAD_PEPTIDE at template residue (1w61A)N218 Warning: unaligning (T0301)T220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)A221 Warning: unaligning (T0301)V221 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)A221 Warning: unaligning (T0301)L258 because of BadResidue code BAD_PEPTIDE in next template residue (1w61A)S254 Warning: unaligning (T0301)R259 because of BadResidue code BAD_PEPTIDE at template residue (1w61A)S254 T0301 6 :QIRIP 1w61A 43 :KKSFT T0301 13 :Y 1w61A 50 :D T0301 16 :GGTSK 1w61A 53 :TEGEA T0301 22 :VFFRLEDLPES 1w61A 58 :ARIVTSGLPHI T0301 36 :PG 1w61A 69 :PG T0301 38 :EARDRLFMRVIGSPDPYAAH 1w61A 82 :ENMDYLRRGIMLEPRGHDDM T0301 70 :KCVILSKSSQPGHDVDYLYGQV 1w61A 102 :FGAFLFDPIEEGADLGIVFMDT T0301 98 :VDWSGNCGNLSTGAGAFALHAGLVDPA 1w61A 124 :GGYLNMCGHNSIAAVTAAVETGIVSVP T0301 127 :PEDGICEVRIWQ 1w61A 151 :AKATNVPVVLDT T0301 141 :IGKTIIAHVPVSGGQ 1w61A 163 :PAGLVRGTAHLQSGT T0301 168 :TFPAAEIVLEFLDP 1w61A 178 :ESEVSNASIINVPS T0301 195 :GNLVDDLEVP 1w61A 194 :YQQDVVVVLP T0301 205 :GVGTFKATMINA 1w61A 205 :PYGEVRVDIAFG T0301 219 :P 1w61A 219 :F T0301 222 :FVNAEEIGYRGTE 1w61A 222 :IVPAEQLGIDISV T0301 240 :NGDPQQLARFERIRVAGA 1w61A 235 :QNLSRLQEAGELLRTEIN T0301 260 :MGL 1w61A 255 :VKV T0301 263 :IKTP 1w61A 260 :PQLP T0301 272 :RQHTPKIAFVAPPRDYRT 1w61A 265 :INTVDCVEIYGPPTNPEA T0301 300 :IDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTL 1w61A 283 :NYKNVVIFGNRQADRSPCGTGTSAKMATLYAKGQL T0301 342 :GERSAVRFGHPSG 1w61A 318 :RIGETFVYESILG T0301 355 :TLRVGAEAS 1w61A 332 :LFQGRVLGE Number of specific fragments extracted= 22 number of extra gaps= 6 total=651 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hzdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hzdA expands to /projects/compbio/data/pdb/1hzd.pdb.gz 1hzdA:# T0301 read from 1hzdA/merged-good-all-a2m # 1hzdA read from 1hzdA/merged-good-all-a2m # adding 1hzdA to template set # found chain 1hzdA in template set Warning: unaligning (T0301)T159 because first residue in template chain is (1hzdA)E74 T0301 160 :GDFELDGVTFPAAE 1hzdA 75 :DELRVRHLEEENRG T0301 174 :IVLEFLDPS 1hzdA 90 :VVLGINRAY T0301 185 :GE 1hzdA 99 :GK T0301 189 :GAIFPT 1hzdA 101 :NSLSKN T0301 205 :GVGTFKATMINAGIPTVFVNA 1hzdA 120 :SDKKVRTIIIRSEVPGIFCAG T0301 234 :ELREEIN 1hzdA 141 :ADLKERA T0301 241 :GDPQQLARFERIRVAGALRMGL 1hzdA 150 :SSSEVGPFVSKIRAVINDIANL T0301 274 :HTPKIAFVAP 1hzdA 172 :PVPTIAAIDG T0301 301 :DLL 1hzdA 182 :LAL T0301 320 :AAVAIGTAA 1hzdA 186 :GGLELALAC Number of specific fragments extracted= 10 number of extra gaps= 0 total=661 Number of alignments=34 # 1hzdA read from 1hzdA/merged-good-all-a2m # found chain 1hzdA in template set T0301 161 :DFELDGVTFPA 1hzdA 76 :ELRVRHLEEEN T0301 174 :IVLEFLDPS 1hzdA 90 :VVLGINRAY T0301 185 :GE 1hzdA 99 :GK T0301 189 :GAIFPT 1hzdA 101 :NSLSKN T0301 206 :VGTFKATMINAGIPTVFVNA 1hzdA 121 :DKKVRTIIIRSEVPGIFCAG T0301 234 :ELREEIN 1hzdA 141 :ADLKERA T0301 241 :GDPQQLARFERIRVAGALRMGL 1hzdA 150 :SSSEVGPFVSKIRAVINDIANL T0301 274 :HTPKIAFVAP 1hzdA 172 :PVPTIAAIDG T0301 302 :LL 1hzdA 183 :AL T0301 317 :M 1hzdA 185 :G T0301 320 :AAVAIGTAA 1hzdA 186 :GGLELALAC Number of specific fragments extracted= 11 number of extra gaps= 0 total=672 Number of alignments=35 # 1hzdA read from 1hzdA/merged-good-all-a2m # found chain 1hzdA in template set T0301 161 :DFELDGVTFPAA 1hzdA 76 :ELRVRHLEEENR T0301 174 :IVLEFLDPS 1hzdA 90 :VVLGINRAY T0301 187 :DGGAIFPT 1hzdA 99 :GKNSLSKN T0301 206 :VGTFKATMINAGIPTVFVNA 1hzdA 121 :DKKVRTIIIRSEVPGIFCAG T0301 234 :ELREEIN 1hzdA 141 :ADLKERA T0301 241 :GDPQQLARFERIRVAGALRMGL 1hzdA 150 :SSSEVGPFVSKIRAVINDIANL T0301 274 :HTPKIAFVA 1hzdA 172 :PVPTIAAID T0301 302 :LLVRA 1hzdA 181 :GLALG T0301 320 :AAVAIGTAA 1hzdA 186 :GGLELALAC Number of specific fragments extracted= 9 number of extra gaps= 0 total=681 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bwzA expands to /projects/compbio/data/pdb/1bwz.pdb.gz 1bwzA:# T0301 read from 1bwzA/merged-good-all-a2m # 1bwzA read from 1bwzA/merged-good-all-a2m # adding 1bwzA to template set # found chain 1bwzA in template set T0301 10 :PATYLRGGTSKGVFFRL 1bwzA 2 :QFSKMHGLGNDFVVVDG T0301 29 :LPESCRVPGEARDRLF 1bwzA 19 :VTQNVFFTPETIRRLA T0301 51 :PDPYAAH 1bwzA 35 :NRHCGIG T0301 68 :TSKCVILSKSSQPGHDVDYLYGQ 1bwzA 42 :FDQLLIVEAPYDPELDFHYRIFN T0301 94 :DK 1bwzA 66 :DG T0301 99 :DWSGNCGNLSTGAGAFALHAGLVD 1bwzA 68 :SEVSQCGNGARCFARFVTLKGLTN T0301 129 :DGICEVR 1bwzA 92 :KKDISVS T0301 140 :NIGKTIIAHV 1bwzA 99 :TQKGNMVLTV T0301 169 :FPAAEIVLEFLDPSDDGEDGGAIFPTGNLVDDLEVP 1bwzA 109 :KDMNQIRVNMGEPIWEPAKIPFTANKFEKNYILRTD T0301 206 :VGTFKATMINAGIPTVFVNAEEIGYRG 1bwzA 145 :IQTVLCGAVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 1bwzA 173 :EQLGPLLE T0301 261 :GL 1bwzA 181 :SH T0301 268 :EAATR 1bwzA 183 :ERFPE T0301 275 :TPKIAFV 1bwzA 188 :RVNAGFM T0301 293 :KLVAAG 1bwzA 195 :QIINKE T0301 301 :DLLVRALSMGK 1bwzA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAAA 1bwzA 213 :ETQACGSGACAAVAVGIM T0301 340 :GGGERSAVRFGHPSGTLRV 1bwzA 231 :QGLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 1bwzA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 19 number of extra gaps= 0 total=700 Number of alignments=37 # 1bwzA read from 1bwzA/merged-good-all-a2m # found chain 1bwzA in template set T0301 10 :PATYLRGGTSKGVFFRL 1bwzA 2 :QFSKMHGLGNDFVVVDG T0301 29 :LPESCRVPGEARDRLF 1bwzA 19 :VTQNVFFTPETIRRLA T0301 51 :PDPYAAHI 1bwzA 35 :NRHCGIGF T0301 69 :SKCVILSKSSQPGHDVDYLYGQ 1bwzA 43 :DQLLIVEAPYDPELDFHYRIFN T0301 93 :IDK 1bwzA 65 :ADG T0301 99 :DWSGNCGNLSTGAGAFALHAGLVD 1bwzA 68 :SEVSQCGNGARCFARFVTLKGLTN T0301 129 :DGICEVR 1bwzA 92 :KKDISVS T0301 140 :NIGKTIIAHV 1bwzA 99 :TQKGNMVLTV T0301 169 :FPAAEIVLEFLDPSDDGEDGGAIFPTGNLVDDLEVPGV 1bwzA 109 :KDMNQIRVNMGEPIWEPAKIPFTANKFEKNYILRTDIQ T0301 208 :TFKATMINAGIPTVFVNAEEIGYRG 1bwzA 147 :TVLCGAVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 1bwzA 173 :EQLGPLLE T0301 261 :GL 1bwzA 184 :RF T0301 273 :QHTPKIAFV 1bwzA 186 :PERVNAGFM T0301 293 :KLVAAG 1bwzA 195 :QIINKE T0301 301 :DLLVRALSMGK 1bwzA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAAA 1bwzA 213 :ETQACGSGACAAVAVGIM T0301 340 :GGGERSAVRFGHPSGTLR 1bwzA 231 :QGLLNNNVQVDLPGGSLM T0301 360 :AEASQANGEWTV 1bwzA 249 :IEWNGVGHPLYM Number of specific fragments extracted= 18 number of extra gaps= 0 total=718 Number of alignments=38 # 1bwzA read from 1bwzA/merged-good-all-a2m # found chain 1bwzA in template set T0301 10 :PATYLRGGTSKGVFFR 1bwzA 2 :QFSKMHGLGNDFVVVD T0301 28 :DLPESCRVPGEARDRLF 1bwzA 18 :GVTQNVFFTPETIRRLA T0301 51 :PDPYAAHI 1bwzA 35 :NRHCGIGF T0301 69 :SKCVILSKSSQPGHDVDYLYGQ 1bwzA 43 :DQLLIVEAPYDPELDFHYRIFN T0301 94 :DK 1bwzA 66 :DG T0301 99 :DWSGNCGNLSTGAGAFALHAGLVDP 1bwzA 68 :SEVSQCGNGARCFARFVTLKGLTNK T0301 130 :GICEVR 1bwzA 93 :KDISVS T0301 140 :NIGKTIIAHV 1bwzA 99 :TQKGNMVLTV T0301 169 :FPAAEIVLEFLDPSDDGEDGGAIFPTGNLVDDLEVPGV 1bwzA 109 :KDMNQIRVNMGEPIWEPAKIPFTANKFEKNYILRTDIQ T0301 208 :TFKATMINAGIPTVFVNAEEIGYRG 1bwzA 147 :TVLCGAVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 1bwzA 173 :EQLGPLLE T0301 272 :RQHTPKIAFV 1bwzA 185 :FPERVNAGFM T0301 293 :KLVAAG 1bwzA 195 :QIINKE T0301 301 :DLLVRALSMGK 1bwzA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAAA 1bwzA 213 :ETQACGSGACAAVAVGIM T0301 340 :GGGERSAVRFGHPSGTLRV 1bwzA 231 :QGLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTV 1bwzA 250 :EWNGVGHPLYM Number of specific fragments extracted= 17 number of extra gaps= 0 total=735 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g6yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2g6yA expands to /projects/compbio/data/pdb/2g6y.pdb.gz 2g6yA:Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 53, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 57, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 59, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 61, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 63, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 65, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 67, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 69, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 251, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 286, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 290, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 292, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 294, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 296, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 298, because occupancy 0.500 <= existing 0.500 in 2g6yA Bad short name: CA1 for alphabet: pdb_atoms Bad short name: C1 for alphabet: pdb_atoms Bad short name: N2 for alphabet: pdb_atoms Bad short name: N3 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: O2 for alphabet: pdb_atoms Bad short name: CA2 for alphabet: pdb_atoms Bad short name: CA3 for alphabet: pdb_atoms Bad short name: CB2 for alphabet: pdb_atoms Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 804, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 892, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 918, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1004, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1008, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1041, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1045, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1047, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1049, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1051, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1058, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1060, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1062, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1064, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1066, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1099, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1101, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1189, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1191, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1320, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1324, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1326, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1328, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1330, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1371, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1380, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1384, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1386, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1388, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1412, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1416, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1418, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1420, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1422, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1424, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1426, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1458, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1462, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1464, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1466, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1468, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1470, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1566, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1570, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1572, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1574, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1677, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1681, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1683, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1685, because occupancy 0.500 <= existing 0.500 in 2g6yA Skipped atom 1687, because occupancy 0.500 <= existing 0.500 in 2g6yA # T0301 read from 2g6yA/merged-good-all-a2m # 2g6yA read from 2g6yA/merged-good-all-a2m # adding 2g6yA to template set # found chain 2g6yA in template set Warning: unaligning (T0301)A113 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2g6yA)F60 Warning: unaligning (T0301)A115 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2g6yA)F60 Warning: unaligning (T0301)K293 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2g6yA)Y165 Warning: unaligning (T0301)L294 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2g6yA)Y165 Warning: unaligning (T0301)V358 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2g6yA)V209 Warning: unaligning (T0301)G359 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2g6yA)V209 T0301 87 :LYGQVSIDKPFVDWS 2g6yA 34 :MTNKMKSTKGALTFS T0301 106 :NLSTGAG 2g6yA 49 :PYLLSHV T0301 116 :LHAGLVDPARI 2g6yA 61 :YHFGTYPSGYE T0301 127 :PEDGICEVRIWQANIGKTIIAHVPV 2g6yA 79 :NNGGYTNTRIEKYEDGGVLHVSFSY T0301 152 :SGGQVQE 2g6yA 106 :EAGRVIG T0301 161 :DFELDGVTFPAA 2g6yA 113 :DFKVMGTGFPED T0301 184 :DGEDGGAIFPTGNLVDDLEVPGVGTFKATM 2g6yA 125 :SVIFTDKIIRSNATVEHLHPMGDNDLDGSF T0301 285 :RDYRTASG 2g6yA 156 :RTFSLRDG T0301 295 :VA 2g6yA 166 :YS T0301 300 :IDLLVRALSMGKLHHA 2g6yA 168 :SVVDSHMHFKSAIHPS T0301 338 :AAGGGERSA 2g6yA 184 :ILQNGGPMF T0301 347 :VRFGHPSGTLR 2g6yA 197 :VEEDHSNTELG T0301 360 :AEASQA 2g6yA 210 :EYQHAF Number of specific fragments extracted= 13 number of extra gaps= 2 total=748 Number of alignments=40 # 2g6yA read from 2g6yA/merged-good-all-a2m # found chain 2g6yA in template set Warning: unaligning (T0301)G112 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2g6yA)F60 Warning: unaligning (T0301)A115 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2g6yA)F60 Warning: unaligning (T0301)K293 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2g6yA)Y165 Warning: unaligning (T0301)L294 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2g6yA)Y165 Warning: unaligning (T0301)V358 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2g6yA)V209 Warning: unaligning (T0301)G359 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2g6yA)V209 T0301 87 :LYGQVSIDKPFVDWSG 2g6yA 34 :MTNKMKSTKGALTFSP T0301 106 :NLSTGA 2g6yA 50 :YLLSHV T0301 116 :LHAGLVDPARI 2g6yA 61 :YHFGTYPSGYE T0301 127 :PEDGICEVRIWQANIGKTIIAHVPV 2g6yA 79 :NNGGYTNTRIEKYEDGGVLHVSFSY T0301 152 :SGGQVQETGDFELDGVTFPA 2g6yA 106 :EAGRVIGDFKVMGTGFPEDS T0301 185 :GEDGGAIFPTGNLVDDLEVPGVGTFKATM 2g6yA 126 :VIFTDKIIRSNATVEHLHPMGDNDLDGSF T0301 286 :DYRTASG 2g6yA 157 :TFSLRDG T0301 295 :VA 2g6yA 166 :YS T0301 300 :IDLLVRALSMGKLHHA 2g6yA 168 :SVVDSHMHFKSAIHPS T0301 338 :AAGGGERS 2g6yA 184 :ILQNGGPM T0301 346 :AVRFGHPSGTLR 2g6yA 196 :RVEEDHSNTELG T0301 360 :AEASQ 2g6yA 210 :EYQHA Number of specific fragments extracted= 12 number of extra gaps= 2 total=760 Number of alignments=41 # 2g6yA read from 2g6yA/merged-good-all-a2m # found chain 2g6yA in template set Warning: unaligning (T0301)G112 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2g6yA)F60 Warning: unaligning (T0301)F114 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2g6yA)F60 Warning: unaligning (T0301)K293 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2g6yA)Y165 Warning: unaligning (T0301)L294 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2g6yA)Y165 Warning: unaligning (T0301)V358 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2g6yA)V209 Warning: unaligning (T0301)G359 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2g6yA)V209 T0301 87 :LYGQVSIDKPFVDWSG 2g6yA 34 :MTNKMKSTKGALTFSP T0301 106 :NLSTGA 2g6yA 50 :YLLSHV T0301 116 :LHAGLVDPARI 2g6yA 61 :YHFGTYPSGYE T0301 127 :PEDGICEVRIWQANIGKTIIAHVPV 2g6yA 79 :NNGGYTNTRIEKYEDGGVLHVSFSY T0301 152 :SGGQVQ 2g6yA 106 :EAGRVI T0301 160 :GDFELDGVTFPA 2g6yA 112 :GDFKVMGTGFPE T0301 184 :D 2g6yA 124 :D T0301 187 :DGGAIFPTGNLVDDLEVPGVGTFKATM 2g6yA 128 :FTDKIIRSNATVEHLHPMGDNDLDGSF T0301 286 :DYRTASG 2g6yA 157 :TFSLRDG T0301 295 :VA 2g6yA 166 :YS T0301 300 :IDLLVRALSMGKLHHA 2g6yA 168 :SVVDSHMHFKSAIHPS T0301 338 :AAGGGERSA 2g6yA 184 :ILQNGGPMF T0301 347 :VRFGHPSGTLR 2g6yA 197 :VEEDHSNTELG T0301 360 :AEASQA 2g6yA 210 :EYQHAF Number of specific fragments extracted= 14 number of extra gaps= 2 total=774 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s7jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1s7jA expands to /projects/compbio/data/pdb/1s7j.pdb.gz 1s7jA:# T0301 read from 1s7jA/merged-good-all-a2m # 1s7jA read from 1s7jA/merged-good-all-a2m # adding 1s7jA to template set # found chain 1s7jA in template set T0301 8 :RIPATYLRG 1s7jA 2 :SYPYYIVDA T0301 17 :GTSKGVFFRLED 1s7jA 17 :KGNPAAVYVLEK T0301 34 :RVPGEARDRLFMRV 1s7jA 29 :WLPEAVMQNIAIEN T0301 67 :STSKCVILSKSSQ 1s7jA 43 :NLSETAFTVKEGQ T0301 85 :D 1s7jA 56 :S T0301 87 :LYGQVSIDKPFVDW 1s7jA 57 :YALRWFTPEREIDL T0301 104 :CGNLSTGAGAFALHAGLVDPARI 1s7jA 71 :CGHATLATAFVLFNYYSVAEETL T0301 128 :EDGICEVRI 1s7jA 98 :QSGPLAVTK T0301 141 :IGKTIIAHVPVSGGQV 1s7jA 107 :KEEYYYLDFPYILPER T0301 167 :VTFP 1s7jA 123 :IPIL T0301 204 :PGVGTF 1s7jA 135 :TKIYEA T0301 215 :NAGIPTVFV 1s7jA 141 :YLGRDLFFV T0301 230 :Y 1s7jA 150 :L T0301 241 :GDPQQLAR 1s7jA 151 :KDEETVAK T0301 249 :FERIRV 1s7jA 163 :FSALKA T0301 262 :L 1s7jA 169 :L T0301 273 :QHTPKIAFVAP 1s7jA 170 :DLGVGVIVTAS T0301 297 :AGDIDLLVRALSMGK 1s7jA 181 :GDSVDFVSRTFFPKL T0301 312 :LHHAMMGTAAVA 1s7jA 203 :CGSAHANLIPYW T0301 327 :AAAI 1s7jA 215 :GKRL T0301 341 :GGERSAVRFGHPS 1s7jA 219 :NQTTLSAYQVSPR T0301 354 :GTLRVGAE 1s7jA 233 :GFLTCEVK T0301 366 :NGEWTVT 1s7jA 241 :ENRVIIG Number of specific fragments extracted= 23 number of extra gaps= 0 total=797 Number of alignments=43 # 1s7jA read from 1s7jA/merged-good-all-a2m # found chain 1s7jA in template set T0301 8 :RIPATYLRG 1s7jA 2 :SYPYYIVDA T0301 17 :G 1s7jA 18 :G T0301 19 :SKGVFFRLED 1s7jA 19 :NPAAVYVLEK T0301 34 :RVPGEARDRLFMRV 1s7jA 29 :WLPEAVMQNIAIEN T0301 67 :STSKCVILSKSSQ 1s7jA 43 :NLSETAFTVKEGQ T0301 85 :D 1s7jA 56 :S T0301 87 :LYGQVSIDKPFVD 1s7jA 57 :YALRWFTPEREID T0301 103 :NCGNLSTGAGAFALHAGLVDPA 1s7jA 70 :LCGHATLATAFVLFNYYSVAEE T0301 131 :IC 1s7jA 92 :TL T0301 148 :HVPVSGGQVQETGD 1s7jA 94 :HFTSQSGPLAVTKK T0301 171 :AAEIVLEFLDPS 1s7jA 108 :EEYYYLDFPYIL T0301 185 :GEDGGAI 1s7jA 120 :PERIPIL T0301 194 :TGNLVDDLE 1s7jA 134 :GTKIYEAYL T0301 217 :GIPTVFV 1s7jA 143 :GRDLFFV T0301 225 :A 1s7jA 150 :L T0301 241 :GDPQQ 1s7jA 151 :KDEET T0301 249 :FE 1s7jA 156 :VA T0301 261 :GLIKTPEEAATRQHTPKIAFVAPPR 1s7jA 158 :KITPDFSALKALDLGVGVIVTASGD T0301 299 :DIDLLVRALSMGK 1s7jA 183 :SVDFVSRTFFPKL T0301 312 :LHHAMMGTAAVA 1s7jA 203 :CGSAHANLIPYW T0301 336 :NLAA 1s7jA 215 :GKRL T0301 341 :GGERSAVRFGHPS 1s7jA 219 :NQTTLSAYQVSPR T0301 354 :GTLRVGAE 1s7jA 233 :GFLTCEVK T0301 366 :NGEWTV 1s7jA 241 :ENRVII Number of specific fragments extracted= 24 number of extra gaps= 0 total=821 Number of alignments=44 # 1s7jA read from 1s7jA/merged-good-all-a2m # found chain 1s7jA in template set T0301 8 :RIPATYLRGG 1s7jA 2 :SYPYYIVDAF T0301 18 :TSKGVFFRLED 1s7jA 18 :GNPAAVYVLEK T0301 34 :RVPGEARDRLFMRV 1s7jA 29 :WLPEAVMQNIAIEN T0301 67 :STSKCVILSKSSQ 1s7jA 43 :NLSETAFTVKEGQ T0301 85 :D 1s7jA 56 :S T0301 87 :LYGQVSIDKPFVDW 1s7jA 57 :YALRWFTPEREIDL T0301 104 :CGNLSTGAGAFALHAGLVDP 1s7jA 71 :CGHATLATAFVLFNYYSVAE T0301 130 :GICEV 1s7jA 91 :ETLHF T0301 139 :ANIGKTIIAH 1s7jA 96 :TSQSGPLAVT T0301 151 :VSGGQVQET 1s7jA 106 :KKEEYYYLD T0301 178 :FLDPS 1s7jA 115 :FPYIL T0301 185 :GEDGGAI 1s7jA 120 :PERIPIL T0301 194 :TGNLVDDLE 1s7jA 134 :GTKIYEAYL T0301 217 :GIPTVFVN 1s7jA 143 :GRDLFFVL T0301 241 :GDPQQLA 1s7jA 151 :KDEETVA T0301 261 :GLIKTPEEAATRQHTPKIAFVAPPRD 1s7jA 158 :KITPDFSALKALDLGVGVIVTASGDS T0301 300 :IDLLVRALSMGK 1s7jA 184 :VDFVSRTFFPKL T0301 312 :LHHAMMGTAAVA 1s7jA 203 :CGSAHANLIPYW T0301 336 :NLAAGG 1s7jA 215 :GKRLNQ T0301 343 :ERSAVRFGHPSG 1s7jA 221 :TTLSAYQVSPRG T0301 355 :TLRVG 1s7jA 234 :FLTCE T0301 362 :AS 1s7jA 239 :VK T0301 366 :NGEWTV 1s7jA 241 :ENRVII Number of specific fragments extracted= 23 number of extra gaps= 0 total=844 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2azpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2azpA expands to /projects/compbio/data/pdb/2azp.pdb.gz 2azpA:# T0301 read from 2azpA/merged-good-all-a2m # 2azpA read from 2azpA/merged-good-all-a2m # adding 2azpA to template set # found chain 2azpA in template set T0301 5 :PQIRIPATYLRGGTSKGVFF 2azpA -1 :HMQRIRIIDSHTGGEPTRLV T0301 26 :LEDLPES 2azpA 20 :IGGFPDL T0301 34 :RVPG 2azpA 27 :GQGD T0301 38 :EARDRLFMRVIGSPD 2azpA 40 :ERHDAWRAACILEPR T0301 65 :TSSTSKCVILSKSSQPGHDVDYLYG 2azpA 55 :GSDVLVGALLCAPVDPEACAGVIFF T0301 93 :IDKPFV 2azpA 80 :NNSGYL T0301 102 :GNCGNLSTGAGAFALHAGLVD 2azpA 86 :GMCGHGTIGLVASLAHLGRIG T0301 129 :DGICEVR 2azpA 107 :PGVHRIE T0301 139 :ANIG 2azpA 114 :TPVG T0301 144 :TIIAHV 2azpA 118 :EVEATL T0301 169 :FPAAEIVLEFLDPS 2azpA 124 :HEDGSVSVRNVPAY T0301 194 :TGNLVDDLEVPGVGTFKATMINAGIPTVFVN 2azpA 138 :RYRRQVSVEVPGIGRVSGDIAWGGNWFFLVA T0301 229 :GYRGTELR 2azpA 169 :GHGQRLAG T0301 240 :NGDPQQLARFERIRVAGAL 2azpA 177 :DNLDALTAYTVAVQQALDD T0301 260 :MGL 2azpA 196 :QDI T0301 264 :KTPEEA 2azpA 199 :RGEDGG T0301 274 :HTPKIAFVA 2azpA 205 :AIDHIELFA T0301 296 :AAGDIDLLVRALSMGKLH 2azpA 214 :DDPHADSRNFVLCPGKAY T0301 314 :HAMMGTAAVAIGTAAAIPGT 2azpA 233 :RSPCGTGTSAKLACLAADGK T0301 341 :GGERSAVRFGHPSG 2azpA 253 :LLPGQPWRQASVIG T0301 355 :TLRVGAEA 2azpA 268 :QFEGRYEW T0301 363 :SQANGEWTVT 2azpA 278 :GQPGGPIVPT Number of specific fragments extracted= 22 number of extra gaps= 0 total=866 Number of alignments=46 # 2azpA read from 2azpA/merged-good-all-a2m # found chain 2azpA in template set T0301 5 :PQIRIPATYLRGGTSKGVFF 2azpA -1 :HMQRIRIIDSHTGGEPTRLV T0301 26 :LEDLPES 2azpA 20 :IGGFPDL T0301 34 :RVPG 2azpA 27 :GQGD T0301 38 :EARDRLFMRVIGSPD 2azpA 40 :ERHDAWRAACILEPR T0301 65 :TSSTSKCVILSKSSQPGHDVDYLYG 2azpA 55 :GSDVLVGALLCAPVDPEACAGVIFF T0301 93 :IDKPF 2azpA 80 :NNSGY T0301 101 :SGNCGNLSTGAGAFALHAGLVD 2azpA 85 :LGMCGHGTIGLVASLAHLGRIG T0301 129 :DGICEV 2azpA 107 :PGVHRI T0301 150 :PVSGGQVQET 2azpA 113 :ETPVGEVEAT T0301 164 :L 2azpA 123 :L T0301 169 :FPAAEIVLEFLDPS 2azpA 124 :HEDGSVSVRNVPAY T0301 194 :TGNLVDDLEVPGVGTFKATMINAGIPTVFVNAEEIGYRG 2azpA 138 :RYRRQVSVEVPGIGRVSGDIAWGGNWFFLVAGHGQRLAG T0301 240 :NGDPQQLARFERIRVAGA 2azpA 177 :DNLDALTAYTVAVQQALD T0301 259 :RMGLIK 2azpA 195 :DQDIRG T0301 270 :ATRQHTPKIAFVA 2azpA 201 :EDGGAIDHIELFA T0301 296 :AAGDIDLLVRALSMGK 2azpA 214 :DDPHADSRNFVLCPGK T0301 312 :LHHAMMGTAAVAIGTAAAIPGT 2azpA 231 :YDRSPCGTGTSAKLACLAADGK T0301 341 :GGERSAVRFGHPSG 2azpA 253 :LLPGQPWRQASVIG T0301 355 :TLRVGAEA 2azpA 268 :QFEGRYEW T0301 363 :SQANGEWTV 2azpA 278 :GQPGGPIVP Number of specific fragments extracted= 20 number of extra gaps= 0 total=886 Number of alignments=47 # 2azpA read from 2azpA/merged-good-all-a2m # found chain 2azpA in template set T0301 5 :PQIRIPATYLRGGTSK 2azpA -1 :HMQRIRIIDSHTGGEP T0301 22 :VFFRLEDLPESCRVP 2azpA 16 :TRLVIGGFPDLGQGD T0301 37 :GEARDRLFMRVIGSPDPYAAHI 2azpA 39 :GERHDAWRAACILEPRGSDVLV T0301 71 :CVILSKSSQPGHDVDYLYG 2azpA 61 :GALLCAPVDPEACAGVIFF T0301 93 :IDKPFV 2azpA 80 :NNSGYL T0301 102 :GNCGNLSTGAGAFALHAGLVDP 2azpA 86 :GMCGHGTIGLVASLAHLGRIGP T0301 130 :GICEVR 2azpA 108 :GVHRIE T0301 139 :ANIG 2azpA 114 :TPVG T0301 144 :TIIAHVP 2azpA 118 :EVEATLH T0301 170 :PAAEIVLEFLDPS 2azpA 125 :EDGSVSVRNVPAY T0301 194 :TGNLVDDLEVPGVGTFKATMINAGIPTVFVN 2azpA 138 :RYRRQVSVEVPGIGRVSGDIAWGGNWFFLVA T0301 229 :GYRGTELR 2azpA 169 :GHGQRLAG T0301 240 :NGDPQQLARFERIRVAGALR 2azpA 177 :DNLDALTAYTVAVQQALDDQ T0301 261 :GLIK 2azpA 197 :DIRG T0301 270 :ATRQHTPKIAFV 2azpA 201 :EDGGAIDHIELF T0301 295 :VAAGDIDLLVRALSMGKLH 2azpA 213 :ADDPHADSRNFVLCPGKAY T0301 314 :HAMMGTAAVAIGTAAAIPGT 2azpA 233 :RSPCGTGTSAKLACLAADGK T0301 341 :GGERSAVRFGHPSGT 2azpA 253 :LLPGQPWRQASVIGS T0301 357 :RVGAEASQ 2azpA 268 :QFEGRYEW T0301 365 :ANGEWTVT 2azpA 280 :PGGPIVPT Number of specific fragments extracted= 20 number of extra gaps= 0 total=906 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t6kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t6kA expands to /projects/compbio/data/pdb/1t6k.pdb.gz 1t6kA:# T0301 read from 1t6kA/merged-good-all-a2m # 1t6kA read from 1t6kA/merged-good-all-a2m # adding 1t6kA to template set # found chain 1t6kA in template set T0301 17 :GTSKGVFFRLEDLP 1t6kA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1t6kA 31 :PAQMQRIAREM T0301 67 :STSKCVILSKSSQPGHD 1t6kA 42 :NLSESTFVLKPRNGGDA T0301 88 :YGQVSIDKPFVDW 1t6kA 59 :LIRIFTPVNELPF T0301 104 :CGNLSTGAGAFALHAG 1t6kA 72 :AGHPLLGTAIALGAHT T0301 128 :EDGICEVRI 1t6kA 88 :DNHRLYLET T0301 141 :IGKTIIAHVPVSGGQVQE 1t6kA 97 :QMGTIAFELERQNGSVIA T0301 162 :FELDGVTFPAAEI 1t6kA 115 :ASMDQPIPTWTAL T0301 185 :GE 1t6kA 128 :GR T0301 201 :LEVPGV 1t6kA 137 :LGISDS T0301 208 :TFKATMINAGIPTVFVNAEEI 1t6kA 143 :TFPIEIYHNGPRHVFVGLPSI T0301 247 :ARFER 1t6kA 164 :DALSA T0301 263 :IKTPEEAATRQHTPKIAFVAPP 1t6kA 169 :LHPDHRALSNFHDMAINCFAGA T0301 291 :SG 1t6kA 191 :GR T0301 301 :DLLVRALSMG 1t6kA 193 :RWRSRMFSPA T0301 315 :AMMGTAAVAIGTAAAIPGTL 1t6kA 209 :AATGSAAGPLAIHLARHGQI T0301 340 :GGGERSAVRFGHPSG 1t6kA 229 :EFGQPVEILQGVEIG T0301 355 :TLRVGAEASQANGE 1t6kA 245 :PSLMFAKAEGRAEQ T0301 371 :VTKA 1t6kA 259 :LTRV Number of specific fragments extracted= 19 number of extra gaps= 0 total=925 Number of alignments=49 # 1t6kA read from 1t6kA/merged-good-all-a2m # found chain 1t6kA in template set T0301 17 :GTSKGVFFRLEDLP 1t6kA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1t6kA 31 :PAQMQRIAREM T0301 67 :STSKCVILSKSSQPGHD 1t6kA 42 :NLSESTFVLKPRNGGDA T0301 88 :YGQVSIDKPFVDW 1t6kA 59 :LIRIFTPVNELPF T0301 104 :CGNLSTGAGAFALHAG 1t6kA 72 :AGHPLLGTAIALGAHT T0301 128 :EDGICEVRI 1t6kA 88 :DNHRLYLET T0301 141 :IGKTIIAHVPVSGGQVQE 1t6kA 97 :QMGTIAFELERQNGSVIA T0301 162 :FELDGVTFPAAEI 1t6kA 115 :ASMDQPIPTWTAL T0301 185 :GE 1t6kA 128 :GR T0301 205 :GVGTFKATMINAGIPTVFVNAEEI 1t6kA 140 :SDSTFPIEIYHNGPRHVFVGLPSI T0301 247 :ARFER 1t6kA 164 :DALSA T0301 262 :LIKTPEEAATRQHT 1t6kA 169 :LHPDHRALSNFHDM T0301 277 :KIAFVAP 1t6kA 183 :AINCFAG T0301 290 :ASG 1t6kA 190 :AGR T0301 301 :DLLVRALSMGKL 1t6kA 193 :RWRSRMFSPAYG T0301 313 :HHAMMGTAAVAIGTAAAIPGTL 1t6kA 207 :EDAATGSAAGPLAIHLARHGQI T0301 340 :GGGERSAVRFGHPSG 1t6kA 229 :EFGQPVEILQGVEIG T0301 355 :TLRVGAEASQANGEW 1t6kA 245 :PSLMFAKAEGRAEQL T0301 372 :TK 1t6kA 260 :TR Number of specific fragments extracted= 19 number of extra gaps= 0 total=944 Number of alignments=50 # 1t6kA read from 1t6kA/merged-good-all-a2m # found chain 1t6kA in template set T0301 17 :GTSKGVFFRLEDLP 1t6kA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1t6kA 31 :PAQMQRIAREM T0301 67 :STSKCVILSKSSQPGHD 1t6kA 42 :NLSESTFVLKPRNGGDA T0301 88 :YGQVSIDKPFVDWS 1t6kA 59 :LIRIFTPVNELPFA T0301 105 :GNLSTGAGAFALHAG 1t6kA 73 :GHPLLGTAIALGAHT T0301 128 :EDGICEVRI 1t6kA 88 :DNHRLYLET T0301 141 :IGKTIIAHVPVSGGQVQE 1t6kA 97 :QMGTIAFELERQNGSVIA T0301 162 :FELDGVTFPAAEI 1t6kA 115 :ASMDQPIPTWTAL T0301 204 :P 1t6kA 128 :G T0301 205 :GVGTFKATMINAGIPTVFVNAEEI 1t6kA 140 :SDSTFPIEIYHNGPRHVFVGLPSI T0301 247 :ARFER 1t6kA 164 :DALSA T0301 262 :LIKTPEEAATRQHTPKIAFVAP 1t6kA 169 :LHPDHRALSNFHDMAINCFAGA T0301 299 :DIDLLVRALSMG 1t6kA 191 :GRRWRSRMFSPA T0301 315 :AMMGTAAVAIGTAAAIPGTL 1t6kA 209 :AATGSAAGPLAIHLARHGQI T0301 340 :GGGERSAVRFGHPSG 1t6kA 229 :EFGQPVEILQGVEIG T0301 355 :TLRVGAEASQANGE 1t6kA 245 :PSLMFAKAEGRAEQ T0301 371 :VTKA 1t6kA 259 :LTRV Number of specific fragments extracted= 17 number of extra gaps= 0 total=961 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oe4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1oe4A expands to /projects/compbio/data/pdb/1oe4.pdb.gz 1oe4A:Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 832, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 2098, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 2100, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 2103, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 2105, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 2107, because occupancy 0.500 <= existing 0.500 in 1oe4A # T0301 read from 1oe4A/merged-good-all-a2m # 1oe4A read from 1oe4A/merged-good-all-a2m # adding 1oe4A to template set # found chain 1oe4A in template set T0301 212 :TMINAGIPTVFVNAEEIGYRGTELREEIN 1oe4A 170 :CFVHNHCPLIFMNHSGKNLTPTDLPKAQR T0301 243 :PQQLARFERIRVAGALRMGL 1oe4A 199 :DTLLEICDEALCQAVRVLGV T0301 276 :PKIAFVA 1oe4A 219 :KLVIGVG Number of specific fragments extracted= 3 number of extra gaps= 0 total=964 Number of alignments=52 # 1oe4A read from 1oe4A/merged-good-all-a2m # found chain 1oe4A in template set T0301 212 :TMINAGIPTVFVN 1oe4A 170 :CFVHNHCPLIFMN T0301 225 :AEEIG 1oe4A 190 :PTDLP T0301 237 :EEIN 1oe4A 195 :KAQR T0301 243 :PQQLARFERIRVAGALRMGL 1oe4A 199 :DTLLEICDEALCQAVRVLGV T0301 264 :K 1oe4A 219 :K T0301 266 :PEEAATRQHTPKIAFVAPP 1oe4A 233 :RKALMAEGIDVTVKGIMHP T0301 309 :M 1oe4A 252 :S Number of specific fragments extracted= 7 number of extra gaps= 0 total=971 Number of alignments=53 # 1oe4A read from 1oe4A/merged-good-all-a2m # found chain 1oe4A in template set T0301 212 :TMINAGIPTVFVNAEEIGYRGTELREEIN 1oe4A 170 :CFVHNHCPLIFMNHSGKNLTPTDLPKAQR T0301 243 :PQQLARFERIRVAGALRMGLI 1oe4A 199 :DTLLEICDEALCQAVRVLGVK T0301 266 :PEEAATRQHTPKIAFVAPPRD 1oe4A 233 :RKALMAEGIDVTVKGIMHPSP Number of specific fragments extracted= 3 number of extra gaps= 0 total=974 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ejxC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ejxC expands to /projects/compbio/data/pdb/1ejx.pdb.gz 1ejxC:Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 391, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 1367, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 1ejxC Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms Skipped atom 1699, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 2582, because occupancy 0.500 <= existing 0.500 in 1ejxC # T0301 read from 1ejxC/merged-good-all-a2m # 1ejxC read from 1ejxC/merged-good-all-a2m # adding 1ejxC to template set # found chain 1ejxC in template set Warning: unaligning (T0301)V304 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ejxC)I1218 Warning: unaligning (T0301)A306 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ejxC)I1218 T0301 91 :VSIDKPFVDWSGNCGN 1ejxC 1030 :IEVEDDLTTYGEEVKF T0301 116 :LHAGLVDPARI 1ejxC 1055 :MGQGQMLAADC T0301 130 :GICEVRIWQANIGKTIIAHVPVSGGQVQETGDFELDG 1ejxC 1067 :DLVLTNALIVDHWGIVKADIGVKDGRIFAIGKAGNPD T0301 170 :PAAEIVLEF 1ejxC 1104 :IQPNVTIPI T0301 185 :GEDGGAIFPTGNLVDDL 1ejxC 1113 :GAATEVIAAEGKIVTAG T0301 209 :FKATMINA 1ejxC 1130 :GIDTHIHW T0301 217 :GIPTVFVNAE 1ejxC 1150 :GVTTMVGGGT T0301 234 :ELREEING 1ejxC 1160 :GPAAGTHA T0301 245 :QLARFERIRVAG 1ejxC 1173 :GPWYISRMLQAA T0301 272 :RQHTPKIAFVA 1ejxC 1185 :DSLPVNIGLLG T0301 283 :PPRDYRT 1ejxC 1201 :QPDALRE T0301 302 :LL 1ejxC 1214 :IG T0301 307 :LSM 1ejxC 1219 :HED T0301 313 :HHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERSA 1ejxC 1222 :WGATPAAIDCALTVADEMDIQVALHSDTLNESGF T0301 347 :VRFGHPSG 1ejxC 1268 :IHTFHTEG Number of specific fragments extracted= 15 number of extra gaps= 0 total=989 Number of alignments=55 # 1ejxC read from 1ejxC/merged-good-all-a2m # found chain 1ejxC in template set Warning: unaligning (T0301)V304 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ejxC)I1218 Warning: unaligning (T0301)A306 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ejxC)I1218 T0301 56 :AHIDGMG 1ejxC 1050 :VIRDGMG T0301 118 :AGLVDPARI 1ejxC 1057 :QGQMLAADC T0301 130 :GICEVRIWQANIGKTIIAHVPVSGGQVQETGDFELDG 1ejxC 1067 :DLVLTNALIVDHWGIVKADIGVKDGRIFAIGKAGNPD T0301 168 :TFPAAEIVL 1ejxC 1104 :IQPNVTIPI T0301 185 :GEDGGAIFPTGNLVDD 1ejxC 1113 :GAATEVIAAEGKIVTA T0301 208 :TFKATMINA 1ejxC 1129 :GGIDTHIHW T0301 217 :GIPTVFVNA 1ejxC 1150 :GVTTMVGGG T0301 231 :RGT 1ejxC 1159 :TGP T0301 236 :REEINGD 1ejxC 1162 :AAGTHAT T0301 245 :QLARFERIRVAG 1ejxC 1173 :GPWYISRMLQAA T0301 272 :RQHTPKIAFVAP 1ejxC 1185 :DSLPVNIGLLGK T0301 284 :PRDYRTA 1ejxC 1202 :PDALREQ T0301 292 :GK 1ejxC 1212 :GV T0301 302 :LL 1ejxC 1214 :IG T0301 307 :LSM 1ejxC 1219 :HED T0301 313 :HHAMMGTAAVAIGTAAAIPGTLVNLAAGGG 1ejxC 1222 :WGATPAAIDCALTVADEMDIQVALHSDTLN T0301 343 :ERSAVRFGHPSG 1ejxC 1264 :GGRTIHTFHTEG Number of specific fragments extracted= 17 number of extra gaps= 0 total=1006 Number of alignments=56 # 1ejxC read from 1ejxC/merged-good-all-a2m # found chain 1ejxC in template set Warning: unaligning (T0301)V304 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ejxC)I1218 Warning: unaligning (T0301)A306 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ejxC)I1218 T0301 117 :HAGLVDPARI 1ejxC 1056 :GQGQMLAADC T0301 130 :GICEVRIWQANIGKTIIAHVPVSGGQVQETGDFELD 1ejxC 1067 :DLVLTNALIVDHWGIVKADIGVKDGRIFAIGKAGNP T0301 169 :FPAAEIVLEF 1ejxC 1103 :DIQPNVTIPI T0301 185 :GEDGGAIFPTGNLVDD 1ejxC 1113 :GAATEVIAAEGKIVTA T0301 208 :TFKATMINA 1ejxC 1129 :GGIDTHIHW T0301 217 :GIPTVFVNAE 1ejxC 1150 :GVTTMVGGGT T0301 232 :GT 1ejxC 1160 :GP T0301 236 :REEINGD 1ejxC 1162 :AAGTHAT T0301 245 :QLARFERIRVAG 1ejxC 1173 :GPWYISRMLQAA T0301 272 :RQHTPKIAFVAPPRDYR 1ejxC 1185 :DSLPVNIGLLGKGNVSQ T0301 302 :LL 1ejxC 1214 :IG T0301 307 :LSMGKLHHA 1ejxC 1219 :HEDWGATPA T0301 317 :MGTAA 1ejxC 1228 :AIDCA T0301 324 :IGTAAAI 1ejxC 1233 :LTVADEM Number of specific fragments extracted= 14 number of extra gaps= 0 total=1020 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qyaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qyaA expands to /projects/compbio/data/pdb/1qya.pdb.gz 1qyaA:Skipped atom 1217, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1231, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1999, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2003, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2005, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2007, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2009, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2148, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2152, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2154, because occupancy 0.500 <= existing 0.500 in 1qyaA # T0301 read from 1qyaA/merged-good-all-a2m # 1qyaA read from 1qyaA/merged-good-all-a2m # adding 1qyaA to template set # found chain 1qyaA in template set Warning: unaligning (T0301)W100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qyaA)H74 Warning: unaligning (T0301)N106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qyaA)H74 Warning: unaligning (T0301)E128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qyaA)K102 Warning: unaligning (T0301)I131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qyaA)K102 Warning: unaligning (T0301)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qyaA)I154 Warning: unaligning (T0301)V198 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qyaA)I154 Warning: unaligning (T0301)E202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qyaA)T159 Warning: unaligning (T0301)V203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qyaA)T159 T0301 17 :GTSKGVFFRLEDLP 1qyaA 18 :GNSAGVVFPADNLS T0301 37 :GEARDRLFMRV 1qyaA 32 :EAQMQLIAREL T0301 67 :STSKCVILSKSSQPGHDVDYL 1qyaA 43 :GHSETAFLLHSDDSDVRIRYF T0301 93 :IDKPFVD 1qyaA 64 :TPTVEVP T0301 107 :LS 1qyaA 75 :AT T0301 109 :TGAGAFALHAGL 1qyaA 78 :AAHYVRAKVLGL T0301 127 :P 1qyaA 98 :S T0301 132 :CEVRIWQANIGKTIIAHV 1qyaA 103 :HRVTIEKHNDDYRISLEQ T0301 154 :GQVQ 1qyaA 121 :GTPG T0301 178 :FLDPSD 1qyaA 125 :FEPPLE T0301 185 :GE 1qyaA 131 :GE T0301 187 :DGGAIFP 1qyaA 144 :TEDDILP T0301 195 :GN 1qyaA 151 :GL T0301 199 :DDL 1qyaA 155 :QVA T0301 204 :PG 1qyaA 160 :GH T0301 210 :KATMINAGI 1qyaA 162 :SKVMIPLKP T0301 223 :VNAEEIGYR 1qyaA 172 :VDIDALSPD T0301 246 :LARFERIRV 1qyaA 181 :LNALTAISK T0301 259 :RMGL 1qyaA 190 :KIGC T0301 275 :TPKIAFVAPP 1qyaA 194 :NGFFPFQIRP T0301 298 :GDIDLLVRALSMGK 1qyaA 204 :GKNETDGRMFSPAI T0301 315 :AMMGTAAVAIGTAA 1qyaA 223 :PVTGNANGPMGAWL T0301 335 :VNLAAGGGERS 1qyaA 237 :VHHNVLPHDGN T0301 346 :AVRFGH 1qyaA 250 :RVKGHQ T0301 352 :PSGTLRVGAEASQA 1qyaA 261 :RDGMIEVTVTIRDN T0301 368 :E 1qyaA 275 :Q T0301 371 :VTKA 1qyaA 276 :PEKV Number of specific fragments extracted= 27 number of extra gaps= 2 total=1047 Number of alignments=58 # 1qyaA read from 1qyaA/merged-good-all-a2m # found chain 1qyaA in template set Warning: unaligning (T0301)N103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qyaA)H74 Warning: unaligning (T0301)N106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qyaA)H74 Warning: unaligning (T0301)I131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qyaA)K102 Warning: unaligning (T0301)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qyaA)I154 Warning: unaligning (T0301)V198 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qyaA)I154 Warning: unaligning (T0301)E202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qyaA)T159 Warning: unaligning (T0301)V203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qyaA)T159 T0301 17 :GTSKGVFFRLEDLP 1qyaA 18 :GNSAGVVFPADNLS T0301 37 :GEARDRLFMRV 1qyaA 32 :EAQMQLIAREL T0301 67 :STSKCVILSKSSQPGHDVDYL 1qyaA 43 :GHSETAFLLHSDDSDVRIRYF T0301 93 :IDKPFVD 1qyaA 64 :TPTVEVP T0301 107 :LSTGAGAFALH 1qyaA 75 :ATVAAHYVRAK T0301 118 :AGL 1qyaA 87 :LGL T0301 125 :RI 1qyaA 93 :TI T0301 132 :CEVRIWQANIGKTIIAHV 1qyaA 103 :HRVTIEKHNDDYRISLEQ T0301 154 :GQVQETG 1qyaA 121 :GTPGFEP T0301 181 :PSD 1qyaA 128 :PLE T0301 185 :GE 1qyaA 131 :GE T0301 187 :DGGAIFP 1qyaA 144 :TEDDILP T0301 195 :GN 1qyaA 151 :GL T0301 199 :DDL 1qyaA 155 :QVA T0301 208 :TFKATMINAGI 1qyaA 160 :GHSKVMIPLKP T0301 223 :VNAEEIGYR 1qyaA 172 :VDIDALSPD T0301 246 :LARFERIRV 1qyaA 181 :LNALTAISK T0301 259 :RMGL 1qyaA 190 :KIGC T0301 275 :TPKIAFVAPP 1qyaA 194 :NGFFPFQIRP T0301 298 :GDIDLLVRALSMGK 1qyaA 204 :GKNETDGRMFSPAI T0301 314 :HAMMGTAAVAIGTAAAIP 1qyaA 222 :DPVTGNANGPMGAWLVHH T0301 338 :AAG 1qyaA 240 :NVL T0301 341 :GGERSAVRFGH 1qyaA 245 :DGNVLRVKGHQ T0301 352 :PSGTLRVGAEASQA 1qyaA 261 :RDGMIEVTVTIRDN T0301 370 :TVTK 1qyaA 275 :QPEK Number of specific fragments extracted= 25 number of extra gaps= 2 total=1072 Number of alignments=59 # 1qyaA read from 1qyaA/merged-good-all-a2m # found chain 1qyaA in template set Warning: unaligning (T0301)W100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qyaA)H74 Warning: unaligning (T0301)N106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qyaA)H74 Warning: unaligning (T0301)E128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qyaA)K102 Warning: unaligning (T0301)I131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qyaA)K102 Warning: unaligning (T0301)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qyaA)I154 Warning: unaligning (T0301)V198 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qyaA)I154 Warning: unaligning (T0301)E202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qyaA)T159 Warning: unaligning (T0301)V203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qyaA)T159 T0301 17 :GTSKGVFFRLEDLP 1qyaA 18 :GNSAGVVFPADNLS T0301 37 :GEARDRLFMRV 1qyaA 32 :EAQMQLIAREL T0301 67 :STSKCVILSKSSQPGHDVDYL 1qyaA 43 :GHSETAFLLHSDDSDVRIRYF T0301 93 :IDKPFVD 1qyaA 64 :TPTVEVP T0301 107 :LSTGAGAFALH 1qyaA 75 :ATVAAHYVRAK T0301 118 :AGL 1qyaA 87 :LGL T0301 123 :P 1qyaA 98 :S T0301 132 :CEVRIWQANIGKTIIAHVP 1qyaA 103 :HRVTIEKHNDDYRISLEQG T0301 155 :QVQ 1qyaA 122 :TPG T0301 178 :FLDPSDD 1qyaA 125 :FEPPLEG T0301 187 :DGGAIFP 1qyaA 144 :TEDDILP T0301 195 :GN 1qyaA 151 :GL T0301 199 :DDL 1qyaA 155 :QVA T0301 208 :TFKATMINAGI 1qyaA 160 :GHSKVMIPLKP T0301 223 :VNAEEIGYR 1qyaA 172 :VDIDALSPD T0301 246 :LARFERIRVAG 1qyaA 181 :LNALTAISKKI T0301 273 :QHTPKIAFVAPPRDY 1qyaA 192 :GCNGFFPFQIRPGKN T0301 301 :DLLVRALSMGK 1qyaA 207 :ETDGRMFSPAI T0301 315 :AMMGTAAVAIGTAAAI 1qyaA 223 :PVTGNANGPMGAWLVH T0301 337 :LAAGGGERSAVRFG 1qyaA 239 :HNVLPHDGNVLRVK T0301 351 :H 1qyaA 255 :Q T0301 352 :PSGTLRVGAEASQA 1qyaA 261 :RDGMIEVTVTIRDN T0301 370 :TVTKA 1qyaA 275 :QPEKV Number of specific fragments extracted= 23 number of extra gaps= 2 total=1095 Number of alignments=60 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 60 Done printing distance constraints # command: