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/T0372/ # command:# Making conformation for sequence T0372 numbered 1 through 305 Created new target T0372 from T0372.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0372/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0372//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0372/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0372//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0372/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0372/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0372/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c27A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c27A expands to /projects/compbio/data/pdb/2c27.pdb.gz 2c27A:# T0372 read from 2c27A/merged-good-all-a2m # 2c27A read from 2c27A/merged-good-all-a2m # adding 2c27A to template set # found chain 2c27A in template set Warning: unaligning (T0372)P3 because first residue in template chain is (2c27A)D5 Warning: unaligning (T0372)D154 because of BadResidue code BAD_PEPTIDE in next template residue (2c27A)P146 T0372 4 :F 2c27A 6 :W # choosing archetypes in rotamer library T0372 5 :KDITLAD 2c27A 8 :SALTADE T0372 12 :RDTITAFTMKSDRRNCDLSFSNL 2c27A 19 :RALVTATTAVDGVAPVGEQVLRE T0372 38 :RFLYDTQFAVIDD 2c27A 42 :LGQQRTEHLLVAG T0372 51 :FLVFKFW 2c27A 62 :IGYLNLS T0372 58 :AGEQLAYMMPVGN 2c27A 73 :AGGAMAELVVHPQ T0372 71 :GD 2c27A 89 :RG T0372 73 :LKAVLRKLIED 2c27A 92 :GTAMARAALAK T0372 87 :EKHNFCMLG 2c27A 103 :TAGRNQFWA T0372 98 :SNMRADLEAILP 2c27A 112 :HGTLDPARATAS T0372 110 :ERFIFTEDRAYAD 2c27A 125 :LGLVGVRELIQMR T0372 131 :ATLK 2c27A 138 :RPLR T0372 151 :TYP 2c27A 142 :DIP T0372 155 :YEYTPI 2c27A 152 :VVIRTY T0372 161 :TPDRIQECLDLEAEWCK 2c27A 159 :GTSDDAELLRVNNAAFA T0372 179 :NNCDQQEGTGNERRALIYA 2c27A 176 :GHPEQGGWTAVQLAERRGE T0372 199 :HNFEALGLT 2c27A 195 :AWFDPDGLI T0372 209 :GILHVN 2c27A 204 :LAFGDS T0372 215 :GKIVAFTFGMPI 2c27A 215 :GRLLGFHWTKVH T0372 227 :NHETFGVHVEKADTS 2c27A 229 :HPGLGEVYVLGVDPA T0372 242 :IDGAYAMINYEFANRI 2c27A 246 :RRGLGQMLTSIGIVSL Number of specific fragments extracted= 21 number of extra gaps= 1 total=21 Number of alignments=1 # 2c27A read from 2c27A/merged-good-all-a2m # found chain 2c27A in template set Warning: unaligning (T0372)I2 because first residue in template chain is (2c27A)D5 Warning: unaligning (T0372)D154 because of BadResidue code BAD_PEPTIDE in next template residue (2c27A)P146 T0372 3 :PFKDITLAD 2c27A 6 :WRSALTADE T0372 12 :RDTITAFTMKSDRRNCDLSFSNLC 2c27A 19 :RALVTATTAVDGVAPVGEQVLREL T0372 39 :FLYDTQFAVIDD 2c27A 43 :GQQRTEHLLVAG T0372 51 :FLVFKF 2c27A 62 :IGYLNL T0372 57 :WAGE 2c27A 71 :RGAG T0372 61 :QLAYMMPVG 2c27A 78 :AELVVHPQS T0372 70 :NGD 2c27A 88 :RRG T0372 73 :LKAVLRKLIED 2c27A 92 :GTAMARAALAK T0372 87 :EKHNFCMLG 2c27A 103 :TAGRNQFWA T0372 99 :NMRADLEAIL 2c27A 113 :GTLDPARATA T0372 109 :PERFIFTEDRAYAD 2c27A 124 :ALGLVGVRELIQMR T0372 131 :ATLKG 2c27A 138 :RPLRD T0372 152 :YP 2c27A 143 :IP T0372 155 :YEYTPI 2c27A 152 :VVIRTY T0372 161 :TPDRIQECLDLEAEWCKVNN 2c27A 159 :GTSDDAELLRVNNAAFAGHP T0372 182 :DQQEGTGNERRALIYA 2c27A 179 :EQGGWTAVQLAERRGE T0372 199 :HNFEALGLT 2c27A 195 :AWFDPDGLI T0372 209 :GILHVN 2c27A 204 :LAFGDS T0372 215 :GKIVAFTFGMPIN 2c27A 215 :GRLLGFHWTKVHP T0372 228 :HETFGVHVEKADTS 2c27A 230 :PGLGEVYVLGVDPA T0372 242 :IDGAYAMINYEFANRIPE 2c27A 246 :RRGLGQMLTSIGIVSLAR Number of specific fragments extracted= 21 number of extra gaps= 1 total=42 Number of alignments=2 # 2c27A read from 2c27A/merged-good-all-a2m # found chain 2c27A in template set T0372 5 :KDITLADRDTITAFTMKS 2c27A 8 :SALTADEQRSVRALVTAT T0372 23 :DRRN 2c27A 30 :GVAP T0372 30 :SFSNLCSWRFLYDTQFAVIDD 2c27A 34 :VGEQVLRELGQQRTEHLLVAG T0372 51 :FLVFKFWAGEQ 2c27A 61 :IIGYLNLSPPR T0372 62 :LAYMMPVGNGD 2c27A 77 :MAELVVHPQSR T0372 73 :LKAVLRKLIEDADK 2c27A 92 :GTAMARAALAKTAG T0372 88 :KHNFCMLGVCSNMRADLEAI 2c27A 106 :RNQFWAHGTLDPARATASAL T0372 111 :RFIFTE 2c27A 126 :GLVGVR T0372 122 :DYIYLRSDLATL 2c27A 132 :ELIQMRRPLRDI T0372 153 :PDYEYTPI 2c27A 150 :DGVVIRTY T0372 161 :TPDRIQECLDLEAEWCKVNNCDQQEGTGN 2c27A 159 :GTSDDAELLRVNNAAFAGHPEQGGWTAVQ T0372 198 :LHNFEALGLT 2c27A 188 :LAERRGEAWF T0372 208 :GGILH 2c27A 202 :LILAF T0372 214 :NGKIVAFTFGMPI 2c27A 214 :PGRLLGFHWTKVH T0372 227 :NHETFGVHVEKADTSI 2c27A 229 :HPGLGEVYVLGVDPAA T0372 243 :DGAYAMINYEFANRIPEQ 2c27A 247 :RGLGQMLTSIGIVSLARR Number of specific fragments extracted= 16 number of extra gaps= 0 total=58 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sqhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sqhA expands to /projects/compbio/data/pdb/1sqh.pdb.gz 1sqhA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0372 read from 1sqhA/merged-good-all-a2m # 1sqhA read from 1sqhA/merged-good-all-a2m # adding 1sqhA to template set # found chain 1sqhA in template set T0372 5 :KDITLAD 1sqhA 11 :RPLSDSE T0372 12 :RDTITAFTMKSDRRNCDLSF 1sqhA 19 :DELLDLYKVKFGIRNFHYLL T0372 32 :SNLCSWR 1sqhA 40 :YNQRKWD T0372 39 :FLYDTQFAVID 1sqhA 63 :SLRKQFYTHRR T0372 51 :FLVFKFWAGEQLAYMMPVGNGD 1sqhA 81 :TYVSLHRDIVQSVSFFSWQPDG T0372 77 :LRKLIED 1sqhA 106 :LWECLEQ T0372 87 :EKHNFCMLGVCSNMRADLEAIL 1sqhA 118 :WTQGALLTNVDLGFCNRVKELA T0372 109 :PERFIFTEDRAYADYIYLRSDLATLK 1sqhA 141 :SRGVTAIQPRQCFGMVLSHEDAFCAK T0372 152 :YPDYEYTPITPDRIQECLDL 1sqhA 171 :PSEFEIRRLRAEDAAMVHDS T0372 179 :NNC 1sqhA 191 :WPN T0372 183 :QQEGTGNERRALIYA 1sqhA 194 :KGEGSLTYLQALVRF T0372 204 :LGLTGGILHVNGKIVAFTFGMPIN 1sqhA 209 :NKSLGICRSDTGELIAWIFQNDFS T0372 233 :VHVEKADTS 1sqhA 234 :LGMLQVLPK T0372 242 :IDGAYAMINYEFANRI 1sqhA 245 :RRGLGGLLAAAMSREI Number of specific fragments extracted= 14 number of extra gaps= 0 total=72 Number of alignments=4 # 1sqhA read from 1sqhA/merged-good-all-a2m # found chain 1sqhA in template set T0372 5 :KDITLAD 1sqhA 11 :RPLSDSE T0372 12 :RDTITAFTMKSDRRNCDLSF 1sqhA 19 :DELLDLYKVKFGIRNFHYLL T0372 32 :SNLCSWR 1sqhA 40 :YNQRKWD T0372 39 :FLYD 1sqhA 63 :SLRK T0372 44 :QFAVIDD 1sqhA 67 :QFYTHRR T0372 51 :FLVFKFWAGEQLAYMMPVGNGD 1sqhA 81 :TYVSLHRDIVQSVSFFSWQPDG T0372 73 :LKAVLRK 1sqhA 106 :LWECLEQ T0372 87 :EKHNFCMLGVCSNMRADLEAIL 1sqhA 118 :WTQGALLTNVDLGFCNRVKELA T0372 109 :PERFIFTEDRAYADYIYLRSDLATLK 1sqhA 141 :SRGVTAIQPRQCFGMVLSHEDAFCAK T0372 152 :YPDYEYTPITPDRIQEC 1sqhA 171 :PSEFEIRRLRAEDAAMV T0372 176 :CKVNN 1sqhA 188 :HDSWP T0372 182 :DQQEGTGNERRALIYA 1sqhA 193 :NKGEGSLTYLQALVRF T0372 204 :LGLT 1sqhA 209 :NKSL T0372 209 :GILHVN 1sqhA 213 :GICRSD T0372 215 :GKIVAFTFGMPIN 1sqhA 220 :GELIAWIFQNDFS T0372 233 :VHVEKADTS 1sqhA 234 :LGMLQVLPK T0372 242 :IDGAYAMINYEFANRIPE 1sqhA 245 :RRGLGGLLAAAMSREIAR Number of specific fragments extracted= 17 number of extra gaps= 0 total=89 Number of alignments=5 # 1sqhA read from 1sqhA/merged-good-all-a2m # found chain 1sqhA in template set Warning: unaligning (T0372)D297 because last residue in template chain is (1sqhA)S303 T0372 4 :FKDITLADRDTITAFTMK 1sqhA 10 :LRPLSDSEVDELLDLYKV T0372 22 :SDRRNCDLSFSNLCSWR 1sqhA 30 :GIRNFHYLLLYNQRKWD T0372 39 :FLYDTQFAVIDD 1sqhA 62 :ISLRKQFYTHRR T0372 51 :FLVFKFWAGEQLAYMMPVGNGDLKAVLRKLIE 1sqhA 81 :TYVSLHRDIVQSVSFFSWQPDGAAELWECLEQ T0372 87 :EKHNFCMLGVCSNMRADLEAILPE 1sqhA 118 :WTQGALLTNVDLGFCNRVKELAVS T0372 111 :RFIFTEDRAYADYIYLRSDLATLK 1sqhA 143 :GVTAIQPRQCFGMVLSHEDAFCAK T0372 153 :PDYEYTPITPDRIQECLDL 1sqhA 172 :SEFEIRRLRAEDAAMVHDS T0372 178 :VNNCDQQ 1sqhA 191 :WPNKGEG T0372 187 :TGNERRALIYA 1sqhA 198 :SLTYLQALVRF T0372 206 :LTGGILHVNG 1sqhA 209 :NKSLGICRSD T0372 216 :KIVAFTFGMPIN 1sqhA 221 :ELIAWIFQNDFS T0372 232 :GVHVEKADTSID 1sqhA 233 :GLGMLQVLPKAE T0372 244 :GAYAMINYEFANRIPE 1sqhA 247 :GLGGLLAAAMSREIAR T0372 260 :Q 1sqhA 267 :T T0372 261 :YIYINR 1sqhA 269 :TAWIVA T0372 268 :EDLGIEG 1sqhA 275 :TNWRSEA T0372 275 :LR 1sqhA 283 :LK T0372 279 :KLSYQPVTILEKYMACLK 1sqhA 285 :RIGYQKDLVNEWIKLVPN Number of specific fragments extracted= 18 number of extra gaps= 0 total=107 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cy2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cy2A expands to /projects/compbio/data/pdb/2cy2.pdb.gz 2cy2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0372 read from 2cy2A/merged-good-all-a2m # 2cy2A read from 2cy2A/merged-good-all-a2m # adding 2cy2A to template set # found chain 2cy2A in template set T0372 156 :EYTPITPDRIQECLDLE 2cy2A 2 :RIRRAGLEDLPGVARVL T0372 173 :AEWCK 2cy2A 20 :DTWRA T0372 178 :VNNCDQQE 2cy2A 26 :YRGVVPEA T0372 186 :GTGNERRALIYALHNFEALGLTGGILHVNGKIVAFTFGMPIN 2cy2A 39 :SYEGQAERWAQRLKTPTWPGRLFVAESESGEVVGFAAFGPDR T0372 228 :HE 2cy2A 85 :PG T0372 230 :TFGVHVEKADTS 2cy2A 88 :TAELWAIYVLPT T0372 242 :IDGAYAMINYEFANRIPE 2cy2A 102 :RKGLGRALFHEGARLLQA T0372 260 :QYIYI 2cy2A 121 :GYGRM Number of specific fragments extracted= 8 number of extra gaps= 0 total=115 Number of alignments=7 # 2cy2A read from 2cy2A/merged-good-all-a2m # found chain 2cy2A in template set T0372 156 :EYTPITPDRIQECLDLE 2cy2A 2 :RIRRAGLEDLPGVARVL T0372 173 :AEWCK 2cy2A 20 :DTWRA T0372 178 :VNNC 2cy2A 26 :YRGV T0372 182 :DQQEGTGNERRALIYALHNF 2cy2A 31 :PEAFLEGLSYEGQAERWAQR T0372 202 :EALGLTGGILHVN 2cy2A 54 :PTWPGRLFVAESE T0372 215 :GKIVAFTFGMPIN 2cy2A 68 :GEVVGFAAFGPDR T0372 228 :HE 2cy2A 85 :PG T0372 230 :TFGVHVEKADTS 2cy2A 88 :TAELWAIYVLPT T0372 242 :IDGAYAMINYEFANRIPE 2cy2A 102 :RKGLGRALFHEGARLLQA T0372 260 :QYIYIN 2cy2A 121 :GYGRML Number of specific fragments extracted= 10 number of extra gaps= 0 total=125 Number of alignments=8 # 2cy2A read from 2cy2A/merged-good-all-a2m # found chain 2cy2A in template set T0372 156 :EYTPITPDRIQECLDLEAEWCKVN 2cy2A 2 :RIRRAGLEDLPGVARVLVDTWRAT T0372 180 :NCDQQ 2cy2A 28 :GVVPE T0372 185 :EGTGNERR 2cy2A 38 :LSYEGQAE T0372 196 :YALHNFEALGLTGGILHV 2cy2A 46 :RWAQRLKTPTWPGRLFVA T0372 214 :NGKIVAFTFGMPIN 2cy2A 67 :SGEVVGFAAFGPDR T0372 228 :HE 2cy2A 85 :PG T0372 230 :TFGVHVEKADTSI 2cy2A 88 :TAELWAIYVLPTW T0372 243 :DGAYAMINYEFANRIPEQ 2cy2A 103 :KGLGRALFHEGARLLQAE T0372 261 :YIYINREE 2cy2A 126 :LVWVLKEN Number of specific fragments extracted= 9 number of extra gaps= 0 total=134 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aj6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aj6A expands to /projects/compbio/data/pdb/2aj6.pdb.gz 2aj6A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 91, because occupancy 0.5 <= existing 0.500 in 2aj6A Skipped atom 95, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 170, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 172, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 174, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 178, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 180, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 301, because occupancy 0.400 <= existing 0.600 in 2aj6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 2aj6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 2aj6A Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 2aj6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 946, because occupancy 0.500 <= existing 0.500 in 2aj6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 950, because occupancy 0.500 <= existing 0.500 in 2aj6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 952, because occupancy 0.500 <= existing 0.500 in 2aj6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 956, because occupancy 0.500 <= existing 0.500 in 2aj6A # T0372 read from 2aj6A/merged-good-all-a2m # 2aj6A read from 2aj6A/merged-good-all-a2m # adding 2aj6A to template set # found chain 2aj6A in template set Warning: unaligning (T0372)N265 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2aj6A)N117 T0372 156 :EYTPIT 2aj6A 0 :HMRTLN T0372 163 :DRIQECLDLEAEWCKVNNCDQQEGTGNERRALIYALHNFEALGLTGGILHVNGKIVAFTFGMPINHE 2aj6A 10 :NYIKQIANIHETLLSQVESNYKCTKLSIALRYEMICSRLEHTNDKIYIYENEGQLIAFIWGHFSNEK T0372 230 :TFGVHVEKADTSID 2aj6A 78 :MVNIELLYVEPQFR T0372 244 :GAYAMINYEFANRIPE 2aj6A 94 :GIATQLKIALEKWAKT T0372 260 :QYIYI 2aj6A 111 :NAKRI Number of specific fragments extracted= 5 number of extra gaps= 1 total=139 Number of alignments=10 # 2aj6A read from 2aj6A/merged-good-all-a2m # found chain 2aj6A in template set Warning: unaligning (T0372)N265 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2aj6A)N117 T0372 156 :EYTPIT 2aj6A 0 :HMRTLN T0372 162 :PDRIQECLDLEAEWCKVNN 2aj6A 9 :HNYIKQIANIHETLLSQVE T0372 182 :DQQEGTGNERRALIYAL 2aj6A 28 :SNYKCTKLSIALRYEMI T0372 199 :HNFEALGLTGGILHVNGKIVAFTFGMPIN 2aj6A 46 :SRLEHTNDKIYIYENEGQLIAFIWGHFSN T0372 228 :HETFGVHVEKADTSID 2aj6A 76 :KSMVNIELLYVEPQFR T0372 244 :GAYAMINYEFANRIPE 2aj6A 94 :GIATQLKIALEKWAKT T0372 260 :QYIYI 2aj6A 111 :NAKRI Number of specific fragments extracted= 7 number of extra gaps= 1 total=146 Number of alignments=11 # 2aj6A read from 2aj6A/merged-good-all-a2m # found chain 2aj6A in template set Warning: unaligning (T0372)Y155 because first residue in template chain is (2aj6A)H-1 T0372 156 :EYTPIT 2aj6A 0 :HMRTLN T0372 162 :PDRIQECLDLEAEWCKVNNCDQQEGTGNERRALIYALHNFEALGLTGGILHVNGKIVAFTFGMPINHET 2aj6A 9 :HNYIKQIANIHETLLSQVESNYKCTKLSIALRYEMICSRLEHTNDKIYIYENEGQLIAFIWGHFSNEKS T0372 232 :GVHVEK 2aj6A 78 :MVNIEL T0372 238 :ADTSID 2aj6A 86 :VEPQFR T0372 244 :GAYAMINYEFANRIP 2aj6A 94 :GIATQLKIALEKWAK Number of specific fragments extracted= 5 number of extra gaps= 0 total=151 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ne9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0372 read from 1ne9A/merged-good-all-a2m # 1ne9A read from 1ne9A/merged-good-all-a2m # found chain 1ne9A in training set T0372 6 :DITLADRDTITAFTMKSDRRNCDLSFSNLCSWRFLYD 1ne9A 2 :VLNLNDPQAVERYEEFMRQSPYGQVTQDLGWAKVKNN T0372 43 :TQFAVID 1ne9A 41 :PVDVYLE T0372 50 :D 1ne9A 49 :D T0372 51 :FLVFKFWA 1ne9A 55 :AAMSMLLG T0372 59 :GEQLAYMM 1ne9A 66 :TDKKFAYA T0372 67 :PVGNGDLKAVLRKLIEDADKE 1ne9A 77 :PVMDVTDVDLLDRLVDEAVKA T0372 88 :KHNFCMLGV 1ne9A 99 :DGRAYVLRF T0372 97 :CSNMRADLEAI 1ne9A 114 :SDEFNTTLQDH T0372 109 :PERFIFTEDR 1ne9A 137 :GMHATIQPRL T0372 119 :AYAD 1ne9A 148 :MVLD T0372 127 :RSDLATLKG 1ne9A 152 :LTKFPDAKT T0372 139 :QAKRNHINRFRNTY 1ne9A 167 :SKTKSKIKRPFRDG T0372 155 :YEYT 1ne9A 181 :VEVH T0372 159 :PITPDRIQECLDLEAEWCKVNNCDQQEGT 1ne9A 186 :GNSATELDEFFKTYTTMAERHGITHRPIE T0372 193 :ALIYALHNFEALGLTGGILHVNGKIVAFTFGMPINHETFGVHVEKADTSIDGAYAMINYEFANRIPE 1ne9A 215 :YFQRMQAAFDADTMRIFVAEREGKLLSTGIALKYGRKIWYMYAGSMDGNTYYAPYAVQSEMIQWALD T0372 260 :QYIYIN 1ne9A 283 :NTDLYD T0372 275 :LRKAKLSYQPVTILEKYMACLKD 1ne9A 289 :LGGIESESTDDSLYVFKHVFVKD Number of specific fragments extracted= 17 number of extra gaps= 0 total=168 Number of alignments=13 # 1ne9A read from 1ne9A/merged-good-all-a2m # found chain 1ne9A in training set T0372 7 :ITLADRDTITAFT 1ne9A 3 :LNLNDPQAVERYE T0372 20 :MKSDRR 1ne9A 19 :RQSPYG T0372 26 :NCDLSFSNL 1ne9A 27 :TQDLGWAKV T0372 38 :RFLYDTQFAVIDD 1ne9A 36 :KNNWEPVDVYLED T0372 51 :FLVFKFWAGE 1ne9A 54 :IAAMSMLLGD T0372 61 :QLAY 1ne9A 69 :KFAY T0372 65 :MMPVGNGDLKAVLRKLIEDADKE 1ne9A 75 :KGPVMDVTDVDLLDRLVDEAVKA T0372 88 :KHNFCMLGVC 1ne9A 99 :DGRAYVLRFD T0372 98 :SNMRADLEA 1ne9A 115 :DEFNTTLQD T0372 108 :LPERFI 1ne9A 124 :HGYVTR T0372 123 :YIYLRSDL 1ne9A 148 :MVLDLTKF T0372 131 :ATLKGK 1ne9A 162 :LDLYPS T0372 140 :AKRNHINRFRNTY 1ne9A 168 :KTKSKIKRPFRDG T0372 155 :YEYT 1ne9A 181 :VEVH T0372 159 :PITPDRIQECLDLEAEWCKVNNCDQQEGT 1ne9A 186 :GNSATELDEFFKTYTTMAERHGITHRPIE T0372 193 :ALIYALHNFEALGLTGGILHVNGKIVAFTFGMPINHETFGVHVEKADTSIDGAYAMINYEFANRIPE 1ne9A 215 :YFQRMQAAFDADTMRIFVAEREGKLLSTGIALKYGRKIWYMYAGSMDGNTYYAPYAVQSEMIQWALD T0372 260 :QYIYIN 1ne9A 283 :NTDLYD T0372 275 :LRKAKLSYQPVTILEKYMACLKD 1ne9A 289 :LGGIESESTDDSLYVFKHVFVKD Number of specific fragments extracted= 18 number of extra gaps= 0 total=186 Number of alignments=14 # 1ne9A read from 1ne9A/merged-good-all-a2m # found chain 1ne9A in training set T0372 8 :TLADRDTITAFTMKSDRRNCDLSFSN 1ne9A 7 :DPQAVERYEEFMRQSPYGQVTQDLGW T0372 35 :CSWRFLYDTQFAVIDD 1ne9A 33 :AKVKNNWEPVDVYLED T0372 51 :FLVFKFWA 1ne9A 55 :AAMSMLLG T0372 60 :EQ 1ne9A 63 :DT T0372 62 :LAYM 1ne9A 69 :KFAY T0372 66 :MPVGNGD 1ne9A 77 :PVMDVTD T0372 73 :LKAVLRKLIEDAD 1ne9A 87 :LDRLVDEAVKALD T0372 89 :HNF 1ne9A 100 :GRA T0372 92 :CMLGVCSNMRADLEAI 1ne9A 109 :PEVAYSDEFNTTLQDH T0372 113 :I 1ne9A 127 :V T0372 115 :TEDRAYAD 1ne9A 128 :TRNRNVAD T0372 124 :I 1ne9A 149 :V T0372 129 :DLATLKGKKF 1ne9A 151 :DLTKFPDAKT T0372 139 :QAKRNHINRFRNT 1ne9A 167 :SKTKSKIKRPFRD T0372 154 :DYEYTP 1ne9A 180 :GVEVHS T0372 160 :ITPDRIQECLDLEAEWCKVNNCDQQEGTG 1ne9A 187 :NSATELDEFFKTYTTMAERHGITHRPIEY T0372 194 :LIYALHNFEALGLTGGILHVNGKIVAFTFGMPINHETFGVHVEKADTSIDGAYAMINYEFANRIPE 1ne9A 216 :FQRMQAAFDADTMRIFVAEREGKLLSTGIALKYGRKIWYMYAGSMDGNTYYAPYAVQSEMIQWALD T0372 260 :QYIYIN 1ne9A 283 :NTDLYD Number of specific fragments extracted= 18 number of extra gaps= 0 total=204 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mk4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0372 read from 1mk4A/merged-good-all-a2m # 1mk4A read from 1mk4A/merged-good-all-a2m # found chain 1mk4A in training set Warning: unaligning (T0372)D154 because first residue in template chain is (1mk4A)H0 T0372 155 :YEYTPITPDRIQECLDLEAEWCKVNNCDQQEGT 1mk4A 1 :MDIRTITSSDYEMVTSVLNEWWGGRQLKEKLPR T0372 193 :ALIYA 1mk4A 34 :LFFEH T0372 201 :FEA 1mk4A 39 :FQD T0372 206 :LT 1mk4A 42 :TS T0372 209 :GILHVNGKIVAFTFGMPI 1mk4A 44 :FITSEHNSMTGFLIGFQS T0372 227 :NHETFGVHVEKADTSID 1mk4A 64 :DPETAYIHFSGVHPDFR T0372 244 :GAYAMINYEFANRIPE 1mk4A 83 :QIGKQLYDVFIETVKQ T0372 260 :QYIYIN 1mk4A 100 :GCTRVK T0372 278 :AKLSYQPVTILEKYM 1mk4A 106 :CVTSPVNKVSIAYHT Number of specific fragments extracted= 9 number of extra gaps= 0 total=213 Number of alignments=16 # 1mk4A read from 1mk4A/merged-good-all-a2m # found chain 1mk4A in training set Warning: unaligning (T0372)D154 because first residue in template chain is (1mk4A)H0 T0372 155 :YEYTPITPDRIQECLDLEAEWCKVNNCDQQEGT 1mk4A 1 :MDIRTITSSDYEMVTSVLNEWWGGRQLKEKLPR T0372 193 :ALIYA 1mk4A 34 :LFFEH T0372 201 :FEAL 1mk4A 39 :FQDT T0372 208 :GGILHVNGKIVAFTFGMPIN 1mk4A 43 :SFITSEHNSMTGFLIGFQSQ T0372 228 :HETFGVHVEKADTSID 1mk4A 65 :PETAYIHFSGVHPDFR T0372 244 :GAYAMINYEFANRIPE 1mk4A 83 :QIGKQLYDVFIETVKQ T0372 260 :QYIYIN 1mk4A 100 :GCTRVK T0372 278 :AKLSYQPVTILEKYMA 1mk4A 106 :CVTSPVNKVSIAYHTK Number of specific fragments extracted= 8 number of extra gaps= 0 total=221 Number of alignments=17 # 1mk4A read from 1mk4A/merged-good-all-a2m # found chain 1mk4A in training set Warning: unaligning (T0372)D154 because first residue in template chain is (1mk4A)H0 T0372 155 :YEYTPITPDRIQECLDLEAEWCKVNNCDQQEGTG 1mk4A 1 :MDIRTITSSDYEMVTSVLNEWWGGRQLKEKLPRL T0372 197 :ALHNFEAL 1mk4A 35 :FFEHFQDT T0372 209 :GILHVNGKIVAFTFGMPI 1mk4A 44 :FITSEHNSMTGFLIGFQS T0372 227 :NHETFGVHVEKADTSIDG 1mk4A 64 :DPETAYIHFSGVHPDFRK T0372 245 :AYAMINYEFANRIPEQ 1mk4A 84 :IGKQLYDVFIETVKQR Number of specific fragments extracted= 5 number of extra gaps= 0 total=226 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fe7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fe7A expands to /projects/compbio/data/pdb/2fe7.pdb.gz 2fe7A:# T0372 read from 2fe7A/merged-good-all-a2m # 2fe7A read from 2fe7A/merged-good-all-a2m # adding 2fe7A to template set # found chain 2fe7A in template set Warning: unaligning (T0372)Y155 because first residue in template chain is (2fe7A)L3 Warning: unaligning (T0372)D243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fe7A)G96 T0372 156 :EYTPITPDRIQECLDLEAEWCKVNNCDQQEGTGNE 2fe7A 4 :EIRPAVPADAEQILAFIIELADYERARHEVVTDVE T0372 193 :ALIYAL 2fe7A 39 :GIRRSL T0372 200 :NFEALGLTGGILHVNGKIVAFTFGMPI 2fe7A 45 :FAEGSPTRALMCLSEGRPIGYAVFFYS T0372 227 :NHE 2fe7A 73 :STW T0372 230 :TFGVHVEKADTSI 2fe7A 80 :GIYLEDLYVTPEY T0372 245 :AYAMINYEFANRIPE 2fe7A 97 :AGRRLLRELAREAVA T0372 260 :QYIYIN 2fe7A 113 :DCGRLE Number of specific fragments extracted= 7 number of extra gaps= 1 total=233 Number of alignments=19 # 2fe7A read from 2fe7A/merged-good-all-a2m # found chain 2fe7A in template set Warning: unaligning (T0372)Y155 because first residue in template chain is (2fe7A)L3 Warning: unaligning (T0372)D243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fe7A)G96 T0372 156 :EYTPITPDRIQECLDLEAEWCKVNNCDQQEGTGNE 2fe7A 4 :EIRPAVPADAEQILAFIIELADYERARHEVVTDVE T0372 193 :ALIYAL 2fe7A 39 :GIRRSL T0372 200 :NFEALGLTGGILHVNGKIVAFTFGMPIN 2fe7A 45 :FAEGSPTRALMCLSEGRPIGYAVFFYSY T0372 230 :TFGVHVEKADTSI 2fe7A 80 :GIYLEDLYVTPEY T0372 245 :AYAMINYEFANRIPE 2fe7A 97 :AGRRLLRELAREAVA T0372 260 :QYIYIN 2fe7A 113 :DCGRLE T0372 280 :LSYQ 2fe7A 122 :LDWN T0372 285 :VTILEKYMA 2fe7A 126 :QPAIDFYRS Number of specific fragments extracted= 8 number of extra gaps= 1 total=241 Number of alignments=20 # 2fe7A read from 2fe7A/merged-good-all-a2m # found chain 2fe7A in template set Warning: unaligning (T0372)Y155 because first residue in template chain is (2fe7A)L3 Warning: unaligning (T0372)D243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fe7A)G96 Warning: unaligning (T0372)G244 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fe7A)G96 T0372 156 :EYTPITPDRIQECLDLEAEWCKVNNCDQQ 2fe7A 4 :EIRPAVPADAEQILAFIIELADYERARHE T0372 185 :EGTGNERRAL 2fe7A 35 :TDVEGIRRSL T0372 200 :NFEALGLTGGILHVNGKIVAFTFGMPI 2fe7A 45 :FAEGSPTRALMCLSEGRPIGYAVFFYS T0372 227 :NHE 2fe7A 73 :STW T0372 231 :FGVHVEK 2fe7A 79 :NGIYLED T0372 238 :ADTSI 2fe7A 88 :VTPEY T0372 245 :AYAMINYEFANRIPEQ 2fe7A 97 :AGRRLLRELAREAVAN Number of specific fragments extracted= 7 number of extra gaps= 1 total=248 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wwzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0372 read from 1wwzA/merged-good-all-a2m # 1wwzA read from 1wwzA/merged-good-all-a2m # found chain 1wwzA in training set T0372 153 :PDYEYTPIT 1wwzA 2 :DEIKIEKLK T0372 162 :PDRIQECLDLEAEWC 1wwzA 14 :KKALNELIDVYMSGY T0372 179 :NNCDQ 1wwzA 29 :EGLEE T0372 184 :QEGTGNERRALIYALHNFEAL 1wwzA 36 :GEGRDYARNYIKWCWKKASDG T0372 208 :GGILHVNGKIVAFTFG 1wwzA 57 :FFVAKVGDKIVGFIVC T0372 224 :MPI 1wwzA 76 :WFS T0372 227 :NHE 1wwzA 81 :EGR T0372 230 :TFGVHVEKADTS 1wwzA 85 :VGAIHEFVVDKK T0372 242 :IDGAYAMINYEFANRIPEQYIYIN 1wwzA 99 :GKGIGRKLLITCLDFLGKYNDTIE T0372 270 :L 1wwzA 123 :L T0372 280 :LSYQPVTILEKYMA 1wwzA 125 :VGEKNYGAMNLYEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=259 Number of alignments=22 # 1wwzA read from 1wwzA/merged-good-all-a2m # found chain 1wwzA in training set T0372 153 :PDYEYTPIT 1wwzA 2 :DEIKIEKLK T0372 162 :PDRIQECLDLEAEWC 1wwzA 14 :KKALNELIDVYMSGY T0372 179 :NNCDQ 1wwzA 29 :EGLEE T0372 184 :QEGTGNERRALIYALHNFEAL 1wwzA 36 :GEGRDYARNYIKWCWKKASDG T0372 208 :GGILHVNGKIVAFTFG 1wwzA 57 :FFVAKVGDKIVGFIVC T0372 224 :MPIN 1wwzA 76 :WFSK T0372 228 :HETF 1wwzA 82 :GRIV T0372 232 :GVHVEKADTS 1wwzA 87 :AIHEFVVDKK T0372 242 :IDGAYAMINYEFANRIPEQYIYIN 1wwzA 99 :GKGIGRKLLITCLDFLGKYNDTIE T0372 270 :LG 1wwzA 123 :LW T0372 280 :LSYQPVTILEKYMAC 1wwzA 125 :VGEKNYGAMNLYEKF Number of specific fragments extracted= 11 number of extra gaps= 0 total=270 Number of alignments=23 # 1wwzA read from 1wwzA/merged-good-all-a2m # found chain 1wwzA in training set T0372 154 :DYEYTPIT 1wwzA 3 :EIKIEKLK T0372 162 :PDRIQECLDLEAEWC 1wwzA 14 :KKALNELIDVYMSGY T0372 179 :NNCDQ 1wwzA 29 :EGLEE T0372 184 :QEGTGNERRALIYALHNFEAL 1wwzA 36 :GEGRDYARNYIKWCWKKASDG T0372 209 :GILHVNGKIVAFTFGMPI 1wwzA 58 :FVAKVGDKIVGFIVCDKD T0372 228 :HE 1wwzA 82 :GR T0372 230 :TFGVHVEKADTSI 1wwzA 85 :VGAIHEFVVDKKF T0372 243 :DGAYAMINYEFANRIPEQYIYI 1wwzA 100 :KGIGRKLLITCLDFLGKYNDTI Number of specific fragments extracted= 8 number of extra gaps= 0 total=278 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tiqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tiqA expands to /projects/compbio/data/pdb/1tiq.pdb.gz 1tiqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0372 read from 1tiqA/merged-good-all-a2m # 1tiqA read from 1tiqA/merged-good-all-a2m # adding 1tiqA to template set # found chain 1tiqA in template set Warning: unaligning (T0372)D154 because first residue in template chain is (1tiqA)S2 T0372 155 :YEYTPITPDRIQECLDLEAEWCK 1tiqA 3 :VKMKKCSREDLQTLQQLSIETFN T0372 178 :V 1tiqA 28 :F T0372 183 :QQEGTGNERRALIY 1tiqA 29 :KEQNSPENMKAYLE T0372 197 :ALHNFEALGLTGGILHVNGKIVAFTFG 1tiqA 50 :LEKELSNMSSQFFFIYFDHEIAGYVKV T0372 224 :MPINHETFGV 1tiqA 84 :EEMGAESLEI T0372 234 :HVEKADTS 1tiqA 95 :RIYIKNSF T0372 242 :IDGAYAMINYEFANRIPE 1tiqA 104 :KHGLGKHLLNKAIEIALE T0372 260 :QYIYIN 1tiqA 123 :NKKNIW T0372 270 :LG 1tiqA 129 :LG T0372 281 :S 1tiqA 133 :E T0372 283 :QP 1tiqA 134 :KN T0372 289 :EKYMACLKDH 1tiqA 136 :ENAIAFYKKM Number of specific fragments extracted= 12 number of extra gaps= 0 total=290 Number of alignments=25 # 1tiqA read from 1tiqA/merged-good-all-a2m # found chain 1tiqA in template set Warning: unaligning (T0372)D154 because first residue in template chain is (1tiqA)S2 T0372 155 :YEYTPITPDRIQECLDLEAEWCKVNN 1tiqA 3 :VKMKKCSREDLQTLQQLSIETFNDTF T0372 183 :QQEGTGNERRALIY 1tiqA 29 :KEQNSPENMKAYLE T0372 198 :LHNFEALGLTGGILHVNGKIVAFTFG 1tiqA 51 :EKELSNMSSQFFFIYFDHEIAGYVKV T0372 224 :MPINHETFGVHVEKADTS 1tiqA 84 :EEMGAESLEIERIYIKNS T0372 242 :IDGAYAMINYEFANRIPE 1tiqA 104 :KHGLGKHLLNKAIEIALE T0372 260 :QYIYIN 1tiqA 123 :NKKNIW T0372 270 :LG 1tiqA 129 :LG T0372 280 :LSYQ 1tiqA 132 :WEKN T0372 285 :VTI 1tiqA 136 :ENA T0372 292 :MACLKDH 1tiqA 139 :IAFYKKM Number of specific fragments extracted= 10 number of extra gaps= 0 total=300 Number of alignments=26 # 1tiqA read from 1tiqA/merged-good-all-a2m # found chain 1tiqA in template set Warning: unaligning (T0372)D154 because first residue in template chain is (1tiqA)S2 T0372 155 :YEYTPITPDRIQECLDLEAEWCKVNNCDQQ 1tiqA 3 :VKMKKCSREDLQTLQQLSIETFNDTFKEQN T0372 185 :EGTGNERR 1tiqA 35 :ENMKAYLE T0372 196 :YALHNFEALGLTGGILHVNGKIVAFTFGMP 1tiqA 49 :QLEKELSNMSSQFFFIYFDHEIAGYVKVNI T0372 226 :INHETFGVHVEKADTSI 1tiqA 86 :MGAESLEIERIYIKNSF T0372 243 :DGAYAMINYEFANRIPE 1tiqA 105 :HGLGKHLLNKAIEIALE T0372 260 :QYIYIN 1tiqA 125 :KNIWLG Number of specific fragments extracted= 6 number of extra gaps= 0 total=306 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yvoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yvoA expands to /projects/compbio/data/pdb/1yvo.pdb.gz 1yvoA:Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 422, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 764, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 766, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 778, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 1yvoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0372 read from 1yvoA/merged-good-all-a2m # 1yvoA read from 1yvoA/merged-good-all-a2m # adding 1yvoA to template set # found chain 1yvoA in template set Warning: unaligning (T0372)E156 because first residue in template chain is (1yvoA)S4 T0372 157 :YTPITPDRIQECLDLEAEWCKVNNC 1yvoA 5 :IRDAGVADLPGILAIYNDAVGNTTA T0372 182 :DQQEGTGNERRALIYA 1yvoA 32 :NETPVDLANRQAWFDT T0372 199 :HNFEALGLT 1yvoA 48 :RARQGYPIL T0372 209 :GILHVNGKIVAFTFGMPIN 1yvoA 57 :VASDAAGEVLGYASYGDWR T0372 230 :TFGVHVEKADTS 1yvoA 83 :TVEHSVYVRDDQ T0372 242 :IDGAYAMINYEFANRIPE 1yvoA 96 :GKGLGVQLLQALIERARA T0372 260 :QYIYIN 1yvoA 115 :GLHVMV Number of specific fragments extracted= 7 number of extra gaps= 0 total=313 Number of alignments=28 # 1yvoA read from 1yvoA/merged-good-all-a2m # found chain 1yvoA in template set Warning: unaligning (T0372)E156 because first residue in template chain is (1yvoA)S4 T0372 157 :YTPITPDRIQECLDLEAEWCKVNNC 1yvoA 5 :IRDAGVADLPGILAIYNDAVGNTTA T0372 182 :DQQEGTGNERRALIYA 1yvoA 32 :NETPVDLANRQAWFDT T0372 199 :HNFEALGLT 1yvoA 48 :RARQGYPIL T0372 209 :GILHVNGKIVAFTFGMPIN 1yvoA 57 :VASDAAGEVLGYASYGDWR T0372 230 :TFGVHVEKADTS 1yvoA 83 :TVEHSVYVRDDQ T0372 242 :IDGAYAMINYEFANRIPE 1yvoA 96 :GKGLGVQLLQALIERARA T0372 260 :QYIYIN 1yvoA 115 :GLHVMV T0372 278 :AKLSYQPVTILEKYMAC 1yvoA 121 :AAIESGNAASIGLHRRL Number of specific fragments extracted= 8 number of extra gaps= 0 total=321 Number of alignments=29 # 1yvoA read from 1yvoA/merged-good-all-a2m # found chain 1yvoA in template set Warning: unaligning (T0372)E156 because first residue in template chain is (1yvoA)S4 T0372 157 :YTPITPDRIQECLDLEAEWCKVN 1yvoA 5 :IRDAGVADLPGILAIYNDAVGNT T0372 182 :DQQEGTGNER 1yvoA 33 :ETPVDLANRQ T0372 196 :YALHNFEALGLTGGILH 1yvoA 43 :AWFDTRARQGYPILVAS T0372 214 :NGKIVAFTFGMPINHE 1yvoA 62 :AGEVLGYASYGDWRPF T0372 230 :TFGVHVEKADTSIDGAYAMINYEFANRIPEQ 1yvoA 84 :VEHSVYVRDDQRGKGLGVQLLQALIERARAQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=326 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vhsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0372 read from 1vhsA/merged-good-all-a2m # 1vhsA read from 1vhsA/merged-good-all-a2m # found chain 1vhsA in training set Warning: unaligning (T0372)D154 because first residue in template chain is (1vhsA)S0 T0372 155 :YEYTPITPDRIQECLDLEAEWCKVNNC 1vhsA 1 :LTLRLAEHRDLEAVVAIYNSTIASRMV T0372 182 :DQQEGTGNERRALIY 1vhsA 30 :DTEPVTPEDRMEWFS T0372 199 :HNFEALGLT 1vhsA 45 :GHTESRPLY T0372 209 :GILHVNGKIVAFTFGMPINHE 1vhsA 54 :VAEDENGNVAAWISFETFYGR T0372 230 :TFGVHVEKADTS 1vhsA 80 :TAEVSIYIDEAC T0372 242 :IDGAYAMINYEFANRIPE 1vhsA 93 :GKGVGSYLLQEALRIAPN T0372 260 :QYIYIN 1vhsA 112 :GIRSLM T0372 270 :L 1vhsA 121 :F T0372 282 :YQPVTILEKYMA 1vhsA 122 :GHNKPSLKLFEK Number of specific fragments extracted= 9 number of extra gaps= 0 total=335 Number of alignments=31 # 1vhsA read from 1vhsA/merged-good-all-a2m # found chain 1vhsA in training set Warning: unaligning (T0372)D154 because first residue in template chain is (1vhsA)S0 T0372 155 :YEYTPITPDRIQECLDLEAEWCKVNNC 1vhsA 1 :LTLRLAEHRDLEAVVAIYNSTIASRMV T0372 182 :DQQEGTGNERRALIYA 1vhsA 30 :DTEPVTPEDRMEWFSG T0372 200 :NFEALGLT 1vhsA 46 :HTESRPLY T0372 209 :GILHVNGKIVAFTFGMPIN 1vhsA 54 :VAEDENGNVAAWISFETFY T0372 228 :HETFGVHVEKADTS 1vhsA 78 :NKTAEVSIYIDEAC T0372 242 :IDGAYAMINYEFANRIPE 1vhsA 93 :GKGVGSYLLQEALRIAPN T0372 260 :QYIYIN 1vhsA 112 :GIRSLM T0372 280 :LSYQPVTILEKYMA 1vhsA 120 :IFGHNKPSLKLFEK Number of specific fragments extracted= 8 number of extra gaps= 0 total=343 Number of alignments=32 # 1vhsA read from 1vhsA/merged-good-all-a2m # found chain 1vhsA in training set Warning: unaligning (T0372)D154 because first residue in template chain is (1vhsA)S0 T0372 155 :YEYTPITPDRIQECLDLEAEWCKVNNCDQQ 1vhsA 1 :LTLRLAEHRDLEAVVAIYNSTIASRMVTAD T0372 185 :EGT 1vhsA 38 :DRM T0372 199 :HNFEAL 1vhsA 41 :EWFSGH T0372 205 :GLTGGILHV 1vhsA 49 :SRPLYVAED T0372 214 :NGKIVAFTFGMPI 1vhsA 59 :NGNVAAWISFETF T0372 227 :NHETFGVHVEKADTSI 1vhsA 77 :YNKTAEVSIYIDEACR T0372 243 :DGAYAMINYEFANRIPE 1vhsA 94 :KGVGSYLLQEALRIAPN Number of specific fragments extracted= 7 number of extra gaps= 0 total=350 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cjwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0372 read from 1cjwA/merged-good-all-a2m # 1cjwA read from 1cjwA/merged-good-all-a2m # found chain 1cjwA in training set T0372 153 :PDYEYTPITPDRIQECLDLEAEWC 1cjwA 33 :PANEFRCLTPEDAAGVFEIEREAF T0372 177 :KVNNC 1cjwA 59 :VSGNC T0372 186 :GTGN 1cjwA 65 :LNLD T0372 193 :ALIYALHNFEAL 1cjwA 69 :EVQHFLTLCPEL T0372 208 :GGILHVNGKIVAFTFGMPINHE 1cjwA 81 :SLGWFVEGRLVAFIIGSLWDEE T0372 230 :TFGV 1cjwA 118 :SAHL T0372 234 :HVEKADTS 1cjwA 123 :ALAVHRSF T0372 242 :IDGAYAMINYEFANRIPE 1cjwA 132 :QQGKGSVLLWRYLHHVGA T0372 260 :QYIYI 1cjwA 152 :AVRRA Number of specific fragments extracted= 9 number of extra gaps= 0 total=359 Number of alignments=34 # 1cjwA read from 1cjwA/merged-good-all-a2m # found chain 1cjwA in training set T0372 153 :PDYEYTPITPDRIQECLDLEAEWC 1cjwA 33 :PANEFRCLTPEDAAGVFEIEREAF T0372 177 :KVNN 1cjwA 58 :SVSG T0372 184 :QEGTGNE 1cjwA 62 :NCPLNLD T0372 193 :ALIYALHNFEAL 1cjwA 69 :EVQHFLTLCPEL T0372 208 :GGILHVNGKIVAFTFGMPINHE 1cjwA 81 :SLGWFVEGRLVAFIIGSLWDEE T0372 230 :TFGVHVEKADTSID 1cjwA 118 :SAHLHALAVHRSFR T0372 244 :GAYAMINYEFANRIPE 1cjwA 134 :GKGSVLLWRYLHHVGA T0372 260 :QYIYI 1cjwA 152 :AVRRA Number of specific fragments extracted= 8 number of extra gaps= 0 total=367 Number of alignments=35 # 1cjwA read from 1cjwA/merged-good-all-a2m # found chain 1cjwA in training set T0372 153 :PDYEYTPITPDRIQECLDLEAEWCKV 1cjwA 33 :PANEFRCLTPEDAAGVFEIEREAFIS T0372 180 :NCDQQEGTGNE 1cjwA 59 :VSGNCPLNLDE T0372 194 :LIYALHNFEAL 1cjwA 70 :VQHFLTLCPEL T0372 208 :GGILHVNGKIVAFTFGMPINHE 1cjwA 81 :SLGWFVEGRLVAFIIGSLWDEE T0372 230 :TFGVHVEKADTSID 1cjwA 118 :SAHLHALAVHRSFR T0372 244 :GAYAMINYEFANRIPEQ 1cjwA 134 :GKGSVLLWRYLHHVGAQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=373 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d4pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2d4pA expands to /projects/compbio/data/pdb/2d4p.pdb.gz 2d4pA:# T0372 read from 2d4pA/merged-good-all-a2m # 2d4pA read from 2d4pA/merged-good-all-a2m # adding 2d4pA to template set # found chain 2d4pA in template set Warning: unaligning (T0372)Y155 because first residue in template chain is (2d4pA)M1 T0372 156 :EYTPITPDRIQECLDLE 2d4pA 2 :RFRPFTEEDLDRLNRLA T0372 180 :N 2d4pA 19 :G T0372 182 :DQQEGT 2d4pA 20 :KRPVSL T0372 193 :ALIYA 2d4pA 26 :GALRF T0372 201 :FEALGLT 2d4pA 31 :FARTGHS T0372 209 :GILHVNGKIVAFTFGMPI 2d4pA 38 :FLAEEGEEPMGFALAQAV T0372 227 :NHE 2d4pA 57 :QGE T0372 230 :TFGV 2d4pA 62 :TVLV T0372 234 :HVEKADTS 2d4pA 67 :RIEGRSVE T0372 242 :IDGAYAMINYEFAN 2d4pA 76 :LRGLLRAVVKSAYD T0372 260 :QYIYIN 2d4pA 91 :GVYEVA T0372 278 :AKLSYQPVTILEKYMACLKDHP 2d4pA 97 :LHLDPERKELEEALKAEGFALG Number of specific fragments extracted= 12 number of extra gaps= 0 total=385 Number of alignments=37 # 2d4pA read from 2d4pA/merged-good-all-a2m # found chain 2d4pA in template set T0372 156 :EYTPITPDRIQECLD 2d4pA 2 :RFRPFTEEDLDRLNR T0372 178 :VNN 2d4pA 17 :LAG T0372 182 :DQQEGT 2d4pA 20 :KRPVSL T0372 193 :ALIYA 2d4pA 26 :GALRF T0372 201 :FEALGLT 2d4pA 31 :FARTGHS T0372 209 :GILHVNGKIVAFTFGMPIN 2d4pA 38 :FLAEEGEEPMGFALAQAVW T0372 228 :HETFGVHVEKADTSIDGAYAMINYEFANRIPE 2d4pA 58 :GEATTVLVTRIEGRSVEALRGLLRAVVKSAYD T0372 260 :QYIYIN 2d4pA 91 :GVYEVA T0372 278 :AKLSYQPVTILEKYMACLKDHPM 2d4pA 97 :LHLDPERKELEEALKAEGFALGP Number of specific fragments extracted= 9 number of extra gaps= 0 total=394 Number of alignments=38 # 2d4pA read from 2d4pA/merged-good-all-a2m # found chain 2d4pA in template set Warning: unaligning (T0372)Y155 because first residue in template chain is (2d4pA)M1 T0372 156 :EYTPITPDRIQECLD 2d4pA 2 :RFRPFTEEDLDRLNR T0372 181 :CDQQEGTGN 2d4pA 19 :GKRPVSLGA T0372 198 :LHNFEALGLT 2d4pA 28 :LRFFARTGHS T0372 209 :GILHVNGKIVAFTFGMPI 2d4pA 38 :FLAEEGEEPMGFALAQAV T0372 227 :NHETFGVHVEKADTSIDGAYAMINYEFANRIPE 2d4pA 57 :QGEATTVLVTRIEGRSVEALRGLLRAVVKSAYD T0372 260 :QYIY 2d4pA 94 :EVAL T0372 267 :EEDLGIEGLRKA 2d4pA 98 :HLDPERKELEEA Number of specific fragments extracted= 7 number of extra gaps= 0 total=401 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z4rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z4rA expands to /projects/compbio/data/pdb/1z4r.pdb.gz 1z4rA:# T0372 read from 1z4rA/merged-good-all-a2m # 1z4rA read from 1z4rA/merged-good-all-a2m # adding 1z4rA to template set # found chain 1z4rA in template set T0372 10 :ADRDTITAFTMKSDRRNCDL 1z4rA 515 :RVLLWLVGLQNVFSHQLPRM T0372 30 :SFSNLCSWRFLYDTQFAVIDDFL 1z4rA 537 :EYIARLVFDPKHKTLALIKDGRV T0372 53 :VFKFWAGE 1z4rA 562 :GICFRMFP T0372 61 :QLAYMM 1z4rA 573 :FTEIVF T0372 67 :PVGN 1z4rA 580 :AVTS T0372 73 :LKAVLRKLIEDADKEKHNFCMLGVCSNMRADLEA 1z4rA 591 :GTHLMNHLKEYHIKHNILYFLTYADEYAIGYFKK T0372 108 :LP 1z4rA 625 :QG Number of specific fragments extracted= 7 number of extra gaps= 0 total=408 Number of alignments=40 # 1z4rA read from 1z4rA/merged-good-all-a2m # found chain 1z4rA in template set T0372 11 :DRDTITAF 1z4rA 535 :PKEYIARL T0372 36 :SWRFLYDTQFAVIDD 1z4rA 543 :VFDPKHKTLALIKDG T0372 51 :FLVFKFWAGE 1z4rA 560 :IGGICFRMFP T0372 61 :QLAY 1z4rA 573 :FTEI T0372 65 :MMPVG 1z4rA 578 :FCAVT T0372 70 :NGD 1z4rA 586 :QVK T0372 73 :LKAVLRKLIEDADKEKHNFCMLGVCSNMRADLEA 1z4rA 591 :GTHLMNHLKEYHIKHNILYFLTYADEYAIGYFKK T0372 108 :LP 1z4rA 625 :QG T0372 127 :RSDL 1z4rA 628 :SKDI T0372 132 :TLKGKKFQAK 1z4rA 632 :KVPKSRYLGY T0372 150 :NTYPDYEYT 1z4rA 643 :KDYEGATLM T0372 159 :PITP 1z4rA 654 :ELNP Number of specific fragments extracted= 12 number of extra gaps= 0 total=420 Number of alignments=41 # 1z4rA read from 1z4rA/merged-good-all-a2m # found chain 1z4rA in template set T0372 164 :RIQECLDLEAEWC 1z4rA 519 :WLVGLQNVFSHQL T0372 179 :NNCDQQE 1z4rA 532 :PRMPKEY T0372 197 :ALHNFEALGLTGGILHVNGKIVAFTFGMPI 1z4rA 539 :IARLVFDPKHKTLALIKDGRVIGGICFRMF T0372 227 :NHETFGVHVEKADTSI 1z4rA 570 :TQGFTEIVFCAVTSNE T0372 243 :DGAYAMINYEFANRIPE 1z4rA 588 :KGYGTHLMNHLKEYHIK T0372 260 :QYIY 1z4rA 606 :NILY Number of specific fragments extracted= 6 number of extra gaps= 0 total=426 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z4eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z4eA expands to /projects/compbio/data/pdb/1z4e.pdb.gz 1z4eA:# T0372 read from 1z4eA/merged-good-all-a2m # 1z4eA read from 1z4eA/merged-good-all-a2m # adding 1z4eA to template set # found chain 1z4eA in template set Warning: unaligning (T0372)D154 because first residue in template chain is (1z4eA)H4 T0372 155 :YEYTPITPDRIQECLDLEAE 1z4eA 5 :VTIREATEGDLEQMVHMLAD T0372 176 :CKVNNCDQQEGT 1z4eA 29 :RKRERYEKPLPV T0372 189 :NERRALIYA 1z4eA 41 :SYVRAFKEI T0372 199 :HNFEAL 1z4eA 50 :KKDKNN T0372 207 :TGGILHVNGKIVAFTFGMPINHE 1z4eA 56 :ELIVACNGEEIVGMLQVTFTPYL T0372 230 :TFGVHVEKADTS 1z4eA 85 :RATIEGVRTHSA T0372 242 :IDGAYAMINYEFANRIPE 1z4eA 99 :GQGIGSQLVCWAIERAKE T0372 260 :QYIYIN 1z4eA 118 :GCHLIQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=434 Number of alignments=43 # 1z4eA read from 1z4eA/merged-good-all-a2m # found chain 1z4eA in template set Warning: unaligning (T0372)D154 because first residue in template chain is (1z4eA)H4 T0372 155 :YEYTPITPDRIQECLDLEAE 1z4eA 5 :VTIREATEGDLEQMVHMLAD T0372 176 :CKVNNCDQQEGT 1z4eA 29 :RKRERYEKPLPV T0372 190 :ERRALIYALHNFEALGL 1z4eA 41 :SYVRAFKEIKKDKNNEL T0372 209 :GILHVNGKIVAFTFGMPIN 1z4eA 58 :IVACNGEEIVGMLQVTFTP T0372 229 :E 1z4eA 78 :L T0372 230 :TFGVHVEKADTSID 1z4eA 85 :RATIEGVRTHSAAR T0372 244 :GAYAMINYEFANRIPE 1z4eA 101 :GIGSQLVCWAIERAKE T0372 260 :QYIYIN 1z4eA 118 :GCHLIQ T0372 279 :KLSYQPVTILEK 1z4eA 128 :KQRPDALRFYEQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=443 Number of alignments=44 # 1z4eA read from 1z4eA/merged-good-all-a2m # found chain 1z4eA in template set Warning: unaligning (T0372)D154 because first residue in template chain is (1z4eA)H4 T0372 155 :YEYTPITPDRIQECLDLEAE 1z4eA 5 :VTIREATEGDLEQMVHMLAD T0372 179 :NNCDQQ 1z4eA 30 :KRERYE T0372 185 :EGTGNERRALI 1z4eA 37 :PLPVSYVRAFK T0372 199 :HNFEALGLTGGILHVNGKIVAFTFGMPINHE 1z4eA 48 :EIKKDKNNELIVACNGEEIVGMLQVTFTPYL T0372 230 :TFGVHVEKADTSID 1z4eA 85 :RATIEGVRTHSAAR T0372 244 :GAYAMINYEFANRIPE 1z4eA 101 :GIGSQLVCWAIERAKE T0372 260 :QYIYI 1z4eA 118 :GCHLI Number of specific fragments extracted= 7 number of extra gaps= 0 total=450 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s3zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1s3zA expands to /projects/compbio/data/pdb/1s3z.pdb.gz 1s3zA:# T0372 read from 1s3zA/merged-good-all-a2m # 1s3zA read from 1s3zA/merged-good-all-a2m # adding 1s3zA to template set # found chain 1s3zA in template set Warning: unaligning (T0372)P153 because first residue in template chain is (1s3zA)S-1 T0372 154 :DYEYTPITPDRIQECLDLEAEW 1s3zA 0 :HMDIRQMNKTHLEHWRGLRKQL T0372 178 :VNNCDQQEGT 1s3zA 22 :WPGHPDDAHL T0372 193 :ALIYA 1s3zA 32 :ADGEE T0372 200 :NFEALGLTGGILHVNGKIVAFTFGMPIN 1s3zA 37 :ILQADHLASFIAMADGVAIGFADASIRH T0372 228 :HETFGVHVEK 1s3zA 71 :DSSPVVFLEG T0372 238 :ADTS 1s3zA 83 :VLPS T0372 242 :IDGAYAMINYEFANRIPE 1s3zA 89 :QRGVAKQLIAAVQRWGTN T0372 260 :QYIYIN 1s3zA 108 :GCREMA T0372 278 :AKLS 1s3zA 114 :SDTS T0372 283 :QPVTILEKYM 1s3zA 118 :PENTISQKVH Number of specific fragments extracted= 10 number of extra gaps= 0 total=460 Number of alignments=46 # 1s3zA read from 1s3zA/merged-good-all-a2m # found chain 1s3zA in template set Warning: unaligning (T0372)P153 because first residue in template chain is (1s3zA)S-1 T0372 154 :DYEYTPITPDRIQECLDLEAEWC 1s3zA 0 :HMDIRQMNKTHLEHWRGLRKQLW T0372 179 :NNCDQQEGT 1s3zA 23 :PGHPDDAHL T0372 193 :ALIY 1s3zA 32 :ADGE T0372 199 :HNFEALGLTGGILHVNGKIVAFTFGMPIN 1s3zA 36 :EILQADHLASFIAMADGVAIGFADASIRH T0372 228 :HE 1s3zA 71 :DS T0372 230 :TFGVHVEKADTS 1s3zA 75 :VVFLEGIFVLPS T0372 242 :IDGAYAMINYEFANRIPE 1s3zA 89 :QRGVAKQLIAAVQRWGTN T0372 260 :QYIYIN 1s3zA 108 :GCREMA T0372 278 :AKLSYQPVTILEKYMA 1s3zA 114 :SDTSPENTISQKVHQA Number of specific fragments extracted= 9 number of extra gaps= 0 total=469 Number of alignments=47 # 1s3zA read from 1s3zA/merged-good-all-a2m # found chain 1s3zA in template set Warning: unaligning (T0372)P153 because first residue in template chain is (1s3zA)S-1 T0372 154 :DYEYTPITPDRIQECLDLEAEWC 1s3zA 0 :HMDIRQMNKTHLEHWRGLRKQLW T0372 179 :NNCDQQEGTGNERR 1s3zA 23 :PGHPDDAHLADGEE T0372 200 :NFEALGLTGGILHVNGKIVAFTFGMPINHET 1s3zA 37 :ILQADHLASFIAMADGVAIGFADASIRHDYV T0372 232 :GVHVEK 1s3zA 75 :VVFLEG T0372 238 :ADTSI 1s3zA 83 :VLPSF T0372 243 :DGAYAMINYEFANRIPE 1s3zA 90 :RGVAKQLIAAVQRWGTN Number of specific fragments extracted= 6 number of extra gaps= 0 total=475 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2beiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2beiA expands to /projects/compbio/data/pdb/2bei.pdb.gz 2beiA:Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 2beiA Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 2beiA Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 2beiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0372 read from 2beiA/merged-good-all-a2m # 2beiA read from 2beiA/merged-good-all-a2m # adding 2beiA to template set # found chain 2beiA in template set Warning: unaligning (T0372)D154 because first residue in template chain is (2beiA)S3 Warning: unaligning (T0372)C181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2beiA)K35 Warning: unaligning (T0372)G186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2beiA)K35 Warning: unaligning (T0372)E202 because of BadResidue code BAD_PEPTIDE in next template residue (2beiA)N49 Warning: unaligning (T0372)A203 because of BadResidue code BAD_PEPTIDE at template residue (2beiA)N49 Warning: unaligning (T0372)N214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2beiA)G68 T0372 155 :YEYTPITPDRIQECLDLEAEWCKVNN 2beiA 4 :VRIREAKEGDCGDILRLIRELAEFEK T0372 187 :TGNE 2beiA 36 :ISEE T0372 193 :ALIYAL 2beiA 40 :ALRADG T0372 200 :NF 2beiA 46 :FG T0372 204 :LGLTGGILHV 2beiA 50 :PFYHCLVAEI T0372 217 :IVAFTFGMPI 2beiA 71 :VVGYGIYYFI T0372 227 :NHE 2beiA 83 :TWK T0372 230 :TFGV 2beiA 88 :TIYL T0372 234 :HVEK 2beiA 93 :DIYV T0372 239 :DTS 2beiA 97 :MPE T0372 242 :IDGAYAMINYEFANRIPE 2beiA 102 :GQGIGSKIIKKVAEVALD T0372 260 :QYIYIN 2beiA 121 :GCSQFR T0372 270 :L 2beiA 127 :L T0372 280 :LS 2beiA 130 :LD T0372 283 :QPVTILEKYMA 2beiA 132 :WNQRAMDLYKA Number of specific fragments extracted= 15 number of extra gaps= 1 total=490 Number of alignments=49 # 2beiA read from 2beiA/merged-good-all-a2m # found chain 2beiA in template set Warning: unaligning (T0372)D154 because first residue in template chain is (2beiA)S3 Warning: unaligning (T0372)C181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2beiA)K35 Warning: unaligning (T0372)G186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2beiA)K35 Warning: unaligning (T0372)A203 because of BadResidue code BAD_PEPTIDE in next template residue (2beiA)N49 Warning: unaligning (T0372)L204 because of BadResidue code BAD_PEPTIDE at template residue (2beiA)N49 Warning: unaligning (T0372)N214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2beiA)G68 T0372 155 :YEYTPITPDRIQECLDLEAEWCKVNN 2beiA 4 :VRIREAKEGDCGDILRLIRELAEFEK T0372 187 :TGNE 2beiA 36 :ISEE T0372 193 :ALIYAL 2beiA 40 :ALRADG T0372 201 :FE 2beiA 46 :FG T0372 205 :G 2beiA 50 :P T0372 206 :LTGGILHV 2beiA 52 :YHCLVAEI T0372 215 :GKIVAFTFGMPIN 2beiA 69 :PCVVGYGIYYFIY T0372 230 :TFGVHVEKADTS 2beiA 88 :TIYLEDIYVMPE T0372 242 :IDGAYAMINYEFANRIPE 2beiA 102 :GQGIGSKIIKKVAEVALD T0372 260 :QYIYIN 2beiA 121 :GCSQFR T0372 270 :L 2beiA 127 :L T0372 280 :LSYQ 2beiA 130 :LDWN T0372 285 :VTILEKYMAC 2beiA 134 :QRAMDLYKAL Number of specific fragments extracted= 13 number of extra gaps= 1 total=503 Number of alignments=50 # 2beiA read from 2beiA/merged-good-all-a2m # found chain 2beiA in template set Warning: unaligning (T0372)D154 because first residue in template chain is (2beiA)S3 Warning: unaligning (T0372)C181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2beiA)K35 Warning: unaligning (T0372)Q184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2beiA)K35 Warning: unaligning (T0372)E202 because of BadResidue code BAD_PEPTIDE in next template residue (2beiA)N49 Warning: unaligning (T0372)A203 because of BadResidue code BAD_PEPTIDE at template residue (2beiA)N49 Warning: unaligning (T0372)N214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2beiA)G68 T0372 155 :YEYTPITPDRIQECLDLEAEWCKVNN 2beiA 4 :VRIREAKEGDCGDILRLIRELAEFEK T0372 185 :EGTGNERRALI 2beiA 36 :ISEEALRADGF T0372 204 :LGLTGGILHV 2beiA 50 :PFYHCLVAEI T0372 216 :KIVAFTFGMPI 2beiA 70 :CVVGYGIYYFI T0372 228 :HE 2beiA 83 :TW T0372 232 :GVHVEK 2beiA 88 :TIYLED T0372 238 :ADTSI 2beiA 96 :VMPEY T0372 243 :DGAYAMINYEFANRIPE 2beiA 103 :QGIGSKIIKKVAEVALD Number of specific fragments extracted= 8 number of extra gaps= 1 total=511 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b6bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b6bA expands to /projects/compbio/data/pdb/1b6b.pdb.gz 1b6bA:# T0372 read from 1b6bA/merged-good-all-a2m # 1b6bA read from 1b6bA/merged-good-all-a2m # adding 1b6bA to template set # found chain 1b6bA in template set T0372 156 :EYTPITPDRIQECLD 1b6bA 36 :EFRCLTPEDAAGVFE T0372 178 :VNNCDQQEGT 1b6bA 56 :FISVSGNCPL T0372 190 :ERRA 1b6bA 66 :NLDE T0372 197 :ALHNFEALGLTGGILHVNGKIVAFTFGMPINHE 1b6bA 70 :VQHFLTLCPELSLGWFVEGRLVAFIIGSLWDEE T0372 230 :TFGV 1b6bA 118 :SAHL T0372 234 :HVEKADTS 1b6bA 123 :ALAVHRSF T0372 242 :IDGAYAMINYEFANRIPE 1b6bA 132 :QQGKGSVLLWRYLHHVGA T0372 260 :QYIYI 1b6bA 152 :AVRRA Number of specific fragments extracted= 8 number of extra gaps= 0 total=519 Number of alignments=52 # 1b6bA read from 1b6bA/merged-good-all-a2m # found chain 1b6bA in template set T0372 156 :EYTPITPDRIQECLD 1b6bA 36 :EFRCLTPEDAAGVFE T0372 178 :VNNCDQQEGT 1b6bA 56 :FISVSGNCPL T0372 190 :ERR 1b6bA 66 :NLD T0372 196 :YALHNFEALGLTGGILHVNGKIVAFTFGMPINHE 1b6bA 69 :EVQHFLTLCPELSLGWFVEGRLVAFIIGSLWDEE T0372 257 :IPEQYIYIN 1b6bA 112 :HRPRGHSAH T0372 270 :LG 1b6bA 121 :LH T0372 276 :RKAKLSYQPVTILEKYMACLKDHP 1b6bA 128 :RSFRQQGKGSVLLWRYLHHVGAQP Number of specific fragments extracted= 7 number of extra gaps= 0 total=526 Number of alignments=53 # 1b6bA read from 1b6bA/merged-good-all-a2m # found chain 1b6bA in template set Warning: unaligning (T0372)D154 because first residue in template chain is (1b6bA)A34 T0372 155 :YEYTPITPDRIQECLD 1b6bA 35 :NEFRCLTPEDAAGVFE T0372 180 :NCDQQ 1b6bA 58 :SVSGN T0372 197 :ALHNFEAL 1b6bA 73 :FLTLCPEL T0372 208 :GGILHVNGKIVAFTFGMPINHE 1b6bA 81 :SLGWFVEGRLVAFIIGSLWDEE T0372 232 :GVHVEKA 1b6bA 118 :SAHLHAL T0372 239 :DTSI 1b6bA 127 :HRSF T0372 243 :DGAYAMINYEFANRIPEQ 1b6bA 133 :QGKGSVLLWRYLHHVGAQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=533 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p0hA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0372 read from 1p0hA/merged-good-all-a2m # 1p0hA read from 1p0hA/merged-good-all-a2m # found chain 1p0hA in training set Warning: unaligning (T0372)G59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p0hA)G74 Warning: unaligning (T0372)Y152 because of BadResidue code BAD_PEPTIDE in next template residue (1p0hA)D150 Warning: unaligning (T0372)P153 because of BadResidue code BAD_PEPTIDE at template residue (1p0hA)D150 Warning: unaligning (T0372)V213 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0hA)G215 T0372 2 :IPF 1p0hA 4 :LDW T0372 5 :KDITLADRDTITAFT 1p0hA 8 :SALTADEQRSVRALV T0372 20 :MKSDRRNCDLSFSNL 1p0hA 27 :AVDGVAPVGEQVLRE T0372 38 :RFLYDTQFAVID 1p0hA 42 :LGQQRTEHLLVA T0372 51 :FLVFKFW 1p0hA 62 :IGYLNLS T0372 60 :EQLAYMMPVGN 1p0hA 75 :GAMAELVVHPQ T0372 71 :GD 1p0hA 89 :RG T0372 73 :LKAVLRKLIED 1p0hA 92 :GTAMARAALAK T0372 87 :EKHNFCMLG 1p0hA 103 :TAGRNQFWA T0372 98 :SNMRADLEAI 1p0hA 112 :HGTLDPARAT T0372 127 :RSDL 1p0hA 122 :ASAL T0372 132 :TL 1p0hA 126 :GL T0372 134 :K 1p0hA 141 :R T0372 151 :T 1p0hA 142 :D T0372 154 :DYEYTPIT 1p0hA 151 :GVVIRTYA T0372 162 :PDRIQECLDLEAEWCK 1p0hA 160 :TSDDAELLRVNNAAFA T0372 179 :NNCDQQEGTGNERRALIYA 1p0hA 176 :GHPEQGGWTAVQLAERRGE T0372 199 :HNFEALGLT 1p0hA 195 :AWFDPDGLI T0372 209 :GILH 1p0hA 204 :LAFG T0372 217 :IVAFTFGMPI 1p0hA 217 :LLGFHWTKVH T0372 227 :NHETFGVHVEKADTS 1p0hA 229 :HPGLGEVYVLGVDPA T0372 242 :IDGAYAMINYEFANRI 1p0hA 246 :RRGLGQMLTSIGIVSL Number of specific fragments extracted= 22 number of extra gaps= 1 total=555 Number of alignments=55 # 1p0hA read from 1p0hA/merged-good-all-a2m # found chain 1p0hA in training set Warning: unaligning (T0372)E60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p0hA)G74 Warning: unaligning (T0372)Y152 because of BadResidue code BAD_PEPTIDE in next template residue (1p0hA)D150 Warning: unaligning (T0372)P153 because of BadResidue code BAD_PEPTIDE at template residue (1p0hA)D150 Warning: unaligning (T0372)N214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0hA)G215 Warning: unaligning (T0372)G215 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p0hA)G215 T0372 2 :IPF 1p0hA 4 :LDW T0372 5 :KDITLAD 1p0hA 8 :SALTADE T0372 12 :RDTITAFTMKSDRRNCDLSFSNLC 1p0hA 19 :RALVTATTAVDGVAPVGEQVLREL T0372 39 :FLYDTQFAVIDD 1p0hA 43 :GQQRTEHLLVAG T0372 51 :FLVFKF 1p0hA 62 :IGYLNL T0372 61 :QLAYMMPVG 1p0hA 78 :AELVVHPQS T0372 70 :NGD 1p0hA 88 :RRG T0372 73 :LKAVLRKLIED 1p0hA 92 :GTAMARAALAK T0372 87 :EKHNFCMLG 1p0hA 103 :TAGRNQFWA T0372 96 :VCSNMRADLEA 1p0hA 114 :TLDPARATASA T0372 108 :LPERFIFTEDRAYAD 1p0hA 125 :LGLVGVRELIQMRRP T0372 127 :RSDLATLK 1p0hA 140 :LRDIPEPT T0372 151 :T 1p0hA 148 :I T0372 154 :DYEYTPIT 1p0hA 151 :GVVIRTYA T0372 162 :PDRIQECLDLEAEWCKVNN 1p0hA 160 :TSDDAELLRVNNAAFAGHP T0372 182 :DQQEGTGNERRALIYA 1p0hA 179 :EQGGWTAVQLAERRGE T0372 199 :HNFEALGLT 1p0hA 195 :AWFDPDGLI T0372 210 :ILHV 1p0hA 204 :LAFG T0372 216 :KIVAFTFGMPIN 1p0hA 216 :RLLGFHWTKVHP T0372 228 :HETFGVHVEKADTS 1p0hA 230 :PGLGEVYVLGVDPA T0372 242 :IDGAYAMINYEFANRIPE 1p0hA 246 :RRGLGQMLTSIGIVSLAR Number of specific fragments extracted= 21 number of extra gaps= 1 total=576 Number of alignments=56 # 1p0hA read from 1p0hA/merged-good-all-a2m # found chain 1p0hA in training set Warning: unaligning (T0372)E60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0hA)G74 Warning: unaligning (T0372)P153 because of BadResidue code BAD_PEPTIDE at template residue (1p0hA)D150 Warning: unaligning (T0372)G215 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p0hA)G215 T0372 4 :FKDITLADRDTITAFTMKS 1p0hA 7 :RSALTADEQRSVRALVTAT T0372 23 :DRRNCD 1p0hA 30 :GVAPVG T0372 32 :SNLCSWRFLYDTQFAVIDD 1p0hA 36 :EQVLRELGQQRTEHLLVAG T0372 51 :FLVFKFWAG 1p0hA 61 :IIGYLNLSP T0372 62 :LAYMMPVGNGD 1p0hA 77 :MAELVVHPQSR T0372 73 :LKAVLRKLIEDADK 1p0hA 92 :GTAMARAALAKTAG T0372 88 :KHNFCMLGVCSNMRADLEAI 1p0hA 106 :RNQFWAHGTLDPARATASAL T0372 111 :RF 1p0hA 126 :GL T0372 115 :TEDRAYADYIYLRSDLATLK 1p0hA 128 :VGVRELIQMRRPLRDIPEPT T0372 154 :DYEYTPIT 1p0hA 151 :GVVIRTYA T0372 162 :PDRIQECLDLEAEWCKVNNCDQQEGTGNER 1p0hA 160 :TSDDAELLRVNNAAFAGHPEQGGWTAVQLA T0372 199 :HNFEAL 1p0hA 190 :ERRGEA T0372 205 :GLTGGIL 1p0hA 200 :DGLILAF T0372 216 :KIVAFTFGMPI 1p0hA 216 :RLLGFHWTKVH T0372 227 :NHETFGVHVEKADTSI 1p0hA 229 :HPGLGEVYVLGVDPAA T0372 243 :DGAYAMINYEFANRIPE 1p0hA 247 :RGLGQMLTSIGIVSLAR Number of specific fragments extracted= 16 number of extra gaps= 1 total=592 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ge3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ge3A expands to /projects/compbio/data/pdb/2ge3.pdb.gz 2ge3A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0372 read from 2ge3A/merged-good-all-a2m # 2ge3A read from 2ge3A/merged-good-all-a2m # adding 2ge3A to template set # found chain 2ge3A in template set Warning: unaligning (T0372)P153 because first residue in template chain is (2ge3A)D6 Warning: unaligning (T0372)V233 because of BadResidue code BAD_PEPTIDE in next template residue (2ge3A)G90 Warning: unaligning (T0372)H234 because of BadResidue code BAD_PEPTIDE at template residue (2ge3A)G90 T0372 154 :DYEYTPITPDRIQECLDLEAEWCKVNNC 2ge3A 7 :TVTIKPIRAEHVESFHRALDAVSRERKY T0372 182 :DQQEGTGNERRALIYALHN 2ge3A 38 :LEAPPLEAVRAFVLDMIEN T0372 203 :ALG 2ge3A 57 :DHP T0372 208 :GGILHVNGKIVAFTFGMPI 2ge3A 60 :QFVAIADGDVIGWCDIRRQ T0372 227 :NHE 2ge3A 80 :RAT T0372 230 :TFG 2ge3A 86 :CGT T0372 235 :VEKADTS 2ge3A 91 :MGILPAY T0372 242 :IDGAYAMINYEFANRIPE 2ge3A 99 :NKGLGARLMRRTLDAAHE T0372 260 :QYIYIN 2ge3A 118 :GLHRIE T0372 270 :LG 2ge3A 124 :LS T0372 280 :LSYQPVTILEKYM 2ge3A 126 :VHADNARAIALYE Number of specific fragments extracted= 11 number of extra gaps= 1 total=603 Number of alignments=58 # 2ge3A read from 2ge3A/merged-good-all-a2m # found chain 2ge3A in template set Warning: unaligning (T0372)P153 because first residue in template chain is (2ge3A)D6 Warning: unaligning (T0372)V233 because of BadResidue code BAD_PEPTIDE in next template residue (2ge3A)G90 Warning: unaligning (T0372)H234 because of BadResidue code BAD_PEPTIDE at template residue (2ge3A)G90 T0372 154 :DYEYTPITPDRIQECLDLEAEWCKVNNC 2ge3A 7 :TVTIKPIRAEHVESFHRALDAVSRERKY T0372 182 :DQQEGTGNE 2ge3A 36 :SFLEAPPLE T0372 193 :ALIYALHNFEALGLTGGILHVNGKIVAFTFGMPIN 2ge3A 45 :AVRAFVLDMIENDHPQFVAIADGDVIGWCDIRRQD T0372 230 :TFG 2ge3A 86 :CGT T0372 235 :VE 2ge3A 91 :MG T0372 238 :ADTS 2ge3A 93 :ILPA T0372 242 :IDGAYAMINYEFANRIPE 2ge3A 99 :NKGLGARLMRRTLDAAHE T0372 260 :QYIYIN 2ge3A 118 :GLHRIE T0372 270 :LG 2ge3A 124 :LS T0372 280 :LSYQPVTILEKYMAC 2ge3A 126 :VHADNARAIALYEKI Number of specific fragments extracted= 10 number of extra gaps= 1 total=613 Number of alignments=59 # 2ge3A read from 2ge3A/merged-good-all-a2m # found chain 2ge3A in template set Warning: unaligning (T0372)P153 because first residue in template chain is (2ge3A)D6 Warning: unaligning (T0372)V233 because of BadResidue code BAD_PEPTIDE in next template residue (2ge3A)G90 Warning: unaligning (T0372)H234 because of BadResidue code BAD_PEPTIDE at template residue (2ge3A)G90 T0372 154 :DYEYTPITPDRIQECLDLEAEWCKVNNC 2ge3A 7 :TVTIKPIRAEHVESFHRALDAVSRERKY T0372 182 :DQQEGTGNERRALIYALHN 2ge3A 38 :LEAPPLEAVRAFVLDMIEN T0372 205 :GLTGGILHVNGKIVAFTFGMPINHE 2ge3A 57 :DHPQFVAIADGDVIGWCDIRRQDRA T0372 230 :TFG 2ge3A 86 :CGT T0372 235 :VEKADTSI 2ge3A 91 :MGILPAYR T0372 243 :DGAYAMINYEFANRIPE 2ge3A 100 :KGLGARLMRRTLDAAHE T0372 260 :QY 2ge3A 118 :GL Number of specific fragments extracted= 7 number of extra gaps= 1 total=620 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n71A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0372 read from 1n71A/merged-good-all-a2m # 1n71A read from 1n71A/merged-good-all-a2m # found chain 1n71A in training set T0372 156 :EYTPIT 1n71A 2 :IISEFD T0372 162 :PDRIQECLDLEAEWCK 1n71A 11 :PVLKDQLSDLLRLTWP T0372 182 :DQQEGT 1n71A 27 :EEYGDS T0372 193 :AL 1n71A 33 :SA T0372 196 :YALHNFEALGLTGGILHVNGKIVAFTFGMPI 1n71A 35 :EEVEEMMNPERIAVAAVDQDELVGFIGAIPQ T0372 227 :NHETFGV 1n71A 67 :GITGWEL T0372 234 :HVEKADTS 1n71A 75 :PLVVESSR T0372 242 :IDGAYAMINYEFANRIPE 1n71A 84 :KNQIGTRLVNYLEKEVAS T0372 260 :QYIYIN 1n71A 103 :GGITIY T0372 270 :L 1n71A 109 :L Number of specific fragments extracted= 10 number of extra gaps= 0 total=630 Number of alignments=61 # 1n71A read from 1n71A/merged-good-all-a2m # found chain 1n71A in training set T0372 156 :EYTPIT 1n71A 2 :IISEFD T0372 162 :PDRIQECLDLEAEWCK 1n71A 11 :PVLKDQLSDLLRLTWP T0372 182 :DQQEGT 1n71A 27 :EEYGDS T0372 193 :ALIYALHNFEALGL 1n71A 33 :SAEEVEEMMNPERI T0372 208 :GGILHVNGKIVAFTFGMPINH 1n71A 47 :AVAAVDQDELVGFIGAIPQYG T0372 229 :ETFGVHVEKADTS 1n71A 69 :TGWELHPLVVESS T0372 242 :IDGAYAMINYEFANRIPE 1n71A 84 :KNQIGTRLVNYLEKEVAS T0372 260 :QYIYIN 1n71A 103 :GGITIY T0372 270 :LG 1n71A 109 :LG Number of specific fragments extracted= 9 number of extra gaps= 0 total=639 Number of alignments=62 # 1n71A read from 1n71A/merged-good-all-a2m # found chain 1n71A in training set Warning: unaligning (T0372)Y155 because first residue in template chain is (1n71A)M1 T0372 156 :EYTPIT 1n71A 2 :IISEFD T0372 162 :PDRIQECLDLEAEWC 1n71A 11 :PVLKDQLSDLLRLTW T0372 178 :VNNCDQQEG 1n71A 26 :PEEYGDSSA T0372 199 :HNFEAL 1n71A 35 :EEVEEM T0372 205 :GLTGGILHVNGKIVAFTFGMPINH 1n71A 44 :ERIAVAAVDQDELVGFIGAIPQYG T0372 229 :ETFGVHVEKADTSID 1n71A 69 :TGWELHPLVVESSRR T0372 244 :GAYAMINYEFANRIPE 1n71A 86 :QIGTRLVNYLEKEVAS Number of specific fragments extracted= 7 number of extra gaps= 0 total=646 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kuxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kuxA expands to /projects/compbio/data/pdb/1kux.pdb.gz 1kuxA:# T0372 read from 1kuxA/merged-good-all-a2m # 1kuxA read from 1kuxA/merged-good-all-a2m # adding 1kuxA to template set # found chain 1kuxA in template set T0372 152 :YPDYEYTPITPDRIQECLDLEAEWC 1kuxA 32 :LPANEFRCLTPEDAAGVFEIEREAF T0372 177 :KVNNC 1kuxA 59 :VSGNC T0372 186 :GTGN 1kuxA 65 :LNLD T0372 193 :ALIYALHNFEAL 1kuxA 69 :EVQHFLTLCPEL T0372 208 :GGILHVNGKIVAFTFGMPINHE 1kuxA 81 :SLGWFVEGRLVAFIIGSLWDEE T0372 230 :TFGV 1kuxA 118 :SAHL T0372 234 :HVEKADTS 1kuxA 123 :ALAVHRSF T0372 242 :IDGAYAMINYEFANRIPE 1kuxA 132 :QQGKGSVLLWRYLHHVGA T0372 260 :QYIYI 1kuxA 152 :AVRRA Number of specific fragments extracted= 9 number of extra gaps= 0 total=655 Number of alignments=64 # 1kuxA read from 1kuxA/merged-good-all-a2m # found chain 1kuxA in template set T0372 153 :PDYEYTPITPDRIQECLDLEAEWC 1kuxA 33 :PANEFRCLTPEDAAGVFEIEREAF T0372 177 :KVNN 1kuxA 58 :SVSG T0372 184 :QEGTGNE 1kuxA 62 :NCPLNLD T0372 193 :ALIYALHNFEAL 1kuxA 69 :EVQHFLTLCPEL T0372 208 :GGILHVNGKIVAFTFGMPINHE 1kuxA 81 :SLGWFVEGRLVAFIIGSLWDEE T0372 230 :TFGVHVEKADTS 1kuxA 118 :SAHLHALAVHRS T0372 242 :IDGAYAMINYEFANRIPE 1kuxA 132 :QQGKGSVLLWRYLHHVGA T0372 260 :QYIYI 1kuxA 152 :AVRRA Number of specific fragments extracted= 8 number of extra gaps= 0 total=663 Number of alignments=65 # 1kuxA read from 1kuxA/merged-good-all-a2m # found chain 1kuxA in template set Warning: unaligning (T0372)Q260 because of BadResidue code BAD_PEPTIDE in next template residue (1kuxA)P151 T0372 153 :PDYEYTPITPDRIQECLDLEAEWCKV 1kuxA 33 :PANEFRCLTPEDAAGVFEIEREAFIS T0372 180 :NCDQQEGTGNE 1kuxA 59 :VSGNCPLNLDE T0372 194 :LIYALHNFEAL 1kuxA 70 :VQHFLTLCPEL T0372 208 :GGILHVNGKIVAFTFGMPINHE 1kuxA 81 :SLGWFVEGRLVAFIIGSLWDEE T0372 230 :TFGVHVEKADTSID 1kuxA 118 :SAHLHALAVHRSFR T0372 244 :GAYAMINYEFANRIPE 1kuxA 134 :GKGSVLLWRYLHHVGA Number of specific fragments extracted= 6 number of extra gaps= 1 total=669 Number of alignments=66 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 66 Done printing distance constraints # command: