# 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/T0292/ # command:# Making conformation for sequence T0292 numbered 1 through 277 Created new target T0292 from T0292.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0292/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0292//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0292/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0292//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0292/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0292/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0292/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z57A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z57A expands to /projects/compbio/data/pdb/1z57.pdb.gz 1z57A:Skipped atom 406, because occupancy 0.35 <= existing 0.650 in 1z57A Skipped atom 408, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1026, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1028, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1181, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1184, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1255, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1257, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1259, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1261, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1263, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1499, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1501, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 2508, because occupancy 0.500 <= existing 0.500 in 1z57A Skipped atom 2512, because occupancy 0.500 <= existing 0.500 in 1z57A Skipped atom 2514, because occupancy 0.500 <= existing 0.500 in 1z57A Skipped atom 2516, because occupancy 0.500 <= existing 0.500 in 1z57A Skipped atom 2518, because occupancy 0.500 <= existing 0.500 in 1z57A # T0292 read from 1z57A/merged-good-all-a2m # 1z57A read from 1z57A/merged-good-all-a2m # adding 1z57A to template set # found chain 1z57A in template set Warning: unaligning (T0292)M84 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1z57A)E242 Warning: unaligning (T0292)E85 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1z57A)E242 T0292 4 :EDYEVLYTIGTGSYGRCQKIRR 1z57A 159 :ARYEIVDTLGEGAFGKVVECID # choosing archetypes in rotamer library T0292 26 :KSDGKILVWKELDY 1z57A 182 :KAGGRHVAVKIVKN T0292 43 :TEAEKQMLVSEVNLLREL 1z57A 196 :VDRYCEAARSEIQVLEHL T0292 61 :KHP 1z57A 219 :NST T0292 64 :NIVRYYDRI 1z57A 223 :RCVQMLEWF T0292 75 :RTNTTLYIV 1z57A 232 :EHHGHICIV T0292 86 :YCE 1z57A 243 :LLG T0292 90 :GDLASVITKG 1z57A 246 :LSTYDFIKEN T0292 102 :ERQYLDEEFVLRVMTQLTLALKECHRRS 1z57A 256 :GFLPFRLDHIRKMAYQICKSVNFLHSNK T0292 135 :VLHRDLKPANVFL 1z57A 284 :LTHTDLKPENILF T0292 149 :GKQNVKLGDFGLARI 1z57A 317 :INPDIKVVDFGSATY T0292 167 :DTSFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKE 1z57A 332 :DDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKE T0292 222 :LAGKIR 1z57A 390 :MMERIL T0292 228 :EGKFR 1z57A 414 :HDRLD T0292 234 :IPYR 1z57A 419 :WDEH T0292 239 :SDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1z57A 447 :HERLFDLIQKMLEYDPAKRITLREALKHPFFDLL Number of specific fragments extracted= 16 number of extra gaps= 1 total=16 Number of alignments=1 # 1z57A read from 1z57A/merged-good-all-a2m # found chain 1z57A in template set Warning: unaligning (T0292)M84 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1z57A)E242 Warning: unaligning (T0292)E85 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1z57A)E242 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKS 1z57A 159 :ARYEIVDTLGEGAFGKVVECIDHK T0292 28 :DGKILVWKELDY 1z57A 184 :GGRHVAVKIVKN T0292 43 :TEAEKQMLVSEVNLLREL 1z57A 196 :VDRYCEAARSEIQVLEHL T0292 61 :KHP 1z57A 219 :NST T0292 64 :NIVRYYDRI 1z57A 223 :RCVQMLEWF T0292 75 :RTNTTLYIV 1z57A 232 :EHHGHICIV T0292 86 :YCEG 1z57A 243 :LLGL T0292 91 :DLASVITKGTKER 1z57A 247 :STYDFIKENGFLP T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1z57A 260 :FRLDHIRKMAYQICKSVNFLHSNK T0292 135 :VLHRDLKPANVFL 1z57A 284 :LTHTDLKPENILF T0292 150 :KQN 1z57A 300 :DYT T0292 153 :VKLGDFGLARI 1z57A 321 :IKVVDFGSATY T0292 167 :DTSFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1z57A 332 :DDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMER T0292 229 :GKFR 1z57A 396 :GPLP T0292 233 :RIPY 1z57A 407 :RKRK T0292 240 :DELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1z57A 448 :ERLFDLIQKMLEYDPAKRITLREALKHPFFDLLK Number of specific fragments extracted= 16 number of extra gaps= 1 total=32 Number of alignments=2 # 1z57A read from 1z57A/merged-good-all-a2m # found chain 1z57A in template set Warning: unaligning (T0292)M84 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1z57A)E242 Warning: unaligning (T0292)E85 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1z57A)E242 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRK 1z57A 159 :ARYEIVDTLGEGAFGKVVECIDH T0292 27 :SDGKILVWKELDYG 1z57A 183 :AGGRHVAVKIVKNV T0292 44 :EAEKQMLVSEVNLLREL 1z57A 197 :DRYCEAARSEIQVLEHL T0292 61 :KHPN 1z57A 219 :NSTF T0292 65 :IVRYYDRIIDRTN 1z57A 224 :CVQMLEWFEHHGH T0292 80 :LYIV 1z57A 237 :ICIV T0292 86 :YCEG 1z57A 243 :LLGL T0292 91 :DLASVITK 1z57A 247 :STYDFIKE T0292 101 :KERQYLDEEFVLRVMTQLTLALKECHRR 1z57A 255 :NGFLPFRLDHIRKMAYQICKSVNFLHSN T0292 134 :TVLHRDLKPANVFL 1z57A 283 :KLTHTDLKPENILF T0292 148 :DGKQNVKLGDFGLARILNHD 1z57A 316 :LINPDIKVVDFGSATYDDEH T0292 171 :AKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1z57A 336 :HSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMER T0292 229 :GKFRR 1z57A 396 :GPLPK T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1z57A 442 :SQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLL Number of specific fragments extracted= 14 number of extra gaps= 1 total=46 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uu3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0292 read from 1uu3A/merged-good-all-a2m # 1uu3A read from 1uu3A/merged-good-all-a2m # found chain 1uu3A in training set Warning: unaligning (T0292)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uu3A)F242 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uu3A)F242 Warning: unaligning (T0292)S259 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uu3A)G332 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAE 1uu3A 78 :RPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKEN T0292 47 :KQMLVSEVNLLRELKHPNIVRYYDRI 1uu3A 124 :VPYVTRERDVMSRLDHPFFVKLYFTF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1uu3A 150 :QDDEKLYFGLSYAKNGELLKYIRKIGS T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1uu3A 177 :FDETCTRFYTAEIVSALEYLHGKG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARI 1uu3A 201 :IIHRDLKPENILLNEDMHIQITDFGTAKV T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1uu3A 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYD T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1uu3A 301 :FPEKFFPKARDLVEKLLVLDATKRL T0292 260 :VEEILENPLILEHHHH 1uu3A 333 :YGPLKAHPFFESVTWE Number of specific fragments extracted= 8 number of extra gaps= 1 total=54 Number of alignments=4 # 1uu3A read from 1uu3A/merged-good-all-a2m # found chain 1uu3A in training set Warning: unaligning (T0292)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uu3A)F242 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uu3A)F242 Warning: unaligning (T0292)S259 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uu3A)G332 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1uu3A 78 :RPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHI T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1uu3A 120 :KENKVPYVTRERDVMSRLDHPFFVKLYFTF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1uu3A 150 :QDDEKLYFGLSYAKNGELLKYIRKIGS T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1uu3A 177 :FDETCTRFYTAEIVSALEYLHGKG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARI 1uu3A 201 :IIHRDLKPENILLNEDMHIQITDFGTAKV T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1uu3A 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYD T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1uu3A 301 :FPEKFFPKARDLVEKLLVLDATKRL T0292 260 :VEEILENPLILEHH 1uu3A 333 :YGPLKAHPFFESVT Number of specific fragments extracted= 8 number of extra gaps= 1 total=62 Number of alignments=5 # 1uu3A read from 1uu3A/merged-good-all-a2m # found chain 1uu3A in training set Warning: unaligning (T0292)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uu3A)F242 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uu3A)F242 Warning: unaligning (T0292)S259 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uu3A)G332 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1uu3A 78 :RPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHI T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1uu3A 120 :KENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEK T0292 80 :LYIVMEYCEGGDLASVITK 1uu3A 155 :LYFGLSYAKNGELLKYIRK T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1uu3A 174 :IGSFDETCTRFYTAEIVSALEYLHGK T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARI 1uu3A 200 :GIIHRDLKPENILLNEDMHIQITDFGTAKV T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1uu3A 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYD T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1uu3A 301 :FPEKFFPKARDLVEKLLVLDATKRL T0292 260 :VEEILENPLILEHHHHH 1uu3A 333 :YGPLKAHPFFESVTWEN Number of specific fragments extracted= 8 number of extra gaps= 1 total=70 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p4oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0292 read from 1p4oA/merged-good-all-a2m # 1p4oA read from 1p4oA/merged-good-all-a2m # found chain 1p4oA in training set T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKS 1p4oA 965 :AREKITMSRELGQGSFGMVYEGVAKG T0292 28 :DGK 1p4oA 993 :KDE T0292 31 :ILVWKELDYG 1p4oA 999 :RVAIKTVNEA T0292 42 :MTEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1p4oA 1009 :ASMRERIEFLNEASVMKEFNCHHVVRLLGVV T0292 75 :RTNTTLYIVMEYCEGGDLASVIT 1p4oA 1040 :SQGQPTLVIMELMTRGDLKSYLR T0292 98 :KGTKERQYLDEEFVLRVMTQLTLALKECHRRS 1p4oA 1069 :ANNPVLAPPSLSKMIQMAGEIADGMAYLNANK T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLAR 1p4oA 1101 :FVHRDLAARNCMVAEDFTVKIGDFGMTR T0292 163 :ILNHDTSFAK 1p4oA 1135 :YYRKGGKGLL T0292 177 :TPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALM 1p4oA 1145 :PVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLA T0292 212 :PPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILEN 1p4oA 1181 :QPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISS Number of specific fragments extracted= 10 number of extra gaps= 0 total=80 Number of alignments=7 # 1p4oA read from 1p4oA/merged-good-all-a2m # found chain 1p4oA in training set T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRK 1p4oA 965 :AREKITMSRELGQGSFGMVYEGVAK T0292 27 :SDG 1p4oA 993 :KDE T0292 30 :KILVWKELDYG 1p4oA 998 :TRVAIKTVNEA T0292 42 :MTEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1p4oA 1009 :ASMRERIEFLNEASVMKEFNCHHVVRLLGVV T0292 75 :RTNTTLYIVMEYCEGGDLASVIT 1p4oA 1040 :SQGQPTLVIMELMTRGDLKSYLR T0292 98 :KGTKERQYLDEEFVLRVMTQLTLALKECHRRS 1p4oA 1069 :ANNPVLAPPSLSKMIQMAGEIADGMAYLNANK T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 1p4oA 1101 :FVHRDLAARNCMVAEDFTVKIGDFGMTRDIYETDYYR T0292 172 :KAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCA 1p4oA 1140 :GKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIAT T0292 210 :LMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1p4oA 1179 :AEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSIKEEME Number of specific fragments extracted= 9 number of extra gaps= 0 total=89 Number of alignments=8 # 1p4oA read from 1p4oA/merged-good-all-a2m # found chain 1p4oA in training set T0292 1 :SRAEDYEVLYTIGTGSYGRCQKIRRK 1p4oA 964 :VAREKITMSRELGQGSFGMVYEGVAK T0292 27 :SD 1p4oA 993 :KD T0292 29 :GKILVWKELDYG 1p4oA 997 :ETRVAIKTVNEA T0292 42 :MTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1p4oA 1009 :ASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQGQP T0292 80 :LYIVMEYCEGGDLASVITKGT 1p4oA 1045 :TLVIMELMTRGDLKSYLRSLR T0292 101 :KERQYLDEEFVLRVMTQLTLALKECHRR 1p4oA 1072 :PVLAPPSLSKMIQMAGEIADGMAYLNAN T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILN 1p4oA 1100 :KFVHRDLAARNCMVAEDFTVKIGDFGMTRDIY T0292 166 :HD 1p4oA 1141 :KG T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCA 1p4oA 1143 :LLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIAT T0292 210 :LMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILEN 1p4oA 1179 :AEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISS T0292 269 :ILEHHHH 1p4oA 1236 :IKEEMEP Number of specific fragments extracted= 11 number of extra gaps= 0 total=100 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xwsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xwsA expands to /projects/compbio/data/pdb/1xws.pdb.gz 1xwsA:Skipped atom 956, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 958, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 960, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1217, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1219, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1221, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1223, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1532, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1534, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1536, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1538, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1540, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1851, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1853, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1859, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1861, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1863, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1865, because occupancy 0.350 <= existing 0.650 in 1xwsA Skipped atom 1867, because occupancy 0.350 <= existing 0.650 in 1xwsA # T0292 read from 1xwsA/merged-good-all-a2m # 1xwsA read from 1xwsA/merged-good-all-a2m # adding 1xwsA to template set # found chain 1xwsA in template set T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMT 1xwsA 34 :LESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRIS T0292 44 :EAE 1xwsA 81 :PNG T0292 52 :SEVNLLREL 1xwsA 88 :MEVVLLKKV T0292 61 :KHPNIVRYYDRI 1xwsA 99 :GFSGVIRLLDWF T0292 75 :RTNTTLYIVMEYCEG 1xwsA 111 :ERPDSFVLILERPEP T0292 90 :GDLASVITKGTK 1xwsA 127 :QDLFDFITERGA T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1xwsA 139 :LQEELARSFFWQVLEAVRHCHNCG T0292 135 :VLHRDLKPANVFL 1xwsA 163 :VLHRDIKDENILI T0292 148 :DGKQNVKLGDFGLARILNHD 1xwsA 177 :LNRGELKLIDFGSGALLKDT T0292 170 :FAKAFVGTPYYMSPEQMNRMSYN 1xwsA 197 :VYTDFDGTRVYSPPEWIRYHRYH T0292 193 :EKSDIWSLGCLLYELCALMPPFTAFS 1xwsA 221 :RSAAVWSLGILLYDMVCGDIPFEHDE T0292 225 :KIREGKF 1xwsA 247 :EIIRGQV T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1xwsA 254 :FFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVL Number of specific fragments extracted= 13 number of extra gaps= 0 total=113 Number of alignments=10 # 1xwsA read from 1xwsA/merged-good-all-a2m # found chain 1xwsA in template set Warning: unaligning (T0292)R2 because first residue in template chain is (1xwsA)P33 T0292 3 :AED 1xwsA 34 :LES T0292 6 :YEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMT 1xwsA 38 :YQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRIS T0292 52 :SEVNLLRELKHP 1xwsA 88 :MEVVLLKKVSSG T0292 64 :NIVRYYDRI 1xwsA 102 :GVIRLLDWF T0292 75 :RTNTTLYIVMEYCEG 1xwsA 111 :ERPDSFVLILERPEP T0292 90 :GDLASVITKGTK 1xwsA 127 :QDLFDFITERGA T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1xwsA 139 :LQEELARSFFWQVLEAVRHCHNCG T0292 135 :VLHRDLKPANVFLD 1xwsA 163 :VLHRDIKDENILID T0292 149 :GKQNVKLGDFGLARILNH 1xwsA 178 :NRGELKLIDFGSGALLKD T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYN 1xwsA 196 :TVYTDFDGTRVYSPPEWIRYHRYH T0292 193 :EKSDIWSLGCLLYELCALMPPFTA 1xwsA 221 :RSAAVWSLGILLYDMVCGDIPFEH T0292 219 :QKE 1xwsA 245 :DEE T0292 226 :IREGKFR 1xwsA 248 :IIRGQVF T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1xwsA 255 :FRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVL Number of specific fragments extracted= 14 number of extra gaps= 0 total=127 Number of alignments=11 # 1xwsA read from 1xwsA/merged-good-all-a2m # found chain 1xwsA in template set T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1xwsA 34 :LESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRI T0292 52 :SEVNLLREL 1xwsA 88 :MEVVLLKKV T0292 61 :KHPNIVRYYDRIIDRTN 1xwsA 99 :GFSGVIRLLDWFERPDS T0292 80 :LYIVMEYCEG 1xwsA 116 :FVLILERPEP T0292 90 :GDLASVITK 1xwsA 127 :QDLFDFITE T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1xwsA 136 :RGALQEELARSFFWQVLEAVRHCHNC T0292 134 :TVLHRDLKPANVFL 1xwsA 162 :GVLHRDIKDENILI T0292 148 :DGKQNVKLGDFGLARILNHD 1xwsA 177 :LNRGELKLIDFGSGALLKDT T0292 170 :FAKAFVGTPYYMSPEQMNRMSYN 1xwsA 197 :VYTDFDGTRVYSPPEWIRYHRYH T0292 193 :EKSDIWSLGCLLYELCALMPPFTAF 1xwsA 221 :RSAAVWSLGILLYDMVCGDIPFEHD T0292 224 :GKIREGKFR 1xwsA 246 :EEIIRGQVF T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHH 1xwsA 255 :FRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLL Number of specific fragments extracted= 12 number of extra gaps= 0 total=139 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ia8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0292 read from 1ia8A/merged-good-all-a2m # 1ia8A read from 1ia8A/merged-good-all-a2m # found chain 1ia8A in training set Warning: unaligning (T0292)S41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ia8A)C48 Warning: unaligning (T0292)A45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ia8A)C48 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYG 1ia8A 5 :FVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMK T0292 46 :E 1ia8A 49 :P T0292 48 :QMLVSEVNLLRELKHPNIVRYYDRI 1ia8A 50 :ENIKKEICINKMLNHENVVKFYGHR T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1ia8A 75 :REGNIQYLFLEYCSGGELFDRIEPDIG T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1ia8A 102 :MPEPDAQRFFHQLMAGVVYLHGIG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTS 1ia8A 126 :ITHRDIKPENLLLDERDNLKISDFGLATVFRYNNR T0292 170 :FAKAFVGTPYYMSPEQMNRMSYN 1ia8A 163 :LLNKMCGTLPYVAPELLKRREFH T0292 193 :EKSDIWSLGCLLYELCALMPPFTAFSQK 1ia8A 187 :EPVDVWSCGIVLTAMLAGELPWDQPSDS T0292 221 :ELAGKIREGKF 1ia8A 216 :QEYSDWKEKKT T0292 233 :RIP 1ia8A 227 :YLN T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1ia8A 232 :KKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKP T0292 274 :HHH 1ia8A 272 :GAK Number of specific fragments extracted= 12 number of extra gaps= 0 total=151 Number of alignments=13 # 1ia8A read from 1ia8A/merged-good-all-a2m # found chain 1ia8A in training set Warning: unaligning (T0292)S41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ia8A)C48 Warning: unaligning (T0292)T43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ia8A)C48 T0292 3 :AEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYG 1ia8A 6 :VEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMK T0292 44 :EA 1ia8A 49 :PE T0292 49 :MLVSEVNLLRELKHPNIVRYYDRI 1ia8A 51 :NIKKEICINKMLNHENVVKFYGHR T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1ia8A 75 :REGNIQYLFLEYCSGGELFDRIEPDIG T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1ia8A 102 :MPEPDAQRFFHQLMAGVVYLHGIG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 1ia8A 126 :ITHRDIKPENLLLDERDNLKISDFGLATVFRYNNRER T0292 172 :KAFVGTPYYMSPEQMNRMSYN 1ia8A 165 :NKMCGTLPYVAPELLKRREFH T0292 193 :EKSDIWSLGCLLYELCALMPPFTAFSQK 1ia8A 187 :EPVDVWSCGIVLTAMLAGELPWDQPSDS T0292 221 :ELAGKIREGKFR 1ia8A 216 :QEYSDWKEKKTY T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1ia8A 229 :NPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPL T0292 275 :HH 1ia8A 273 :AK Number of specific fragments extracted= 11 number of extra gaps= 0 total=162 Number of alignments=14 # 1ia8A read from 1ia8A/merged-good-all-a2m # found chain 1ia8A in training set Warning: unaligning (T0292)S41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ia8A)C48 Warning: unaligning (T0292)T43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ia8A)C48 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYG 1ia8A 5 :FVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMK T0292 44 :E 1ia8A 49 :P T0292 48 :QMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1ia8A 50 :ENIKKEICINKMLNHENVVKFYGHRREGNI T0292 80 :LYIVMEYCEGGDLASVITK 1ia8A 80 :QYLFLEYCSGGELFDRIEP T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1ia8A 99 :DIGMPEPDAQRFFHQLMAGVVYLHGI T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 1ia8A 125 :GITHRDIKPENLLLDERDNLKISDFGLATVFRYN T0292 168 :TSFAKAFVGTPYYMSPEQMNRMSYN 1ia8A 161 :ERLLNKMCGTLPYVAPELLKRREFH T0292 193 :EKSDIWSLGCLLYELCALMPPFTAFSQK 1ia8A 187 :EPVDVWSCGIVLTAMLAGELPWDQPSDS T0292 221 :ELAGKIREGKFRR 1ia8A 216 :QEYSDWKEKKTYL T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 1ia8A 230 :PWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKKGA Number of specific fragments extracted= 10 number of extra gaps= 0 total=172 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bdwA expands to /projects/compbio/data/pdb/2bdw.pdb.gz 2bdwA:# T0292 read from 2bdwA/merged-good-all-a2m # 2bdwA read from 2bdwA/merged-good-all-a2m # adding 2bdwA to template set # found chain 2bdwA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRI 2bdwA 11 :DNYDVKEELGKGAFSVVRRCVHKTTGLEFAAKIINTKKLSARDFQKLEREARICRKLQHPNIVRLHDSI T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 2bdwA 80 :QEESFHYLVFDLVTGGELFEDIVAREF T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2bdwA 107 :YSEADASHCIQQILESIAYCHSNG T0292 135 :VLHRDLKPANVFL 2bdwA 131 :IVHRNLKPENLLL T0292 148 :DGKQNVKLGDFGLARILNHD 2bdwA 147 :AKGAAVKLADFGLAIEVNDS T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRY 2bdwA 168 :EAWHGFAGTPGYLSPEVLKKDPYSKPVDIWACGVILYILLVGYPPFWDEDQHRLYAQIKAGAYDYPSPEW T0292 239 :SDELNEIITRMLNLKDYHRPSVEEILENPLILEH 2bdwA 241 :TPEAKSLIDSMLTVNPKKRITADQALKVPWICNR T0292 273 :HH 2bdwA 279 :SA Number of specific fragments extracted= 8 number of extra gaps= 0 total=180 Number of alignments=16 # 2bdwA read from 2bdwA/merged-good-all-a2m # found chain 2bdwA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRI 2bdwA 11 :DNYDVKEELGKGAFSVVRRCVHKTTGLEFAAKIINTKKLSARDFQKLEREARICRKLQHPNIVRLHDSI T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 2bdwA 80 :QEESFHYLVFDLVTGGELFEDIVAREF T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2bdwA 107 :YSEADASHCIQQILESIAYCHSNG T0292 135 :VLHRDLKPANVFL 2bdwA 131 :IVHRNLKPENLLL T0292 148 :DGKQNVKLGDFGLARILNHD 2bdwA 147 :AKGAAVKLADFGLAIEVNDS T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 2bdwA 168 :EAWHGFAGTPGYLSPEVLKKDPYSKPVDIWACGVILYILLVGYPPFWDEDQHRLYAQIKAGAYD T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 2bdwA 235 :PEWDTVTPEAKSLIDSMLTVNPKKRITADQALKVPWICNRE Number of specific fragments extracted= 7 number of extra gaps= 0 total=187 Number of alignments=17 # 2bdwA read from 2bdwA/merged-good-all-a2m # found chain 2bdwA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 2bdwA 11 :DNYDVKEELGKGAFSVVRRCVHKTTGLEFAAKIINTKKLSARDFQKLEREARICRKLQHPNIVRLHDSIQEESF T0292 80 :LYIVMEYCEGGDLASVITK 2bdwA 85 :HYLVFDLVTGGELFEDIVA T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 2bdwA 104 :REFYSEADASHCIQQILESIAYCHSN T0292 134 :TVLHRDLKPANVFL 2bdwA 130 :GIVHRNLKPENLLL T0292 148 :DGKQNVKLGDFGLARILNHD 2bdwA 147 :AKGAAVKLADFGLAIEVNDS T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 2bdwA 168 :EAWHGFAGTPGYLSPEVLKKDPYSKPVDIWACGVILYILLVGYPPFWDEDQHRLYAQIKAGAYDY T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILE 2bdwA 236 :EWDTVTPEAKSLIDSMLTVNPKKRITADQALKVPWICN Number of specific fragments extracted= 7 number of extra gaps= 0 total=194 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2eueA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2eueA expands to /projects/compbio/data/pdb/2eue.pdb.gz 2eueA:# T0292 read from 2eueA/merged-good-all-a2m # 2eueA read from 2eueA/merged-good-all-a2m # adding 2eueA to template set # found chain 2eueA in template set Warning: unaligning (T0292)L9 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eueA)K59 Warning: unaligning (T0292)Y10 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eueA)K59 Warning: unaligning (T0292)G18 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)A67 Warning: unaligning (T0292)R19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)K68 Warning: unaligning (T0292)S41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2eueA)M96 Warning: unaligning (T0292)T79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eueA)I128 Warning: unaligning (T0292)L80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eueA)I128 Warning: unaligning (T0292)V83 because of BadResidue code BAD_PEPTIDE in next template residue (2eueA)I132 Warning: unaligning (T0292)M84 because of BadResidue code BAD_PEPTIDE at template residue (2eueA)I132 Warning: unaligning (T0292)A161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2eueA)P215 Warning: unaligning (T0292)P178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)P215 Warning: unaligning (T0292)N187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2eueA)G230 Warning: unaligning (T0292)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)G230 T0292 2 :RAEDYEV 2eueA 51 :HIGNYQI T0292 20 :CQKIRRKSDGKILVWKELDYG 2eueA 69 :VKLAYHTTTGQKVALKIINKK T0292 47 :KQMLVSEVNLLRELKHPNIVRYYDRI 2eueA 97 :QGRIEREISYLRLLRHPHIIKLYDVI T0292 75 :RTNT 2eueA 123 :KSKD T0292 81 :YI 2eueA 129 :IM T0292 85 :EYCE 2eueA 133 :EYAG T0292 90 :GDLASVITKGTK 2eueA 137 :NELFDYIVQRDK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2eueA 149 :MSEQEARRFFQQIISAVEYCHRHK T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGL 2eueA 173 :IVHRDLKPENLLLDEHLNVKIADFGL T0292 179 :YYMSPEQM 2eueA 216 :NYAAPEVI T0292 193 :EKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKF 2eueA 231 :PEVDVWSCGVILYVMLCRRLPFDDESIPVLFKNISNGVY T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 2eueA 270 :TLPKFLSPGAAGLIKRMLIVNPLNRISIHEIMQDDWFKVD Number of specific fragments extracted= 12 number of extra gaps= 4 total=206 Number of alignments=19 # 2eueA read from 2eueA/merged-good-all-a2m # found chain 2eueA in template set Warning: unaligning (T0292)L9 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eueA)K59 Warning: unaligning (T0292)Y10 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eueA)K59 Warning: unaligning (T0292)G18 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)A67 Warning: unaligning (T0292)R19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)K68 Warning: unaligning (T0292)T43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)M96 Warning: unaligning (T0292)T79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eueA)I128 Warning: unaligning (T0292)L80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eueA)I128 Warning: unaligning (T0292)V83 because of BadResidue code BAD_PEPTIDE in next template residue (2eueA)I132 Warning: unaligning (T0292)M84 because of BadResidue code BAD_PEPTIDE at template residue (2eueA)I132 Warning: unaligning (T0292)A161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2eueA)P215 Warning: unaligning (T0292)P178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)P215 Warning: unaligning (T0292)N187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2eueA)G230 Warning: unaligning (T0292)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)G230 T0292 2 :RAEDYEV 2eueA 51 :HIGNYQI T0292 20 :CQKIRRKSDGKILVWKELDY 2eueA 69 :VKLAYHTTTGQKVALKIINK T0292 44 :EAEK 2eueA 97 :QGRI T0292 51 :VSEVNLLRELKHPNIVRYYDRI 2eueA 101 :EREISYLRLLRHPHIIKLYDVI T0292 75 :RTNT 2eueA 123 :KSKD T0292 81 :YI 2eueA 129 :IM T0292 85 :EYCEG 2eueA 133 :EYAGN T0292 91 :DLASVITKGTK 2eueA 138 :ELFDYIVQRDK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2eueA 149 :MSEQEARRFFQQIISAVEYCHRHK T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGL 2eueA 173 :IVHRDLKPENLLLDEHLNVKIADFGL T0292 179 :YYMSPEQM 2eueA 216 :NYAAPEVI T0292 193 :EKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 2eueA 231 :PEVDVWSCGVILYVMLCRRLPFDDESIPVLFKNISNGVYT T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHH 2eueA 271 :LPKFLSPGAAGLIKRMLIVNPLNRISIHEIMQDDWFKVDLPE Number of specific fragments extracted= 13 number of extra gaps= 4 total=219 Number of alignments=20 # 2eueA read from 2eueA/merged-good-all-a2m # found chain 2eueA in template set Warning: unaligning (T0292)L9 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eueA)K59 Warning: unaligning (T0292)Y10 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eueA)K59 Warning: unaligning (T0292)G18 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)A67 Warning: unaligning (T0292)R19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)K68 Warning: unaligning (T0292)T43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)M96 Warning: unaligning (T0292)N77 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eueA)I128 Warning: unaligning (T0292)L80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eueA)I128 Warning: unaligning (T0292)V83 because of BadResidue code BAD_PEPTIDE in next template residue (2eueA)I132 Warning: unaligning (T0292)M84 because of BadResidue code BAD_PEPTIDE at template residue (2eueA)I132 Warning: unaligning (T0292)A161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2eueA)P215 Warning: unaligning (T0292)P178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)P215 Warning: unaligning (T0292)N187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2eueA)G230 Warning: unaligning (T0292)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eueA)G230 T0292 3 :AEDYEV 2eueA 52 :IGNYQI T0292 20 :CQKIRRKSDGKILVWKELDY 2eueA 69 :VKLAYHTTTGQKVALKIINK T0292 44 :EA 2eueA 97 :QG T0292 49 :MLVSEVNLLRELKHPNIVRYYDRIIDRT 2eueA 99 :RIEREISYLRLLRHPHIIKLYDVIKSKD T0292 81 :YI 2eueA 129 :IM T0292 85 :EYCE 2eueA 133 :EYAG T0292 90 :GDLASVITK 2eueA 137 :NELFDYIVQ T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 2eueA 146 :RDKMSEQEARRFFQQIISAVEYCHRH T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGL 2eueA 172 :KIVHRDLKPENLLLDEHLNVKIADFGL T0292 179 :YYMSPEQM 2eueA 216 :NYAAPEVI T0292 193 :EKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 2eueA 231 :PEVDVWSCGVILYVMLCRRLPFDDESIPVLFKNISNGVYT T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHH 2eueA 271 :LPKFLSPGAAGLIKRMLIVNPLNRISIHEIMQDDWFKVDLPE Number of specific fragments extracted= 12 number of extra gaps= 4 total=231 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rdqE/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0292 read from 1rdqE/merged-good-all-a2m # 1rdqE read from 1rdqE/merged-good-all-a2m # found chain 1rdqE in training set Warning: unaligning (T0292)C87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)A124 Warning: unaligning (T0292)E88 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)A124 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rdqE)L198 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rdqE)L198 Warning: unaligning (T0292)M189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)G214 Warning: unaligning (T0292)S190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)G214 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTE 1rdqE 39 :QLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKVVK T0292 45 :AEKQMLVSEVNLLRELKHPNIVRYYDRI 1rdqE 83 :KQIEHTLNEKRILQAVNFPFLVKLEFSF T0292 75 :RTNTTLYIVMEY 1rdqE 111 :KDNSNLYMVMEY T0292 89 :GGDLASVITKGTK 1rdqE 125 :GGEMFSHLRRIGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1rdqE 138 :FSEPHARFYAAQIVLTFEYLHSLD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILN 1rdqE 162 :LIYRDLKPENLLIDQQGYIQVTDFGFAKRVK T0292 169 :SFA 1rdqE 193 :GRT T0292 175 :VGTPYYMSPEQMNR 1rdqE 199 :CGTPEALAPEIILS T0292 191 :YNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKF 1rdqE 215 :YNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKV T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRP 1rdqE 256 :RFPSHFSSDLKDLLRNLLQVDLTKRF T0292 260 :VEEILENPLILEH 1rdqE 288 :VNDIKNHKWFATT Number of specific fragments extracted= 11 number of extra gaps= 2 total=242 Number of alignments=22 # 1rdqE read from 1rdqE/merged-good-all-a2m # found chain 1rdqE in training set Warning: unaligning (T0292)C87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)A124 Warning: unaligning (T0292)E88 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)A124 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rdqE)L198 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rdqE)L198 Warning: unaligning (T0292)M189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)G214 Warning: unaligning (T0292)S190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)G214 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1rdqE 39 :QLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1rdqE 81 :KLKQIEHTLNEKRILQAVNFPFLVKLEFSF T0292 75 :RTNTTLYIVMEY 1rdqE 111 :KDNSNLYMVMEY T0292 89 :GGDLASVITKGTK 1rdqE 125 :GGEMFSHLRRIGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1rdqE 138 :FSEPHARFYAAQIVLTFEYLHSLD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILN 1rdqE 162 :LIYRDLKPENLLIDQQGYIQVTDFGFAKRVK T0292 169 :SFA 1rdqE 193 :GRT T0292 175 :VGTPYYMSPEQMNR 1rdqE 199 :CGTPEALAPEIILS T0292 191 :YNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1rdqE 215 :YNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1rdqE 257 :FPSHFSSDLKDLLRNLLQVDLTKRF T0292 259 :SVEEILENPLILEHH 1rdqE 287 :GVNDIKNHKWFATTD Number of specific fragments extracted= 11 number of extra gaps= 2 total=253 Number of alignments=23 # 1rdqE read from 1rdqE/merged-good-all-a2m # found chain 1rdqE in training set Warning: unaligning (T0292)C87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)A124 Warning: unaligning (T0292)E88 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)A124 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rdqE)L198 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rdqE)L198 Warning: unaligning (T0292)M189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)G214 Warning: unaligning (T0292)S190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)G214 T0292 1 :SRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1rdqE 38 :AQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1rdqE 81 :KLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSN T0292 80 :LYIVMEY 1rdqE 116 :LYMVMEY T0292 89 :GGDLASVITK 1rdqE 125 :GGEMFSHLRR T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1rdqE 135 :IGRFSEPHARFYAAQIVLTFEYLHSL T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 1rdqE 161 :DLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGR T0292 171 :A 1rdqE 195 :T T0292 175 :VGTPYYMSPEQMNR 1rdqE 199 :CGTPEALAPEIILS T0292 191 :YNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1rdqE 215 :YNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1rdqE 257 :FPSHFSSDLKDLLRNLLQVDLTKRF T0292 261 :EEILENPLILEHH 1rdqE 289 :NDIKNHKWFATTD Number of specific fragments extracted= 11 number of extra gaps= 2 total=264 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t4hA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0292 read from 1t4hA/merged-good-all-a2m # 1t4hA read from 1t4hA/merged-good-all-a2m # found chain 1t4hA in training set Warning: unaligning (T0292)F170 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)A380 Warning: unaligning (T0292)A171 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)A380 Warning: unaligning (T0292)Y191 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)D400 Warning: unaligning (T0292)N192 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)D400 Warning: unaligning (T0292)L270 because last residue in template chain is (1t4hA)Q480 T0292 4 :EDYEVLY 1t4hA 218 :GRFLKFD T0292 11 :TIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRII 1t4hA 226 :EIGRGSFKTVYKGLDTETTVEVAWCELQDRKLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWE T0292 74 :DRTNTTLYIVMEYCEGGDLASVITKGTK 1t4hA 291 :VKGKKCIVLVTELMTSGTLKTYLKRFKV T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1t4hA 319 :MKIKVLRSWCRQILKGLQFLHTRT T0292 133 :HTVLHRDLKPANVFL 1t4hA 343 :PPIIHRDLKCDNIFI T0292 148 :DGKQNVKLGDFGLARILNHD 1t4hA 359 :GPTGSVKIGDLGLATLKRAS T0292 172 :KAFVGTPYYMSPEQM 1t4hA 381 :KAVIGTPEFMAPEMY T0292 188 :RMS 1t4hA 396 :EEK T0292 193 :EKSDIWSLGCLLYELCALMPPFTA 1t4hA 401 :ESVDVYAFGMCMLEMATSEYPYSE T0292 217 :FSQKELAGKIREGKFRRIPYRY 1t4hA 426 :QNAAQIYRRVTSGVKPASFDKV T0292 239 :SDELNEIITRMLNLKDYHRPSVEEILENPLI 1t4hA 449 :IPEVKEIIEGCIRQNKDERYSIKDLLNHAFF Number of specific fragments extracted= 11 number of extra gaps= 2 total=275 Number of alignments=25 # 1t4hA read from 1t4hA/merged-good-all-a2m # found chain 1t4hA in training set Warning: unaligning (T0292)F170 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)A380 Warning: unaligning (T0292)A171 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)A380 Warning: unaligning (T0292)Y191 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)D400 Warning: unaligning (T0292)N192 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)D400 Warning: unaligning (T0292)L270 because last residue in template chain is (1t4hA)Q480 T0292 4 :EDYEVLY 1t4hA 218 :GRFLKFD T0292 11 :TIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRII 1t4hA 226 :EIGRGSFKTVYKGLDTETTVEVAWCELQDRKLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWE T0292 74 :DRTNTTLYIVMEYCEGGDLASVITKGTK 1t4hA 291 :VKGKKCIVLVTELMTSGTLKTYLKRFKV T0292 106 :LDEEFVLRVMTQLTLALKECHRRSDG 1t4hA 319 :MKIKVLRSWCRQILKGLQFLHTRTPP T0292 135 :VLHRDLKPANVFL 1t4hA 345 :IIHRDLKCDNIFI T0292 148 :DGKQNVKLGDFGLARILNHD 1t4hA 359 :GPTGSVKIGDLGLATLKRAS T0292 172 :KAFVGTPYYMSPEQMN 1t4hA 381 :KAVIGTPEFMAPEMYE T0292 189 :MS 1t4hA 397 :EK T0292 193 :EKSDIWSLGCLLYELCALMPPFTA 1t4hA 401 :ESVDVYAFGMCMLEMATSEYPYSE T0292 217 :FSQKELAGKIREGKFRRIPYRYS 1t4hA 426 :QNAAQIYRRVTSGVKPASFDKVA T0292 240 :DELNEIITRMLNLKDYHRPSVEEILENPLI 1t4hA 450 :PEVKEIIEGCIRQNKDERYSIKDLLNHAFF Number of specific fragments extracted= 11 number of extra gaps= 2 total=286 Number of alignments=26 # 1t4hA read from 1t4hA/merged-good-all-a2m # found chain 1t4hA in training set Warning: unaligning (T0292)F170 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)A380 Warning: unaligning (T0292)A171 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)A380 Warning: unaligning (T0292)Y191 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)D400 Warning: unaligning (T0292)N192 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)D400 Warning: unaligning (T0292)L270 because last residue in template chain is (1t4hA)Q480 T0292 8 :VLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIID 1t4hA 223 :FDIEIGRGSFKTVYKGLDTETTVEVAWCELQDRKLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWES T0292 75 :RTNTTLYIVMEYCEGGDLASVITK 1t4hA 292 :KGKKCIVLVTELMTSGTLKTYLKR T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1t4hA 316 :FKVMKIKVLRSWCRQILKGLQFLHTR T0292 132 :GHTVLHRDLKPANVFL 1t4hA 342 :TPPIIHRDLKCDNIFI T0292 148 :DGKQNVKLGDFGLARILNHD 1t4hA 359 :GPTGSVKIGDLGLATLKRAS T0292 172 :KAFVGTPYYMSPEQMN 1t4hA 381 :KAVIGTPEFMAPEMYE T0292 189 :MS 1t4hA 397 :EK T0292 193 :EKSDIWSLGCLLYELCALMPPFTA 1t4hA 401 :ESVDVYAFGMCMLEMATSEYPYSE T0292 217 :FSQKELAGKIREGKFRRIPYRY 1t4hA 426 :QNAAQIYRRVTSGVKPASFDKV T0292 239 :SDELNEIITRMLNLKDYHRPSVEEILENPLI 1t4hA 449 :IPEVKEIIEGCIRQNKDERYSIKDLLNHAFF Number of specific fragments extracted= 10 number of extra gaps= 2 total=296 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1csn/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1csn expands to /projects/compbio/data/pdb/1csn.pdb.gz 1csn:Warning: there is no chain 1csn will retry with 1csnA # T0292 read from 1csn/merged-good-all-a2m # 1csn read from 1csn/merged-good-all-a2m # adding 1csn to template set # found chain 1csn in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGS 1csn 10 :VHYKVGRRIGEGSFGVIFEGTNLLNNQQVAIKFEPRRS T0292 42 :MTE 1csn 49 :APQ T0292 50 :LVSEVNLLREL 1csn 52 :LRDEYRTYKLL T0292 61 :KHPNIVRYYDRI 1csn 64 :GCTGIPNVYYFG T0292 75 :RTNTTLYIVMEYCE 1csn 76 :QEGLHNVLVIDLLG T0292 90 :GDLASVITKGTKE 1csn 90 :PSLEDLLDLCGRK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1csn 103 :FSVKTVAMAAKQMLARVQSIHEKS T0292 135 :VLHRDLKPANVFLDGKQN 1csn 127 :LVYRDIKPDNFLIGRPNS T0292 153 :VKLGDFGLARILNHDTSFAKA 1csn 150 :IYVVDFGMVKFYRDPVTKQHI T0292 174 :FVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFS 1csn 178 :LSGTARYMSINTHLGREQSRRDDLEALGHVFMYFLRGSLPWQGLK T0292 219 :QKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILEN 1csn 230 :YERIGEKKQSTPLRELCAGFPEEFYKYMHYARNLAFDATPDYDYLQGL Number of specific fragments extracted= 11 number of extra gaps= 0 total=307 Number of alignments=28 # 1csn read from 1csn/merged-good-all-a2m # found chain 1csn in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1csn 10 :VHYKVGRRIGEGSFGVIFEGTNLLNNQQVAIKFEPRRSD T0292 43 :T 1csn 51 :Q T0292 50 :LVSEVNLLREL 1csn 52 :LRDEYRTYKLL T0292 61 :KHPNIVRYYDRI 1csn 64 :GCTGIPNVYYFG T0292 75 :RTNTTLYIVMEYCE 1csn 76 :QEGLHNVLVIDLLG T0292 90 :GDLASVITKGTKE 1csn 90 :PSLEDLLDLCGRK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1csn 103 :FSVKTVAMAAKQMLARVQSIHEKS T0292 135 :VLHRDLKPANVFLDGKQ 1csn 127 :LVYRDIKPDNFLIGRPN T0292 152 :NVKLGDFGLARILNHDTSFA 1csn 149 :MIYVVDFGMVKFYRDPVTKQ T0292 172 :KAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTA 1csn 176 :KNLSGTARYMSINTHLGREQSRRDDLEALGHVFMYFLRGSLPWQG T0292 217 :FSQKELAGKIRE 1csn 224 :ATNKQKYERIGE T0292 229 :GKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENP 1csn 240 :TPLRELCAGFPEEFYKYMHYARNLAFDATPDYDYLQGLF Number of specific fragments extracted= 12 number of extra gaps= 0 total=319 Number of alignments=29 # 1csn read from 1csn/merged-good-all-a2m # found chain 1csn in template set T0292 5 :DYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1csn 11 :HYKVGRRIGEGSFGVIFEGTNLLNNQQVAIKFEPRRSD T0292 43 :T 1csn 51 :Q T0292 50 :LVSEVNLLREL 1csn 52 :LRDEYRTYKLL T0292 61 :KHPNIVRYYDRIIDRTN 1csn 64 :GCTGIPNVYYFGQEGLH T0292 80 :LYIVMEYCE 1csn 81 :NVLVIDLLG T0292 90 :GDLASVITK 1csn 90 :PSLEDLLDL T0292 102 :ERQYLDEEFVLRVMTQLTLALKECHRR 1csn 99 :CGRKFSVKTVAMAAKQMLARVQSIHEK T0292 134 :TVLHRDLKPANVFL 1csn 126 :SLVYRDIKPDNFLI T0292 148 :DGKQNVKLGDFGLARILN 1csn 145 :KNANMIYVVDFGMVKFYR T0292 166 :HDTSFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFS 1csn 170 :IPYREKKNLSGTARYMSINTHLGREQSRRDDLEALGHVFMYFLRGSLPWQGLK T0292 219 :QKELAGKIREGK 1csn 230 :YERIGEKKQSTP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILE 1csn 245 :LCAGFPEEFYKYMHYARNLAFDATPDYDYLQG Number of specific fragments extracted= 12 number of extra gaps= 0 total=331 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1blxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1blxA expands to /projects/compbio/data/pdb/1blx.pdb.gz 1blxA:# T0292 read from 1blxA/merged-good-all-a2m # 1blxA read from 1blxA/merged-good-all-a2m # adding 1blxA to template set # found chain 1blxA in template set Warning: unaligning (T0292)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1blxA)K29 Warning: unaligning (T0292)K22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1blxA)K29 Warning: unaligning (T0292)T43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1blxA)S57 Warning: unaligning (T0292)A45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1blxA)S57 Warning: unaligning (T0292)I72 because of BadResidue code BAD_PEPTIDE in next template residue (1blxA)T84 Warning: unaligning (T0292)I73 because of BadResidue code BAD_PEPTIDE at template residue (1blxA)T84 Warning: unaligning (T0292)A143 because of BadResidue code BAD_PEPTIDE in next template residue (1blxA)N150 Warning: unaligning (T0292)N144 because of BadResidue code BAD_PEPTIDE at template residue (1blxA)N150 Warning: unaligning (T0292)D167 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1blxA)Q173 Warning: unaligning (T0292)T168 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1blxA)Q173 Warning: unaligning (T0292)A173 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1blxA)V179 Warning: unaligning (T0292)F174 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1blxA)V179 T0292 3 :AEDYEVLYTIGTGSYGRC 1blxA 10 :DQQYECVAEIGEGAYGKV T0292 23 :IRRKS 1blxA 30 :ARDLK T0292 28 :DGKILVWKELDY 1blxA 36 :GGRFVALKRVRV T0292 40 :GSM 1blxA 53 :GMP T0292 46 :EKQMLVSEVN 1blxA 58 :TIREVAVLRH T0292 57 :LRELKHPNIVRYYDR 1blxA 68 :LETFEHPNVVRLFDV T0292 74 :DRTNTTLYIVMEYCE 1blxA 88 :TDRETKLTLVFEHVD T0292 90 :GDLASVITKG 1blxA 103 :QDLTTYLDKV T0292 102 :ERQYLDEEFVLRVMTQLTLALKECHRRS 1blxA 113 :PEPGVPTETIKDMMFQLLRGLDFLHSHR T0292 135 :VLHRDLKP 1blxA 141 :VVHRDLKP T0292 145 :VFLDGKQNVKLGDFGLAR 1blxA 151 :ILVTSSGQIKLADFGLAR T0292 164 :LNH 1blxA 169 :IYS T0292 169 :SFAK 1blxA 174 :MALT T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1blxA 180 :VVTLWYRAPEVLLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGKILD T0292 229 :GKFRRIPYRY 1blxA 245 :RDVALPRQAF T0292 239 :SDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 1blxA 270 :DELGKDLLLKCLTFNPAKRISAYSALSHPYFQDLERCKE Number of specific fragments extracted= 16 number of extra gaps= 6 total=347 Number of alignments=31 # 1blxA read from 1blxA/merged-good-all-a2m # found chain 1blxA in template set Warning: unaligning (T0292)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1blxA)K29 Warning: unaligning (T0292)K22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1blxA)K29 Warning: unaligning (T0292)T43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1blxA)S57 Warning: unaligning (T0292)E44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1blxA)S57 Warning: unaligning (T0292)I72 because of BadResidue code BAD_PEPTIDE in next template residue (1blxA)T84 Warning: unaligning (T0292)I73 because of BadResidue code BAD_PEPTIDE at template residue (1blxA)T84 Warning: unaligning (T0292)A143 because of BadResidue code BAD_PEPTIDE in next template residue (1blxA)N150 Warning: unaligning (T0292)N144 because of BadResidue code BAD_PEPTIDE at template residue (1blxA)N150 Warning: unaligning (T0292)D167 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1blxA)Q173 Warning: unaligning (T0292)T168 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1blxA)Q173 Warning: unaligning (T0292)A173 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1blxA)V179 Warning: unaligning (T0292)F174 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1blxA)V179 T0292 2 :RAED 1blxA 8 :RADQ T0292 6 :YEVLYTIGTGSYGRC 1blxA 13 :YECVAEIGEGAYGKV T0292 23 :IRRKS 1blxA 30 :ARDLK T0292 28 :DGKILVWKELDY 1blxA 36 :GGRFVALKRVRV T0292 40 :GSM 1blxA 53 :GMP T0292 50 :LVSEVNLLREL 1blxA 58 :TIREVAVLRHL T0292 61 :KHPNIVRYYDR 1blxA 72 :EHPNVVRLFDV T0292 74 :DRTNTT 1blxA 86 :SRTDRE T0292 80 :LYIVMEYCEG 1blxA 94 :LTLVFEHVDQ T0292 91 :DLASVITKGTKER 1blxA 104 :DLTTYLDKVPEPG T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1blxA 117 :VPTETIKDMMFQLLRGLDFLHSHR T0292 135 :VLHRDLKP 1blxA 141 :VVHRDLKP T0292 145 :VFLDGKQNVKLGDFGLARI 1blxA 151 :ILVTSSGQIKLADFGLARI T0292 165 :NH 1blxA 170 :YS T0292 169 :SFAK 1blxA 174 :MALT T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYR 1blxA 180 :VVTLWYRAPEVLLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGKILDVIGLPGEED T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 1blxA 269 :IDELGKDLLLKCLTFNPAKRISAYSALSHPYFQDLERCKE Number of specific fragments extracted= 17 number of extra gaps= 6 total=364 Number of alignments=32 # 1blxA read from 1blxA/merged-good-all-a2m # found chain 1blxA in template set Warning: unaligning (T0292)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1blxA)K29 Warning: unaligning (T0292)K22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1blxA)K29 Warning: unaligning (T0292)T43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1blxA)S57 Warning: unaligning (T0292)E44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1blxA)S57 Warning: unaligning (T0292)I72 because of BadResidue code BAD_PEPTIDE in next template residue (1blxA)T84 Warning: unaligning (T0292)I73 because of BadResidue code BAD_PEPTIDE at template residue (1blxA)T84 Warning: unaligning (T0292)A143 because of BadResidue code BAD_PEPTIDE in next template residue (1blxA)N150 Warning: unaligning (T0292)N144 because of BadResidue code BAD_PEPTIDE at template residue (1blxA)N150 Warning: unaligning (T0292)H166 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1blxA)Q173 Warning: unaligning (T0292)D167 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1blxA)Q173 Warning: unaligning (T0292)A173 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1blxA)V179 Warning: unaligning (T0292)F174 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1blxA)V179 T0292 3 :AEDYEVLYTIGTGSYGRC 1blxA 10 :DQQYECVAEIGEGAYGKV T0292 23 :IRRKSD 1blxA 30 :ARDLKN T0292 29 :GKILVWKELDY 1blxA 37 :GRFVALKRVRV T0292 40 :GS 1blxA 53 :GM T0292 50 :LVSEVNLLREL 1blxA 58 :TIREVAVLRHL T0292 61 :KHPNIVRYYDR 1blxA 72 :EHPNVVRLFDV T0292 74 :DRTNTTLYIVMEYCEG 1blxA 88 :TDRETKLTLVFEHVDQ T0292 91 :DLASVITK 1blxA 104 :DLTTYLDK T0292 101 :KERQYLDEEFVLRVMTQLTLALKECHRR 1blxA 112 :VPEPGVPTETIKDMMFQLLRGLDFLHSH T0292 134 :TVLHRDLKP 1blxA 140 :RVVHRDLKP T0292 145 :VFLDGKQNVKLGDFGLARILN 1blxA 151 :ILVTSSGQIKLADFGLARIYS T0292 169 :SFAK 1blxA 174 :MALT T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1blxA 180 :VVTLWYRAPEVLLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGKILDVIGLP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 1blxA 265 :FVTDIDELGKDLLLKCLTFNPAKRISAYSALSHPYFQDLERCKE Number of specific fragments extracted= 14 number of extra gaps= 6 total=378 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xh9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xh9A expands to /projects/compbio/data/pdb/1xh9.pdb.gz 1xh9A:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0292 read from 1xh9A/merged-good-all-a2m # 1xh9A read from 1xh9A/merged-good-all-a2m # adding 1xh9A to template set # found chain 1xh9A in template set Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xh9A)L198 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xh9A)L198 Warning: unaligning (T0292)M189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xh9A)G214 Warning: unaligning (T0292)S190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xh9A)G214 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTE 1xh9A 39 :HLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKVVK T0292 45 :AEKQMLVSEVNLLRELKHPNIVRYYDRI 1xh9A 83 :KEIEHTLNEKRILQAVNFPFLVKLEFSF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1xh9A 111 :KDNSNLYMVMEYAPGGEMFSHLRRIGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1xh9A 138 :FSEPHARFYAAQIVLTFEYLHSLD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILN 1xh9A 162 :LIYRDLKPENLMIDQQGYIKVTDFGLAKRVK T0292 169 :SFA 1xh9A 193 :GRT T0292 175 :VGTPYYMSPEQMNR 1xh9A 199 :CGTPEYLAPEIILS T0292 191 :YNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKF 1xh9A 215 :YNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKV T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRP 1xh9A 256 :RFPSHFSSDLKDLLRNLLQVDLTKRF T0292 260 :VEEILENPLILEH 1xh9A 288 :VNDIKNHKWFATT Number of specific fragments extracted= 10 number of extra gaps= 1 total=388 Number of alignments=34 # 1xh9A read from 1xh9A/merged-good-all-a2m # found chain 1xh9A in template set Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xh9A)L198 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xh9A)L198 Warning: unaligning (T0292)M189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xh9A)G214 Warning: unaligning (T0292)S190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xh9A)G214 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1xh9A 39 :HLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1xh9A 81 :KLKEIEHTLNEKRILQAVNFPFLVKLEFSF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1xh9A 111 :KDNSNLYMVMEYAPGGEMFSHLRRIGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1xh9A 138 :FSEPHARFYAAQIVLTFEYLHSLD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILN 1xh9A 162 :LIYRDLKPENLMIDQQGYIKVTDFGLAKRVK T0292 169 :SFA 1xh9A 193 :GRT T0292 175 :VGTPYYMSPEQMNR 1xh9A 199 :CGTPEYLAPEIILS T0292 191 :YNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1xh9A 215 :YNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1xh9A 257 :FPSHFSSDLKDLLRNLLQVDLTKRF T0292 259 :SVEEILENPLILEHH 1xh9A 287 :GVNDIKNHKWFATTD Number of specific fragments extracted= 10 number of extra gaps= 1 total=398 Number of alignments=35 # 1xh9A read from 1xh9A/merged-good-all-a2m # found chain 1xh9A in template set Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xh9A)L198 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xh9A)L198 Warning: unaligning (T0292)M189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xh9A)G214 Warning: unaligning (T0292)S190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xh9A)G214 T0292 1 :SRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1xh9A 38 :AHLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1xh9A 81 :KLKEIEHTLNEKRILQAVNFPFLVKLEFSFKDNSN T0292 80 :LYIVMEYCEGGDLASVITK 1xh9A 116 :LYMVMEYAPGGEMFSHLRR T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1xh9A 135 :IGRFSEPHARFYAAQIVLTFEYLHSL T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 1xh9A 161 :DLIYRDLKPENLMIDQQGYIKVTDFGLAKRVKGR T0292 171 :A 1xh9A 195 :T T0292 175 :VGTPYYMSPEQMNR 1xh9A 199 :CGTPEYLAPEIILS T0292 191 :YNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1xh9A 215 :YNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1xh9A 257 :FPSHFSSDLKDLLRNLLQVDLTKRF T0292 261 :EEILENPLILEH 1xh9A 289 :NDIKNHKWFATT Number of specific fragments extracted= 10 number of extra gaps= 1 total=408 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jvpP/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jvpP expands to /projects/compbio/data/pdb/1jvp.pdb.gz 1jvpP:Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 175, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 177, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 643, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 645, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 679, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1015, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1182, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1184, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1186, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1188, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1190, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1192, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1194, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1196, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1200, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1202, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1204, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1212, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1214, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1220, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1222, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1224, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1226, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1230, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1232, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1234, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1288, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1290, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1292, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1336, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2006, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2008, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2010, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2012, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2014, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2016, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2018, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2020, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2022, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2024, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2026, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2028, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2030, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2032, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2034, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2036, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2038, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2040, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2042, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2046, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2048, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2050, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2052, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2054, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2056, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2058, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2062, because occupancy 0.500 <= existing 0.500 in 1jvpP # T0292 read from 1jvpP/merged-good-all-a2m # 1jvpP read from 1jvpP/merged-good-all-a2m # adding 1jvpP to template set # found chain 1jvpP in template set Warning: unaligning (T0292)A3 because first residue in template chain is (1jvpP)M1 Warning: unaligning (T0292)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V44 Warning: unaligning (T0292)M42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V44 Warning: unaligning (T0292)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V163 Warning: unaligning (T0292)V175 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V163 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKEL 1jvpP 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKI T0292 43 :TEAE 1jvpP 45 :PSTA T0292 51 :VSEVNLLRELKHPNIVRYYDRI 1jvpP 49 :IREISLLKELNHPNIVKLLDVI T0292 75 :RTNTTLYIVMEYCE 1jvpP 71 :HTENKLYLVFEFLH T0292 90 :GDLASVITKG 1jvpP 85 :QDLKKFMDAS T0292 102 :ERQYLDEEFVLRVMTQLTLALKECHRRS 1jvpP 95 :ALTGIPLPLIKSYLFQLLQGLAFCHSHR T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARI 1jvpP 123 :VLHRDLKPQNLLINTEGAIKLADFGLARA T0292 176 :GTPYYMSPEQMNR 1jvpP 164 :VTLWYRAPEILLG T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1jvpP 178 :KYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFR T0292 229 :GKFRRIP 1jvpP 238 :PSFPKWA T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH 1jvpP 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPV Number of specific fragments extracted= 11 number of extra gaps= 0 total=419 Number of alignments=37 # 1jvpP read from 1jvpP/merged-good-all-a2m # found chain 1jvpP in template set Warning: unaligning (T0292)A3 because first residue in template chain is (1jvpP)M1 Warning: unaligning (T0292)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V44 Warning: unaligning (T0292)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V163 Warning: unaligning (T0292)V175 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V163 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKEL 1jvpP 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKI T0292 43 :TEAEK 1jvpP 45 :PSTAI T0292 52 :SEVNLLRELKHPNIVRYYDRI 1jvpP 50 :REISLLKELNHPNIVKLLDVI T0292 75 :RTNTTLYIVMEYCEG 1jvpP 71 :HTENKLYLVFEFLHQ T0292 91 :DLASVITKGTKER 1jvpP 86 :DLKKFMDASALTG T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1jvpP 99 :IPLPLIKSYLFQLLQGLAFCHSHR T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARI 1jvpP 123 :VLHRDLKPQNLLINTEGAIKLADFGLARA T0292 176 :GTPYYMSPEQMNR 1jvpP 164 :VTLWYRAPEILLG T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYR 1jvpP 178 :KYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVV T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1jvpP 255 :LDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVT T0292 274 :HHHH 1jvpP 295 :HLRL Number of specific fragments extracted= 11 number of extra gaps= 0 total=430 Number of alignments=38 # 1jvpP read from 1jvpP/merged-good-all-a2m # found chain 1jvpP in template set Warning: unaligning (T0292)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V44 Warning: unaligning (T0292)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V163 Warning: unaligning (T0292)V175 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V163 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKEL 1jvpP 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKI T0292 43 :TEAEK 1jvpP 45 :PSTAI T0292 52 :SEVNLLRELKHPNIVRYYDRIIDRTN 1jvpP 50 :REISLLKELNHPNIVKLLDVIHTENK T0292 80 :LYIVMEYCEG 1jvpP 76 :LYLVFEFLHQ T0292 91 :DLASVITK 1jvpP 86 :DLKKFMDA T0292 101 :KERQYLDEEFVLRVMTQLTLALKECHRR 1jvpP 94 :SALTGIPLPLIKSYLFQLLQGLAFCHSH T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARI 1jvpP 122 :RVLHRDLKPQNLLINTEGAIKLADFGLARA T0292 176 :GTPYYMSPEQMNR 1jvpP 164 :VTLWYRAPEILLG T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1jvpP 178 :KYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH 1jvpP 251 :VVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPV Number of specific fragments extracted= 10 number of extra gaps= 0 total=440 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p4fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1p4fA expands to /projects/compbio/data/pdb/1p4f.pdb.gz 1p4fA:Skipped atom 166, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 168, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 170, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 172, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 174, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 178, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 180, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 1110, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 1112, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 1114, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 1116, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 1118, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 1120, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 1122, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 1124, because occupancy 0.500 <= existing 0.500 in 1p4fA Skipped atom 1126, because occupancy 0.500 <= existing 0.500 in 1p4fA # T0292 read from 1p4fA/merged-good-all-a2m # 1p4fA read from 1p4fA/merged-good-all-a2m # adding 1p4fA to template set # found chain 1p4fA in template set Warning: unaligning (T0292)T79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p4fA)V89 Warning: unaligning (T0292)L80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p4fA)V89 Warning: unaligning (T0292)V95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p4fA)T112 Warning: unaligning (T0292)D107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p4fA)T112 Warning: unaligning (T0292)Q151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p4fA)P155 Warning: unaligning (T0292)N152 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p4fA)P155 Warning: unaligning (T0292)E271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p4fA)Q292 T0292 2 :RAED 1p4fA 8 :NVDD T0292 6 :YEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 1p4fA 13 :YDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKK T0292 40 :GSMTEA 1p4fA 49 :TKSSRR T0292 47 :KQMLVSEVNLLRELKHPNIVRYYDRI 1p4fA 58 :REDIEREVSILKEIQHPNVITLHEVY T0292 75 :RTNT 1p4fA 84 :ENKT T0292 81 :YIVMEYCEGGDLAS 1p4fA 90 :ILILELVAGGELFD T0292 108 :EEFVLRVMTQLTLALKECHRRS 1p4fA 113 :EEEATEFLKQILNGVYYLHSLQ T0292 135 :VLHRDLKPANVFL 1p4fA 135 :IAHFDLKPENIML T0292 148 :DGK 1p4fA 149 :DRN T0292 153 :VKLGDFGLARILNHD 1p4fA 157 :IKIIDFGLAHKIDFG T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIP 1p4fA 172 :NEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFED T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLIL 1p4fA 242 :SNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIK Number of specific fragments extracted= 12 number of extra gaps= 2 total=452 Number of alignments=40 # 1p4fA read from 1p4fA/merged-good-all-a2m # found chain 1p4fA in template set Warning: unaligning (T0292)T79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p4fA)V89 Warning: unaligning (T0292)L80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p4fA)V89 Warning: unaligning (T0292)V95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p4fA)T112 Warning: unaligning (T0292)D107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p4fA)T112 Warning: unaligning (T0292)Q151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p4fA)P155 Warning: unaligning (T0292)E271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p4fA)Q292 T0292 1 :SRAED 1p4fA 7 :ENVDD T0292 6 :YEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 1p4fA 13 :YDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKK T0292 40 :GSMTEAE 1p4fA 54 :RGVSRED T0292 50 :LVSEVNLLRELKHPNIVRYYDRI 1p4fA 61 :IEREVSILKEIQHPNVITLHEVY T0292 75 :RTNT 1p4fA 84 :ENKT T0292 81 :YIVMEYCEGGDLAS 1p4fA 90 :ILILELVAGGELFD T0292 108 :EEFVLRVMTQLTLALKECHRRS 1p4fA 113 :EEEATEFLKQILNGVYYLHSLQ T0292 135 :VLHRDLKPANVFL 1p4fA 135 :IAHFDLKPENIML T0292 148 :DGK 1p4fA 149 :DRN T0292 152 :NVKLGDFGLARILNHD 1p4fA 156 :RIKIIDFGLAHKIDFG T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIP 1p4fA 172 :NEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFED T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLIL 1p4fA 242 :SNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIK Number of specific fragments extracted= 12 number of extra gaps= 2 total=464 Number of alignments=41 # 1p4fA read from 1p4fA/merged-good-all-a2m # found chain 1p4fA in template set Warning: unaligning (T0292)N77 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p4fA)V89 Warning: unaligning (T0292)L80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p4fA)V89 Warning: unaligning (T0292)V95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p4fA)T112 Warning: unaligning (T0292)D107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p4fA)T112 Warning: unaligning (T0292)E271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p4fA)Q292 T0292 3 :AEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 1p4fA 10 :DDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKK T0292 43 :T 1p4fA 57 :S T0292 47 :KQMLVSEVNLLRELKHPNIVRYYDRIIDRT 1p4fA 58 :REDIEREVSILKEIQHPNVITLHEVYENKT T0292 81 :YIVMEYCEGGDLAS 1p4fA 90 :ILILELVAGGELFD T0292 108 :EEFVLRVMTQLTLALKECHRR 1p4fA 113 :EEEATEFLKQILNGVYYLHSL T0292 134 :TVLHRDLKPANVFL 1p4fA 134 :QIAHFDLKPENIML T0292 148 :DGK 1p4fA 149 :DRN T0292 152 :NVKLGDFGLARILNHD 1p4fA 156 :RIKIIDFGLAHKIDFG T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1p4fA 172 :NEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEF T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLIL 1p4fA 240 :YFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIK Number of specific fragments extracted= 10 number of extra gaps= 1 total=474 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b9hA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b9hA expands to /projects/compbio/data/pdb/2b9h.pdb.gz 2b9hA:# T0292 read from 2b9hA/merged-good-all-a2m # 2b9hA read from 2b9hA/merged-good-all-a2m # adding 2b9hA to template set # found chain 2b9hA in template set Warning: unaligning (T0292)N165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b9hA)V180 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b9hA)V180 T0292 3 :AEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 2b9hA 10 :SSDFQLKSLLGEGAYGVVCSATHKPTGEIVAIKKIEP T0292 43 :TEAEK 2b9hA 47 :FDKPL T0292 48 :QMLVSEVNLLRELKHPNIVRYYDRII 2b9hA 54 :LRTLREIKILKHFKHENIITIFNIQR T0292 74 :DRTNTTLYIVMEYCE 2b9hA 83 :FENFNEVYIIQELMQ T0292 90 :GDLASVITKGT 2b9hA 98 :TDLHRVISTQM T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2b9hA 109 :LSDDHIQYFIYQTLRAVKVLHGSN T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARIL 2b9hA 133 :VIHRDLKPSNLLINSNCDLKVCDFGLARII T0292 173 :AFVGTPYYMSPEQM 2b9hA 181 :EFVATRWYRAPEVM T0292 187 :NRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 2b9hA 196 :TSAKYSRAMDVWSCGCILAELFLRRPIFPGRDYRHQLLLIFG T0292 231 :FRRIP 2b9hA 263 :LPMYP T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 2b9hA 276 :PRVNPKGIDLLQRMLVFDPAKRITAKEALEHPYLQTY Number of specific fragments extracted= 11 number of extra gaps= 0 total=485 Number of alignments=43 # 2b9hA read from 2b9hA/merged-good-all-a2m # found chain 2b9hA in template set Warning: unaligning (T0292)N165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b9hA)V180 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b9hA)V180 T0292 3 :AEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 2b9hA 10 :SSDFQLKSLLGEGAYGVVCSATHKPTGEIVAIKKIEP T0292 40 :G 2b9hA 48 :D T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRII 2b9hA 49 :KPLFALRTLREIKILKHFKHENIITIFNIQR T0292 74 :D 2b9hA 82 :S T0292 75 :RTNTTLYIVMEYCEG 2b9hA 84 :ENFNEVYIIQELMQT T0292 91 :DLASVITKGT 2b9hA 99 :DLHRVISTQM T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2b9hA 109 :LSDDHIQYFIYQTLRAVKVLHGSN T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARIL 2b9hA 133 :VIHRDLKPSNLLINSNCDLKVCDFGLARII T0292 173 :AFVGTPYYMSPEQMNR 2b9hA 181 :EFVATRWYRAPEVMLT T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYR 2b9hA 198 :AKYSRAMDVWSCGCILAELFLRRPIFPGRDYRHQLLLIFGIIGTPHSDN T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 2b9hA 278 :VNPKGIDLLQRMLVFDPAKRITAKEALEHPYLQTYH Number of specific fragments extracted= 11 number of extra gaps= 0 total=496 Number of alignments=44 # 2b9hA read from 2b9hA/merged-good-all-a2m # found chain 2b9hA in template set Warning: unaligning (T0292)N165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b9hA)V180 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b9hA)V180 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 2b9hA 11 :SDFQLKSLLGEGAYGVVCSATHKPTGEIVAIKKIEP T0292 42 :MTEAEKQMLVSEVNLLRELKHPNIVRYYDRIID 2b9hA 48 :DKPLFALRTLREIKILKHFKHENIITIFNIQRP T0292 75 :RTNTTLYIVMEYCEG 2b9hA 84 :ENFNEVYIIQELMQT T0292 91 :DLASVITK 2b9hA 99 :DLHRVIST T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 2b9hA 107 :QMLSDDHIQYFIYQTLRAVKVLHGS T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARIL 2b9hA 132 :NVIHRDLKPSNLLINSNCDLKVCDFGLARII T0292 173 :AFVGTPYYMSPEQMNR 2b9hA 181 :EFVATRWYRAPEVMLT T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 2b9hA 198 :AKYSRAMDVWSCGCILAELFLRRPIFPGRDYRHQLLLIFG T0292 229 :GKFRR 2b9hA 240 :GTPHS T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 2b9hA 274 :MFPRVNPKGIDLLQRMLVFDPAKRITAKEALEHPYLQTYHDPND Number of specific fragments extracted= 10 number of extra gaps= 0 total=506 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bfxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bfxA expands to /projects/compbio/data/pdb/2bfx.pdb.gz 2bfxA:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0292 read from 2bfxA/merged-good-all-a2m # 2bfxA read from 2bfxA/merged-good-all-a2m # adding 2bfxA to template set # found chain 2bfxA in template set Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bfxA)M249 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bfxA)M249 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAE 2bfxA 89 :TIDDFDIGRPLGKGKFGNVYLAREKQNKFIMALKVLFKSQLEKEG T0292 47 :KQMLVSEVNLLRELKHPNIVRYYDRI 2bfxA 135 :EHQLRREIEIQSHLRHPNILRMYNYF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 2bfxA 161 :HDRKRIYLMLEFAPRGELYKELQKHGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2bfxA 188 :FDEQRSATFMEELADALHYCHERK T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARIL 2bfxA 212 :VIHRDIKPENLLMGYKGELKIADFGWSVHA T0292 167 :DTSFA 2bfxA 242 :PSLRR T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKF 2bfxA 250 :CGTLDYLPPEMIEGKTHDEKVDLWCAGVLCYEFLVGMPPFDSPSHTETHRRIVNVDL T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 2bfxA 307 :KFPPFLSDGSKDLISKLLRYHPPQRLPLKGVMEHPWVKAN T0292 275 :HH 2bfxA 350 :VL Number of specific fragments extracted= 9 number of extra gaps= 0 total=515 Number of alignments=46 # 2bfxA read from 2bfxA/merged-good-all-a2m # found chain 2bfxA in template set Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bfxA)M249 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bfxA)M249 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 2bfxA 89 :TIDDFDIGRPLGKGKFGNVYLAREKQNKFIMALKVLFKSQL T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 2bfxA 131 :KEGVEHQLRREIEIQSHLRHPNILRMYNYF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 2bfxA 161 :HDRKRIYLMLEFAPRGELYKELQKHGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2bfxA 188 :FDEQRSATFMEELADALHYCHERK T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILN 2bfxA 212 :VIHRDIKPENLLMGYKGELKIADFGWSVHAP T0292 168 :TSFA 2bfxA 243 :SLRR T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 2bfxA 250 :CGTLDYLPPEMIEGKTHDEKVDLWCAGVLCYEFLVGMPPFDSPSHTETHRRIVNVDLK T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 2bfxA 308 :FPPFLSDGSKDLISKLLRYHPPQRLPLKGVMEHPWVKANSRRVL Number of specific fragments extracted= 8 number of extra gaps= 0 total=523 Number of alignments=47 # 2bfxA read from 2bfxA/merged-good-all-a2m # found chain 2bfxA in template set Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bfxA)M249 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bfxA)M249 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 2bfxA 89 :TIDDFDIGRPLGKGKFGNVYLAREKQNKFIMALKVLFKSQL T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 2bfxA 131 :KEGVEHQLRREIEIQSHLRHPNILRMYNYFHDRKR T0292 80 :LYIVMEYCEGGDLASVITK 2bfxA 166 :IYLMLEFAPRGELYKELQK T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 2bfxA 185 :HGRFDEQRSATFMEELADALHYCHER T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 2bfxA 211 :KVIHRDIKPENLLMGYKGELKIADFGWSVHAPSL T0292 170 :FA 2bfxA 245 :RR T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 2bfxA 250 :CGTLDYLPPEMIEGKTHDEKVDLWCAGVLCYEFLVGMPPFDSPSHTETHRRIVNVDLK T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 2bfxA 308 :FPPFLSDGSKDLISKLLRYHPPQRLPLKGVMEHPWVKANSRRVL Number of specific fragments extracted= 8 number of extra gaps= 0 total=531 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gz8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0292 read from 1gz8A/merged-good-all-a2m # 1gz8A read from 1gz8A/merged-good-all-a2m # found chain 1gz8A in training set Warning: unaligning (T0292)A3 because first residue in template chain is (1gz8A)M1 Warning: unaligning (T0292)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gz8A)K20 Warning: unaligning (T0292)K22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gz8A)K20 Warning: unaligning (T0292)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)V44 Warning: unaligning (T0292)M42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)V44 Warning: unaligning (T0292)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)K178 Warning: unaligning (T0292)S190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)K178 Warning: unaligning (T0292)N192 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)S181 Warning: unaligning (T0292)Y236 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)P253 T0292 4 :EDYEVLYTIGTGSYGRC 1gz8A 2 :ENFQKVEKIGEGTYGVV T0292 23 :IRRKSDGKILVWKEL 1gz8A 21 :ARNKLTGEVVALKKI T0292 43 :TEA 1gz8A 45 :PST T0292 50 :LVSEVNLLRELKHPNIVRYYDRI 1gz8A 48 :AIREISLLKELNHPNIVKLLDVI T0292 75 :RTNTTLYIVMEYCE 1gz8A 71 :HTENKLYLVFEFLH T0292 90 :GDLASVITKG 1gz8A 85 :QDLKKFMDAS T0292 102 :ERQYLDEEFVLRVMTQLTLALKECHRRS 1gz8A 95 :ALTGIPLPLIKSYLFQLLQGLAFCHSHR T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKAFVGTPYYMSPEQMN 1gz8A 123 :VLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILL T0292 191 :Y 1gz8A 179 :Y T0292 193 :EKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1gz8A 182 :TAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFR T0292 229 :GKFRRIP 1gz8A 238 :PSFPKWA T0292 237 :RYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH 1gz8A 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPV Number of specific fragments extracted= 12 number of extra gaps= 3 total=543 Number of alignments=49 # 1gz8A read from 1gz8A/merged-good-all-a2m # found chain 1gz8A in training set Warning: unaligning (T0292)A3 because first residue in template chain is (1gz8A)M1 Warning: unaligning (T0292)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gz8A)K20 Warning: unaligning (T0292)K22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gz8A)K20 Warning: unaligning (T0292)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)V44 Warning: unaligning (T0292)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)K178 Warning: unaligning (T0292)M189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)K178 Warning: unaligning (T0292)Y191 because of BadResidue code BAD_PEPTIDE in next template residue (1gz8A)S181 Warning: unaligning (T0292)N192 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)S181 T0292 4 :EDYEVLYTIGTGSYGRC 1gz8A 2 :ENFQKVEKIGEGTYGVV T0292 23 :IRRKSDGKILVWKEL 1gz8A 21 :ARNKLTGEVVALKKI T0292 43 :TEA 1gz8A 45 :PST T0292 50 :LVSEVNLLRELKHPNIVRYYDRI 1gz8A 48 :AIREISLLKELNHPNIVKLLDVI T0292 75 :RTNTTLYIVMEYCEG 1gz8A 71 :HTENKLYLVFEFLHQ T0292 91 :DLASVITKGTKER 1gz8A 86 :DLKKFMDASALTG T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1gz8A 99 :IPLPLIKSYLFQLLQGLAFCHSHR T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKAFVGTPYYMSPEQMN 1gz8A 123 :VLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILL T0292 190 :S 1gz8A 179 :Y T0292 193 :EKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYR 1gz8A 182 :TAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVV T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1gz8A 255 :LDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVT T0292 274 :HHHH 1gz8A 295 :HLRL Number of specific fragments extracted= 12 number of extra gaps= 2 total=555 Number of alignments=50 # 1gz8A read from 1gz8A/merged-good-all-a2m # found chain 1gz8A in training set Warning: unaligning (T0292)A3 because first residue in template chain is (1gz8A)M1 Warning: unaligning (T0292)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gz8A)K20 Warning: unaligning (T0292)K22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gz8A)K20 Warning: unaligning (T0292)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)V44 Warning: unaligning (T0292)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)K178 Warning: unaligning (T0292)M189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)K178 Warning: unaligning (T0292)Y191 because of BadResidue code BAD_PEPTIDE in next template residue (1gz8A)S181 Warning: unaligning (T0292)N192 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)S181 Warning: unaligning (T0292)P235 because of BadResidue code BAD_PEPTIDE in next template residue (1gz8A)P253 Warning: unaligning (T0292)Y236 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)P253 T0292 4 :EDYEVLYTIGTGSYGRC 1gz8A 2 :ENFQKVEKIGEGTYGVV T0292 23 :IRRKSDGKILVWKEL 1gz8A 21 :ARNKLTGEVVALKKI T0292 43 :TEAE 1gz8A 45 :PSTA T0292 51 :VSEVNLLRELKHPNIVRYYDRIIDRTN 1gz8A 49 :IREISLLKELNHPNIVKLLDVIHTENK T0292 80 :LYIVMEYCEG 1gz8A 76 :LYLVFEFLHQ T0292 91 :DLASVITK 1gz8A 86 :DLKKFMDA T0292 101 :KERQYLDEEFVLRVMTQLTLALKECHRR 1gz8A 94 :SALTGIPLPLIKSYLFQLLQGLAFCHSH T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKAFVGTPYYMSPEQMN 1gz8A 122 :RVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILL T0292 190 :S 1gz8A 179 :Y T0292 193 :EKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1gz8A 182 :TAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTP T0292 234 :I 1gz8A 251 :V T0292 237 :RYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH 1gz8A 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPV Number of specific fragments extracted= 12 number of extra gaps= 3 total=567 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2evaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2evaA expands to /projects/compbio/data/pdb/2eva.pdb.gz 2evaA:Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 2evaA Skipped atom 696, because occupancy 0.500 <= existing 0.500 in 2evaA Skipped atom 698, because occupancy 0.500 <= existing 0.500 in 2evaA Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2evaA # T0292 read from 2evaA/merged-good-all-a2m # 2evaA read from 2evaA/merged-good-all-a2m # adding 2evaA to template set # found chain 2evaA in template set Warning: unaligning (T0292)L160 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2evaA)G191 Warning: unaligning (T0292)G176 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2evaA)G191 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRR 2evaA 32 :DYKEIEVEEVVGRGAFGVVCKAKW T0292 28 :DGKILVWKELDYG 2evaA 56 :RAKDVAIKQIESE T0292 45 :AEKQMLVSEVNLLRELKHPNIVRYYDRI 2evaA 69 :SERKAFIVELRQLSRVNHPNIVKLYGAC T0292 75 :RTNT 2evaA 97 :LNPV T0292 81 :YIVMEYCEGGDLASVITKGTK 2evaA 101 :CLVMEYAEGGSLYNVLHGAEP T0292 105 :YLDEEFVLRVMTQLTLALKECHRRSDGG 2evaA 124 :YYTAAHAMSWCLQCSQGVAYLHSMQPKA T0292 135 :VLHRDLKPANVFLDGK 2evaA 152 :LIHRDLKPPNLLLVAG T0292 151 :QNVKLGDFG 2evaA 169 :TVLKICDFG T0292 177 :TPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFT 2evaA 192 :SAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFD T0292 216 :AFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILEN 2evaA 233 :GGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKI T0292 267 :PLILEH 2evaA 289 :RYFPGA T0292 274 :HHHH 2evaA 296 :EPLQ Number of specific fragments extracted= 12 number of extra gaps= 0 total=579 Number of alignments=52 # 2evaA read from 2evaA/merged-good-all-a2m # found chain 2evaA in template set Warning: unaligning (T0292)L160 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2evaA)G191 Warning: unaligning (T0292)G176 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2evaA)G191 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRK 2evaA 32 :DYKEIEVEEVVGRGAFGVVCKAKWR T0292 29 :GKILVWKELDYG 2evaA 57 :AKDVAIKQIESE T0292 45 :AEKQMLVSEVNLLRELKHPNIVRYYDRI 2evaA 69 :SERKAFIVELRQLSRVNHPNIVKLYGAC T0292 75 :RTNT 2evaA 97 :LNPV T0292 81 :YIVMEYCEGGDLASVITKGTKERQ 2evaA 101 :CLVMEYAEGGSLYNVLHGAEPLPY T0292 106 :LDEEFVLRVMTQLTLALKECHRRSDGG 2evaA 125 :YTAAHAMSWCLQCSQGVAYLHSMQPKA T0292 135 :VLHRDLKPANVFLDGKQ 2evaA 152 :LIHRDLKPPNLLLVAGG T0292 152 :NVKLGDFG 2evaA 170 :VLKICDFG T0292 177 :TPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFT 2evaA 192 :SAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFD T0292 216 :AFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILEN 2evaA 233 :GGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKI T0292 267 :PLILEHH 2evaA 288 :MRYFPGA T0292 275 :HH 2evaA 296 :EP Number of specific fragments extracted= 12 number of extra gaps= 0 total=591 Number of alignments=53 # 2evaA read from 2evaA/merged-good-all-a2m # found chain 2evaA in template set Warning: unaligning (T0292)L160 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2evaA)G191 Warning: unaligning (T0292)G176 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2evaA)G191 T0292 1 :SRAEDYEVLYTIGTGSYGRCQKIRRK 2evaA 31 :IDYKEIEVEEVVGRGAFGVVCKAKWR T0292 29 :GKILVWKELDYGS 2evaA 57 :AKDVAIKQIESES T0292 46 :EKQMLVSEVNLLRELKHPNIVRYYDRIIDR 2evaA 70 :ERKAFIVELRQLSRVNHPNIVKLYGACLNP T0292 80 :LYIVMEYCEGGDLASVITK 2evaA 100 :VCLVMEYAEGGSLYNVLHG T0292 100 :TKERQYLDEEFVLRVMTQLTLALKECHRR 2evaA 119 :AEPLPYYTAAHAMSWCLQCSQGVAYLHSM T0292 131 :GGHTVLHRDLKPANVFL 2evaA 148 :QPKALIHRDLKPPNLLL T0292 148 :DGKQNVKLGDFG 2evaA 166 :AGGTVLKICDFG T0292 177 :TPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFT 2evaA 192 :SAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFD T0292 216 :AFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILEN 2evaA 233 :GGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKI T0292 267 :PLILEHHH 2evaA 289 :RYFPGADE Number of specific fragments extracted= 10 number of extra gaps= 0 total=601 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mq4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mq4A expands to /projects/compbio/data/pdb/1mq4.pdb.gz 1mq4A:# T0292 read from 1mq4A/merged-good-all-a2m # 1mq4A read from 1mq4A/merged-good-all-a2m # adding 1mq4A to template set # found chain 1mq4A in template set Warning: unaligning (T0292)H166 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1mq4A)P282 Warning: unaligning (T0292)D167 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1mq4A)P282 Warning: unaligning (T0292)F170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mq4A)T288 Warning: unaligning (T0292)A173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mq4A)T288 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAE 1mq4A 129 :ALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAG T0292 47 :KQMLVSEVNLLRELKHPNIVRYYDRI 1mq4A 175 :EHQLRREVEIQSHLRHPNILRLYGYF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1mq4A 201 :HDATRVYLILEYAPLGTVYRELQKLSK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1mq4A 228 :FDEQRTATYITELANALSYCHSKR T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLAR 1mq4A 252 :VIHRDIKPENLLLGSAGELKIADFGWSV T0292 165 :N 1mq4A 280 :H T0292 168 :TS 1mq4A 283 :SS T0292 174 :FVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKF 1mq4A 289 :LCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEF T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILE 1mq4A 347 :TFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITA Number of specific fragments extracted= 9 number of extra gaps= 1 total=610 Number of alignments=55 # 1mq4A read from 1mq4A/merged-good-all-a2m # found chain 1mq4A in template set Warning: unaligning (T0292)L164 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1mq4A)P282 Warning: unaligning (T0292)N165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1mq4A)P282 Warning: unaligning (T0292)F170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mq4A)T288 Warning: unaligning (T0292)A173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mq4A)T288 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1mq4A 129 :ALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQL T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1mq4A 171 :KAGVEHQLRREVEIQSHLRHPNILRLYGYF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1mq4A 201 :HDATRVYLILEYAPLGTVYRELQKLSK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1mq4A 228 :FDEQRTATYITELANALSYCHSKR T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARI 1mq4A 252 :VIHRDIKPENLLLGSAGELKIADFGWSVH T0292 166 :H 1mq4A 283 :S T0292 169 :S 1mq4A 284 :S T0292 174 :FVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1mq4A 289 :LCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFT T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILE 1mq4A 348 :FPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITA Number of specific fragments extracted= 9 number of extra gaps= 1 total=619 Number of alignments=56 # 1mq4A read from 1mq4A/merged-good-all-a2m # found chain 1mq4A in template set Warning: unaligning (T0292)L164 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1mq4A)P282 Warning: unaligning (T0292)N165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1mq4A)P282 Warning: unaligning (T0292)F170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mq4A)T288 Warning: unaligning (T0292)A173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mq4A)T288 Warning: unaligning (T0292)H274 because last residue in template chain is (1mq4A)S388 T0292 1 :SRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1mq4A 128 :WALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQL T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1mq4A 171 :KAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATR T0292 80 :LYIVMEYCEGGDLASVITK 1mq4A 206 :VYLILEYAPLGTVYRELQK T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1mq4A 225 :LSKFDEQRTATYITELANALSYCHSK T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARI 1mq4A 251 :RVIHRDIKPENLLLGSAGELKIADFGWSVH T0292 166 :HD 1mq4A 283 :SS T0292 174 :FVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1mq4A 289 :LCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFT T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1mq4A 348 :FPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANS Number of specific fragments extracted= 8 number of extra gaps= 1 total=627 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e1xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1e1xA expands to /projects/compbio/data/pdb/1e1x.pdb.gz 1e1xA:# T0292 read from 1e1xA/merged-good-all-a2m # 1e1xA read from 1e1xA/merged-good-all-a2m # adding 1e1xA to template set # found chain 1e1xA in template set Warning: unaligning (T0292)A3 because first residue in template chain is (1e1xA)M1 Warning: unaligning (T0292)L37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1e1xA)V44 Warning: unaligning (T0292)M42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1e1xA)V44 Warning: unaligning (T0292)C87 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)H84 Warning: unaligning (T0292)E88 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)H84 Warning: unaligning (T0292)N192 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)S181 Warning: unaligning (T0292)A216 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)D206 Warning: unaligning (T0292)F217 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)D206 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKE 1e1xA 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKK T0292 43 :TEAE 1e1xA 45 :PSTA T0292 51 :VSEVNLLRELKHPNIVRYYDRI 1e1xA 49 :IREISLLKELNHPNIVKLLDVI T0292 75 :RTNTTLYIVMEY 1e1xA 71 :HTENKLYLVFEF T0292 90 :GDLASVITKG 1e1xA 85 :QDLKKFMDAS T0292 102 :ERQYLDEEFVLRVMTQLTLALKECHRRS 1e1xA 95 :ALTGIPLPLIKSYLFQLLQGLAFCHSHR T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKAFVGTPYYMSPEQMNRMSY 1e1xA 123 :VLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKY T0292 193 :EKSDIWSLGCLLYELCALMPPFT 1e1xA 182 :TAVDIWSLGCIFAEMVTRRALFP T0292 218 :SQKELAGKIRE 1e1xA 207 :SEIDQLFRIFR T0292 229 :GKFRRIP 1e1xA 238 :PSFPKWA T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH 1e1xA 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPV Number of specific fragments extracted= 11 number of extra gaps= 3 total=638 Number of alignments=58 # 1e1xA read from 1e1xA/merged-good-all-a2m # found chain 1e1xA in template set Warning: unaligning (T0292)A3 because first residue in template chain is (1e1xA)M1 Warning: unaligning (T0292)L37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1e1xA)V44 Warning: unaligning (T0292)C87 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)H84 Warning: unaligning (T0292)G89 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)H84 Warning: unaligning (T0292)Y191 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)S181 Warning: unaligning (T0292)N192 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)S181 Warning: unaligning (T0292)A216 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)D206 Warning: unaligning (T0292)F217 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)D206 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKE 1e1xA 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKK T0292 43 :TEAEK 1e1xA 45 :PSTAI T0292 52 :SEVNLLRELKHPNIVRYYDRI 1e1xA 50 :REISLLKELNHPNIVKLLDVI T0292 75 :RTNTTLYIVMEY 1e1xA 71 :HTENKLYLVFEF T0292 90 :GDLASVITKGTKER 1e1xA 85 :QDLKKFMDASALTG T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1e1xA 99 :IPLPLIKSYLFQLLQGLAFCHSHR T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKAFVGTPYYMSPEQMNR 1e1xA 123 :VLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLG T0292 189 :MS 1e1xA 178 :KY T0292 193 :EKSDIWSLGCLLYELCALMPPFT 1e1xA 182 :TAVDIWSLGCIFAEMVTRRALFP T0292 218 :SQKELAGKIREGKFRRIPYR 1e1xA 207 :SEIDQLFRIFRTLGTPDEVV T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1e1xA 255 :LDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVT T0292 274 :HHHH 1e1xA 295 :HLRL Number of specific fragments extracted= 12 number of extra gaps= 3 total=650 Number of alignments=59 # 1e1xA read from 1e1xA/merged-good-all-a2m # found chain 1e1xA in template set Warning: unaligning (T0292)A3 because first residue in template chain is (1e1xA)M1 Warning: unaligning (T0292)L37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1e1xA)V44 Warning: unaligning (T0292)C87 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)H84 Warning: unaligning (T0292)E88 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)H84 Warning: unaligning (T0292)Y191 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)S181 Warning: unaligning (T0292)N192 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)S181 Warning: unaligning (T0292)A216 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)D206 Warning: unaligning (T0292)F217 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)D206 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKE 1e1xA 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKK T0292 43 :TEAEKQ 1e1xA 45 :PSTAIR T0292 53 :EVNLLRELKHPNIVRYYDRIIDRTN 1e1xA 51 :EISLLKELNHPNIVKLLDVIHTENK T0292 80 :LYIVMEY 1e1xA 76 :LYLVFEF T0292 90 :GDLASVITK 1e1xA 85 :QDLKKFMDA T0292 101 :KERQYLDEEFVLRVMTQLTLALKECHRR 1e1xA 94 :SALTGIPLPLIKSYLFQLLQGLAFCHSH T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKAFVGTPYYMSPEQMNR 1e1xA 122 :RVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLG T0292 189 :MS 1e1xA 178 :KY T0292 193 :EKSDIWSLGCLLYELCALMPPFT 1e1xA 182 :TAVDIWSLGCIFAEMVTRRALFP T0292 218 :SQKELAGKIREGKFRR 1e1xA 207 :SEIDQLFRIFRTLGTP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH 1e1xA 251 :VVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPV Number of specific fragments extracted= 11 number of extra gaps= 3 total=661 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zrzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zrzA expands to /projects/compbio/data/pdb/1zrz.pdb.gz 1zrzA:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0292 read from 1zrzA/merged-good-all-a2m # 1zrzA read from 1zrzA/merged-good-all-a2m # adding 1zrzA to template set # found chain 1zrzA in template set Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zrzA)F404 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zrzA)F404 Warning: unaligning (T0292)A216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zrzA)Q455 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTE 1zrzA 241 :GLQDFDLLRVIGRGSYAKVLLVRLKKTDRIYAMKVVKKELVND T0292 45 :AEKQMLVSEVNLLREL 1zrzA 285 :EDIDWVQTEKHVFEQA T0292 61 :KHPNIVRYYDRI 1zrzA 302 :NHPFLVGLHSCF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1zrzA 314 :QTESRLFFVIEYVNGGDLMFHMQRQRK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1zrzA 341 :LPEEHARFYSAEISLALNYLHERG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 1zrzA 365 :IIYRDLKLDNVLLDSEGHIKLTDYGMCKEGLRPGDTT T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPF 1zrzA 405 :CGTPNYIAPEILRGEDYGFSVDWWALGVLMFEMMAGRSPF T0292 217 :FSQKELAGKIREGKF 1zrzA 456 :NTEDYLFQVILEKQI T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRPS 1zrzA 471 :RIPRSMSVKAASVLKSFLNKDPKERLG T0292 260 :VEEILENPLILEH 1zrzA 504 :FADIQGHPFFRNV Number of specific fragments extracted= 10 number of extra gaps= 0 total=671 Number of alignments=61 # 1zrzA read from 1zrzA/merged-good-all-a2m # found chain 1zrzA in template set Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zrzA)F404 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zrzA)F404 Warning: unaligning (T0292)T215 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zrzA)Q455 Warning: unaligning (T0292)F217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zrzA)Q455 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1zrzA 241 :GLQDFDLLRVIGRGSYAKVLLVRLKKTDRIYAMKVVKKELV T0292 43 :TEAEKQMLVSEVNLLREL 1zrzA 283 :DDEDIDWVQTEKHVFEQA T0292 61 :KHPNIVRYYDRI 1zrzA 302 :NHPFLVGLHSCF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1zrzA 314 :QTESRLFFVIEYVNGGDLMFHMQRQRK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1zrzA 341 :LPEEHARFYSAEISLALNYLHERG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 1zrzA 365 :IIYRDLKLDNVLLDSEGHIKLTDYGMCKEGLRPGDTT T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPF 1zrzA 405 :CGTPNYIAPEILRGEDYGFSVDWWALGVLMFEMMAGRSPF T0292 218 :SQKE 1zrzA 456 :NTED T0292 222 :LAGKIREGKFR 1zrzA 461 :LFQVILEKQIR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1zrzA 472 :IPRSMSVKAASVLKSFLNKDPKERL T0292 259 :SVEEILENPLILEHH 1zrzA 503 :GFADIQGHPFFRNVD T0292 274 :H 1zrzA 525 :Q Number of specific fragments extracted= 12 number of extra gaps= 0 total=683 Number of alignments=62 # 1zrzA read from 1zrzA/merged-good-all-a2m # found chain 1zrzA in template set Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zrzA)F404 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zrzA)F404 Warning: unaligning (T0292)A216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zrzA)Q455 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1zrzA 241 :GLQDFDLLRVIGRGSYAKVLLVRLKKTDRIYAMKVVKKELV T0292 43 :TEAEKQMLVSEVNLLREL 1zrzA 283 :DDEDIDWVQTEKHVFEQA T0292 61 :KHPNIVRYYDRIIDRTN 1zrzA 302 :NHPFLVGLHSCFQTESR T0292 80 :LYIVMEYCEGGDLASVITK 1zrzA 319 :LFFVIEYVNGGDLMFHMQR T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1zrzA 338 :QRKLPEEHARFYSAEISLALNYLHER T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 1zrzA 364 :GIIYRDLKLDNVLLDSEGHIKLTDYGMCKEGLRPGDTT T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPF 1zrzA 405 :CGTPNYIAPEILRGEDYGFSVDWWALGVLMFEMMAGRSPF T0292 217 :FSQKELAGKIREGKFR 1zrzA 456 :NTEDYLFQVILEKQIR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPS 1zrzA 472 :IPRSMSVKAASVLKSFLNKDPKERLG T0292 260 :VEEILENPLILEHH 1zrzA 504 :FADIQGHPFFRNVD Number of specific fragments extracted= 10 number of extra gaps= 0 total=693 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pme/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pme expands to /projects/compbio/data/pdb/1pme.pdb.gz 1pme:Warning: there is no chain 1pme will retry with 1pmeA # T0292 read from 1pme/merged-good-all-a2m # 1pme read from 1pme/merged-good-all-a2m # adding 1pme to template set # found chain 1pme in template set Warning: unaligning (T0292)G13 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pme)Y36 Warning: unaligning (T0292)Y17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pme)Y36 Warning: unaligning (T0292)K150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pme)D162 Warning: unaligning (T0292)N152 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pme)D162 T0292 3 :AEDYEVLYTI 1pme 22 :GPRYTNLSYI T0292 18 :GRCQKIRRKSDGKILVWKELDYGS 1pme 37 :GMVCSAYDNVNKVRVAIKKISPFE T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT 1pme 61 :HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIE T0292 79 :TLYIVMEYC 1pme 100 :DVYLVTHLM T0292 89 :GGDLASVITK 1pme 109 :GADLYKLLKT T0292 100 :TK 1pme 119 :QH T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1pme 121 :LSNDHICYFLYQILRGLKYIHSAN T0292 135 :VLHRDLKPANVFLDG 1pme 145 :VLHRDLKPSNLLLNT T0292 153 :VKLGDFGLARILNHDT 1pme 163 :LKICDFGLARVADPDH T0292 169 :SFAKAFVGTPYYMSPEQMNRMS 1pme 182 :GFLTEYVATRWYRAPEIMLNSK T0292 191 :YNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1pme 205 :YTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILG T0292 229 :GKFRRIP 1pme 268 :PHKNKVP T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1pme 280 :PNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQY T0292 273 :HHHH 1pme 323 :PIAE Number of specific fragments extracted= 14 number of extra gaps= 0 total=707 Number of alignments=64 # 1pme read from 1pme/merged-good-all-a2m # found chain 1pme in template set Warning: unaligning (T0292)G13 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pme)Y36 Warning: unaligning (T0292)Y17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pme)Y36 Warning: unaligning (T0292)K150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pme)D162 Warning: unaligning (T0292)N152 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pme)D162 T0292 3 :AEDYEVLYTI 1pme 22 :GPRYTNLSYI T0292 18 :GRCQKIRRKSDGKILVWKELDYGS 1pme 37 :GMVCSAYDNVNKVRVAIKKISPFE T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT 1pme 61 :HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIE T0292 79 :TLYIVMEYC 1pme 100 :DVYLVTHLM T0292 89 :GGDLASVITKGT 1pme 109 :GADLYKLLKTQH T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1pme 121 :LSNDHICYFLYQILRGLKYIHSAN T0292 135 :VLHRDLKPANVFLDG 1pme 145 :VLHRDLKPSNLLLNT T0292 153 :VKLGDFGLARILNHDTSFA 1pme 163 :LKICDFGLARVADPDHDHT T0292 172 :KAFVGTPYYMSPEQMNR 1pme 185 :TEYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPY 1pme 203 :KGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQE T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1pme 282 :ADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYY T0292 274 :H 1pme 326 :E Number of specific fragments extracted= 12 number of extra gaps= 0 total=719 Number of alignments=65 # 1pme read from 1pme/merged-good-all-a2m # found chain 1pme in template set Warning: unaligning (T0292)G13 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pme)Y36 Warning: unaligning (T0292)Y17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pme)Y36 Warning: unaligning (T0292)K150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pme)D162 Warning: unaligning (T0292)N152 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pme)D162 T0292 4 :EDYEVLYTI 1pme 23 :PRYTNLSYI T0292 18 :GRCQKIRRKSDGKILVWKELDYGS 1pme 37 :GMVCSAYDNVNKVRVAIKKISPFE T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT 1pme 61 :HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIE T0292 79 :TLYIVMEYCE 1pme 100 :DVYLVTHLMG T0292 90 :GDLASVITK 1pme 110 :ADLYKLLKT T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 1pme 119 :QHLSNDHICYFLYQILRGLKYIHSA T0292 134 :TVLHRDLKPANVFLDG 1pme 144 :NVLHRDLKPSNLLLNT T0292 153 :VKLGDFGLARILNHD 1pme 163 :LKICDFGLARVADPD T0292 168 :TSFAKAFVGTPYYMSPEQMNR 1pme 181 :TGFLTEYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1pme 203 :KGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 1pme 278 :LFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSD Number of specific fragments extracted= 11 number of extra gaps= 0 total=730 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fgkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fgkA expands to /projects/compbio/data/pdb/1fgk.pdb.gz 1fgkA:Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 1fgkA # T0292 read from 1fgkA/merged-good-all-a2m # 1fgkA read from 1fgkA/merged-good-all-a2m # adding 1fgkA to template set # found chain 1fgkA in template set Warning: unaligning (T0292)G13 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fgkA)Q491 Warning: unaligning (T0292)R19 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)Q491 Warning: unaligning (T0292)S27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)P505 Warning: unaligning (T0292)R103 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)E592 T0292 2 :RAEDYEVLYTI 1fgkA 474 :PRDRLVLGKPL T0292 20 :CQKIR 1fgkA 492 :VVLAE T0292 28 :DG 1fgkA 506 :NR T0292 30 :KILVWKEL 1fgkA 509 :TKVAVKML T0292 39 :YGSMTEAEKQMLVSEVNLLREL 1fgkA 517 :KSDATEKDLSDLISEMEMMKMI T0292 61 :KHPNIVRYYDRI 1fgkA 540 :KHKNIINLLGAC T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1fgkA 552 :TQDGPLYVIVEYASKGNLREYLQARRP T0292 104 :QYLDEEFVLRVMTQLTLALKECHRRS 1fgkA 593 :EQLSSKDLVSCAYQVARGMEYLASKK T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKAFVGTP 1fgkA 619 :CIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRL T0292 179 :YYMSPEQMNRMSYNEKSDIWSLGCLLYELCA 1fgkA 665 :KWMAPEALFDRIYTHQSDVWSFGVLLWEIFT T0292 210 :LMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILEN 1fgkA 697 :GGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVED Number of specific fragments extracted= 11 number of extra gaps= 0 total=741 Number of alignments=67 # 1fgkA read from 1fgkA/merged-good-all-a2m # found chain 1fgkA in template set Warning: unaligning (T0292)G13 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fgkA)Q491 Warning: unaligning (T0292)R19 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)Q491 Warning: unaligning (T0292)R103 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)E592 T0292 2 :RAEDYEVLYTI 1fgkA 474 :PRDRLVLGKPL T0292 20 :CQKIRRK 1fgkA 492 :VVLAEAI T0292 30 :KILVWKELDYG 1fgkA 509 :TKVAVKMLKSD T0292 42 :MTEAEKQMLVSEVNLLREL 1fgkA 520 :ATEKDLSDLISEMEMMKMI T0292 61 :KHPNIVRYYDRI 1fgkA 540 :KHKNIINLLGAC T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1fgkA 552 :TQDGPLYVIVEYASKGNLREYLQARRP T0292 104 :QYLDEEFVLRVMTQLTLALKECHRRS 1fgkA 593 :EQLSSKDLVSCAYQVARGMEYLASKK T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNH 1fgkA 619 :CIHRDLAARNVLVTEDNVMKIADFGLARDIHH T0292 167 :DTSFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCA 1fgkA 653 :YYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFT T0292 210 :LMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPL 1fgkA 697 :GGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLD Number of specific fragments extracted= 10 number of extra gaps= 0 total=751 Number of alignments=68 # 1fgkA read from 1fgkA/merged-good-all-a2m # found chain 1fgkA in template set Warning: unaligning (T0292)G13 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fgkA)Q491 Warning: unaligning (T0292)R19 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)Q491 Warning: unaligning (T0292)R103 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)E592 T0292 1 :SRAEDYEVLYTI 1fgkA 473 :LPRDRLVLGKPL T0292 20 :CQKIRRK 1fgkA 492 :VVLAEAI T0292 30 :KILVWKELDYG 1fgkA 509 :TKVAVKMLKSD T0292 42 :MTEAEKQMLVSEVNLLREL 1fgkA 520 :ATEKDLSDLISEMEMMKMI T0292 61 :KHPNIVRYYDRIIDRTN 1fgkA 540 :KHKNIINLLGACTQDGP T0292 80 :LYIVMEYCEGGDLASVITKGT 1fgkA 557 :LYVIVEYASKGNLREYLQARR T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 1fgkA 593 :EQLSSKDLVSCAYQVARGMEYLASK T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILN 1fgkA 618 :KCIHRDLAARNVLVTEDNVMKIADFGLARDIH T0292 166 :HDTSFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCA 1fgkA 652 :DYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFT T0292 210 :LMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILEN 1fgkA 697 :GGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVED Number of specific fragments extracted= 10 number of extra gaps= 0 total=761 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hcl/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hcl expands to /projects/compbio/data/pdb/1hcl.pdb.gz 1hcl:Warning: there is no chain 1hcl will retry with 1hclA Skipped atom 1022, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 1024, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 1026, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 1028, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 1030, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 2093, because occupancy 0.370 <= existing 0.660 in 1hcl # T0292 read from 1hcl/merged-good-all-a2m # 1hcl read from 1hcl/merged-good-all-a2m # adding 1hcl to template set # found chain 1hcl in template set Warning: unaligning (T0292)A3 because first residue in template chain is (1hcl)M1 Warning: unaligning (T0292)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hcl)T41 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKEL 1hcl 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKI T0292 40 :GSMTEA 1hcl 42 :EGVPST T0292 50 :LVSEVNLLRELKHPNIVRYYDRI 1hcl 48 :AIREISLLKELNHPNIVKLLDVI T0292 75 :RTNTTLYIVMEYCE 1hcl 71 :HTENKLYLVFEFLH T0292 90 :GDLASVITKG 1hcl 85 :QDLKKFMDAS T0292 102 :ERQYLDEEFVLRVMTQLTLALKECHRRS 1hcl 95 :ALTGIPLPLIKSYLFQLLQGLAFCHSHR T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKAFVGTPYYMSPEQMNRMSY 1hcl 123 :VLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKY T0292 192 :NEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1hcl 181 :STAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFR T0292 229 :GKFRRIP 1hcl 238 :PSFPKWA T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH 1hcl 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPV Number of specific fragments extracted= 10 number of extra gaps= 0 total=771 Number of alignments=70 # 1hcl read from 1hcl/merged-good-all-a2m # found chain 1hcl in template set Warning: unaligning (T0292)A3 because first residue in template chain is (1hcl)M1 Warning: unaligning (T0292)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hcl)T41 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKEL 1hcl 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKI T0292 40 :GSMTEA 1hcl 42 :EGVPST T0292 50 :LVSEVNLLRELKHPNIVRYYDRI 1hcl 48 :AIREISLLKELNHPNIVKLLDVI T0292 75 :RTNTTLYIVMEYCEG 1hcl 71 :HTENKLYLVFEFLHQ T0292 91 :DLASVITKGTKER 1hcl 86 :DLKKFMDASALTG T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1hcl 99 :IPLPLIKSYLFQLLQGLAFCHSHR T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKAFVGTPYYMSPEQMNR 1hcl 123 :VLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLG T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYR 1hcl 178 :KYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVV T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1hcl 255 :LDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVT T0292 274 :HHH 1hcl 295 :HLR Number of specific fragments extracted= 10 number of extra gaps= 0 total=781 Number of alignments=71 # 1hcl read from 1hcl/merged-good-all-a2m # found chain 1hcl in template set Warning: unaligning (T0292)A3 because first residue in template chain is (1hcl)M1 Warning: unaligning (T0292)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hcl)T41 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKEL 1hcl 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKI T0292 40 :GSMTEAE 1hcl 42 :EGVPSTA T0292 51 :VSEVNLLRELKHPNIVRYYDRIIDRTN 1hcl 49 :IREISLLKELNHPNIVKLLDVIHTENK T0292 80 :LYIVMEYCEG 1hcl 76 :LYLVFEFLHQ T0292 91 :DLASVITK 1hcl 86 :DLKKFMDA T0292 101 :KERQYLDEEFVLRVMTQLTLALKECHRR 1hcl 94 :SALTGIPLPLIKSYLFQLLQGLAFCHSH T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKAFVGTPYYMSPEQMNR 1hcl 122 :RVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLG T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1hcl 178 :KYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH 1hcl 251 :VVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPV Number of specific fragments extracted= 9 number of extra gaps= 0 total=790 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h1wA expands to /projects/compbio/data/pdb/1h1w.pdb.gz 1h1wA:Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1026, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1028, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1h1wA Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Skipped atom 1432, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1436, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1986, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1988, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2280, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2282, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2284, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2286, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2288, because occupancy 0.500 <= existing 0.500 in 1h1wA # T0292 read from 1h1wA/merged-good-all-a2m # 1h1wA read from 1h1wA/merged-good-all-a2m # adding 1h1wA to template set # found chain 1h1wA in template set Warning: unaligning (T0292)H166 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)A237 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)F242 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)F242 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAE 1h1wA 78 :RPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKEN T0292 47 :KQMLVSEVNLLRELKHPNIVRYYDRI 1h1wA 124 :VPYVTRERDVMSRLDHPFFVKLYFTF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1h1wA 150 :QDDEKLYFGLSYAKNGELLKYIRKIGS T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1h1wA 177 :FDETCTRFYTAEIVSALEYLHGKG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILN 1h1wA 201 :IIHRDLKPENILLNEDMHIQITDFGTAKVLS T0292 170 :FA 1h1wA 238 :RA T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1h1wA 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYD T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1h1wA 301 :FPEKFFPKARDLVEKLLVLDATKRL T0292 259 :SVEEILENPLILEHHHH 1h1wA 332 :GYGPLKAHPFFESVTWE Number of specific fragments extracted= 9 number of extra gaps= 0 total=799 Number of alignments=73 # 1h1wA read from 1h1wA/merged-good-all-a2m # found chain 1h1wA in template set Warning: unaligning (T0292)H166 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)A237 Warning: unaligning (T0292)A171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)A237 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)F242 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)F242 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1h1wA 78 :RPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHI T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1h1wA 120 :KENKVPYVTRERDVMSRLDHPFFVKLYFTF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1h1wA 150 :QDDEKLYFGLSYAKNGELLKYIRKIGS T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1h1wA 177 :FDETCTRFYTAEIVSALEYLHGKG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILN 1h1wA 201 :IIHRDLKPENILLNEDMHIQITDFGTAKVLS T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1h1wA 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYD T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1h1wA 301 :FPEKFFPKARDLVEKLLVLDATKRL T0292 259 :SVEEILENPLILEHH 1h1wA 332 :GYGPLKAHPFFESVT Number of specific fragments extracted= 8 number of extra gaps= 0 total=807 Number of alignments=74 # 1h1wA read from 1h1wA/merged-good-all-a2m # found chain 1h1wA in template set Warning: unaligning (T0292)H166 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)A237 Warning: unaligning (T0292)S169 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)A237 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)F242 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)F242 T0292 1 :SRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1h1wA 77 :KRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHI T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1h1wA 120 :KENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEK T0292 80 :LYIVMEYCEGGDLASVITK 1h1wA 155 :LYFGLSYAKNGELLKYIRK T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1h1wA 174 :IGSFDETCTRFYTAEIVSALEYLHGK T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILN 1h1wA 200 :GIIHRDLKPENILLNEDMHIQITDFGTAKVLS T0292 170 :FA 1h1wA 238 :RA T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1h1wA 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYD T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1h1wA 301 :FPEKFFPKARDLVEKLLVLDATKRL T0292 259 :SVEEILENPLILEHHHHH 1h1wA 332 :GYGPLKAHPFFESVTWEN Number of specific fragments extracted= 9 number of extra gaps= 0 total=816 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f3mC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f3mC expands to /projects/compbio/data/pdb/1f3m.pdb.gz 1f3mC:# T0292 read from 1f3mC/merged-good-all-a2m # 1f3mC read from 1f3mC/merged-good-all-a2m # adding 1f3mC to template set # found chain 1f3mC in template set Warning: unaligning (T0292)N165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f3mC)T423 Warning: unaligning (T0292)A173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f3mC)T423 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAE 1f3mC 268 :KKYTRFEKIGQGASGTVYTAMDVATGQEVAIRQMNLQQQPKKE T0292 49 :MLVSEVNLLRELKHPNIVRYYDRI 1f3mC 311 :LIINEILVMRENKNPNIVNYLDSY T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGT 1f3mC 335 :LVGDELWVVMEYLAGGSLTDVVTETC T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1f3mC 361 :MDEGQIAAVCRECLQALEFLHSNQ T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARIL 1f3mC 385 :VIHRDIKSDNILLGMDGSVKLTDFGFCAQI T0292 174 :FVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRI 1f3mC 424 :MVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPEL T0292 235 :PYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHH 1f3mC 487 :PEKLSAIFRDFLNRCLDMDVEKRGSAKELLQHQFLKIAKP Number of specific fragments extracted= 7 number of extra gaps= 0 total=823 Number of alignments=76 # 1f3mC read from 1f3mC/merged-good-all-a2m # found chain 1f3mC in template set Warning: unaligning (T0292)N165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f3mC)T423 Warning: unaligning (T0292)A173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f3mC)T423 T0292 5 :DYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1f3mC 269 :KYTRFEKIGQGASGTVYTAMDVATGQEVAIRQMNLQQQ T0292 43 :TEAE 1f3mC 308 :KKEL T0292 50 :LVSEVNLLRELKHPNIVRYYDRI 1f3mC 312 :IINEILVMRENKNPNIVNYLDSY T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGT 1f3mC 335 :LVGDELWVVMEYLAGGSLTDVVTETC T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1f3mC 361 :MDEGQIAAVCRECLQALEFLHSNQ T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARIL 1f3mC 385 :VIHRDIKSDNILLGMDGSVKLTDFGFCAQI T0292 174 :FVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRI 1f3mC 424 :MVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPEL T0292 235 :PYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHH 1f3mC 487 :PEKLSAIFRDFLNRCLDMDVEKRGSAKELLQHQFLKIAKP Number of specific fragments extracted= 8 number of extra gaps= 0 total=831 Number of alignments=77 # 1f3mC read from 1f3mC/merged-good-all-a2m # found chain 1f3mC in template set Warning: unaligning (T0292)N165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f3mC)T423 Warning: unaligning (T0292)A173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f3mC)T423 T0292 5 :DYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1f3mC 269 :KYTRFEKIGQGASGTVYTAMDVATGQEVAIRQMNLQQQ T0292 44 :E 1f3mC 308 :K T0292 47 :KQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1f3mC 309 :KELIINEILVMRENKNPNIVNYLDSYLVGDE T0292 80 :LYIVMEYCEGGDLASVITK 1f3mC 340 :LWVVMEYLAGGSLTDVVTE T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 1f3mC 359 :TCMDEGQIAAVCRECLQALEFLHSN T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARIL 1f3mC 384 :QVIHRDIKSDNILLGMDGSVKLTDFGFCAQI T0292 174 :FVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1f3mC 424 :MVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPE T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHH 1f3mC 486 :NPEKLSAIFRDFLNRCLDMDVEKRGSAKELLQHQFLKIAKP Number of specific fragments extracted= 8 number of extra gaps= 0 total=839 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bikB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0292 read from 2bikB/merged-good-all-a2m # 2bikB read from 2bikB/merged-good-all-a2m # found chain 2bikB in training set Warning: unaligning (T0292)S239 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bikB)E262 Warning: unaligning (T0292)E241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bikB)E262 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMT 2bikB 36 :SQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRIS T0292 44 :EAE 2bikB 81 :PNG T0292 52 :SEVNLLREL 2bikB 88 :MEVVLLKKV T0292 61 :KHPNIVRYYDRI 2bikB 99 :GFSGVIRLLDWF T0292 75 :RTNTTLYIVMEYCEG 2bikB 111 :ERPDSFVLILERPEP T0292 90 :GDLASVITKGTK 2bikB 127 :QDLFDFITERGA T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2bikB 139 :LQEELARSFFWQVLEAVRHCHNCG T0292 135 :VLHRDLKPANVFLDGK 2bikB 163 :VLHRDIKDENILIDLN T0292 151 :QNVKLGDFGLARILNHD 2bikB 180 :GELKLIDFGSGALLKDT T0292 170 :FAKAFVGTPYYMSPEQMNRMSYN 2bikB 197 :VYTDFDGTRVYSPPEWIRYHRYH T0292 193 :EKSDIWSLGCLLYELCALMPPFTAFS 2bikB 221 :RSAAVWSLGILLYDMVCGDIPFEHDE T0292 225 :KIREGKF 2bikB 247 :EIIGGQV T0292 233 :RIPYRY 2bikB 254 :FFRQRV T0292 242 :LNEIITRMLNLKDYHRPSVEEILENPLILEH 2bikB 263 :CQHLIRWCLALRPSDRPTFEEIQNHPWMQDV Number of specific fragments extracted= 14 number of extra gaps= 0 total=853 Number of alignments=79 # 2bikB read from 2bikB/merged-good-all-a2m # found chain 2bikB in training set Warning: unaligning (T0292)S239 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bikB)E262 Warning: unaligning (T0292)E241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bikB)E262 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMT 2bikB 36 :SQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRIS T0292 52 :SEVNLLRELKHP 2bikB 88 :MEVVLLKKVSSG T0292 64 :NIVRYYDRI 2bikB 102 :GVIRLLDWF T0292 75 :RTNTTLYIVMEYCEG 2bikB 111 :ERPDSFVLILERPEP T0292 90 :GDLASVITKGTK 2bikB 127 :QDLFDFITERGA T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2bikB 139 :LQEELARSFFWQVLEAVRHCHNCG T0292 135 :VLHRDLKPANVFLD 2bikB 163 :VLHRDIKDENILID T0292 149 :GKQNVKLGDFGLARILNH 2bikB 178 :NRGELKLIDFGSGALLKD T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYN 2bikB 196 :TVYTDFDGTRVYSPPEWIRYHRYH T0292 193 :EKSDIWSLGCLLYELCALMPPFTA 2bikB 221 :RSAAVWSLGILLYDMVCGDIPFEH T0292 219 :QKE 2bikB 245 :DEE T0292 226 :IREGKFR 2bikB 248 :IIGGQVF T0292 234 :IPYRY 2bikB 255 :FRQRV T0292 242 :LNEIITRMLNLKDYHRPSVEEILENPLILEHH 2bikB 263 :CQHLIRWCLALRPSDRPTFEEIQNHPWMQDVL Number of specific fragments extracted= 14 number of extra gaps= 0 total=867 Number of alignments=80 # 2bikB read from 2bikB/merged-good-all-a2m # found chain 2bikB in training set Warning: unaligning (T0292)S239 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bikB)E262 Warning: unaligning (T0292)E241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bikB)E262 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 2bikB 36 :SQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRI T0292 52 :SEVNLLREL 2bikB 88 :MEVVLLKKV T0292 61 :KHPNIVRYYDRIIDRTN 2bikB 99 :GFSGVIRLLDWFERPDS T0292 80 :LYIVMEYCEG 2bikB 116 :FVLILERPEP T0292 90 :GDLASVITK 2bikB 127 :QDLFDFITE T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 2bikB 136 :RGALQEELARSFFWQVLEAVRHCHNC T0292 134 :TVLHRDLKPANVFL 2bikB 162 :GVLHRDIKDENILI T0292 148 :DGKQNVKLGDFGLARILNHD 2bikB 177 :LNRGELKLIDFGSGALLKDT T0292 170 :FAKAFVGTPYYMSPEQMNRMSYN 2bikB 197 :VYTDFDGTRVYSPPEWIRYHRYH T0292 193 :EKSDIWSLGCLLYELCALMPPFTAF 2bikB 221 :RSAAVWSLGILLYDMVCGDIPFEHD T0292 224 :GKIREGKFR 2bikB 246 :EEIIGGQVF T0292 234 :IPYRY 2bikB 255 :FRQRV T0292 242 :LNEIITRMLNLKDYHRPSVEEILENPLILEHHH 2bikB 263 :CQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLL Number of specific fragments extracted= 13 number of extra gaps= 0 total=880 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a19B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a19B expands to /projects/compbio/data/pdb/2a19.pdb.gz 2a19B:# T0292 read from 2a19B/merged-good-all-a2m # 2a19B read from 2a19B/merged-good-all-a2m # adding 2a19B to template set # found chain 2a19B in template set Warning: unaligning (T0292)S41 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E303 Warning: unaligning (T0292)A45 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E303 Warning: unaligning (T0292)D74 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a19B)R356 Warning: unaligning (T0292)R103 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E384 Warning: unaligning (T0292)Q104 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E384 Warning: unaligning (T0292)F170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a19B)R447 Warning: unaligning (T0292)A173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a19B)R447 T0292 5 :DYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYG 2a19B 266 :DFKEIELIGSGGFGQVFKAKHRIDGKTYVIKRVKYN T0292 46 :E 2a19B 304 :K T0292 50 :LVSEVNLLRELKHPNIVRYYDRII 2a19B 305 :AEREVKALAKLDHVNIVHYNGCWD T0292 75 :RTNTTLYIVMEYCEGGDLASVITKG 2a19B 357 :SKTKCLFIQMEFCDKGTLEQWIEKR T0292 102 :E 2a19B 382 :R T0292 105 :YLDEEFVLRVMTQLTLALKECHRRS 2a19B 385 :KLDKVLALELFEQITKGVDYIHSKK T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTS 2a19B 410 :LINRDLKPSNIFLVDTKQVKIGDFGLVTSLKNDGK T0292 174 :FVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALM 2a19B 448 :SKGTLRYMSPEQISSQDYGKEVDLYALGLILAELLHVC T0292 214 :FTAFSQKELAGKIREG 2a19B 486 :DTAFETSKFFTDLRDG T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRPSVEEILEN 2a19B 502 :IISDIFDKKEKTLLQKLLSKKPEDRPNTSEILRT Number of specific fragments extracted= 10 number of extra gaps= 2 total=890 Number of alignments=82 # 2a19B read from 2a19B/merged-good-all-a2m # found chain 2a19B in template set Warning: unaligning (T0292)S41 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E303 Warning: unaligning (T0292)E44 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E303 Warning: unaligning (T0292)K101 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E384 Warning: unaligning (T0292)E102 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E384 Warning: unaligning (T0292)A171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a19B)R447 Warning: unaligning (T0292)A173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a19B)R447 Warning: unaligning (T0292)H272 because last residue in template chain is (2a19B)K541 T0292 5 :DYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYG 2a19B 266 :DFKEIELIGSGGFGQVFKAKHRIDGKTYVIKRVKYN T0292 45 :A 2a19B 304 :K T0292 50 :LVSEVNLLRELKHPNIVRYYDRIID 2a19B 305 :AEREVKALAKLDHVNIVHYNGCWDG T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGT 2a19B 357 :SKTKCLFIQMEFCDKGTLEQWIEKRR T0292 103 :R 2a19B 385 :K T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2a19B 386 :LDKVLALELFEQITKGVDYIHSKK T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTS 2a19B 410 :LINRDLKPSNIFLVDTKQVKIGDFGLVTSLKNDGK T0292 174 :FVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALM 2a19B 448 :SKGTLRYMSPEQISSQDYGKEVDLYALGLILAELLHVC T0292 217 :FSQKEL 2a19B 486 :DTAFET T0292 223 :AGKIREGK 2a19B 495 :FTDLRDGI T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILE 2a19B 503 :ISDIFDKKEKTLLQKLLSKKPEDRPNTSEILRTLTVWK Number of specific fragments extracted= 11 number of extra gaps= 2 total=901 Number of alignments=83 # 2a19B read from 2a19B/merged-good-all-a2m # found chain 2a19B in template set Warning: unaligning (T0292)S41 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E303 Warning: unaligning (T0292)M42 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E303 Warning: unaligning (T0292)R103 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E384 Warning: unaligning (T0292)Q104 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E384 Warning: unaligning (T0292)A171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a19B)R447 Warning: unaligning (T0292)A173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a19B)R447 T0292 5 :DYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYG 2a19B 266 :DFKEIELIGSGGFGQVFKAKHRIDGKTYVIKRVKYN T0292 51 :VSEVNLLRELKHPNIVRYYDRIID 2a19B 306 :EREVKALAKLDHVNIVHYNGCWDG T0292 79 :TLYIVMEYCEGGDLASVITK 2a19B 361 :CLFIQMEFCDKGTLEQWIEK T0292 101 :KE 2a19B 381 :RR T0292 105 :YLDEEFVLRVMTQLTLALKECHRR 2a19B 385 :KLDKVLALELFEQITKGVDYIHSK T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 2a19B 409 :KLINRDLKPSNIFLVDTKQVKIGDFGLVTSLKND T0292 169 :SF 2a19B 443 :GK T0292 174 :FVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALM 2a19B 448 :SKGTLRYMSPEQISSQDYGKEVDLYALGLILAELLHVC T0292 214 :FTAFSQKELAGKIREGK 2a19B 486 :DTAFETSKFFTDLRDGI T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILEN 2a19B 503 :ISDIFDKKEKTLLQKLLSKKPEDRPNTSEILRT Number of specific fragments extracted= 10 number of extra gaps= 2 total=911 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kobA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kobA expands to /projects/compbio/data/pdb/1kob.pdb.gz 1kobA:# T0292 read from 1kobA/merged-good-all-a2m # 1kobA read from 1kobA/merged-good-all-a2m # adding 1kobA to template set # found chain 1kobA in template set T0292 3 :AEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYG 1kobA 50 :YDYYDILEELGSGAFGVVHRCVEKATGRVFVAKFINTP T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1kobA 88 :YPLDKYTVKNEISIMNQLHHPKLINLHDAF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTKE 1kobA 118 :EDKYEMVLILEFLSGGELFDRIAAEDYK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1kobA 146 :MSEAEVINYMRQACEGLKHMHEHS T0292 135 :VLHRDLKPANVFLDGKQN 1kobA 170 :IVHLDIKPENIMCETKKA T0292 153 :VKLGDFGLARILNHD 1kobA 190 :VKIIDFGLATKLNPD T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYR 1kobA 205 :EIVKVTTATAEFAAPEIVDREPVGFYTDMWAIGVLGYVLLSGLSPFAGEDDLETLQNVKRCDWEFDEDA T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1kobA 277 :VSPEAKDFIKNLLQKEPRKRLTVHDALEHPWLKGD T0292 273 :HHHHH 1kobA 314 :NLTSR Number of specific fragments extracted= 9 number of extra gaps= 0 total=920 Number of alignments=85 # 1kobA read from 1kobA/merged-good-all-a2m # found chain 1kobA in template set T0292 2 :RAED 1kobA 48 :SVYD T0292 6 :YEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYG 1kobA 53 :YDILEELGSGAFGVVHRCVEKATGRVFVAKFINTP T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1kobA 88 :YPLDKYTVKNEISIMNQLHHPKLINLHDAF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTKE 1kobA 118 :EDKYEMVLILEFLSGGELFDRIAAEDYK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1kobA 146 :MSEAEVINYMRQACEGLKHMHEHS T0292 135 :VLHRDLKPANVFL 1kobA 170 :IVHLDIKPENIMC T0292 148 :DGKQNVKLGDFGLARILNHDTSFAK 1kobA 185 :KKASSVKIIDFGLATKLNPDEIVKV T0292 174 :FVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYR 1kobA 210 :TTATAEFAAPEIVDREPVGFYTDMWAIGVLGYVLLSGLSPFAGEDDLETLQNVKRCDWEFDEDA T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 1kobA 277 :VSPEAKDFIKNLLQKEPRKRLTVHDALEHPWLKGDHSNLT Number of specific fragments extracted= 9 number of extra gaps= 0 total=929 Number of alignments=86 # 1kobA read from 1kobA/merged-good-all-a2m # found chain 1kobA in template set T0292 3 :AEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYG 1kobA 50 :YDYYDILEELGSGAFGVVHRCVEKATGRVFVAKFINTP T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1kobA 88 :YPLDKYTVKNEISIMNQLHHPKLINLHDAFEDKYE T0292 80 :LYIVMEYCEGGDLASVITK 1kobA 123 :MVLILEFLSGGELFDRIAA T0292 102 :ERQYLDEEFVLRVMTQLTLALKECHRR 1kobA 142 :EDYKMSEAEVINYMRQACEGLKHMHEH T0292 134 :TVLHRDLKPANVFL 1kobA 169 :SIVHLDIKPENIMC T0292 148 :DGKQNVKLGDFGLARILNHD 1kobA 185 :KKASSVKIIDFGLATKLNPD T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1kobA 205 :EIVKVTTATAEFAAPEIVDREPVGFYTDMWAIGVLGYVLLSGLSPFAGEDDLETLQNVKRCDWEF T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHH 1kobA 273 :AFSSVSPEAKDFIKNLLQKEPRKRLTVHDALEHPWLKGDHSN Number of specific fragments extracted= 8 number of extra gaps= 0 total=937 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vzoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0292 read from 1vzoA/merged-good-all-a2m # 1vzoA read from 1vzoA/merged-good-all-a2m # found chain 1vzoA in training set Warning: unaligning (T0292)D70 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vzoA)A120 Warning: unaligning (T0292)R71 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vzoA)A120 Warning: unaligning (T0292)N192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vzoA)D233 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRR 1vzoA 45 :GIENFELLKVLGTGAYGKVFLVRK T0292 26 :KSDGKILVWKELDY 1vzoA 72 :HDTGKLYAMKVLKK T0292 40 :GSMTE 1vzoA 96 :EHTRT T0292 53 :EVNLLREL 1vzoA 101 :ERQVLEHI T0292 61 :KHPNIVRYY 1vzoA 110 :QSPFLVTLH T0292 72 :I 1vzoA 121 :F T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1vzoA 122 :QTETKLHLILDYINGGELFTHLSQRER T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1vzoA 149 :FTEHEVQIYVGEIVLALEHLHKLG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 1vzoA 173 :IIYRDIKLENILLDSNGHVVLTDFGLSKEFVAD T0292 168 :TSFAKAFVGTPYYMSPEQMNR 1vzoA 207 :TERAYDFCGTIEYMAPDIVRG T0292 193 :EKSDIWSLGCLLYELCALMPPF 1vzoA 234 :KAVDWWSLGVLMYELLTGASPF T0292 215 :TAFSQKELAGKIREGKF 1vzoA 260 :EKNSQAEISRRILKSEP T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRP 1vzoA 277 :PYPQEMSALAKDLIQRLLMKDPKKRL T0292 260 :VEEILENPLILEH 1vzoA 309 :ADEIKEHLFFQKI Number of specific fragments extracted= 14 number of extra gaps= 1 total=951 Number of alignments=88 # 1vzoA read from 1vzoA/merged-good-all-a2m # found chain 1vzoA in training set Warning: unaligning (T0292)D70 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vzoA)A120 Warning: unaligning (T0292)R71 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vzoA)A120 Warning: unaligning (T0292)N192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vzoA)D233 Warning: unaligning (T0292)S259 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vzoA)D308 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRR 1vzoA 45 :GIENFELLKVLGTGAYGKVFLVRK T0292 26 :KSDGKILVWKELDY 1vzoA 72 :HDTGKLYAMKVLKK T0292 40 :GSM 1vzoA 96 :EHT T0292 43 :TE 1vzoA 100 :TE T0292 54 :VNLLREL 1vzoA 102 :RQVLEHI T0292 61 :KHPNIVRYY 1vzoA 110 :QSPFLVTLH T0292 72 :I 1vzoA 121 :F T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1vzoA 122 :QTETKLHLILDYINGGELFTHLSQRER T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1vzoA 149 :FTEHEVQIYVGEIVLALEHLHKLG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 1vzoA 173 :IIYRDIKLENILLDSNGHVVLTDFGLSKEFVADETER T0292 172 :KAFVGTPYYMSPEQMNR 1vzoA 211 :YDFCGTIEYMAPDIVRG T0292 193 :EKSDIWSLGCLLYELCALMPPF 1vzoA 234 :KAVDWWSLGVLMYELLTGASPF T0292 215 :TAFSQKELAGKIREGKFR 1vzoA 260 :EKNSQAEISRRILKSEPP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1vzoA 278 :YPQEMSALAKDLIQRLLMKDPKKRL T0292 260 :VEEILENPLILEHH 1vzoA 309 :ADEIKEHLFFQKIN T0292 274 :HHH 1vzoA 330 :KVP Number of specific fragments extracted= 16 number of extra gaps= 2 total=967 Number of alignments=89 # 1vzoA read from 1vzoA/merged-good-all-a2m # found chain 1vzoA in training set Warning: unaligning (T0292)D70 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vzoA)A120 Warning: unaligning (T0292)R71 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vzoA)A120 Warning: unaligning (T0292)N192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vzoA)D233 Warning: unaligning (T0292)S259 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vzoA)D308 T0292 1 :SRAEDYEVLYTIGTGSYGRCQKIRRK 1vzoA 44 :VGIENFELLKVLGTGAYGKVFLVRKI T0292 27 :SDGKILVWKELDY 1vzoA 73 :DTGKLYAMKVLKK T0292 40 :GSM 1vzoA 96 :EHT T0292 43 :TE 1vzoA 100 :TE T0292 54 :VNLLREL 1vzoA 102 :RQVLEHI T0292 61 :KHPNIVRYY 1vzoA 110 :QSPFLVTLH T0292 72 :IIDRTN 1vzoA 121 :FQTETK T0292 80 :LYIVMEYCEGGDLASVITK 1vzoA 127 :LHLILDYINGGELFTHLSQ T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1vzoA 146 :RERFTEHEVQIYVGEIVLALEHLHKL T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 1vzoA 172 :GIIYRDIKLENILLDSNGHVVLTDFGLSKEFVAD T0292 168 :TSFAKAFVGTPYYMSPEQMNR 1vzoA 207 :TERAYDFCGTIEYMAPDIVRG T0292 193 :EKSDIWSLGCLLYELCALMPPF 1vzoA 234 :KAVDWWSLGVLMYELLTGASPF T0292 215 :TAFSQKELAGKIREGKFR 1vzoA 260 :EKNSQAEISRRILKSEPP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1vzoA 278 :YPQEMSALAKDLIQRLLMKDPKKRL T0292 260 :VEEILENPLILEHH 1vzoA 309 :ADEIKEHLFFQKIN Number of specific fragments extracted= 15 number of extra gaps= 2 total=982 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wbsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wbsA expands to /projects/compbio/data/pdb/1wbs.pdb.gz 1wbsA:# T0292 read from 1wbsA/merged-good-all-a2m # 1wbsA read from 1wbsA/merged-good-all-a2m # adding 1wbsA to template set # found chain 1wbsA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1wbsA 22 :ERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARS T0292 78 :TTLYIVMEYCE 1wbsA 100 :NDVYLVTHLMG T0292 90 :GDLASVITKGT 1wbsA 111 :ADLNNIVKCQK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1wbsA 122 :LTDDHVQFLIYQILRGLKYIHSAD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLA 1wbsA 146 :IIHRDLKPSNLAVNEDCELKILDFGLA T0292 165 :NHDTSFAKAFVGTPYYMSPEQMNR 1wbsA 173 :RHTDDEMTGYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1wbsA 198 :MHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILR T0292 230 :KFRRIPYR 1wbsA 261 :SLTQMPKM T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1wbsA 277 :ANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQY T0292 276 :HH 1wbsA 321 :DP Number of specific fragments extracted= 10 number of extra gaps= 0 total=992 Number of alignments=91 # 1wbsA read from 1wbsA/merged-good-all-a2m # found chain 1wbsA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIID 1wbsA 22 :ERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTP T0292 75 :RTN 1wbsA 96 :LEE T0292 78 :TTLYIVMEYCEG 1wbsA 100 :NDVYLVTHLMGA T0292 91 :DLASVITKGT 1wbsA 112 :DLNNIVKCQK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1wbsA 122 :LTDDHVQFLIYQILRGLKYIHSAD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLAR 1wbsA 146 :IIHRDLKPSNLAVNEDCELKILDFGLAR T0292 166 :HDTSFAKAFVGTPYYMSPEQMNR 1wbsA 174 :HTDDEMTGYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTA 1wbsA 198 :MHYNQTVDIWSVGCIMAELLTGRTLFPG T0292 217 :FSQKELAGKIREGKFRRIPYR 1wbsA 250 :ISSESARNYIQSLTQMPKMNF T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1wbsA 277 :ANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYH T0292 274 :H 1wbsA 321 :D Number of specific fragments extracted= 11 number of extra gaps= 0 total=1003 Number of alignments=92 # 1wbsA read from 1wbsA/merged-good-all-a2m # found chain 1wbsA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIID 1wbsA 22 :ERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTP T0292 75 :RTNTTLYIVMEYCEG 1wbsA 97 :EEFNDVYLVTHLMGA T0292 91 :DLASVITK 1wbsA 112 :DLNNIVKC T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 1wbsA 120 :QKLTDDHVQFLIYQILRGLKYIHSA T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLA 1wbsA 145 :DIIHRDLKPSNLAVNEDCELKILDFGLA T0292 165 :NHDTSFAKAFVGTPYYMSPEQMNR 1wbsA 173 :RHTDDEMTGYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1wbsA 198 :MHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 1wbsA 273 :VFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDD Number of specific fragments extracted= 8 number of extra gaps= 0 total=1011 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1apmE/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1apmE expands to /projects/compbio/data/pdb/1apm.pdb.gz 1apmE:Skipped atom 336, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 338, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 340, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 342, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 344, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 346, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 348, because occupancy 0.460 <= existing 0.540 in 1apmE # T0292 read from 1apmE/merged-good-all-a2m # 1apmE read from 1apmE/merged-good-all-a2m # adding 1apmE to template set # found chain 1apmE in template set T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTE 1apmE 39 :QLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKVVK T0292 45 :AEKQMLVSEVNLLRELKHPNIVRYYDRI 1apmE 83 :KQIEHTLNEKRILQAVNFPFLVKLEFSF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1apmE 111 :KDNSNLYMVMEYVAGGEMFSHLRRIGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1apmE 138 :FAEPHARFYAAQIVLTFEYLHSLD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILN 1apmE 162 :LIYRDLKPENLLIDQQGYIQVTDFGFAKRVK T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKF 1apmE 193 :GRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKV T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRP 1apmE 256 :RFPSHFSSDLKDLLRNLLQVDLTKRF T0292 260 :VEEILENPLILEH 1apmE 288 :VNDIKNHKWFATT Number of specific fragments extracted= 8 number of extra gaps= 0 total=1019 Number of alignments=94 # 1apmE read from 1apmE/merged-good-all-a2m # found chain 1apmE in template set T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1apmE 39 :QLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1apmE 81 :KLKQIEHTLNEKRILQAVNFPFLVKLEFSF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1apmE 111 :KDNSNLYMVMEYVAGGEMFSHLRRIGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1apmE 138 :FAEPHARFYAAQIVLTFEYLHSLD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILN 1apmE 162 :LIYRDLKPENLLIDQQGYIQVTDFGFAKRVK T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1apmE 193 :GRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1apmE 257 :FPSHFSSDLKDLLRNLLQVDLTKRF T0292 259 :SVEEILENPLILEHH 1apmE 287 :GVNDIKNHKWFATTD Number of specific fragments extracted= 8 number of extra gaps= 0 total=1027 Number of alignments=95 # 1apmE read from 1apmE/merged-good-all-a2m # found chain 1apmE in template set T0292 1 :SRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1apmE 38 :AQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1apmE 81 :KLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSN T0292 80 :LYIVMEYCEGGDLASVITK 1apmE 116 :LYMVMEYVAGGEMFSHLRR T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1apmE 135 :IGRFAEPHARFYAAQIVLTFEYLHSL T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 1apmE 161 :DLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGR T0292 171 :AKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1apmE 195 :TWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1apmE 257 :FPSHFSSDLKDLLRNLLQVDLTKRF T0292 261 :EEILENPLILEHH 1apmE 289 :NDIKNHKWFATTD Number of specific fragments extracted= 8 number of extra gaps= 0 total=1035 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xjdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xjdA expands to /projects/compbio/data/pdb/1xjd.pdb.gz 1xjdA:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0292 read from 1xjdA/merged-good-all-a2m # 1xjdA read from 1xjdA/merged-good-all-a2m # adding 1xjdA to template set # found chain 1xjdA in template set Warning: unaligning (T0292)A3 because first residue in template chain is (1xjdA)I377 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjdA)F539 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjdA)F539 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAE 1xjdA 378 :EDFILHKMLGKGSFGKVFLAEFKKTNQFFAIKALKKDVVLMDD T0292 47 :KQMLVSEVNLLREL 1xjdA 422 :VECTMVEKRVLSLA T0292 61 :KHPNIVRYYDRI 1xjdA 437 :EHPFLTHMFCTF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1xjdA 449 :QTKENLFFVMEYLNGGDLMYHIQSCHK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1xjdA 476 :FDLSRATFYAAEIILGLQFLHSKG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 1xjdA 500 :IVYRDLKLDNILLDKDGHIKIADFGMCKENMLGDAKT T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKF 1xjdA 540 :CGTPDYIAPEILLGQKYNHSVDWWSFGVLLYEMLIGQSPFHGQDEEELFHSIRMDNP T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRP 1xjdA 597 :FYPRWLEKEAKDLLVKLFVREPEKRL T0292 263 :ILENPLILEH 1xjdA 628 :IRQHPLFREI Number of specific fragments extracted= 9 number of extra gaps= 0 total=1044 Number of alignments=97 # 1xjdA read from 1xjdA/merged-good-all-a2m # found chain 1xjdA in template set Warning: unaligning (T0292)A3 because first residue in template chain is (1xjdA)I377 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjdA)F539 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjdA)F539 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1xjdA 378 :EDFILHKMLGKGSFGKVFLAEFKKTNQFFAIKALKKDVV T0292 43 :TEAEKQMLVSEVNLLREL 1xjdA 418 :MDDDVECTMVEKRVLSLA T0292 61 :KHPNIVRYYDRI 1xjdA 437 :EHPFLTHMFCTF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1xjdA 449 :QTKENLFFVMEYLNGGDLMYHIQSCHK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1xjdA 476 :FDLSRATFYAAEIILGLQFLHSKG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 1xjdA 500 :IVYRDLKLDNILLDKDGHIKIADFGMCKENMLGDAKT T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1xjdA 540 :CGTPDYIAPEILLGQKYNHSVDWWSFGVLLYEMLIGQSPFHGQDEEELFHSIRMDNPF T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1xjdA 598 :YPRWLEKEAKDLLVKLFVREPEKRL T0292 259 :S 1xjdA 627 :D T0292 263 :ILENPLILEHH 1xjdA 628 :IRQHPLFREIN T0292 274 :HHH 1xjdA 646 :EID Number of specific fragments extracted= 11 number of extra gaps= 0 total=1055 Number of alignments=98 # 1xjdA read from 1xjdA/merged-good-all-a2m # found chain 1xjdA in template set Warning: unaligning (T0292)A3 because first residue in template chain is (1xjdA)I377 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjdA)F539 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjdA)F539 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1xjdA 378 :EDFILHKMLGKGSFGKVFLAEFKKTNQFFAIKALKKDVV T0292 43 :TEAEKQMLVSEVNLLREL 1xjdA 418 :MDDDVECTMVEKRVLSLA T0292 61 :KHPNIVRYYDRIIDRTN 1xjdA 437 :EHPFLTHMFCTFQTKEN T0292 80 :LYIVMEYCEGGDLASVITK 1xjdA 454 :LFFVMEYLNGGDLMYHIQS T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1xjdA 473 :CHKFDLSRATFYAAEIILGLQFLHSK T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 1xjdA 499 :GIVYRDLKLDNILLDKDGHIKIADFGMCKENMLGDAKT T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1xjdA 540 :CGTPDYIAPEILLGQKYNHSVDWWSFGVLLYEMLIGQSPFHGQDEEELFHSIRMDNPF T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1xjdA 598 :YPRWLEKEAKDLLVKLFVREPEKRL T0292 263 :ILENPLILEHH 1xjdA 628 :IRQHPLFREIN Number of specific fragments extracted= 9 number of extra gaps= 0 total=1064 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yhvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yhvA expands to /projects/compbio/data/pdb/1yhv.pdb.gz 1yhvA:# T0292 read from 1yhvA/merged-good-all-a2m # 1yhvA read from 1yhvA/merged-good-all-a2m # adding 1yhvA to template set # found chain 1yhvA in template set Warning: unaligning (T0292)D167 because of BadResidue code BAD_PEPTIDE in next template residue (1yhvA)Q418 Warning: unaligning (T0292)T168 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)Q418 Warning: unaligning (T0292)S169 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)S419 T0292 3 :AEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAE 1yhvA 267 :KKKYTRFEKIGQGASGTVYTAMDVATGQEVAIRQMNLQQQPKKE T0292 49 :MLVSEVNLLRELKHPNIVRYYDRI 1yhvA 311 :LIINEILVMRENKNPNIVNYLDSY T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGT 1yhvA 335 :LVGDELWVVMEYLAGGSLTDVVTETC T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1yhvA 361 :MDEGQIAAVCRECLQALEFLHSNQ T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNH 1yhvA 385 :VIHRDIKSDNILLGMDGSVKLTDFGFCAQITP T0292 170 :FAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRI 1yhvA 420 :KRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPEL T0292 235 :PYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHH 1yhvA 487 :PEKLSAIFRDFLNRCLDMDVEKRGSAKELLQHQFLKIAKP Number of specific fragments extracted= 7 number of extra gaps= 1 total=1071 Number of alignments=100 # 1yhvA read from 1yhvA/merged-good-all-a2m # found chain 1yhvA in template set Warning: unaligning (T0292)D167 because of BadResidue code BAD_PEPTIDE in next template residue (1yhvA)Q418 Warning: unaligning (T0292)T168 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)Q418 Warning: unaligning (T0292)S169 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)S419 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEA 1yhvA 268 :KKYTRFEKIGQGASGTVYTAMDVATGQEVAIRQMNLQQQPKK T0292 48 :QMLVSEVNLLRELKHPNIVRYYDRI 1yhvA 310 :ELIINEILVMRENKNPNIVNYLDSY T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGT 1yhvA 335 :LVGDELWVVMEYLAGGSLTDVVTETC T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1yhvA 361 :MDEGQIAAVCRECLQALEFLHSNQ T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNH 1yhvA 385 :VIHRDIKSDNILLGMDGSVKLTDFGFCAQITP T0292 170 :FAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRI 1yhvA 420 :KRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPEL T0292 235 :PYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHH 1yhvA 487 :PEKLSAIFRDFLNRCLDMDVEKRGSAKELLQHQFLKIAKP Number of specific fragments extracted= 7 number of extra gaps= 1 total=1078 Number of alignments=101 # 1yhvA read from 1yhvA/merged-good-all-a2m # found chain 1yhvA in template set Warning: unaligning (T0292)D167 because of BadResidue code BAD_PEPTIDE in next template residue (1yhvA)Q418 Warning: unaligning (T0292)T168 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)Q418 Warning: unaligning (T0292)S169 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)S419 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1yhvA 268 :KKYTRFEKIGQGASGTVYTAMDVATGQEVAIRQMNLQQQ T0292 44 :E 1yhvA 308 :K T0292 47 :KQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1yhvA 309 :KELIINEILVMRENKNPNIVNYLDSYLVGDE T0292 80 :LYIVMEYCEGGDLASVITK 1yhvA 340 :LWVVMEYLAGGSLTDVVTE T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 1yhvA 359 :TCMDEGQIAAVCRECLQALEFLHSN T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNH 1yhvA 384 :QVIHRDIKSDNILLGMDGSVKLTDFGFCAQITP T0292 170 :FAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1yhvA 420 :KRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPE T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHH 1yhvA 486 :NPEKLSAIFRDFLNRCLDMDVEKRGSAKELLQHQFLKIAKP Number of specific fragments extracted= 8 number of extra gaps= 1 total=1086 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ac3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ac3A expands to /projects/compbio/data/pdb/2ac3.pdb.gz 2ac3A:# T0292 read from 2ac3A/merged-good-all-a2m # 2ac3A read from 2ac3A/merged-good-all-a2m # adding 2ac3A to template set # found chain 2ac3A in template set Warning: unaligning (T0292)Y10 because of BadResidue code BAD_PEPTIDE in next template residue (2ac3A)V89 Warning: unaligning (T0292)T11 because of BadResidue code BAD_PEPTIDE at template residue (2ac3A)V89 Warning: unaligning (T0292)S41 because of BadResidue code BAD_PEPTIDE in next template residue (2ac3A)G120 Warning: unaligning (T0292)M42 because of BadResidue code BAD_PEPTIDE at template residue (2ac3A)G120 Warning: unaligning (T0292)T79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ac3A)F155 Warning: unaligning (T0292)L80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ac3A)F155 Warning: unaligning (T0292)R162 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ac3A)C251 Warning: unaligning (T0292)V175 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ac3A)C251 Warning: unaligning (T0292)R232 because of BadResidue code BAD_PEPTIDE in next template residue (2ac3A)F329 Warning: unaligning (T0292)I234 because of BadResidue code BAD_PEPTIDE at template residue (2ac3A)F329 Warning: unaligning (T0292)L270 because last residue in template chain is (2ac3A)Q369 T0292 5 :DYEVL 2ac3A 82 :VYQLQ T0292 12 :IGTGSYGRCQKIRRKSDGKILVWKELDYG 2ac3A 90 :LGEGAHARVQTCINLITSQEYAVKIIEKQ T0292 43 :TEA 2ac3A 121 :HIR T0292 48 :QMLVSEVNLLREL 2ac3A 124 :SRVFREVEMLYQC T0292 61 :KHPNIVRYYDRI 2ac3A 138 :GHRNVLELIEFF T0292 75 :RTNT 2ac3A 150 :EEED T0292 81 :YIVMEYCEGGDLASVITKGTK 2ac3A 156 :YLVFEKMRGGSILSHIHKRRH T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2ac3A 177 :FNELEASVVVQDVASALDFLHNKG T0292 135 :VLHRDLKPANVFLDGKQN 2ac3A 201 :IAHRDLKPENILCEHPNQ T0292 153 :VKLGDFGLA 2ac3A 222 :VKICDFDLG T0292 176 :GTPYYMSPEQMNRMS 2ac3A 252 :GSAEYMAPEVVEAFS T0292 191 :YNEKSDIWSLGCLLYELCALMPPFTAFS 2ac3A 272 :YDKRCDLWSLGVILYILLSGYPPFVGRC T0292 219 :QKELAGKIREGKF 2ac3A 315 :QNMLFESIQEGKY T0292 235 :P 2ac3A 330 :P T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLI 2ac3A 335 :AHISCAAKDLISKLLVRDAKQRLSAAQVLQHPWV Number of specific fragments extracted= 15 number of extra gaps= 4 total=1101 Number of alignments=103 # 2ac3A read from 2ac3A/merged-good-all-a2m # found chain 2ac3A in template set Warning: unaligning (T0292)Y10 because of BadResidue code BAD_PEPTIDE in next template residue (2ac3A)V89 Warning: unaligning (T0292)T11 because of BadResidue code BAD_PEPTIDE at template residue (2ac3A)V89 Warning: unaligning (T0292)S41 because of BadResidue code BAD_PEPTIDE in next template residue (2ac3A)G120 Warning: unaligning (T0292)M42 because of BadResidue code BAD_PEPTIDE at template residue (2ac3A)G120 Warning: unaligning (T0292)T79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ac3A)F155 Warning: unaligning (T0292)L80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ac3A)F155 Warning: unaligning (T0292)R162 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ac3A)C251 Warning: unaligning (T0292)V175 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ac3A)C251 Warning: unaligning (T0292)R233 because of BadResidue code BAD_PEPTIDE in next template residue (2ac3A)F329 Warning: unaligning (T0292)I234 because of BadResidue code BAD_PEPTIDE at template residue (2ac3A)F329 Warning: unaligning (T0292)L270 because last residue in template chain is (2ac3A)Q369 T0292 2 :RAED 2ac3A 78 :RFED T0292 6 :YEVL 2ac3A 83 :YQLQ T0292 12 :IGTGSYGRCQKIRRKSDGKILVWKELDYG 2ac3A 90 :LGEGAHARVQTCINLITSQEYAVKIIEKQ T0292 43 :T 2ac3A 122 :I T0292 47 :KQMLVSEVNLLREL 2ac3A 123 :RSRVFREVEMLYQC T0292 61 :KHPNIVRYYDRI 2ac3A 138 :GHRNVLELIEFF T0292 75 :RTNT 2ac3A 150 :EEED T0292 81 :YIVMEYCEGGDLASVITKGTK 2ac3A 156 :YLVFEKMRGGSILSHIHKRRH T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2ac3A 177 :FNELEASVVVQDVASALDFLHNKG T0292 135 :VLHRDLKPANVFL 2ac3A 201 :IAHRDLKPENILC T0292 148 :DGKQ 2ac3A 215 :HPNQ T0292 152 :NVKLGDFGLA 2ac3A 221 :PVKICDFDLG T0292 176 :GTPYYMSPEQMNRMS 2ac3A 252 :GSAEYMAPEVVEAFS T0292 191 :YNEKSDIWSLGCLLYELCALMPPFTA 2ac3A 272 :YDKRCDLWSLGVILYILLSGYPPFVG T0292 218 :S 2ac3A 311 :C T0292 219 :QKELAGKIREGKFR 2ac3A 314 :CQNMLFESIQEGKY T0292 235 :P 2ac3A 330 :P T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLI 2ac3A 335 :AHISCAAKDLISKLLVRDAKQRLSAAQVLQHPWV Number of specific fragments extracted= 18 number of extra gaps= 4 total=1119 Number of alignments=104 # 2ac3A read from 2ac3A/merged-good-all-a2m # found chain 2ac3A in template set Warning: unaligning (T0292)S41 because of BadResidue code BAD_PEPTIDE in next template residue (2ac3A)G120 Warning: unaligning (T0292)M42 because of BadResidue code BAD_PEPTIDE at template residue (2ac3A)G120 Warning: unaligning (T0292)N77 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ac3A)F155 Warning: unaligning (T0292)L80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ac3A)F155 Warning: unaligning (T0292)R162 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ac3A)C251 Warning: unaligning (T0292)V175 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ac3A)C251 Warning: unaligning (T0292)R232 because of BadResidue code BAD_PEPTIDE in next template residue (2ac3A)F329 Warning: unaligning (T0292)R233 because of BadResidue code BAD_PEPTIDE at template residue (2ac3A)F329 Warning: unaligning (T0292)L270 because last residue in template chain is (2ac3A)Q369 T0292 12 :IGTGSYGRCQKIRRKSDGKILVWKELDYG 2ac3A 90 :LGEGAHARVQTCINLITSQEYAVKIIEKQ T0292 43 :T 2ac3A 122 :I T0292 47 :KQMLVSEVNLLREL 2ac3A 123 :RSRVFREVEMLYQC T0292 61 :KHPNIVRYYDRIIDRT 2ac3A 138 :GHRNVLELIEFFEEED T0292 81 :YIVMEYCEGGDLASVITK 2ac3A 156 :YLVFEKMRGGSILSHIHK T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 2ac3A 174 :RRHFNELEASVVVQDVASALDFLHNK T0292 134 :TVLHRDLKPANVFL 2ac3A 200 :GIAHRDLKPENILC T0292 148 :DGK 2ac3A 215 :HPN T0292 151 :QNVKLGDFGLA 2ac3A 220 :SPVKICDFDLG T0292 176 :GTPYYMSPEQMNR 2ac3A 252 :GSAEYMAPEVVEA T0292 191 :YNEKSDIWSLGCLLYELCALMPPFT 2ac3A 272 :YDKRCDLWSLGVILYILLSGYPPFV T0292 216 :AFS 2ac3A 300 :GSD T0292 219 :QKELAGKIREGKF 2ac3A 315 :QNMLFESIQEGKY T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLI 2ac3A 333 :DWAHISCAAKDLISKLLVRDAKQRLSAAQVLQHPWV Number of specific fragments extracted= 14 number of extra gaps= 3 total=1133 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tvoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tvoA expands to /projects/compbio/data/pdb/1tvo.pdb.gz 1tvoA:# T0292 read from 1tvoA/merged-good-all-a2m # 1tvoA read from 1tvoA/merged-good-all-a2m # adding 1tvoA to template set # found chain 1tvoA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGS 1tvoA 23 :PRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFE T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT 1tvoA 61 :HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIE T0292 79 :TLYIVMEYCE 1tvoA 100 :DVYIVQDLME T0292 90 :GDLASVI 1tvoA 110 :TDLYKLL T0292 98 :KGTK 1tvoA 117 :KTQH T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1tvoA 121 :LSNDHICYFLYQILRGLKYIHSAN T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDT 1tvoA 145 :VLHRDLKPSNLLLNTTCDLKICDFGLARVADPDH T0292 169 :SFAKAFVGTPYYMSPEQMNR 1tvoA 182 :GFLTEYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1tvoA 203 :KGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILG T0292 229 :GKFRRI 1tvoA 267 :LPHKNK T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1tvoA 280 :PNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQY Number of specific fragments extracted= 11 number of extra gaps= 0 total=1144 Number of alignments=106 # 1tvoA read from 1tvoA/merged-good-all-a2m # found chain 1tvoA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGS 1tvoA 23 :PRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFE T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT 1tvoA 61 :HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIE T0292 79 :TLYIVMEYCEG 1tvoA 100 :DVYIVQDLMET T0292 91 :DLASVITKGT 1tvoA 111 :DLYKLLKTQH T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1tvoA 121 :LSNDHICYFLYQILRGLKYIHSAN T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 1tvoA 145 :VLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHT T0292 172 :KAFVGTPYYMSPEQMNR 1tvoA 185 :TEYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYR 1tvoA 203 :KGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQED T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1tvoA 282 :ADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYY T0292 274 :H 1tvoA 326 :E Number of specific fragments extracted= 10 number of extra gaps= 0 total=1154 Number of alignments=107 # 1tvoA read from 1tvoA/merged-good-all-a2m # found chain 1tvoA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGS 1tvoA 23 :PRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFE T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT 1tvoA 61 :HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIE T0292 79 :TLYIVMEYCEG 1tvoA 100 :DVYIVQDLMET T0292 91 :DLASVITK 1tvoA 111 :DLYKLLKT T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 1tvoA 119 :QHLSNDHICYFLYQILRGLKYIHSA T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 1tvoA 144 :NVLHRDLKPSNLLLNTTCDLKICDFGLARVADPD T0292 168 :TSFAKAFVGTPYYMSPEQMNR 1tvoA 181 :TGFLTEYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1tvoA 203 :KGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILG T0292 229 :GKFRR 1tvoA 245 :GSPSQ T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH 1tvoA 278 :LFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPS Number of specific fragments extracted= 10 number of extra gaps= 0 total=1164 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ac5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ac5A expands to /projects/compbio/data/pdb/2ac5.pdb.gz 2ac5A:Skipped atom 1257, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1265, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1269, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1275, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1277, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1279, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1281, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1283, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1285, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1287, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1289, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1291, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1293, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1295, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1305, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1307, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1309, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1311, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1313, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1315, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1321, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1325, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1327, because occupancy 0.500 <= existing 0.500 in 2ac5A Skipped atom 1329, because occupancy 0.500 <= existing 0.500 in 2ac5A # T0292 read from 2ac5A/merged-good-all-a2m # 2ac5A read from 2ac5A/merged-good-all-a2m # adding 2ac5A to template set # found chain 2ac5A in template set Warning: unaligning (T0292)G159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ac5A)P250 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ac5A)P250 Warning: unaligning (T0292)E271 because last residue in template chain is (2ac5A)G370 T0292 3 :AED 2ac5A 79 :FED T0292 6 :YEVLYT 2ac5A 83 :YQLQED T0292 12 :IGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEA 2ac5A 90 :LGEGAHARVQTCINLITSQEYAVKIIEKQPGHIR T0292 48 :QMLVSEVNLLREL 2ac5A 124 :SRVFREVEMLYQC T0292 61 :KHPNIVRYYDRI 2ac5A 138 :GHRNVLELIEFF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 2ac5A 150 :EEEDRFYLVFEKMRGGSILSHIHKRRH T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2ac5A 177 :FNELEASVVVQDVASALDFLHNKG T0292 135 :VLHRDLKPANVFLDGKQN 2ac5A 201 :IAHRDLKPENILCEHPNQ T0292 153 :VKLGDF 2ac5A 222 :VKICDF T0292 175 :VGTPYYMSPEQMNRMS 2ac5A 251 :CGSAEYMAPEVVEAFS T0292 191 :YNEKSDIWSLGCLLYELCALMPPFTAFS 2ac5A 272 :YDKRCDLWSLGVILYILLSGYPPFVGRC T0292 219 :QKELAGKIREGKFR 2ac5A 315 :QNMLFESIQEGKYE T0292 234 :IP 2ac5A 329 :FP T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLIL 2ac5A 335 :AHISCAAKDLISKLLVRDAKQRLSAAQVLQHPWVQ Number of specific fragments extracted= 14 number of extra gaps= 0 total=1178 Number of alignments=109 # 2ac5A read from 2ac5A/merged-good-all-a2m # found chain 2ac5A in template set Warning: unaligning (T0292)G159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ac5A)P250 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ac5A)P250 Warning: unaligning (T0292)E271 because last residue in template chain is (2ac5A)G370 T0292 2 :RAED 2ac5A 78 :RFED T0292 6 :YEVLYT 2ac5A 83 :YQLQED T0292 12 :IGTGSYGRCQKIRRKSDGKILVWKELDYGSM 2ac5A 90 :LGEGAHARVQTCINLITSQEYAVKIIEKQPG T0292 43 :T 2ac5A 122 :I T0292 47 :KQMLVSEVNLLREL 2ac5A 123 :RSRVFREVEMLYQC T0292 61 :KHPNIVRYYDRI 2ac5A 138 :GHRNVLELIEFF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 2ac5A 150 :EEEDRFYLVFEKMRGGSILSHIHKRRH T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2ac5A 177 :FNELEASVVVQDVASALDFLHNKG T0292 135 :VLHRDLKPANVFL 2ac5A 201 :IAHRDLKPENILC T0292 148 :DGKQ 2ac5A 215 :HPNQ T0292 152 :NVKLGDF 2ac5A 221 :PVKICDF T0292 175 :VGTPYYMSPEQMNRMS 2ac5A 251 :CGSAEYMAPEVVEAFS T0292 191 :YNEKSDIWSLGCLLYELCALMPPFTA 2ac5A 272 :YDKRCDLWSLGVILYILLSGYPPFVG T0292 218 :S 2ac5A 311 :C T0292 219 :QKELAGKIREGKFRRIP 2ac5A 314 :CQNMLFESIQEGKYEFP T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLIL 2ac5A 335 :AHISCAAKDLISKLLVRDAKQRLSAAQVLQHPWVQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=1194 Number of alignments=110 # 2ac5A read from 2ac5A/merged-good-all-a2m # found chain 2ac5A in template set Warning: unaligning (T0292)G159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ac5A)P250 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ac5A)P250 Warning: unaligning (T0292)E271 because last residue in template chain is (2ac5A)G370 T0292 2 :RAED 2ac5A 78 :RFED T0292 6 :YEVLYT 2ac5A 83 :YQLQED T0292 12 :IGTGSYGRCQKIRRKSDGKILVWKELDYGSM 2ac5A 90 :LGEGAHARVQTCINLITSQEYAVKIIEKQPG T0292 43 :T 2ac5A 122 :I T0292 47 :KQMLVSEVNLLREL 2ac5A 123 :RSRVFREVEMLYQC T0292 61 :KHPNIVRYYDRIIDRTN 2ac5A 138 :GHRNVLELIEFFEEEDR T0292 80 :LYIVMEYCEGGDLASVITK 2ac5A 155 :FYLVFEKMRGGSILSHIHK T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 2ac5A 174 :RRHFNELEASVVVQDVASALDFLHNK T0292 134 :TVLHRDLKPANVFL 2ac5A 200 :GIAHRDLKPENILC T0292 148 :DGK 2ac5A 215 :HPN T0292 151 :QNVKLGDF 2ac5A 220 :SPVKICDF T0292 175 :VGTPYYMSPEQMNR 2ac5A 251 :CGSAEYMAPEVVEA T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFS 2ac5A 270 :SIYDKRCDLWSLGVILYILLSGYPPFVGRC T0292 219 :QKELAGKIREGKFR 2ac5A 315 :QNMLFESIQEGKYE T0292 234 :IP 2ac5A 329 :FP T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLIL 2ac5A 335 :AHISCAAKDLISKLLVRDAKQRLSAAQVLQHPWVQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=1210 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3erk/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3erk expands to /projects/compbio/data/pdb/3erk.pdb.gz 3erk:Warning: there is no chain 3erk will retry with 3erkA # T0292 read from 3erk/merged-good-all-a2m # 3erk read from 3erk/merged-good-all-a2m # adding 3erk to template set # found chain 3erk in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGS 3erk 21 :PRYTNLSYIGEGAYGMVCSAYDNLNKVRVAIKKISPFE T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT 3erk 59 :HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIE T0292 79 :TLYIVMEYCE 3erk 98 :DVYIVQDLME T0292 90 :GDLASVITKG 3erk 108 :TDLYKLLKTQ T0292 101 :K 3erk 118 :H T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 3erk 119 :LSNDHICYFLYQILRGLKYIHSAN T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDT 3erk 143 :VLHRDLKPSNLLLNTTCDLKICDFGLARVADPDH T0292 169 :SFAKAFVGTPYYMSPEQMNR 3erk 180 :GFLTEYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 3erk 201 :KGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILG T0292 229 :GKFRRIP 3erk 266 :PHKNKVP T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 3erk 278 :PNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQY Number of specific fragments extracted= 11 number of extra gaps= 0 total=1221 Number of alignments=112 # 3erk read from 3erk/merged-good-all-a2m # found chain 3erk in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGS 3erk 21 :PRYTNLSYIGEGAYGMVCSAYDNLNKVRVAIKKISPFE T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT 3erk 59 :HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIE T0292 79 :TLYIVMEYCEG 3erk 98 :DVYIVQDLMET T0292 91 :DLASVITKGT 3erk 109 :DLYKLLKTQH T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 3erk 119 :LSNDHICYFLYQILRGLKYIHSAN T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 3erk 143 :VLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHT T0292 172 :KAFVGTPYYMSPEQMNR 3erk 183 :TEYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPY 3erk 201 :KGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQE T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 3erk 280 :ADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYY T0292 274 :H 3erk 324 :E Number of specific fragments extracted= 10 number of extra gaps= 0 total=1231 Number of alignments=113 # 3erk read from 3erk/merged-good-all-a2m # found chain 3erk in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGS 3erk 21 :PRYTNLSYIGEGAYGMVCSAYDNLNKVRVAIKKISPFE T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT 3erk 59 :HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIE T0292 79 :TLYIVMEYCEG 3erk 98 :DVYIVQDLMET T0292 91 :DLASVITK 3erk 109 :DLYKLLKT T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 3erk 117 :QHLSNDHICYFLYQILRGLKYIHSA T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 3erk 142 :NVLHRDLKPSNLLLNTTCDLKICDFGLARVADPD T0292 168 :TSFAKAFVGTPYYMSPEQMNR 3erk 179 :TGFLTEYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 3erk 201 :KGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH 3erk 276 :LFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPS Number of specific fragments extracted= 9 number of extra gaps= 0 total=1240 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bvaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bvaA expands to /projects/compbio/data/pdb/2bva.pdb.gz 2bvaA:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0292 read from 2bvaA/merged-good-all-a2m # 2bvaA read from 2bvaA/merged-good-all-a2m # adding 2bvaA to template set # found chain 2bvaA in template set Warning: unaligning (T0292)N152 because of BadResidue code BAD_PEPTIDE in next template residue (2bvaA)V454 Warning: unaligning (T0292)V153 because of BadResidue code BAD_PEPTIDE at template residue (2bvaA)V454 Warning: unaligning (T0292)G156 because of BadResidue code BAD_PEPTIDE in next template residue (2bvaA)D458 Warning: unaligning (T0292)D157 because of BadResidue code BAD_PEPTIDE at template residue (2bvaA)D458 Warning: unaligning (T0292)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bvaA)E468 Warning: unaligning (T0292)D167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bvaA)E468 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bvaA)L475 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bvaA)L475 Warning: unaligning (T0292)T177 because of BadResidue code BAD_PEPTIDE in next template residue (2bvaA)P479 Warning: unaligning (T0292)P178 because of BadResidue code BAD_PEPTIDE at template residue (2bvaA)P479 T0292 51 :VSEVNLLRELKHPNIVRYYDRI 2bvaA 364 :FNEVVIMRDYQHENVVEMYNSY T0292 75 :RTNTTLYIVMEYCEGGDLAS 2bvaA 386 :LVGDELWVVMEFLEGGALTD T0292 96 :ITKGTK 2bvaA 406 :IVTHTR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2bvaA 412 :MNEEQIAAVCLAVLQALSVLHAQG T0292 135 :VLHRDLKPANVFLDGKQ 2bvaA 436 :VIHRDIKSDSILLTHDG T0292 154 :KL 2bvaA 455 :KL T0292 158 :FGLARI 2bvaA 459 :FGFCAQ T0292 168 :TSFA 2bvaA 469 :VPRR T0292 175 :VG 2bvaA 476 :VG T0292 179 :YYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRI 2bvaA 480 :YWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRL T0292 235 :PYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 2bvaA 538 :LHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAG Number of specific fragments extracted= 11 number of extra gaps= 3 total=1251 Number of alignments=115 # 2bvaA read from 2bvaA/merged-good-all-a2m # found chain 2bvaA in template set Warning: unaligning (T0292)N152 because of BadResidue code BAD_PEPTIDE in next template residue (2bvaA)V454 Warning: unaligning (T0292)V153 because of BadResidue code BAD_PEPTIDE at template residue (2bvaA)V454 Warning: unaligning (T0292)G156 because of BadResidue code BAD_PEPTIDE in next template residue (2bvaA)D458 Warning: unaligning (T0292)D157 because of BadResidue code BAD_PEPTIDE at template residue (2bvaA)D458 Warning: unaligning (T0292)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bvaA)E468 Warning: unaligning (T0292)D167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bvaA)E468 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bvaA)L475 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bvaA)L475 Warning: unaligning (T0292)T177 because of BadResidue code BAD_PEPTIDE in next template residue (2bvaA)P479 Warning: unaligning (T0292)P178 because of BadResidue code BAD_PEPTIDE at template residue (2bvaA)P479 T0292 51 :VSEVNLLRELKHPNIVRYYDRI 2bvaA 364 :FNEVVIMRDYQHENVVEMYNSY T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGT 2bvaA 386 :LVGDELWVVMEFLEGGALTDIVTHTR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2bvaA 412 :MNEEQIAAVCLAVLQALSVLHAQG T0292 135 :VLHRDLKPANVFLDGKQ 2bvaA 436 :VIHRDIKSDSILLTHDG T0292 154 :KL 2bvaA 455 :KL T0292 158 :FGLARI 2bvaA 459 :FGFCAQ T0292 168 :TSFA 2bvaA 469 :VPRR T0292 175 :VG 2bvaA 476 :VG T0292 179 :YYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRI 2bvaA 480 :YWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRL T0292 235 :PYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 2bvaA 538 :LHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAG Number of specific fragments extracted= 10 number of extra gaps= 3 total=1261 Number of alignments=116 # 2bvaA read from 2bvaA/merged-good-all-a2m # found chain 2bvaA in template set Warning: unaligning (T0292)N152 because of BadResidue code BAD_PEPTIDE in next template residue (2bvaA)V454 Warning: unaligning (T0292)V153 because of BadResidue code BAD_PEPTIDE at template residue (2bvaA)V454 Warning: unaligning (T0292)G156 because of BadResidue code BAD_PEPTIDE in next template residue (2bvaA)D458 Warning: unaligning (T0292)D157 because of BadResidue code BAD_PEPTIDE at template residue (2bvaA)D458 Warning: unaligning (T0292)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bvaA)E468 Warning: unaligning (T0292)D167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bvaA)E468 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bvaA)L475 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bvaA)L475 Warning: unaligning (T0292)T177 because of BadResidue code BAD_PEPTIDE in next template residue (2bvaA)P479 Warning: unaligning (T0292)P178 because of BadResidue code BAD_PEPTIDE at template residue (2bvaA)P479 T0292 51 :VSEVNLLRELKHPNIVRYYDRIIDRTN 2bvaA 364 :FNEVVIMRDYQHENVVEMYNSYLVGDE T0292 80 :LYIVMEYCEGGDLASVITK 2bvaA 391 :LWVVMEFLEGGALTDIVTH T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 2bvaA 410 :TRMNEEQIAAVCLAVLQALSVLHAQ T0292 134 :TVLHRDLKPANVFLDGKQ 2bvaA 435 :GVIHRDIKSDSILLTHDG T0292 154 :KL 2bvaA 455 :KL T0292 158 :FGLARI 2bvaA 459 :FGFCAQ T0292 168 :TSFA 2bvaA 469 :VPRR T0292 175 :VG 2bvaA 476 :VG T0292 179 :YYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 2bvaA 480 :YWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHH 2bvaA 537 :NLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGP Number of specific fragments extracted= 10 number of extra gaps= 3 total=1271 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s9jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1s9jA expands to /projects/compbio/data/pdb/1s9j.pdb.gz 1s9jA:# T0292 read from 1s9jA/merged-good-all-a2m # 1s9jA read from 1s9jA/merged-good-all-a2m # adding 1s9jA to template set # found chain 1s9jA in template set Warning: unaligning (T0292)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1s9jA)K84 Warning: unaligning (T0292)K22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1s9jA)K84 Warning: unaligning (T0292)A171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s9jA)V224 Warning: unaligning (T0292)V175 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s9jA)V224 Warning: unaligning (T0292)T215 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s9jA)P306 T0292 2 :RAEDYEVLYTIGTGSYGRC 1s9jA 64 :KDDDFEKISELGAGNGGVV T0292 23 :IRRKSDGKILVWKELDYG 1s9jA 85 :VSHKPSGLVMARKLIHLE T0292 42 :MTEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1s9jA 103 :IKPAIRNQIIRELQVLHECNSPYIVGFYGAF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1s9jA 134 :YSDGEISICMEHMDGGSLDQVLKKAGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRSD 1s9jA 161 :IPEQILGKVSIAVIKGLTYLREKHK T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNH 1s9jA 186 :IMHRDVKPSNILVNSRGEIKLCDFGVSGQLID T0292 169 :SF 1s9jA 218 :SM T0292 176 :GTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPF 1s9jA 225 :GTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPI T0292 216 :AFSQKELAGKIREGKFRRIP 1s9jA 307 :PMAIFELLDYIVNEPPPKLP T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLIL 1s9jA 328 :GVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIK Number of specific fragments extracted= 10 number of extra gaps= 1 total=1281 Number of alignments=118 # 1s9jA read from 1s9jA/merged-good-all-a2m # found chain 1s9jA in template set Warning: unaligning (T0292)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1s9jA)K84 Warning: unaligning (T0292)K22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1s9jA)K84 Warning: unaligning (T0292)A171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s9jA)V224 Warning: unaligning (T0292)V175 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s9jA)V224 T0292 2 :RAEDYEVLYTIGTGSYGRC 1s9jA 64 :KDDDFEKISELGAGNGGVV T0292 23 :IRRKSDGKILVWKELDYGS 1s9jA 85 :VSHKPSGLVMARKLIHLEI T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1s9jA 104 :KPAIRNQIIRELQVLHECNSPYIVGFYGAF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1s9jA 134 :YSDGEISICMEHMDGGSLDQVLKKAGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRSD 1s9jA 161 :IPEQILGKVSIAVIKGLTYLREKHK T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNH 1s9jA 186 :IMHRDVKPSNILVNSRGEIKLCDFGVSGQLID T0292 169 :SF 1s9jA 218 :SM T0292 176 :GTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTA 1s9jA 225 :GTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIPP T0292 217 :FSQKELAGKIREGKFRRIP 1s9jA 308 :MAIFELLDYIVNEPPPKLP T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLIL 1s9jA 328 :GVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIK Number of specific fragments extracted= 10 number of extra gaps= 1 total=1291 Number of alignments=119 # 1s9jA read from 1s9jA/merged-good-all-a2m # found chain 1s9jA in template set Warning: unaligning (T0292)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1s9jA)K84 Warning: unaligning (T0292)K22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1s9jA)K84 Warning: unaligning (T0292)A171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s9jA)V224 Warning: unaligning (T0292)V175 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s9jA)V224 T0292 2 :RAEDYEVLYTIGTGSYGRC 1s9jA 64 :KDDDFEKISELGAGNGGVV T0292 23 :IRRKSDGKILVWKELDYG 1s9jA 85 :VSHKPSGLVMARKLIHLE T0292 42 :MTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1s9jA 103 :IKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGE T0292 80 :LYIVMEYCEGGDLASVITK 1s9jA 139 :ISICMEHMDGGSLDQVLKK T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRRS 1s9jA 158 :AGRIPEQILGKVSIAVIKGLTYLREKH T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 1s9jA 185 :KIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDS T0292 170 :F 1s9jA 219 :M T0292 176 :GTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFS 1s9jA 225 :GTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIPPPD T0292 219 :QKELAGKIREGKFRR 1s9jA 310 :IFELLDYIVNEPPPK T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLIL 1s9jA 326 :PSGVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIK Number of specific fragments extracted= 10 number of extra gaps= 1 total=1301 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tkiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tkiA expands to /projects/compbio/data/pdb/1tki.pdb.gz 1tkiA:# T0292 read from 1tkiA/merged-good-all-a2m # 1tkiA read from 1tkiA/merged-good-all-a2m # adding 1tkiA to template set # found chain 1tkiA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELD 1tkiA 22 :EKYMIAEDLGRGEFGIVHRCVETSSKKTYMAKFVK T0292 42 :MTEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1tkiA 57 :VKGTDQVLVKKEISILNIARHRNILHLHESF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTKE 1tkiA 88 :ESMEELVMIFEFISGLDIFERINTSAFE T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1tkiA 116 :LNEREIVSYVHQVCEALQFLHSHN T0292 135 :VLHRDLKPANVFLDGKQN 1tkiA 140 :IGHFDIRPENIIYQTRRS T0292 153 :VKLGDFGLARILNHD 1tkiA 160 :IKIIEFGQARQLKPG T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRI 1tkiA 175 :DNFRLLFTAPEYYAPEVHQHDVVSTATDMWSLGTLVYVLLSGINPFLAETNQQIIENIMNAEYTFD T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1tkiA 245 :KEISIEAMDFVDRLLVKERKSRMTASEALQHPWLKQK T0292 274 :H 1tkiA 287 :T Number of specific fragments extracted= 9 number of extra gaps= 0 total=1310 Number of alignments=121 # 1tkiA read from 1tkiA/merged-good-all-a2m # found chain 1tkiA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 1tkiA 22 :EKYMIAEDLGRGEFGIVHRCVETSSKKTYMAKFVKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1tkiA 58 :KGTDQVLVKKEISILNIARHRNILHLHESF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTKE 1tkiA 88 :ESMEELVMIFEFISGLDIFERINTSAFE T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1tkiA 116 :LNEREIVSYVHQVCEALQFLHSHN T0292 135 :VLHRDLKPANVFL 1tkiA 140 :IGHFDIRPENIIY T0292 148 :DGKQNVKLGDFGLARILNHDT 1tkiA 155 :RRSSTIKIIEFGQARQLKPGD T0292 170 :FAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIP 1tkiA 176 :NFRLLFTAPEYYAPEVHQHDVVSTATDMWSLGTLVYVLLSGINPFLAETNQQIIENIMNAEYTFDE T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1tkiA 245 :KEISIEAMDFVDRLLVKERKSRMTASEALQHPWLKQKI T0292 274 :H 1tkiA 286 :S Number of specific fragments extracted= 9 number of extra gaps= 0 total=1319 Number of alignments=122 # 1tkiA read from 1tkiA/merged-good-all-a2m # found chain 1tkiA in template set T0292 3 :AEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 1tkiA 21 :YEKYMIAEDLGRGEFGIVHRCVETSSKKTYMAKFVKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1tkiA 58 :KGTDQVLVKKEISILNIARHRNILHLHESFESMEE T0292 80 :LYIVMEYCEGGDLASVITK 1tkiA 93 :LVMIFEFISGLDIFERINT T0292 102 :ERQYLDEEFVLRVMTQLTLALKECHRR 1tkiA 112 :SAFELNEREIVSYVHQVCEALQFLHSH T0292 134 :TVLHRDLKPANVFL 1tkiA 139 :NIGHFDIRPENIIY T0292 148 :DGKQNVKLGDFGLARILNHD 1tkiA 155 :RRSSTIKIIEFGQARQLKPG T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1tkiA 175 :DNFRLLFTAPEYYAPEVHQHDVVSTATDMWSLGTLVYVLLSGINPFLAETNQQIIENIMNAEYTF T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLILE 1tkiA 245 :KEISIEAMDFVDRLLVKERKSRMTASEALQHPWLKQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=1327 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gfsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gfsA expands to /projects/compbio/data/pdb/2gfs.pdb.gz 2gfsA:Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1230, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1232, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1234, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1238, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1290, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1294, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1296, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1880, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1882, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1884, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1886, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1888, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1890, because occupancy 0.500 <= existing 0.500 in 2gfsA Skipped atom 1892, because occupancy 0.500 <= existing 0.500 in 2gfsA # T0292 read from 2gfsA/merged-good-all-a2m # 2gfsA read from 2gfsA/merged-good-all-a2m # adding 2gfsA to template set # found chain 2gfsA in template set Warning: unaligning (T0292)D38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfsA)R57 Warning: unaligning (T0292)Y39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfsA)R57 Warning: unaligning (T0292)G40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfsA)P58 Warning: unaligning (T0292)F158 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gfsA)H174 Warning: unaligning (T0292)H166 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfsA)H174 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKEL 2gfsA 22 :ERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKL T0292 41 :SMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 2gfsA 59 :FQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARS T0292 78 :TTLYIVMEYC 2gfsA 100 :NDVYLVTHLM T0292 89 :GGDLASVI 2gfsA 110 :GADLNNIV T0292 98 :KGTK 2gfsA 118 :KCQK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2gfsA 122 :LTDDHVQFLIYQILRGLKYIHSAD T0292 135 :VLHRDLKPANVFLDGKQNVKLGD 2gfsA 146 :IIHRDLKPSNLAVNEDCELKILD T0292 167 :DTSFAKAFVGTPYYMSPEQMNR 2gfsA 175 :TDDEMTGYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 2gfsA 198 :MHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILR T0292 229 :GKFRRIPYR 2gfsA 260 :QSLTQMPKM T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 2gfsA 277 :ANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQY Number of specific fragments extracted= 11 number of extra gaps= 1 total=1338 Number of alignments=124 # 2gfsA read from 2gfsA/merged-good-all-a2m # found chain 2gfsA in template set Warning: unaligning (T0292)D38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfsA)R57 Warning: unaligning (T0292)Y39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfsA)R57 Warning: unaligning (T0292)G40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfsA)P58 Warning: unaligning (T0292)F158 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gfsA)H174 Warning: unaligning (T0292)I163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfsA)H174 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKEL 2gfsA 22 :ERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKL T0292 41 :SMTEAEKQMLVSEVNLLRELKHPNIVRYYDRII 2gfsA 59 :FQSIIHAKRTYRELRLLKHMKHENVIGLLDVFT T0292 74 :DRTN 2gfsA 95 :SLEE T0292 78 :TTLYIVMEYC 2gfsA 100 :NDVYLVTHLM T0292 89 :GGDLASVITKGT 2gfsA 110 :GADLNNIVKCQK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2gfsA 122 :LTDDHVQFLIYQILRGLKYIHSAD T0292 135 :VLHRDLKPANVFLDGKQNVKLGD 2gfsA 146 :IIHRDLKPSNLAVNEDCELKILD T0292 167 :DTSFAKAFVGTPYYMSPEQMNR 2gfsA 175 :TDDEMTGYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 2gfsA 198 :MHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGT T0292 234 :IP 2gfsA 242 :PG T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 2gfsA 277 :ANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYH Number of specific fragments extracted= 11 number of extra gaps= 1 total=1349 Number of alignments=125 # 2gfsA read from 2gfsA/merged-good-all-a2m # found chain 2gfsA in template set Warning: unaligning (T0292)D38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfsA)R57 Warning: unaligning (T0292)Y39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfsA)R57 Warning: unaligning (T0292)G40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfsA)P58 Warning: unaligning (T0292)F158 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gfsA)H174 Warning: unaligning (T0292)I163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfsA)H174 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKEL 2gfsA 22 :ERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKL T0292 41 :SMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIID 2gfsA 59 :FQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTP T0292 75 :RTNTTLYIVMEYCE 2gfsA 97 :EEFNDVYLVTHLMG T0292 90 :GDLASVITK 2gfsA 111 :ADLNNIVKC T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 2gfsA 120 :QKLTDDHVQFLIYQILRGLKYIHSA T0292 134 :TVLHRDLKPANVFLDGKQNVKLGD 2gfsA 145 :DIIHRDLKPSNLAVNEDCELKILD T0292 164 :LN 2gfsA 175 :TD T0292 169 :SFAKAFVGTPYYMSPEQMNR 2gfsA 177 :DEMTGYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 2gfsA 198 :MHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 2gfsA 273 :VFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDD Number of specific fragments extracted= 10 number of extra gaps= 1 total=1359 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r3cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r3cA expands to /projects/compbio/data/pdb/1r3c.pdb.gz 1r3cA:Skipped atom 2616, because occupancy 0.500 <= existing 0.500 in 1r3cA Skipped atom 2618, because occupancy 0.500 <= existing 0.500 in 1r3cA Skipped atom 2620, because occupancy 0.500 <= existing 0.500 in 1r3cA Skipped atom 2622, because occupancy 0.500 <= existing 0.500 in 1r3cA Skipped atom 2624, because occupancy 0.500 <= existing 0.500 in 1r3cA Skipped atom 2626, because occupancy 0.500 <= existing 0.500 in 1r3cA Skipped atom 2628, because occupancy 0.500 <= existing 0.500 in 1r3cA Skipped atom 2630, because occupancy 0.500 <= existing 0.500 in 1r3cA Skipped atom 2632, because occupancy 0.500 <= existing 0.500 in 1r3cA Skipped atom 2634, because occupancy 0.500 <= existing 0.500 in 1r3cA Skipped atom 2636, because occupancy 0.500 <= existing 0.500 in 1r3cA # T0292 read from 1r3cA/merged-good-all-a2m # 1r3cA read from 1r3cA/merged-good-all-a2m # adding 1r3cA to template set # found chain 1r3cA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1r3cA 22 :ERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARS T0292 78 :TTLYIVMEYCE 1r3cA 100 :NDVYLVTHLMG T0292 90 :GDLASVI 1r3cA 111 :ADLNNIV T0292 98 :KGTK 1r3cA 118 :KCQK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1r3cA 122 :LTDDHVQFLIYQILRGLKYIHSAD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLA 1r3cA 146 :IIHRDLKPSNLAVNEDSELKILDFGLA T0292 165 :NHDTSFAKAFVGTPYYMSPEQMNR 1r3cA 173 :RHTDDEMTGYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1r3cA 198 :MHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILR T0292 229 :GKFRRIPYR 1r3cA 260 :QSLTQMPKM T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1r3cA 277 :ANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQY Number of specific fragments extracted= 10 number of extra gaps= 0 total=1369 Number of alignments=127 # 1r3cA read from 1r3cA/merged-good-all-a2m # found chain 1r3cA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRII 1r3cA 22 :ERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFT T0292 74 :DRTN 1r3cA 95 :SLEE T0292 78 :TTLYIVMEYCEG 1r3cA 100 :NDVYLVTHLMGA T0292 91 :DLASVITKGT 1r3cA 112 :DLNNIVKCQK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1r3cA 122 :LTDDHVQFLIYQILRGLKYIHSAD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLA 1r3cA 146 :IIHRDLKPSNLAVNEDSELKILDFGLA T0292 165 :NHDTSFAKAFVGTPYYMSPEQMNR 1r3cA 173 :RHTDDEMTGYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTA 1r3cA 198 :MHYNQTVDIWSVGCIMAELLTGRTLFPG T0292 217 :FSQKELAGKIREGKFRRIPYR 1r3cA 250 :ISSESARNYIQSLTQMPKMNF T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1r3cA 277 :ANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYH Number of specific fragments extracted= 10 number of extra gaps= 0 total=1379 Number of alignments=128 # 1r3cA read from 1r3cA/merged-good-all-a2m # found chain 1r3cA in template set T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIID 1r3cA 22 :ERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTP T0292 75 :RTNTTLYIVMEYCEG 1r3cA 97 :EEFNDVYLVTHLMGA T0292 91 :DLASVITK 1r3cA 112 :DLNNIVKC T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 1r3cA 120 :QKLTDDHVQFLIYQILRGLKYIHSA T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGL 1r3cA 145 :DIIHRDLKPSNLAVNEDSELKILDFGL T0292 164 :LNHDTSFAKAFVGTPYYMSPEQMNR 1r3cA 172 :ARHTDDEMTGYVATRWYRAPEIMLN T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1r3cA 198 :MHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 1r3cA 273 :VFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDD Number of specific fragments extracted= 8 number of extra gaps= 0 total=1387 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1omwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1omwA expands to /projects/compbio/data/pdb/1omw.pdb.gz 1omwA:# T0292 read from 1omwA/merged-good-all-a2m # 1omwA read from 1omwA/merged-good-all-a2m # adding 1omwA to template set # found chain 1omwA in template set Warning: unaligning (T0292)Y6 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)S192 Warning: unaligning (T0292)E7 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)S192 Warning: unaligning (T0292)G18 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)E204 Warning: unaligning (T0292)R19 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)E204 Warning: unaligning (T0292)S27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1omwA)T213 Warning: unaligning (T0292)D28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1omwA)T213 T0292 2 :RAED 1omwA 187 :TMND T0292 8 :VLYTIGTGSY 1omwA 193 :VHRIIGRGGF T0292 20 :CQKIRRK 1omwA 205 :VYGCRKA T0292 29 :GKILVWKELDYGSMTEAE 1omwA 214 :GKMYAMKCLDKKRIKMKQ T0292 47 :KQMLVSEVNLLREL 1omwA 233 :ETLALNERIMLSLV T0292 61 :KHPNIVRYYDRI 1omwA 250 :DCPFIVCMSYAF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1omwA 262 :HTPDKLSFILDLMNGGDLHYHLSQHGV T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1omwA 289 :FSEADMRFYAAEIILGLEHMHNRF T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNH 1omwA 313 :VVYRDLKPANILLDEHGHVRISDLGLACDFSK T0292 169 :SFAKAFVGTPYYMSPEQMNR 1omwA 345 :KKPHASVGTHGYMAPEVLQK T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPF 1omwA 366 :VAYDSSADWFSLGCMLFKLLRGHSPF T0292 215 :TAFSQKELAGKIREGKF 1omwA 395 :KTKDKHEIDRMTLTMAV T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRP 1omwA 412 :ELPDSFSPELRSLLEGLLQRDVNRRL T0292 260 :VEEILENPLILEH 1omwA 444 :AQEVKESPFFRSL Number of specific fragments extracted= 14 number of extra gaps= 3 total=1401 Number of alignments=130 # 1omwA read from 1omwA/merged-good-all-a2m # found chain 1omwA in template set Warning: unaligning (T0292)Y6 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)S192 Warning: unaligning (T0292)E7 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)S192 Warning: unaligning (T0292)G18 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)E204 Warning: unaligning (T0292)R19 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)E204 Warning: unaligning (T0292)S27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1omwA)T213 Warning: unaligning (T0292)D28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1omwA)T213 T0292 3 :AED 1omwA 188 :MND T0292 8 :VLYTIGTGSY 1omwA 193 :VHRIIGRGGF T0292 20 :CQKIRRK 1omwA 205 :VYGCRKA T0292 29 :GKILVWKELDYGSM 1omwA 214 :GKMYAMKCLDKKRI T0292 43 :TEAEKQMLVSEVNLLREL 1omwA 229 :MKQGETLALNERIMLSLV T0292 61 :KHPNIVRYYDRI 1omwA 250 :DCPFIVCMSYAF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1omwA 262 :HTPDKLSFILDLMNGGDLHYHLSQHGV T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1omwA 289 :FSEADMRFYAAEIILGLEHMHNRF T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNH 1omwA 313 :VVYRDLKPANILLDEHGHVRISDLGLACDFSK T0292 169 :SFAKAFVGTPYYMSPEQM 1omwA 345 :KKPHASVGTHGYMAPEVL T0292 187 :NRMSYNEKSDIWSLGCLLYELCALMPPFTA 1omwA 364 :KGVAYDSSADWFSLGCMLFKLLRGHSPFRQ T0292 217 :FSQKELAGKIREGKFR 1omwA 397 :KDKHEIDRMTLTMAVE T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1omwA 413 :LPDSFSPELRSLLEGLLQRDVNRRL T0292 259 :SVEEILENPLILEHH 1omwA 443 :GAQEVKESPFFRSLD Number of specific fragments extracted= 14 number of extra gaps= 3 total=1415 Number of alignments=131 # 1omwA read from 1omwA/merged-good-all-a2m # found chain 1omwA in template set Warning: unaligning (T0292)Y6 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)S192 Warning: unaligning (T0292)E7 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)S192 Warning: unaligning (T0292)G18 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)E204 Warning: unaligning (T0292)R19 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)E204 Warning: unaligning (T0292)S27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1omwA)T213 Warning: unaligning (T0292)D28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1omwA)T213 T0292 2 :RAED 1omwA 187 :TMND T0292 8 :VLYTIGTGSY 1omwA 193 :VHRIIGRGGF T0292 20 :CQKIRRK 1omwA 205 :VYGCRKA T0292 29 :GKILVWKELDYGSM 1omwA 214 :GKMYAMKCLDKKRI T0292 43 :TEAEKQMLVSEVNLLREL 1omwA 229 :MKQGETLALNERIMLSLV T0292 61 :KHPNIVRYYDRIIDRTN 1omwA 250 :DCPFIVCMSYAFHTPDK T0292 80 :LYIVMEYCEGGDLASVITK 1omwA 267 :LSFILDLMNGGDLHYHLSQ T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1omwA 286 :HGVFSEADMRFYAAEIILGLEHMHNR T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 1omwA 312 :FVVYRDLKPANILLDEHGHVRISDLGLACDFSKK T0292 170 :FAKAFVGTPYYMSPEQMNR 1omwA 346 :KPHASVGTHGYMAPEVLQK T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFT 1omwA 366 :VAYDSSADWFSLGCMLFKLLRGHSPFR T0292 216 :AFSQKELAGKIREGKFR 1omwA 396 :TKDKHEIDRMTLTMAVE T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1omwA 413 :LPDSFSPELRSLLEGLLQRDVNRRL T0292 259 :SVEEILENPLILEH 1omwA 443 :GAQEVKESPFFRSL Number of specific fragments extracted= 14 number of extra gaps= 3 total=1429 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o6yA expands to /projects/compbio/data/pdb/1o6y.pdb.gz 1o6yA:# T0292 read from 1o6yA/merged-good-all-a2m # 1o6yA read from 1o6yA/merged-good-all-a2m # adding 1o6yA to template set # found chain 1o6yA in template set Warning: unaligning (T0292)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)A180 Warning: unaligning (T0292)N165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6yA)A180 Warning: unaligning (T0292)G224 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6yA)Q227 Warning: unaligning (T0292)K225 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6yA)Q227 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAE 1o6yA 9 :DRYELGEILGFGGMSEVHLARDLRLHRDVAVKVLRADLARDPS T0292 47 :KQMLVSEVNLLRELKHPNIVRYYDRII 1o6yA 53 :YLRFRREAQNAAALNHPAIVAVYDTGE T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1o6yA 83 :PAGPLPYIVMEYVDGVTLRDIVHTEGP T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1o6yA 110 :MTPKRAIEVIADACQALNFSHQNG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARI 1o6yA 134 :IIHRDVKPANIMISATNAVKVMDFGIARA T0292 179 :YYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELA 1o6yA 181 :QYLSPEQARGDSVDARSDVYSLGCVLYEVLTGEPPFTGDSPVSVA T0292 226 :IREGKFRRIP 1o6yA 228 :HVREDPIPPS T0292 236 :YRYSDELNEIITRMLNLKDYHRPS 1o6yA 241 :EGLSADLDAVVLKALAKNPENRYQ T0292 260 :VEEILEN 1o6yA 266 :AAEMRAD Number of specific fragments extracted= 9 number of extra gaps= 2 total=1438 Number of alignments=133 # 1o6yA read from 1o6yA/merged-good-all-a2m # found chain 1o6yA in template set Warning: unaligning (T0292)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)A180 Warning: unaligning (T0292)N165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6yA)A180 Warning: unaligning (T0292)G224 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6yA)Q227 Warning: unaligning (T0292)K225 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6yA)Q227 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1o6yA 9 :DRYELGEILGFGGMSEVHLARDLRLHRDVAVKVLRADLA T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRII 1o6yA 49 :DPSFYLRFRREAQNAAALNHPAIVAVYDTGE T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1o6yA 83 :PAGPLPYIVMEYVDGVTLRDIVHTEGP T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1o6yA 110 :MTPKRAIEVIADACQALNFSHQNG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARI 1o6yA 134 :IIHRDVKPANIMISATNAVKVMDFGIARA T0292 179 :YYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELA 1o6yA 181 :QYLSPEQARGDSVDARSDVYSLGCVLYEVLTGEPPFTGDSPVSVA T0292 226 :IREGKFRRIPYR 1o6yA 228 :HVREDPIPPSAR T0292 238 :YSDELNEIITRMLNLKDYHRP 1o6yA 243 :LSADLDAVVLKALAKNPENRY T0292 259 :SVEEILENPL 1o6yA 265 :TAAEMRADLV Number of specific fragments extracted= 9 number of extra gaps= 2 total=1447 Number of alignments=134 # 1o6yA read from 1o6yA/merged-good-all-a2m # found chain 1o6yA in template set Warning: unaligning (T0292)L164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)A180 Warning: unaligning (T0292)N165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6yA)A180 Warning: unaligning (T0292)G224 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6yA)Q227 Warning: unaligning (T0292)K225 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6yA)Q227 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1o6yA 9 :DRYELGEILGFGGMSEVHLARDLRLHRDVAVKVLRADLA T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIID 1o6yA 49 :DPSFYLRFRREAQNAAALNHPAIVAVYDTGEA T0292 75 :RTNTTLYIVMEYCEGGDLASVITK 1o6yA 83 :PAGPLPYIVMEYVDGVTLRDIVHT T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1o6yA 107 :EGPMTPKRAIEVIADACQALNFSHQN T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARI 1o6yA 133 :GIIHRDVKPANIMISATNAVKVMDFGIARA T0292 179 :YYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELA 1o6yA 181 :QYLSPEQARGDSVDARSDVYSLGCVLYEVLTGEPPFTGDSPVSVA T0292 226 :IREGKFRR 1o6yA 228 :HVREDPIP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPS 1o6yA 239 :RHEGLSADLDAVVLKALAKNPENRYQ T0292 260 :VEEILEN 1o6yA 266 :AAEMRAD Number of specific fragments extracted= 9 number of extra gaps= 2 total=1456 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cdkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cdkA expands to /projects/compbio/data/pdb/1cdk.pdb.gz 1cdkA:# T0292 read from 1cdkA/merged-good-all-a2m # 1cdkA read from 1cdkA/merged-good-all-a2m # adding 1cdkA to template set # found chain 1cdkA in template set Warning: unaligning (T0292)A93 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)S130 Warning: unaligning (T0292)S94 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)S130 Warning: unaligning (T0292)V95 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)H131 Warning: unaligning (T0292)R138 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)D166 Warning: unaligning (T0292)D139 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)D166 Warning: unaligning (T0292)L164 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K192 Warning: unaligning (T0292)N165 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)K192 Warning: unaligning (T0292)P178 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)E203 Warning: unaligning (T0292)Y179 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)E203 Warning: unaligning (T0292)Q219 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)I244 Warning: unaligning (T0292)K220 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)I244 Warning: unaligning (T0292)L250 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)Q274 Warning: unaligning (T0292)N251 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)Q274 Warning: unaligning (T0292)D254 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)T278 Warning: unaligning (T0292)Y255 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)T278 Warning: unaligning (T0292)V260 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)V288 Warning: unaligning (T0292)N266 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K295 Warning: unaligning (T0292)P267 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)K295 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTE 1cdkA 39 :HLDQFERIKTLGTGSFGRVMLVKHKETGNHFAMKILDKQKVVK T0292 45 :AEKQMLVSEVNLLRELKHPNIVRYYDRI 1cdkA 83 :KQIEHTLNEKRILQAVNFPFLVKLEYSF T0292 75 :RTNTTLYIVMEYCEGGDL 1cdkA 111 :KDNSNLYMVMEYVPGGEM T0292 96 :ITKGTK 1cdkA 132 :LRRIGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1cdkA 138 :FSEPHARFYAAQIVLTFEYLHSLD T0292 135 :VLH 1cdkA 162 :LIY T0292 140 :LKPANVFLDGKQNVKLGDFGLARI 1cdkA 167 :LKPENLLIDQQGYIQVTDFGFAKR T0292 169 :SFAKAFVGT 1cdkA 193 :GRTWTLCGT T0292 180 :YMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFS 1cdkA 204 :YLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQ T0292 221 :ELAGKIREGKF 1cdkA 245 :QIYEKIVSGKV T0292 233 :RIPYRYSDELNEIITRM 1cdkA 256 :RFPSHFSSDLKDLLRNL T0292 252 :LK 1cdkA 275 :VD T0292 256 :HRP 1cdkA 279 :KRF T0292 261 :EEILE 1cdkA 289 :NDIKN T0292 268 :LILEH 1cdkA 296 :WFATT Number of specific fragments extracted= 15 number of extra gaps= 9 total=1471 Number of alignments=136 # 1cdkA read from 1cdkA/merged-good-all-a2m # found chain 1cdkA in template set Warning: unaligning (T0292)A93 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)S130 Warning: unaligning (T0292)S94 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)S130 Warning: unaligning (T0292)V95 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)H131 Warning: unaligning (T0292)R138 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)D166 Warning: unaligning (T0292)D139 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)D166 Warning: unaligning (T0292)L164 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K192 Warning: unaligning (T0292)N165 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)K192 Warning: unaligning (T0292)P178 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)E203 Warning: unaligning (T0292)Y179 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)E203 Warning: unaligning (T0292)Q219 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)I244 Warning: unaligning (T0292)K220 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)I244 Warning: unaligning (T0292)L250 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)Q274 Warning: unaligning (T0292)N251 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)Q274 Warning: unaligning (T0292)D254 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)T278 Warning: unaligning (T0292)Y255 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)T278 Warning: unaligning (T0292)S259 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)V288 Warning: unaligning (T0292)V260 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)V288 Warning: unaligning (T0292)N266 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K295 Warning: unaligning (T0292)P267 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)K295 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1cdkA 39 :HLDQFERIKTLGTGSFGRVMLVKHKETGNHFAMKILDKQKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1cdkA 81 :KLKQIEHTLNEKRILQAVNFPFLVKLEYSF T0292 75 :RTNTTLYIVMEYCEGGDL 1cdkA 111 :KDNSNLYMVMEYVPGGEM T0292 96 :ITKGTK 1cdkA 132 :LRRIGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1cdkA 138 :FSEPHARFYAAQIVLTFEYLHSLD T0292 135 :VLH 1cdkA 162 :LIY T0292 140 :LKPANVFLDGKQNVKLGDFGLARI 1cdkA 167 :LKPENLLIDQQGYIQVTDFGFAKR T0292 169 :SFAKAFVGT 1cdkA 193 :GRTWTLCGT T0292 180 :YMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFS 1cdkA 204 :YLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQ T0292 221 :ELAGKIREGKFR 1cdkA 245 :QIYEKIVSGKVR T0292 234 :IPYRYSDELNEIITRM 1cdkA 257 :FPSHFSSDLKDLLRNL T0292 252 :LK 1cdkA 275 :VD T0292 256 :HRP 1cdkA 279 :KRF T0292 261 :EEILE 1cdkA 289 :NDIKN T0292 268 :LILEHH 1cdkA 296 :WFATTD Number of specific fragments extracted= 15 number of extra gaps= 9 total=1486 Number of alignments=137 # 1cdkA read from 1cdkA/merged-good-all-a2m # found chain 1cdkA in template set Warning: unaligning (T0292)A93 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)S130 Warning: unaligning (T0292)S94 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)S130 Warning: unaligning (T0292)V95 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)H131 Warning: unaligning (T0292)R138 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)D166 Warning: unaligning (T0292)D139 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)D166 Warning: unaligning (T0292)L164 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K192 Warning: unaligning (T0292)N165 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)K192 Warning: unaligning (T0292)P178 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)E203 Warning: unaligning (T0292)Y179 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)E203 Warning: unaligning (T0292)Q219 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)I244 Warning: unaligning (T0292)K220 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)I244 Warning: unaligning (T0292)L250 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)Q274 Warning: unaligning (T0292)N251 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)Q274 Warning: unaligning (T0292)D254 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)T278 Warning: unaligning (T0292)Y255 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)T278 Warning: unaligning (T0292)N266 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K295 Warning: unaligning (T0292)P267 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)K295 T0292 1 :SRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1cdkA 38 :AHLDQFERIKTLGTGSFGRVMLVKHKETGNHFAMKILDKQKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1cdkA 81 :KLKQIEHTLNEKRILQAVNFPFLVKLEYSFKDNSN T0292 80 :LYIVMEYCEGGDL 1cdkA 116 :LYMVMEYVPGGEM T0292 96 :ITK 1cdkA 132 :LRR T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1cdkA 135 :IGRFSEPHARFYAAQIVLTFEYLHSL T0292 134 :TVLH 1cdkA 161 :DLIY T0292 140 :LKPANVFLDGKQNVKLGDFGLARI 1cdkA 167 :LKPENLLIDQQGYIQVTDFGFAKR T0292 166 :HD 1cdkA 193 :GR T0292 171 :AKAFVGT 1cdkA 195 :TWTLCGT T0292 180 :YMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFS 1cdkA 204 :YLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQ T0292 221 :ELAGKIREGKFR 1cdkA 245 :QIYEKIVSGKVR T0292 234 :IPYRYSDELNEIITRM 1cdkA 257 :FPSHFSSDLKDLLRNL T0292 252 :LK 1cdkA 275 :VD T0292 256 :HRP 1cdkA 279 :KRF T0292 261 :EEILE 1cdkA 289 :NDIKN T0292 268 :LILEHH 1cdkA 296 :WFATTD Number of specific fragments extracted= 16 number of extra gaps= 8 total=1502 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q8uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1q8uA expands to /projects/compbio/data/pdb/1q8u.pdb.gz 1q8uA:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 1579, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 1581, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 1583, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 1585, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 1587, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 1589, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 1q8uA Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 1q8uA Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0292 read from 1q8uA/merged-good-all-a2m # 1q8uA read from 1q8uA/merged-good-all-a2m # adding 1q8uA to template set # found chain 1q8uA in template set Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1q8uA)L198 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1q8uA)L198 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTE 1q8uA 39 :HLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKVVK T0292 45 :AEKQMLVSEVNLLRELKHPNIVRYYDRI 1q8uA 83 :KQIEHTLNEKRILQAVNFPFLVKLEFSF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1q8uA 111 :KDNSNLYMVMEYVPGGEMFSHLRRIGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1q8uA 138 :FSEPHARFYAAQIVLTFEYLHSLD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILN 1q8uA 162 :LIYRDLKPENLLIDQQGYIQVTDFGFAKRVK T0292 169 :SFA 1q8uA 193 :GRT T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKF 1q8uA 199 :CGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKV T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRP 1q8uA 256 :RFPSHFSSDLKDLLRNLLQVDLTKRF T0292 260 :VEEILENPLILEH 1q8uA 288 :VNDIKNHKWFATT Number of specific fragments extracted= 9 number of extra gaps= 0 total=1511 Number of alignments=139 # 1q8uA read from 1q8uA/merged-good-all-a2m # found chain 1q8uA in template set Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1q8uA)L198 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1q8uA)L198 T0292 2 :RAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1q8uA 39 :HLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1q8uA 81 :KLKQIEHTLNEKRILQAVNFPFLVKLEFSF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1q8uA 111 :KDNSNLYMVMEYVPGGEMFSHLRRIGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1q8uA 138 :FSEPHARFYAAQIVLTFEYLHSLD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILN 1q8uA 162 :LIYRDLKPENLLIDQQGYIQVTDFGFAKRVK T0292 169 :SFA 1q8uA 193 :GRT T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1q8uA 199 :CGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1q8uA 257 :FPSHFSSDLKDLLRNLLQVDLTKRF T0292 259 :SVEEILENPLILEHH 1q8uA 287 :GVNDIKNHKWFATTD Number of specific fragments extracted= 9 number of extra gaps= 0 total=1520 Number of alignments=140 # 1q8uA read from 1q8uA/merged-good-all-a2m # found chain 1q8uA in template set Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1q8uA)L198 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1q8uA)L198 T0292 1 :SRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1q8uA 38 :AHLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1q8uA 81 :KLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSN T0292 80 :LYIVMEYCEGGDLASVITK 1q8uA 116 :LYMVMEYVPGGEMFSHLRR T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1q8uA 135 :IGRFSEPHARFYAAQIVLTFEYLHSL T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 1q8uA 161 :DLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGR T0292 171 :A 1q8uA 195 :T T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1q8uA 199 :CGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1q8uA 257 :FPSHFSSDLKDLLRNLLQVDLTKRF T0292 261 :EEILENPLILEH 1q8uA 289 :NDIKNHKWFATT Number of specific fragments extracted= 9 number of extra gaps= 0 total=1529 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zzlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zzlA expands to /projects/compbio/data/pdb/1zzl.pdb.gz 1zzlA:# T0292 read from 1zzlA/merged-good-all-a2m # 1zzlA read from 1zzlA/merged-good-all-a2m # adding 1zzlA to template set # found chain 1zzlA in template set Warning: unaligning (T0292)K30 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)R49 Warning: unaligning (T0292)I31 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)R49 Warning: unaligning (T0292)S94 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)I116 Warning: unaligning (T0292)V95 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)I116 Warning: unaligning (T0292)L164 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zzlA)D176 Warning: unaligning (T0292)N165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zzlA)D176 Warning: unaligning (T0292)H166 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)E178 Warning: unaligning (T0292)D167 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)E178 Warning: unaligning (T0292)N192 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)Q202 Warning: unaligning (T0292)E193 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)Q202 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDG 1zzlA 22 :ERYQNLSPVGSGAYGSVCAAFDTKTG T0292 32 :LVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1zzlA 50 :VAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARS T0292 78 :TTLYIVMEYCEG 1zzlA 100 :NDVYLVTHLMGA T0292 91 :DLA 1zzlA 112 :DLN T0292 96 :I 1zzlA 117 :V T0292 98 :KGTK 1zzlA 118 :KCQK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1zzlA 122 :LTDDHVQFLIYQILRGLKYIHSAD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARI 1zzlA 146 :IIHRDLKPSNLAVNEDCELKILDFGLARH T0292 168 :TSFA 1zzlA 179 :MTGY T0292 175 :VGTPYYMSPEQMNR 1zzlA 183 :VATRWYRAPEIMLN T0292 189 :MSY 1zzlA 198 :MHY T0292 194 :KSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1zzlA 203 :TVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILR T0292 230 :KFRRIPYR 1zzlA 261 :SLTQMPKM T0292 239 :SDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1zzlA 278 :NPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQY Number of specific fragments extracted= 14 number of extra gaps= 4 total=1543 Number of alignments=142 # 1zzlA read from 1zzlA/merged-good-all-a2m # found chain 1zzlA in template set Warning: unaligning (T0292)K30 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)R49 Warning: unaligning (T0292)I31 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)R49 Warning: unaligning (T0292)S94 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)I116 Warning: unaligning (T0292)V95 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)I116 Warning: unaligning (T0292)D167 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zzlA)D176 Warning: unaligning (T0292)T168 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zzlA)D176 Warning: unaligning (T0292)S169 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)E178 Warning: unaligning (T0292)F170 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)E178 Warning: unaligning (T0292)N192 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)Q202 Warning: unaligning (T0292)E193 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)Q202 Warning: unaligning (T0292)G229 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)V239 Warning: unaligning (T0292)K230 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)V239 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDG 1zzlA 22 :ERYQNLSPVGSGAYGSVCAAFDTKTG T0292 32 :LVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRII 1zzlA 50 :VAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFT T0292 74 :DRTN 1zzlA 95 :SLEE T0292 78 :TTLYIVMEYCEG 1zzlA 100 :NDVYLVTHLMGA T0292 91 :DLA 1zzlA 112 :DLN T0292 96 :ITKGT 1zzlA 117 :VKCQK T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1zzlA 122 :LTDDHVQFLIYQILRGLKYIHSAD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARI 1zzlA 146 :IIHRDLKPSNLAVNEDCELKILDFGLARH T0292 171 :AKAFVGTPYYMSPEQMNR 1zzlA 179 :MTGYVATRWYRAPEIMLN T0292 189 :MSY 1zzlA 198 :MHY T0292 194 :KSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1zzlA 203 :TVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILR T0292 231 :FRRI 1zzlA 240 :GTPG T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1zzlA 277 :ANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYH Number of specific fragments extracted= 13 number of extra gaps= 5 total=1556 Number of alignments=143 # 1zzlA read from 1zzlA/merged-good-all-a2m # found chain 1zzlA in template set Warning: unaligning (T0292)K30 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)R49 Warning: unaligning (T0292)I31 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)R49 Warning: unaligning (T0292)S94 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)I116 Warning: unaligning (T0292)V95 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)I116 Warning: unaligning (T0292)L164 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zzlA)D176 Warning: unaligning (T0292)N165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zzlA)D176 Warning: unaligning (T0292)H166 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)E178 Warning: unaligning (T0292)D167 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)E178 Warning: unaligning (T0292)N192 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)Q202 Warning: unaligning (T0292)E193 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)Q202 Warning: unaligning (T0292)G229 because of BadResidue code BAD_PEPTIDE in next template residue (1zzlA)V239 Warning: unaligning (T0292)K230 because of BadResidue code BAD_PEPTIDE at template residue (1zzlA)V239 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDG 1zzlA 22 :ERYQNLSPVGSGAYGSVCAAFDTKTG T0292 32 :LVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIID 1zzlA 50 :VAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTP T0292 75 :RTNTTLYIVMEYCEG 1zzlA 97 :EEFNDVYLVTHLMGA T0292 91 :DLA 1zzlA 112 :DLN T0292 96 :ITK 1zzlA 117 :VKC T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 1zzlA 120 :QKLTDDHVQFLIYQILRGLKYIHSA T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARI 1zzlA 145 :DIIHRDLKPSNLAVNEDCELKILDFGLARH T0292 171 :AKAFVGTPYYMSPEQMNR 1zzlA 179 :MTGYVATRWYRAPEIMLN T0292 189 :MSY 1zzlA 198 :MHY T0292 194 :KSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1zzlA 203 :TVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILR T0292 231 :FRR 1zzlA 240 :GTP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 1zzlA 273 :VFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDD Number of specific fragments extracted= 12 number of extra gaps= 5 total=1568 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j1bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0292 read from 1j1bA/merged-good-all-a2m # 1j1bA read from 1j1bA/merged-good-all-a2m # found chain 1j1bA in training set T0292 6 :YEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTE 1j1bA 56 :YTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFK T0292 52 :SEVNLLRELKHPNIVRYYDRII 1j1bA 96 :RELQIMRKLDHCNIVRLRYFFY T0292 74 :DRTNTTLYIVMEYCE 1j1bA 122 :KKDEVYLNLVLDYVP T0292 90 :GDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRS 1j1bA 137 :ETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFG T0292 135 :VLHRDLKPANVFLDGK 1j1bA 177 :ICHRDIKPQNLLLDPD T0292 151 :QNVKLGDFGLARILNHD 1j1bA 194 :AVLKLCDFGSAKQLVRG T0292 169 :SFAKAFVGTPYYMSPEQMNR 1j1bA 211 :EPNVSYICSRYYRAPELIFG T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1j1bA 232 :TDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIK T0292 229 :GKFRRI 1j1bA 291 :FKFPQI T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1j1bA 307 :PRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1578 Number of alignments=145 # 1j1bA read from 1j1bA/merged-good-all-a2m # found chain 1j1bA in training set T0292 1 :SRAED 1j1bA 49 :DRPQE T0292 6 :YEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1j1bA 56 :YTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKR T0292 52 :SEVNLLRELKHPNIVRYYDRIID 1j1bA 96 :RELQIMRKLDHCNIVRLRYFFYS T0292 75 :RTNTT 1j1bA 121 :EKKDE T0292 80 :LYIVMEYCEG 1j1bA 128 :LNLVLDYVPE T0292 91 :DLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRS 1j1bA 138 :TVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFG T0292 135 :VLHRDLKPANVFLDGKQ 1j1bA 177 :ICHRDIKPQNLLLDPDT T0292 152 :NVKLGDFGLARILNHD 1j1bA 195 :VLKLCDFGSAKQLVRG T0292 169 :SFAKAFVGTPYYMSPEQMNR 1j1bA 211 :EPNVSYICSRYYRAPELIFG T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIRE 1j1bA 232 :TDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIK T0292 238 :YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1j1bA 309 :TPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELR Number of specific fragments extracted= 11 number of extra gaps= 0 total=1589 Number of alignments=146 # 1j1bA read from 1j1bA/merged-good-all-a2m # found chain 1j1bA in training set T0292 6 :YEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1j1bA 56 :YTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKR T0292 52 :SEVNLLRELKHPNIVRYYDRIID 1j1bA 96 :RELQIMRKLDHCNIVRLRYFFYS T0292 75 :RTNTTLYIVMEYCE 1j1bA 123 :KDEVYLNLVLDYVP T0292 90 :GDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRR 1j1bA 137 :ETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSF T0292 134 :TVLHRDLKPANVFLDGK 1j1bA 176 :GICHRDIKPQNLLLDPD T0292 151 :QNVKLGDFGLARILNHD 1j1bA 194 :AVLKLCDFGSAKQLVRG T0292 169 :SFAKAFVGTPYYMSPEQMNR 1j1bA 211 :EPNVSYICSRYYRAPELIFG T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1j1bA 232 :TDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTP T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 1j1bA 305 :FRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNV Number of specific fragments extracted= 9 number of extra gaps= 0 total=1598 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1phk/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1phk expands to /projects/compbio/data/pdb/1phk.pdb.gz 1phk:Warning: there is no chain 1phk will retry with 1phkA # T0292 read from 1phk/merged-good-all-a2m # 1phk read from 1phk/merged-good-all-a2m # adding 1phk to template set # found chain 1phk in template set T0292 3 :AEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 1phk 16 :YENYEPKEILGRGVSSVVRRCIHKPTCKEYAVKIIDV T0292 40 :GSMTEAE 1phk 56 :GSFSAEE T0292 47 :KQMLVSEVNLLREL 1phk 67 :REATLKEVDILRKV T0292 61 :KHPNIVRYYDRI 1phk 82 :GHPNIIQLKDTY T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1phk 94 :ETNTFFFLVFDLMKKGELFDYLTEKVT T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1phk 121 :LSEKETRKIMRALLEVICALHKLN T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 1phk 145 :IVHRDLKPENILLDDDMNIKLTDFGFSCQLDPG T0292 169 :SFAKAFVGTPYYMSPEQMN 1phk 178 :EKLREVCGTPSYLAPEIIE T0292 188 :RMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRY 1phk 203 :HPGYGKEVDMWSTGVIMYTLLAGSPPFWHRKQMLMLRMIMSGNYQFGSPEW T0292 239 :SDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1phk 257 :SDTVKDLVSRFLVVQPQKRYTAEEALAHPFFQQY Number of specific fragments extracted= 10 number of extra gaps= 0 total=1608 Number of alignments=148 # 1phk read from 1phk/merged-good-all-a2m # found chain 1phk in template set Warning: unaligning (T0292)H273 because last residue in template chain is (1phk)V291 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 1phk 17 :ENYEPKEILGRGVSSVVRRCIHKPTCKEYAVKIIDV T0292 40 :GSMTEAEKQM 1phk 56 :GSFSAEEVQE T0292 50 :LVSEVNLLREL 1phk 70 :TLKEVDILRKV T0292 61 :KHPNIVRYYDRI 1phk 82 :GHPNIIQLKDTY T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1phk 94 :ETNTFFFLVFDLMKKGELFDYLTEKVT T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1phk 121 :LSEKETRKIMRALLEVICALHKLN T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 1phk 145 :IVHRDLKPENILLDDDMNIKLTDFGFSCQLDPG T0292 169 :SFAKAFVGTPYYMSPEQM 1phk 178 :EKLREVCGTPSYLAPEII T0292 187 :NRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1phk 202 :NHPGYGKEVDMWSTGVIMYTLLAGSPPFWHRKQMLMLRMIMSGNYQ T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1phk 251 :PEWDDYSDTVKDLVSRFLVVQPQKRYTAEEALAHPFFQQY Number of specific fragments extracted= 10 number of extra gaps= 0 total=1618 Number of alignments=149 # 1phk read from 1phk/merged-good-all-a2m # found chain 1phk in template set Warning: unaligning (T0292)H273 because last residue in template chain is (1phk)V291 T0292 3 :AEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 1phk 16 :YENYEPKEILGRGVSSVVRRCIHKPTCKEYAVKIIDV T0292 40 :GSMTEA 1phk 56 :GSFSAE T0292 46 :EKQMLVSEVNLLREL 1phk 66 :LREATLKEVDILRKV T0292 61 :KHPNIVRYYDRIIDRTN 1phk 82 :GHPNIIQLKDTYETNTF T0292 80 :LYIVMEYCEGGDLASVITK 1phk 99 :FFLVFDLMKKGELFDYLTE T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1phk 118 :KVTLSEKETRKIMRALLEVICALHKL T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHD 1phk 144 :NIVHRDLKPENILLDDDMNIKLTDFGFSCQLDPG T0292 169 :SFAKAFVGTPYYMSPEQMN 1phk 178 :EKLREVCGTPSYLAPEIIE T0292 189 :MSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1phk 204 :PGYGKEVDMWSTGVIMYTLLAGSPPFWHRKQMLMLRMIMSGNYQF T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEH 1phk 252 :EWDDYSDTVKDLVSRFLVVQPQKRYTAEEALAHPFFQQY Number of specific fragments extracted= 10 number of extra gaps= 0 total=1628 Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c30A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c30A expands to /projects/compbio/data/pdb/2c30.pdb.gz 2c30A:Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 699, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 701, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 904, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 906, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 908, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1238, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1240, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1242, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1244, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1246, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1248, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1278, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1280, because occupancy 0.350 <= existing 0.650 in 2c30A Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Skipped atom 1523, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1525, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1533, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1535, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1537, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1539, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1541, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1762, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1764, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1820, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1822, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1824, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1826, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1828, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1955, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1957, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1959, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 2309, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 2311, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 2313, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 2315, because occupancy 0.500 <= existing 0.500 in 2c30A # T0292 read from 2c30A/merged-good-all-a2m # 2c30A read from 2c30A/merged-good-all-a2m # adding 2c30A to template set # found chain 2c30A in template set Warning: unaligning (T0292)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)L423 Warning: unaligning (T0292)K22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)L423 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c30A)L561 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c30A)L561 Warning: unaligning (T0292)E228 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)S616 Warning: unaligning (T0292)G229 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)S616 Warning: unaligning (T0292)R237 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2c30A)V627 Warning: unaligning (T0292)Y238 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2c30A)V627 T0292 6 :YEVLYTIGTGSYGRC 2c30A 407 :LDSYVKIGEGSTGIV T0292 23 :IRRKSDGKILVWKELDYGSMTEAE 2c30A 424 :AREKHSGRQVAVKMMDLRKQQRRE T0292 49 :MLVSEVNLLRELKHPNIVRYYDRI 2c30A 448 :LLFNEVVIMRDYQHFNVVEMYKSY T0292 75 :RTNTTLYIVMEYCEGGDLASVITKG 2c30A 472 :LVGEELWVLMEFLQGGALTDIVSQV T0292 101 :K 2c30A 497 :R T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2c30A 498 :LNEEQIATVCEAVLQALAYLHAQG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 2c30A 522 :VIHRDIKSDSILLTLDGRVKLSDFGFCAQISKDVPKR T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIR 2c30A 562 :VGTPYWMAPEVISRSLYATEVDIWSLGIMVIEMVDGEPPYFSDSPVQAMKRLR T0292 230 :KFRRI 2c30A 617 :PPPKL T0292 235 :PY 2c30A 624 :SH T0292 239 :SDELNEIITRMLNLKDYHRPSVEEILENPLILEHHH 2c30A 628 :SPVLRDFLERMLVRDPQERATAQELLDHPFLLQTGL Number of specific fragments extracted= 11 number of extra gaps= 3 total=1639 Number of alignments=151 # 2c30A read from 2c30A/merged-good-all-a2m # found chain 2c30A in template set Warning: unaligning (T0292)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)L423 Warning: unaligning (T0292)K22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)L423 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c30A)L561 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c30A)L561 Warning: unaligning (T0292)E228 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)S616 Warning: unaligning (T0292)G229 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)S616 Warning: unaligning (T0292)Y238 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2c30A)V627 T0292 6 :YEVLYTIGTGSYGRC 2c30A 407 :LDSYVKIGEGSTGIV T0292 23 :IRRKSDGKILVWKELDYGSMTEA 2c30A 424 :AREKHSGRQVAVKMMDLRKQQRR T0292 48 :QMLVSEVNLLRELKHPNIVRYYDRI 2c30A 447 :ELLFNEVVIMRDYQHFNVVEMYKSY T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGT 2c30A 472 :LVGEELWVLMEFLQGGALTDIVSQVR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2c30A 498 :LNEEQIATVCEAVLQALAYLHAQG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 2c30A 522 :VIHRDIKSDSILLTLDGRVKLSDFGFCAQISKDVPKR T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIR 2c30A 562 :VGTPYWMAPEVISRSLYATEVDIWSLGIMVIEMVDGEPPYFSDSPVQAMKRLR T0292 230 :KFRRIPYR 2c30A 617 :PPPKLKNS T0292 239 :SDELNEIITRMLNLKDYHRPSVEEILENPLILEHH 2c30A 628 :SPVLRDFLERMLVRDPQERATAQELLDHPFLLQTG Number of specific fragments extracted= 9 number of extra gaps= 3 total=1648 Number of alignments=152 # 2c30A read from 2c30A/merged-good-all-a2m # found chain 2c30A in template set Warning: unaligning (T0292)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)L423 Warning: unaligning (T0292)K22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)L423 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c30A)L561 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c30A)L561 Warning: unaligning (T0292)E228 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)S616 Warning: unaligning (T0292)G229 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)S616 Warning: unaligning (T0292)R237 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2c30A)V627 Warning: unaligning (T0292)Y238 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2c30A)V627 T0292 6 :YEVLYTIGTGSYGRC 2c30A 407 :LDSYVKIGEGSTGIV T0292 23 :IRRKSDGKILVWKELDYGSMTE 2c30A 424 :AREKHSGRQVAVKMMDLRKQQR T0292 47 :KQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 2c30A 446 :RELLFNEVVIMRDYQHFNVVEMYKSYLVGEE T0292 80 :LYIVMEYCEGGDLASVITK 2c30A 477 :LWVLMEFLQGGALTDIVSQ T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 2c30A 496 :VRLNEEQIATVCEAVLQALAYLHAQ T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 2c30A 521 :GVIHRDIKSDSILLTLDGRVKLSDFGFCAQISKDVPKR T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIR 2c30A 562 :VGTPYWMAPEVISRSLYATEVDIWSLGIMVIEMVDGEPPYFSDSPVQAMKRLR T0292 230 :KFRR 2c30A 617 :PPPK T0292 234 :IPY 2c30A 623 :NSH T0292 239 :SDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH 2c30A 628 :SPVLRDFLERMLVRDPQERATAQELLDHPFLLQTGLPE Number of specific fragments extracted= 10 number of extra gaps= 3 total=1658 Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jksA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0292 read from 1jksA/merged-good-all-a2m # 1jksA read from 1jksA/merged-good-all-a2m # found chain 1jksA in training set Warning: unaligning (T0292)K150 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1jksA)V152 Warning: unaligning (T0292)Q151 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jksA)V152 Warning: unaligning (T0292)E271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jksA)P291 T0292 2 :RAED 1jksA 8 :NVDD T0292 6 :YEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 1jksA 13 :YDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKK T0292 41 :SMTEA 1jksA 50 :KSSRR T0292 46 :EKQMLVSEVNLLRELKHPNIVRYYDRI 1jksA 57 :SREDIEREVSILKEIQHPNVITLHEVY T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1jksA 84 :ENKTDVILILELVAGGELFDFLAEKES T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1jksA 111 :LTEEEATEFLKQILNGVYYLHSLQ T0292 135 :VLHRDLKPANVFL 1jksA 135 :IAHFDLKPENIML T0292 148 :DG 1jksA 149 :DR T0292 153 :VKLGDFGLARILNHD 1jksA 157 :IKIIDFGLAHKIDFG T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIP 1jksA 172 :NEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFED T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLIL 1jksA 242 :SNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIK Number of specific fragments extracted= 11 number of extra gaps= 1 total=1669 Number of alignments=154 # 1jksA read from 1jksA/merged-good-all-a2m # found chain 1jksA in training set Warning: unaligning (T0292)K150 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1jksA)V152 Warning: unaligning (T0292)Q151 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jksA)V152 Warning: unaligning (T0292)E271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jksA)P291 T0292 1 :SRAED 1jksA 7 :ENVDD T0292 6 :YEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 1jksA 13 :YDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKK T0292 40 :GSMTEAE 1jksA 54 :RGVSRED T0292 50 :LVSEVNLLRELKHPNIVRYYDRI 1jksA 61 :IEREVSILKEIQHPNVITLHEVY T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1jksA 84 :ENKTDVILILELVAGGELFDFLAEKES T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1jksA 111 :LTEEEATEFLKQILNGVYYLHSLQ T0292 135 :VLHRDLKPANVFL 1jksA 135 :IAHFDLKPENIML T0292 148 :DG 1jksA 149 :DR T0292 152 :NVKLGDFGLARILNHD 1jksA 156 :RIKIIDFGLAHKIDFG T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIP 1jksA 172 :NEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFED T0292 236 :YRYSDELNEIITRMLNLKDYHRPSVEEILENPLIL 1jksA 242 :SNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIK Number of specific fragments extracted= 11 number of extra gaps= 1 total=1680 Number of alignments=155 # 1jksA read from 1jksA/merged-good-all-a2m # found chain 1jksA in training set Warning: unaligning (T0292)D148 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jksA)V152 Warning: unaligning (T0292)E271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jksA)P291 T0292 3 :AEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 1jksA 10 :DDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKK T0292 43 :TE 1jksA 57 :SR T0292 48 :QMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1jksA 59 :EDIEREVSILKEIQHPNVITLHEVYENKTD T0292 80 :LYIVMEYCEGGDLASVITK 1jksA 89 :VILILELVAGGELFDFLAE T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1jksA 108 :KESLTEEEATEFLKQILNGVYYLHSL T0292 134 :TVLHRDLKPANVFL 1jksA 134 :QIAHFDLKPENIML T0292 149 :GKQNVKLGDFGLARILNHD 1jksA 153 :PKPRIKIIDFGLAHKIDFG T0292 169 :SFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 1jksA 172 :NEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEF T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLIL 1jksA 240 :YFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIK Number of specific fragments extracted= 9 number of extra gaps= 1 total=1689 Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o6lA expands to /projects/compbio/data/pdb/1o6l.pdb.gz 1o6lA:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0292 read from 1o6lA/merged-good-all-a2m # 1o6lA read from 1o6lA/merged-good-all-a2m # adding 1o6lA to template set # found chain 1o6lA in template set Warning: unaligning (T0292)Y6 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6lA)D153 Warning: unaligning (T0292)E7 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6lA)D153 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6lA)F310 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6lA)F310 T0292 2 :RAED 1o6lA 148 :TMND T0292 8 :VLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTE 1o6lA 154 :YLKLLGKGTFGKVILVREKATGRYYAMKILRKEVIIA T0292 45 :AEKQMLVSEVNLLRELKHPNIVRYYDRI 1o6lA 192 :DEVAHTVTESRVLQNTRHPFLTALKYAF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1o6lA 220 :QTHDRLCFVMEYANGGELFFHLSRERV T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1o6lA 247 :FTEERARFYGAEIVSALEYLHSRD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 1o6lA 271 :VVYRDIKLENLMLDKDGHIKITDFGLCKEGISDGATM T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKF 1o6lA 311 :CGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHERLFELILMEEI T0292 233 :RIPYRYSDELNEIITRMLNLKDYHRPS 1o6lA 368 :RFPRTLSPEAKSLLAGLLKKDPKQRLG T0292 260 :VEEILENPLILEH 1o6lA 400 :AKEVMEHRFFLSI Number of specific fragments extracted= 9 number of extra gaps= 1 total=1698 Number of alignments=157 # 1o6lA read from 1o6lA/merged-good-all-a2m # found chain 1o6lA in template set Warning: unaligning (T0292)Y6 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6lA)D153 Warning: unaligning (T0292)E7 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6lA)D153 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6lA)F310 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6lA)F310 T0292 2 :RAED 1o6lA 148 :TMND T0292 8 :VLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1o6lA 154 :YLKLLGKGTFGKVILVREKATGRYYAMKILRKEVI T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRI 1o6lA 190 :AKDEVAHTVTESRVLQNTRHPFLTALKYAF T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGTK 1o6lA 220 :QTHDRLCFVMEYANGGELFFHLSRERV T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1o6lA 247 :FTEERARFYGAEIVSALEYLHSRD T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 1o6lA 271 :VVYRDIKLENLMLDKDGHIKITDFGLCKEGISDGATM T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1o6lA 311 :CGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHERLFELILMEEIR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1o6lA 369 :FPRTLSPEAKSLLAGLLKKDPKQRL T0292 260 :VEEILENPLILEHH 1o6lA 400 :AKEVMEHRFFLSIN T0292 274 :HH 1o6lA 421 :KL Number of specific fragments extracted= 10 number of extra gaps= 1 total=1708 Number of alignments=158 # 1o6lA read from 1o6lA/merged-good-all-a2m # found chain 1o6lA in template set Warning: unaligning (T0292)Y6 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6lA)D153 Warning: unaligning (T0292)E7 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6lA)D153 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6lA)F310 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6lA)F310 T0292 1 :SRAED 1o6lA 147 :VTMND T0292 8 :VLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1o6lA 154 :YLKLLGKGTFGKVILVREKATGRYYAMKILRKEVI T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1o6lA 190 :AKDEVAHTVTESRVLQNTRHPFLTALKYAFQTHDR T0292 80 :LYIVMEYCEGGDLASVITK 1o6lA 225 :LCFVMEYANGGELFFHLSR T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1o6lA 244 :ERVFTEERARFYGAEIVSALEYLHSR T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 1o6lA 270 :DVVYRDIKLENLMLDKDGHIKITDFGLCKEGISDGATM T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1o6lA 311 :CGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHERLFELILMEEIR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRP 1o6lA 369 :FPRTLSPEAKSLLAGLLKKDPKQRL T0292 260 :VEEILENPLILEHH 1o6lA 400 :AKEVMEHRFFLSIN Number of specific fragments extracted= 9 number of extra gaps= 1 total=1717 Number of alignments=159 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f57A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f57A expands to /projects/compbio/data/pdb/2f57.pdb.gz 2f57A:Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 2f57A Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2f57A Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2f57A Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Skipped atom 1969, because occupancy 0.500 <= existing 0.500 in 2f57A Skipped atom 1973, because occupancy 0.500 <= existing 0.500 in 2f57A Skipped atom 1975, because occupancy 0.500 <= existing 0.500 in 2f57A # T0292 read from 2f57A/merged-good-all-a2m # 2f57A read from 2f57A/merged-good-all-a2m # adding 2f57A to template set # found chain 2f57A in template set Warning: unaligning (T0292)G15 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2f57A)S459 Warning: unaligning (T0292)S16 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2f57A)S459 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f57A)L603 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f57A)L603 T0292 3 :AEDYEVLYTIGT 2f57A 446 :REYLANFIKIGE T0292 17 :YGRCQKIRRKSDGKILVWKELDYGSMT 2f57A 460 :TGIVCIATEKHTGKQVAVKKMDLRKQQ T0292 46 :EKQMLVSEVNLLRELKHPNIVRYYDRI 2f57A 487 :RRELLFNEVVIMRDYHHDNVVDMYSSY T0292 75 :RTNTTLYIVMEYCEGGDLAS 2f57A 514 :LVGDELWVVMEFLEGGALTD T0292 96 :ITKGTK 2f57A 534 :IVTHTR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2f57A 540 :MNEEQIATVCLSVLRALSYLHNQG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 2f57A 564 :VIHRDIKSDSILLTSDGRIKLSDFGFCAQVSKEVPKR T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRI 2f57A 604 :VGTPYWMAPEVISRLPYGTEVDIWSLGIMVIEMIDGEPPYFNEPPLQAMRRIRDSLPPRV T0292 235 :PYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHH 2f57A 666 :LHKVSSVLRGFLDLMLVREPSQRATAQELLGHPFLKLAGP Number of specific fragments extracted= 9 number of extra gaps= 1 total=1726 Number of alignments=160 # 2f57A read from 2f57A/merged-good-all-a2m # found chain 2f57A in template set Warning: unaligning (T0292)G15 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2f57A)S459 Warning: unaligning (T0292)S16 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2f57A)S459 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f57A)L603 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f57A)L603 T0292 2 :RAED 2f57A 444 :DPRE T0292 6 :YEVLYTIGT 2f57A 449 :LANFIKIGE T0292 17 :YGRCQKIRRKSDGKILVWKELDYGSMT 2f57A 460 :TGIVCIATEKHTGKQVAVKKMDLRKQQ T0292 46 :EKQMLVSEVNLLRELKHPNIVRYYDRI 2f57A 487 :RRELLFNEVVIMRDYHHDNVVDMYSSY T0292 75 :RTNTTLYIVMEYCEGGDLASVITKGT 2f57A 514 :LVGDELWVVMEFLEGGALTDIVTHTR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 2f57A 540 :MNEEQIATVCLSVLRALSYLHNQG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 2f57A 564 :VIHRDIKSDSILLTSDGRIKLSDFGFCAQVSKEVPKR T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRI 2f57A 604 :VGTPYWMAPEVISRLPYGTEVDIWSLGIMVIEMIDGEPPYFNEPPLQAMRRIRDSLPPRV T0292 235 :PYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHH 2f57A 666 :LHKVSSVLRGFLDLMLVREPSQRATAQELLGHPFLKLAGP Number of specific fragments extracted= 9 number of extra gaps= 1 total=1735 Number of alignments=161 # 2f57A read from 2f57A/merged-good-all-a2m # found chain 2f57A in template set Warning: unaligning (T0292)G15 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2f57A)S459 Warning: unaligning (T0292)S16 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2f57A)S459 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f57A)L603 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f57A)L603 T0292 2 :RAEDYEVLYTIGT 2f57A 445 :PREYLANFIKIGE T0292 17 :YGRCQKIRRKSDGKILVWKELDYGSM 2f57A 460 :TGIVCIATEKHTGKQVAVKKMDLRKQ T0292 47 :KQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 2f57A 488 :RELLFNEVVIMRDYHHDNVVDMYSSYLVGDE T0292 80 :LYIVMEYCEGGDLASVITK 2f57A 519 :LWVVMEFLEGGALTDIVTH T0292 104 :QYLDEEFVLRVMTQLTLALKECHRR 2f57A 538 :TRMNEEQIATVCLSVLRALSYLHNQ T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFA 2f57A 563 :GVIHRDIKSDSILLTSDGRIKLSDFGFCAQVSKEVPKR T0292 175 :VGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRR 2f57A 604 :VGTPYWMAPEVISRLPYGTEVDIWSLGIMVIEMIDGEPPYFNEPPLQAMRRIRDSLPPR T0292 234 :IPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHH 2f57A 665 :DLHKVSSVLRGFLDLMLVREPSQRATAQELLGHPFLKLAGPP Number of specific fragments extracted= 8 number of extra gaps= 1 total=1743 Number of alignments=162 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zy4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zy4A expands to /projects/compbio/data/pdb/1zy4.pdb.gz 1zy4A:# T0292 read from 1zy4A/merged-good-all-a2m # 1zy4A read from 1zy4A/merged-good-all-a2m # adding 1zy4A to template set # found chain 1zy4A in template set Warning: unaligning (T0292)H166 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zy4A)A888 Warning: unaligning (T0292)P178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zy4A)A888 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 1zy4A 597 :SDFEEIAVLGQGAFGQVVKARNALDSRYYAIKKIRH T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTN 1zy4A 633 :TEEKLSTILSEVMLLASLNHQYVVRYYAAWLERRN T0292 78 :TTLYIVMEYCEGGDLASVITKGTKE 1zy4A 782 :STLFIQMEYCENGTLYDLIHSENLN T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1zy4A 807 :QQRDEYWRLFRQILEALSYIHSQG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILN 1zy4A 831 :IIHRDLKPMNIFIDESRNVKIGDFGLAKNVH T0292 179 :YYMSPEQMNRM 1zy4A 889 :MYVATEVLDGT T0292 190 :SYNEKSDIWSLGCLLYELC 1zy4A 901 :HYNEKIDMYSLGIIFFEMI T0292 212 :PPFTA 1zy4A 920 :YPFST T0292 217 :FSQKELAGKIREGKFR 1zy4A 926 :MERVNILKKLRSVSIE T0292 234 :IPYRY 1zy4A 942 :FPPDF T0292 239 :SDELNEIITRMLNLKDYHRPSVEEILENPLILE 1zy4A 951 :MKVEKKIIRLLIDHDPNKRPGARTLLNSGWLPV Number of specific fragments extracted= 11 number of extra gaps= 0 total=1754 Number of alignments=163 # 1zy4A read from 1zy4A/merged-good-all-a2m # found chain 1zy4A in template set Warning: unaligning (T0292)P178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zy4A)A888 T0292 5 :DYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDY 1zy4A 598 :DFEEIAVLGQGAFGQVVKARNALDSRYYAIKKIRH T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDRIID 1zy4A 633 :TEEKLSTILSEVMLLASLNHQYVVRYYAAWLE T0292 76 :TNTTLYIVMEYCEGGDLASVITKGTKE 1zy4A 780 :KKSTLFIQMEYCENGTLYDLIHSENLN T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1zy4A 807 :QQRDEYWRLFRQILEALSYIHSQG T0292 135 :VLHRDLKPANVFLDGKQNVKLGDFGLARILN 1zy4A 831 :IIHRDLKPMNIFIDESRNVKIGDFGLAKNVH T0292 179 :YYMSPEQMNR 1zy4A 889 :MYVATEVLDG T0292 189 :MSYNEKSDIWSLGCLLYELCA 1zy4A 900 :GHYNEKIDMYSLGIIFFEMIY T0292 212 :PPFTAFSQKELAGKIREGKFR 1zy4A 921 :PFSTGMERVNILKKLRSVSIE T0292 234 :IPYRYS 1zy4A 942 :FPPDFD T0292 240 :DELNEIITRMLNLKDYHRPSVEEILENPLILEHH 1zy4A 952 :KVEKKIIRLLIDHDPNKRPGARTLLNSGWLPVKH Number of specific fragments extracted= 10 number of extra gaps= 0 total=1764 Number of alignments=164 # 1zy4A read from 1zy4A/merged-good-all-a2m # found chain 1zy4A in template set Warning: unaligning (T0292)P178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zy4A)A888 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYG 1zy4A 597 :SDFEEIAVLGQGAFGQVVKARNALDSRYYAIKKIRHT T0292 44 :EAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNT 1zy4A 634 :EEKLSTILSEVMLLASLNHQYVVRYYAAWLERRNF T0292 79 :TLYIVMEYCEGGDLASVITKGTKER 1zy4A 783 :TLFIQMEYCENGTLYDLIHSENLNQ T0292 107 :DEEFVLRVMTQLTLALKECHRR 1zy4A 808 :QRDEYWRLFRQILEALSYIHSQ T0292 134 :TVLHRDLKPANVFLDGKQNVKLGDFGLARILN 1zy4A 830 :GIIHRDLKPMNIFIDESRNVKIGDFGLAKNVH T0292 179 :YYMSPEQMNR 1zy4A 889 :MYVATEVLDG T0292 189 :MSYNEKSDIWSLGCLLYELC 1zy4A 900 :GHYNEKIDMYSLGIIFFEMI T0292 211 :MPPFTAFSQKELAGKIREGKFR 1zy4A 920 :YPFSTGMERVNILKKLRSVSIE T0292 234 :IPYRYS 1zy4A 942 :FPPDFD T0292 240 :DELNEIITRMLNLKDYHRPSVEEILENPLIL 1zy4A 952 :KVEKKIIRLLIDHDPNKRPGARTLLNSGWLP Number of specific fragments extracted= 10 number of extra gaps= 0 total=1774 Number of alignments=165 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cmkE/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cmkE expands to /projects/compbio/data/pdb/1cmk.pdb.gz 1cmkE:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0292 read from 1cmkE/merged-good-all-a2m # 1cmkE read from 1cmkE/merged-good-all-a2m # adding 1cmkE to template set # found chain 1cmkE in template set Warning: unaligning (T0292)R2 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L40 Warning: unaligning (T0292)A3 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L40 Warning: unaligning (T0292)I72 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)K111 Warning: unaligning (T0292)R75 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)K111 Warning: unaligning (T0292)T76 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)N113 Warning: unaligning (T0292)N77 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)N113 Warning: unaligning (T0292)Q151 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cmkE)Y179 Warning: unaligning (T0292)N152 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cmkE)Y179 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L198 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L198 Warning: unaligning (T0292)V175 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)G200 Warning: unaligning (T0292)G176 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)G200 Warning: unaligning (T0292)D240 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)D264 Warning: unaligning (T0292)E241 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)D264 Warning: unaligning (T0292)L264 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)N293 Warning: unaligning (T0292)E265 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)N293 Warning: unaligning (T0292)P267 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cmkE)W296 Warning: unaligning (T0292)L268 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cmkE)W296 Warning: unaligning (T0292)I269 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)A298 Warning: unaligning (T0292)L270 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)A298 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTE 1cmkE 41 :DQFERIKTLGTGSFGRVMLVKHKETGNHFAMKILDKQKVVK T0292 45 :AEKQMLVSEVNLLRELKHPNIVRYYDR 1cmkE 83 :KQIEHTLNEKRILQAVNFPFLVKLEYS T0292 78 :TTLYIVMEYCEGGDLASVITKGTK 1cmkE 114 :SNLYMVMEYVPGGEMFSHLRRIGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1cmkE 138 :FSEPHARFYAAQIVLTFEYLHSLD T0292 135 :VLHRDLKPANVFLDGK 1cmkE 162 :LIYRDLKPENLLIDQQ T0292 153 :VKLGDFGLARILN 1cmkE 180 :IQVTDFGFAKRVK T0292 169 :SFA 1cmkE 193 :GRT T0292 177 :TPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKF 1cmkE 201 :TPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKV T0292 233 :RIPYRYS 1cmkE 256 :RFPSHFS T0292 242 :LNEIITRMLNLKDYHRP 1cmkE 265 :LKDLLRNLLQVDLTKRF T0292 260 :VEEI 1cmkE 288 :VNDI T0292 266 :N 1cmkE 294 :H T0292 271 :EH 1cmkE 299 :TT Number of specific fragments extracted= 13 number of extra gaps= 6 total=1787 Number of alignments=166 # 1cmkE read from 1cmkE/merged-good-all-a2m # found chain 1cmkE in template set Warning: unaligning (T0292)R2 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L40 Warning: unaligning (T0292)A3 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L40 Warning: unaligning (T0292)I72 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)K111 Warning: unaligning (T0292)R75 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)K111 Warning: unaligning (T0292)T76 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)N113 Warning: unaligning (T0292)N77 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)N113 Warning: unaligning (T0292)Q151 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cmkE)Y179 Warning: unaligning (T0292)N152 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cmkE)Y179 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L198 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L198 Warning: unaligning (T0292)V175 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)G200 Warning: unaligning (T0292)G176 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)G200 Warning: unaligning (T0292)D240 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)D264 Warning: unaligning (T0292)E241 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)D264 Warning: unaligning (T0292)L264 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)N293 Warning: unaligning (T0292)E265 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)N293 Warning: unaligning (T0292)P267 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cmkE)W296 Warning: unaligning (T0292)L268 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cmkE)W296 Warning: unaligning (T0292)I269 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)A298 Warning: unaligning (T0292)L270 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)A298 T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1cmkE 41 :DQFERIKTLGTGSFGRVMLVKHKETGNHFAMKILDKQKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDR 1cmkE 81 :KLKQIEHTLNEKRILQAVNFPFLVKLEYS T0292 78 :TTLYIVMEYCEGGDLASVITKGTK 1cmkE 114 :SNLYMVMEYVPGGEMFSHLRRIGR T0292 106 :LDEEFVLRVMTQLTLALKECHRRS 1cmkE 138 :FSEPHARFYAAQIVLTFEYLHSLD T0292 135 :VLHRDLKPANVFLDGK 1cmkE 162 :LIYRDLKPENLLIDQQ T0292 153 :VKLGDFGLARILN 1cmkE 180 :IQVTDFGFAKRVK T0292 169 :SFA 1cmkE 193 :GRT T0292 177 :TPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1cmkE 201 :TPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVR T0292 234 :IPYRYS 1cmkE 257 :FPSHFS T0292 242 :LNEIITRMLNLKDYHRP 1cmkE 265 :LKDLLRNLLQVDLTKRF T0292 259 :SVEEI 1cmkE 287 :GVNDI T0292 266 :N 1cmkE 294 :H T0292 271 :EHH 1cmkE 299 :TTD Number of specific fragments extracted= 13 number of extra gaps= 6 total=1800 Number of alignments=167 # 1cmkE read from 1cmkE/merged-good-all-a2m # found chain 1cmkE in template set Warning: unaligning (T0292)R2 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L40 Warning: unaligning (T0292)A3 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L40 Warning: unaligning (T0292)I72 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)K111 Warning: unaligning (T0292)I73 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)K111 Warning: unaligning (T0292)D74 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)N113 Warning: unaligning (T0292)R75 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)N113 Warning: unaligning (T0292)Q151 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cmkE)Y179 Warning: unaligning (T0292)N152 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cmkE)Y179 Warning: unaligning (T0292)K172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L198 Warning: unaligning (T0292)F174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L198 Warning: unaligning (T0292)V175 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)G200 Warning: unaligning (T0292)G176 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)G200 Warning: unaligning (T0292)D240 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)D264 Warning: unaligning (T0292)E241 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)D264 Warning: unaligning (T0292)L264 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)N293 Warning: unaligning (T0292)E265 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)N293 Warning: unaligning (T0292)P267 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cmkE)W296 Warning: unaligning (T0292)L268 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cmkE)W296 Warning: unaligning (T0292)I269 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)A298 Warning: unaligning (T0292)L270 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)A298 T0292 1 :S 1cmkE 38 :A T0292 4 :EDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSM 1cmkE 41 :DQFERIKTLGTGSFGRVMLVKHKETGNHFAMKILDKQKV T0292 43 :TEAEKQMLVSEVNLLRELKHPNIVRYYDR 1cmkE 81 :KLKQIEHTLNEKRILQAVNFPFLVKLEYS T0292 76 :TN 1cmkE 114 :SN T0292 80 :LYIVMEYCEGGDLASVITK 1cmkE 116 :LYMVMEYVPGGEMFSHLRR T0292 103 :RQYLDEEFVLRVMTQLTLALKECHRR 1cmkE 135 :IGRFSEPHARFYAAQIVLTFEYLHSL T0292 134 :TVLHRDLKPANVFLDGK 1cmkE 161 :DLIYRDLKPENLLIDQQ T0292 153 :VKLGDFGLARILNHD 1cmkE 180 :IQVTDFGFAKRVKGR T0292 171 :A 1cmkE 195 :T T0292 177 :TPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFR 1cmkE 201 :TPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVR T0292 234 :IPYRYS 1cmkE 257 :FPSHFS T0292 242 :LNEIITRMLNLKDYHRP 1cmkE 265 :LKDLLRNLLQVDLTKRF T0292 261 :EEI 1cmkE 289 :NDI T0292 266 :N 1cmkE 294 :H T0292 271 :EH 1cmkE 299 :TT Number of specific fragments extracted= 15 number of extra gaps= 6 total=1815 Number of alignments=168 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 168 Adding 1737 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -469.2074, CN propb: -469.2074 weights: 0.5769 constraints: 555 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 555 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 555 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 1182 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 1182 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 1737 # command: