parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0338/ # command:# Making conformation for sequence T0338 numbered 1 through 256 Created new target T0338 from T0338.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0338/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0338//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0338/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0338//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0338/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0338/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0338/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qmzB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qmzB expands to /projects/compbio/data/pdb/1qmz.pdb.gz 1qmzB:# T0338 read from 1qmzB/merged-good-all-a2m # 1qmzB read from 1qmzB/merged-good-all-a2m # adding 1qmzB to template set # found chain 1qmzB in template set Warning: unaligning (T0338)R158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qmzB)P324 Warning: unaligning (T0338)T179 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qmzB)P346 Warning: unaligning (T0338)F180 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qmzB)P346 Warning: unaligning (T0338)W214 because of BadResidue code BAD_PEPTIDE in next template residue (1qmzB)T380 Warning: unaligning (T0338)W215 because of BadResidue code BAD_PEPTIDE at template residue (1qmzB)T380 T0338 2 :SSRWFFTREQLENTPSR 1qmzB 181 :DIHTYLREMEVKCKPKV # choosing archetypes in rotamer library T0338 19 :RCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 1qmzB 199 :YMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEE T0338 103 :ACLHPLEPLLDTKCDAY 1qmzB 270 :IYPPEVAEFVYITDDTY T0338 122 :QTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLV 1qmzB 287 :TKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQ T0338 159 :ASKDLAQTSYFMATNSLHLT 1qmzB 325 :ANCKVESLAMFLGELSLIDA T0338 181 :CLQYKPTVIACVCIHLACKWSNWE 1qmzB 347 :YLKYLPSVIAGAAFHLALYTVTGQ T0338 206 :PVSTDGKH 1qmzB 371 :SWPESLIR T0338 216 :E 1qmzB 381 :G T0338 222 :VTLELLDELTHEFLQILEKTPNRLKKIRNWRANQ 1qmzB 382 :YTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKN Number of specific fragments extracted= 9 number of extra gaps= 3 total=9 Number of alignments=1 # 1qmzB read from 1qmzB/merged-good-all-a2m # found chain 1qmzB in template set Warning: unaligning (T0338)R158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qmzB)P324 Warning: unaligning (T0338)T179 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qmzB)P346 Warning: unaligning (T0338)F180 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qmzB)P346 Warning: unaligning (T0338)W215 because of BadResidue code BAD_PEPTIDE in next template residue (1qmzB)T380 Warning: unaligning (T0338)E216 because of BadResidue code BAD_PEPTIDE at template residue (1qmzB)T380 T0338 3 :SRWFFTREQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 1qmzB 183 :HTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEE T0338 103 :ACLHPLEPLLDTKCDAYL 1qmzB 270 :IYPPEVAEFVYITDDTYT T0338 123 :TRELVILETIMLQTLGFEITIEHPHTDVVKCTQLV 1qmzB 288 :KKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQ T0338 159 :ASKDLAQTSYFMATNSLHLT 1qmzB 325 :ANCKVESLAMFLGELSLIDA T0338 181 :CLQYKPTVIACVCIHLACKWSNW 1qmzB 347 :YLKYLPSVIAGAAFHLALYTVTG T0338 206 :PVSTDGKHW 1qmzB 370 :QSWPESLIR T0338 221 :TVTLELLDELTHEFLQILEKTPNRLKKIRNWRANQ 1qmzB 381 :GYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKN Number of specific fragments extracted= 7 number of extra gaps= 3 total=16 Number of alignments=2 # 1qmzB read from 1qmzB/merged-good-all-a2m # found chain 1qmzB in template set Warning: unaligning (T0338)R158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qmzB)P324 Warning: unaligning (T0338)T179 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qmzB)P346 Warning: unaligning (T0338)F180 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qmzB)P346 Warning: unaligning (T0338)D219 because of BadResidue code BAD_PEPTIDE in next template residue (1qmzB)T380 Warning: unaligning (T0338)P220 because of BadResidue code BAD_PEPTIDE at template residue (1qmzB)T380 T0338 4 :RWFFTREQLENTPSRRCG 1qmzB 184 :TYLREMEVKCKPKVGYMK T0338 22 :VE 1qmzB 206 :IT T0338 28 :LSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHA 1qmzB 208 :NSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITD T0338 119 :YLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLV 1qmzB 284 :DTYTKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQ T0338 159 :ASKDLAQTSYFMATNSLHLT 1qmzB 325 :ANCKVESLAMFLGELSLIDA T0338 181 :CLQYKPTVIACVCIHLACKWSNWEIPVS 1qmzB 347 :YLKYLPSVIAGAAFHLALYTVTGQSWPE T0338 215 :WEYV 1qmzB 375 :SLIR T0338 221 :TVTLELLDELTHEFLQILEKTPN 1qmzB 381 :GYTLESLKPCLMDLHQTYLKAPQ Number of specific fragments extracted= 8 number of extra gaps= 3 total=24 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c9bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c9bA expands to /projects/compbio/data/pdb/1c9b.pdb.gz 1c9bA:# T0338 read from 1c9bA/merged-good-all-a2m # 1c9bA read from 1c9bA/merged-good-all-a2m # adding 1c9bA to template set # found chain 1c9bA in template set T0338 33 :QAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 1c9bA 116 :NAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEG T0338 104 :CLHPLEPLLDT 1c9bA 173 :VPRTFKEICAV T0338 117 :DAY 1c9bA 184 :SRI T0338 122 :QTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLH 1c9bA 187 :SKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVE T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIPV 1c9bA 242 :LDLVPGRSPISVAAAAIYMASQASAEKRTQ T0338 209 :TDGKHWWE 1c9bA 272 :KEIGDIAG T0338 222 :VTLELLDELTHEF 1c9bA 280 :VADVTIRQSYRLI Number of specific fragments extracted= 7 number of extra gaps= 0 total=31 Number of alignments=4 # 1c9bA read from 1c9bA/merged-good-all-a2m # found chain 1c9bA in template set T0338 21 :G 1c9bA 116 :N T0338 34 :AANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHAC 1c9bA 117 :AFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRIS T0338 123 :TRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLH 1c9bA 188 :KKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVE T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIP 1c9bA 242 :LDLVPGRSPISVAAAAIYMASQASAEKRT T0338 221 :TVTLELLDELTHEF 1c9bA 279 :GVADVTIRQSYRLI T0338 242 :PNRLKKI 1c9bA 293 :YPRAPDL Number of specific fragments extracted= 6 number of extra gaps= 0 total=37 Number of alignments=5 # 1c9bA read from 1c9bA/merged-good-all-a2m # found chain 1c9bA in template set T0338 34 :AANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKV 1c9bA 117 :AFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAV T0338 119 :YLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLH 1c9bA 184 :SRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVE T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIPVS 1c9bA 242 :LDLVPGRSPISVAAAAIYMASQASAEKRTQK T0338 215 :WEYVDPTVTLELLDELTHEF 1c9bA 273 :EIGDIAGVADVTIRQSYRLI Number of specific fragments extracted= 4 number of extra gaps= 0 total=41 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xo2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0338/1xo2A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0338/1xo2A/merged-good-all-a2m.gz for input Trying 1xo2A/merged-good-all-a2m Error: Couldn't open file 1xo2A/merged-good-all-a2m or 1xo2A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vywB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0338/1vywB/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0338/1vywB/merged-good-all-a2m.gz for input Trying 1vywB/merged-good-all-a2m Error: Couldn't open file 1vywB/merged-good-all-a2m or 1vywB/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tfb/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tfb expands to /projects/compbio/data/pdb/1tfb.pdb.gz 1tfb:Warning: there is no chain 1tfb will retry with 1tfbA # T0338 read from 1tfb/merged-good-all-a2m # 1tfb read from 1tfb/merged-good-all-a2m # adding 1tfb to template set # found chain 1tfb in template set T0338 32 :QQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVA 1tfb 115 :MNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVS T0338 113 :D 1tfb 185 :R T0338 119 :Y 1tfb 186 :I T0338 122 :QTRELVILETIMLQTLGFEIT 1tfb 187 :SKKEIGRCFKLILKALETSVD T0338 157 :VRASKDLAQTSYFMATNSLH 1tfb 222 :LCLPKQVQMAATHIARKAVE T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIPV 1tfb 242 :LDLVPGRSPISVAAAAIYMASQASAEKRTQ T0338 212 :KHWWEYVD 1tfb 272 :KEIGDIAG Number of specific fragments extracted= 7 number of extra gaps= 0 total=48 Number of alignments=7 # 1tfb read from 1tfb/merged-good-all-a2m # found chain 1tfb in template set T0338 33 :QAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHAC 1tfb 116 :NAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRIS T0338 123 :TRELVILETIMLQTLGFEITIEH 1tfb 188 :KKEIGRCFKLILKALETSVDLIT T0338 157 :VRASKDLAQTSYFMATNSLH 1tfb 222 :LCLPKQVQMAATHIARKAVE T0338 178 :TTFCLQYKPTVIACVCIHLACKWS 1tfb 242 :LDLVPGRSPISVAAAAIYMASQAS T0338 202 :NWEIPVSTDG 1tfb 303 :DFKFDTPVDK Number of specific fragments extracted= 5 number of extra gaps= 0 total=53 Number of alignments=8 # 1tfb read from 1tfb/merged-good-all-a2m # found chain 1tfb in template set T0338 33 :QAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKV 1tfb 116 :NAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAV T0338 119 :YLQQTRELVILETIMLQTLGFEI 1tfb 184 :SRISKKEIGRCFKLILKALETSV T0338 157 :VRASKDLAQTSYFMATNSLH 1tfb 222 :LCLPKQVQMAATHIARKAVE T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIP 1tfb 242 :LDLVPGRSPISVAAAAIYMASQASAEKRT Number of specific fragments extracted= 4 number of extra gaps= 0 total=57 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1rB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0338/1h1rB/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0338/1h1rB/merged-good-all-a2m.gz for input Trying 1h1rB/merged-good-all-a2m Error: Couldn't open file 1h1rB/merged-good-all-a2m or 1h1rB/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oiuB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0338/1oiuB/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0338/1oiuB/merged-good-all-a2m.gz for input Trying 1oiuB/merged-good-all-a2m Error: Couldn't open file 1oiuB/merged-good-all-a2m or 1oiuB/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5qB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f5qB expands to /projects/compbio/data/pdb/1f5q.pdb.gz 1f5qB:Skipped atom 2781, because occupancy 0.5 <= existing 0.500 in 1f5qB Skipped atom 2783, because occupancy 0.500 <= existing 0.500 in 1f5qB Skipped atom 2785, because occupancy 0.500 <= existing 0.500 in 1f5qB Skipped atom 2787, because occupancy 0.500 <= existing 0.500 in 1f5qB Skipped atom 2789, because occupancy 0.500 <= existing 0.500 in 1f5qB Skipped atom 2791, because occupancy 0.500 <= existing 0.500 in 1f5qB # T0338 read from 1f5qB/merged-good-all-a2m # 1f5qB read from 1f5qB/merged-good-all-a2m # adding 1f5qB to template set # found chain 1f5qB in template set T0338 8 :TREQLE 1f5qB 27 :SEREHD T0338 19 :RCGVEADKEL 1f5qB 35 :MVGVNVDQHF T0338 29 :SCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 1f5qB 47 :QYRKVLTTWMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRA T0338 103 :ACLHPLEPLLDTKCDAY 1f5qB 108 :YMPIKATQLAYLCGGAT T0338 122 :QTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1f5qB 125 :TADKLLTLEVKSLDTLSWVADRCLSTDLICYILHIMHAPRE T0338 163 :LAQTSYFMATNSLH 1f5qB 170 :IYNLCRPKIFCALC T0338 178 :TTFCLQYKPTVIACVCIHLAC 1f5qB 184 :DGRSAMKRPVLITLACMHLTM T0338 216 :EYV 1f5qB 220 :KSL T0338 221 :TVTLELLDELTHEFLQILEKTPNRLKKI 1f5qB 223 :YITKEELHQCCDLVDIAIVSFDENYFKI Number of specific fragments extracted= 9 number of extra gaps= 0 total=66 Number of alignments=10 # 1f5qB read from 1f5qB/merged-good-all-a2m # found chain 1f5qB in template set T0338 9 :REQL 1f5qB 31 :HDAR T0338 19 :RCGVEAD 1f5qB 35 :MVGVNVD T0338 26 :KELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 1f5qB 44 :FTSQYRKVLTTWMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRA T0338 103 :ACLHPLEPLLDTKCDAYL 1f5qB 108 :YMPIKATQLAYLCGGATT T0338 123 :TRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1f5qB 126 :ADKLLTLEVKSLDTLSWVADRCLSTDLICYILHIMHAPRE T0338 163 :LAQTSYFMATNSLH 1f5qB 170 :IYNLCRPKIFCALC T0338 178 :TTFCLQYKPTVIACVCIHLAC 1f5qB 184 :DGRSAMKRPVLITLACMHLTM T0338 201 :S 1f5qB 205 :N T0338 210 :DGK 1f5qB 206 :QKY T0338 221 :TVTLELLDELTHEFLQILEKTPNRLKK 1f5qB 223 :YITKEELHQCCDLVDIAIVSFDENYFK Number of specific fragments extracted= 10 number of extra gaps= 0 total=76 Number of alignments=11 # 1f5qB read from 1f5qB/merged-good-all-a2m # found chain 1f5qB in template set T0338 19 :RCGVEADKELSCRQQAAN 1f5qB 12 :SSLLNEEDCRQMIYRSER T0338 37 :LIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQ 1f5qB 55 :WMFCVCKDLRQDNNVFPLAVALLDELFLSTRIDRENYQSTAAVALHIAGKVRAY T0338 91 :ARKLEHVIKVAH 1f5qB 110 :PIKATQLAYLCG T0338 119 :YLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1f5qB 122 :GATTADKLLTLEVKSLDTLSWVADRCLSTDLICYILHIMHAPRE T0338 163 :LAQTSYFMATNSLH 1f5qB 170 :IYNLCRPKIFCALC T0338 178 :TTFCLQYKPTVIACVCIHLACK 1f5qB 184 :DGRSAMKRPVLITLACMHLTMN T0338 201 :SNWE 1f5qB 206 :QKYD T0338 215 :WEYVDPTVTLELLDELTHEFLQILEKTPNR 1f5qB 217 :GVCKSLYITKEELHQCCDLVDIAIVSFDEN Number of specific fragments extracted= 8 number of extra gaps= 0 total=84 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d3uB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d3uB expands to /projects/compbio/data/pdb/1d3u.pdb.gz 1d3uB:# T0338 read from 1d3uB/merged-good-all-a2m # 1d3uB read from 1d3uB/merged-good-all-a2m # adding 1d3uB to template set # found chain 1d3uB in template set T0338 24 :ADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVE 1d3uB 1102 :SDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLL T0338 103 :ACLHPLEPLLDT 1d3uB 1167 :KVPRTLDEIADI T0338 117 :DAY 1d3uB 1179 :ARV T0338 122 :QTRELVILETIMLQTLGFE 1d3uB 1182 :DKKEIGRSYRFIARNLNLT T0338 143 :IEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLH 1d3uB 1205 :FVKPTDYVNKFADELGLSEKVRRRAIEILDEAYK T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIPV 1d3uB 1239 :RGLTSGKSPAGLVAAALYIASLLEGEKRTQ T0338 209 :TDGKHWWE 1d3uB 1269 :REVAEVAR T0338 222 :VTLELLDELTHEFLQI 1d3uB 1277 :VTEVTVRNRYKELVEK Number of specific fragments extracted= 8 number of extra gaps= 0 total=92 Number of alignments=13 # 1d3uB read from 1d3uB/merged-good-all-a2m # found chain 1d3uB in template set T0338 25 :DKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHAC 1d3uB 1103 :DAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVD T0338 123 :TRELVILETIMLQTLGFE 1d3uB 1183 :KKEIGRSYRFIARNLNLT T0338 144 :EHPHTDVVKCTQLVRASKDLAQTSYFMATNSLH 1d3uB 1206 :VKPTDYVNKFADELGLSEKVRRRAIEILDEAYK T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIP 1d3uB 1239 :RGLTSGKSPAGLVAAALYIASLLEGEKRT T0338 221 :TVTLELLDELTHEFLQI 1d3uB 1276 :RVTEVTVRNRYKELVEK Number of specific fragments extracted= 5 number of extra gaps= 0 total=97 Number of alignments=14 # 1d3uB read from 1d3uB/merged-good-all-a2m # found chain 1d3uB in template set T0338 28 :LSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAH 1d3uB 1106 :ERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIAR T0338 121 :QQTRELVILETIMLQTLGFE 1d3uB 1181 :VDKKEIGRSYRFIARNLNLT T0338 142 :T 1d3uB 1205 :F T0338 144 :EHPHTDVVKCTQLVRASKDLAQTSYFMATNSLH 1d3uB 1206 :VKPTDYVNKFADELGLSEKVRRRAIEILDEAYK T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIPVS 1d3uB 1239 :RGLTSGKSPAGLVAAALYIASLLEGEKRTQR T0338 215 :WEYVDPTVTLELLDELTHEFLQI 1d3uB 1270 :EVAEVARVTEVTVRNRYKELVEK Number of specific fragments extracted= 6 number of extra gaps= 0 total=103 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kxu/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kxu expands to /projects/compbio/data/pdb/1kxu.pdb.gz 1kxu:Warning: there is no chain 1kxu will retry with 1kxuA # T0338 read from 1kxu/merged-good-all-a2m # 1kxu read from 1kxu/merged-good-all-a2m # adding 1kxu to template set # found chain 1kxu in template set T0338 4 :RWFFTREQLEN 1kxu 27 :NRKFRCKAVAN T0338 15 :TPSRRCGVEADKELSCRQQAANLIQEMGQRLN 1kxu 41 :LPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFK T0338 47 :VSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVA 1kxu 75 :MPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNL T0338 113 :DTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1kxu 130 :RESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYP T0338 163 :LAQTSYFMATNSLH 1kxu 187 :LRKTADDFLNRIAL T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVD 1kxu 201 :TDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKENR T0338 222 :VTLELLDELTHEFLQILEKTP 1kxu 243 :TCLSQLLDIMKSMRNLVKKYE T0338 243 :NRLKKIRNWR 1kxu 267 :SEEVAVLKQK Number of specific fragments extracted= 8 number of extra gaps= 0 total=111 Number of alignments=16 # 1kxu read from 1kxu/merged-good-all-a2m # found chain 1kxu in template set T0338 12 :LENTPSRRCGVEADKELSCRQQAANLIQEMGQRLN 1kxu 38 :GKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFK T0338 47 :VSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVI 1kxu 75 :MPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFV T0338 110 :PLLDTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1kxu 127 :GNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYP T0338 163 :LAQTSYFMATNSLH 1kxu 187 :LRKTADDFLNRIAL T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVD 1kxu 201 :TDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKENR T0338 222 :VTLELLDELTHEFLQILEKTP 1kxu 243 :TCLSQLLDIMKSMRNLVKKYE T0338 243 :NRLKKIRN 1kxu 268 :EEVAVLKQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=118 Number of alignments=17 # 1kxu read from 1kxu/merged-good-all-a2m # found chain 1kxu in template set T0338 15 :TPSRRCGVEADKELSCRQQAANLIQEMGQRLN 1kxu 41 :LPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFK T0338 47 :VSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVI 1kxu 75 :MPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFV T0338 110 :PLLDTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1kxu 127 :GNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYP T0338 163 :LAQTSYFMATNSLH 1kxu 187 :LRKTADDFLNRIAL T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIPVSTDGKHWWEYVDP 1kxu 201 :TDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKENRT T0338 223 :TLELLDELTHEFLQILEKTPNRL 1kxu 244 :CLSQLLDIMKSMRNLVKKYEPPR Number of specific fragments extracted= 6 number of extra gaps= 0 total=124 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zp2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0338/1zp2A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0338/1zp2A/merged-good-all-a2m.gz for input Trying 1zp2A/merged-good-all-a2m Error: Couldn't open file 1zp2A/merged-good-all-a2m or 1zp2A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jkw/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jkw expands to /projects/compbio/data/pdb/1jkw.pdb.gz 1jkw:Warning: there is no chain 1jkw will retry with 1jkwA # T0338 read from 1jkw/merged-good-all-a2m # 1jkw read from 1jkw/merged-good-all-a2m # adding 1jkw to template set # found chain 1jkw in template set T0338 4 :RWFFTREQLEN 1jkw 27 :NRKFRCKAVAN T0338 15 :TPSRRCGVEADKELSCRQQAANLIQEMGQRLN 1jkw 41 :LPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFK T0338 47 :VSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVA 1jkw 75 :MPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNL T0338 113 :DTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRAS 1jkw 130 :RESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTR T0338 161 :KDLAQTSYFMATNSLH 1jkw 185 :EILRKTADDFLNRIAL T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEI 1jkw 201 :TDAYLLYTPSQIALTAILSSASRAGITM T0338 209 :TD 1jkw 229 :ES T0338 211 :GKHWWEYVDPTVTLELLDELTHEFLQILEKTP 1jkw 232 :LSESLMLKENRTCLSQLLDIMKSMRNLVKKYE T0338 243 :NRLKKIRNWRA 1jkw 267 :SEEVAVLKQKL Number of specific fragments extracted= 9 number of extra gaps= 0 total=133 Number of alignments=19 # 1jkw read from 1jkw/merged-good-all-a2m # found chain 1jkw in template set T0338 11 :QLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLN 1jkw 37 :NGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFK T0338 47 :VSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVI 1jkw 75 :MPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFV T0338 110 :PLLDTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1jkw 127 :GNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYP T0338 163 :LAQTSYFMATNSLH 1jkw 187 :LRKTADDFLNRIAL T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIPV 1jkw 201 :TDAYLLYTPSQIALTAILSSASRAGITMES T0338 208 :STDG 1jkw 238 :LKEN T0338 221 :TVTLELLDELTHEFLQILEKTP 1jkw 242 :RTCLSQLLDIMKSMRNLVKKYE T0338 243 :NRLKKIRN 1jkw 268 :EEVAVLKQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=141 Number of alignments=20 # 1jkw read from 1jkw/merged-good-all-a2m # found chain 1jkw in template set T0338 15 :TPSRRCGVEADKELSCRQQAANLIQEMGQRLN 1jkw 41 :LPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFK T0338 47 :VSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVI 1jkw 75 :MPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFV T0338 110 :PLLDTKCDAYLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1jkw 127 :GNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYP T0338 163 :LAQTSYFMATNSLH 1jkw 187 :LRKTADDFLNRIAL T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIPVSTD 1jkw 201 :TDAYLLYTPSQIALTAILSSASRAGITMESYLS T0338 215 :WEYVDPTVTLELLDELTHEFLQILEKTPNRL 1jkw 236 :LMLKENRTCLSQLLDIMKSMRNLVKKYEPPR Number of specific fragments extracted= 6 number of extra gaps= 0 total=147 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w98B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w98B expands to /projects/compbio/data/pdb/1w98.pdb.gz 1w98B:# T0338 read from 1w98B/merged-good-all-a2m # 1w98B read from 1w98B/merged-good-all-a2m # adding 1w98B to template set # found chain 1w98B in template set Warning: unaligning (T0338)L226 because of BadResidue code BAD_PEPTIDE in next template residue (1w98B)I309 Warning: unaligning (T0338)L227 because of BadResidue code BAD_PEPTIDE at template residue (1w98B)I309 T0338 3 :SRWFFTREQLENTPSR 1w98B 101 :VWKIMLNKEKTYLRDQ T0338 19 :RCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMH 1w98B 118 :FLEQHPLLQPKMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMAT T0338 66 :HSFTKFNKNIISSTALFLAAKVEE 1w98B 166 :ENVVKTLLQLIGISSLFIAAKLEE T0338 103 :ACLHPLEPLLDTKCDAY 1w98B 190 :IYPPKLHQFAYVTDGAC T0338 122 :QTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1w98B 207 :SGDEILTMELMIMKALKWRLSPLTIVSWLNVYMQVAYLNDL T0338 163 :LAQTS 1w98B 260 :FIQIA T0338 169 :FMATNSLH 1w98B 265 :ELLDLCVL T0338 178 :TTFCLQYKPTVIACVCIHL 1w98B 273 :DVDCLEFPYGILAASALYH T0338 206 :PVSTD 1w98B 292 :FSSSE T0338 211 :GKHWWE 1w98B 298 :MQKVSG T0338 222 :VTLE 1w98B 304 :YQWC T0338 228 :DELTHEFLQILEK 1w98B 310 :ENCVKWMVPFAMV T0338 249 :R 1w98B 323 :I Number of specific fragments extracted= 13 number of extra gaps= 1 total=160 Number of alignments=22 # 1w98B read from 1w98B/merged-good-all-a2m # found chain 1w98B in template set Warning: unaligning (T0338)L226 because of BadResidue code BAD_PEPTIDE in next template residue (1w98B)I309 Warning: unaligning (T0338)L227 because of BadResidue code BAD_PEPTIDE at template residue (1w98B)I309 T0338 3 :SRWFFTREQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMH 1w98B 102 :WKIMLNKEKTYLRDQHFLEQHPLLQPKMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMAT T0338 66 :HSFTKFNKNIISSTALFLAAKVEE 1w98B 166 :ENVVKTLLQLIGISSLFIAAKLEE T0338 103 :ACLHPLEPLLDTKCDAYL 1w98B 190 :IYPPKLHQFAYVTDGACS T0338 123 :TRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1w98B 208 :GDEILTMELMIMKALKWRLSPLTIVSWLNVYMQVAYLNDL T0338 163 :LAQTS 1w98B 260 :FIQIA T0338 169 :FMATNSLH 1w98B 265 :ELLDLCVL T0338 178 :TTFCLQYKPTVIACVCIHL 1w98B 273 :DVDCLEFPYGILAASALYH T0338 197 :ACKWS 1w98B 298 :MQKVS T0338 221 :TVTLE 1w98B 303 :GYQWC T0338 228 :DELTHEFLQILEKTP 1w98B 310 :ENCVKWMVPFAMVIR Number of specific fragments extracted= 10 number of extra gaps= 1 total=170 Number of alignments=23 # 1w98B read from 1w98B/merged-good-all-a2m # found chain 1w98B in template set Warning: unaligning (T0338)L226 because of BadResidue code BAD_PEPTIDE in next template residue (1w98B)I309 Warning: unaligning (T0338)L227 because of BadResidue code BAD_PEPTIDE at template residue (1w98B)I309 T0338 18 :RRCGVE 1w98B 121 :QHPLLQ T0338 28 :LSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHH 1w98B 127 :PKMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQ T0338 67 :SFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHA 1w98B 167 :NVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTD T0338 119 :YLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1w98B 204 :GACSGDEILTMELMIMKALKWRLSPLTIVSWLNVYMQVAYLNDL T0338 163 :LAQTSYFMATNSL 1w98B 260 :FIQIAELLDLCVL T0338 178 :TTFCLQYKPTVIACVCIHL 1w98B 273 :DVDCLEFPYGILAASALYH T0338 210 :DGKHWWEYVDPTVTLE 1w98B 292 :FSSSELMQKVSGYQWC T0338 228 :DELTHEFLQILEKTP 1w98B 310 :ENCVKWMVPFAMVIR Number of specific fragments extracted= 8 number of extra gaps= 1 total=178 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1volA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1volA expands to /projects/compbio/data/pdb/1vol.pdb.gz 1volA:# T0338 read from 1volA/merged-good-all-a2m # 1volA read from 1volA/merged-good-all-a2m # adding 1volA to template set # found chain 1volA in template set Warning: unaligning (T0338)C181 because of BadResidue code BAD_PEPTIDE in next template residue (1volA)P246 Warning: unaligning (T0338)L182 because of BadResidue code BAD_PEPTIDE at template residue (1volA)P246 T0338 34 :AANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 1volA 117 :AFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEG T0338 104 :CLHPLEPLLDT 1volA 173 :VPRTFKEICAV T0338 117 :DAY 1volA 184 :SRI T0338 122 :QTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLH 1volA 187 :SKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVE T0338 178 :TTF 1volA 242 :LDL T0338 183 :QYKPTVIACVCIHLACKWSNWEIPV 1volA 247 :GRSPISVAAAAIYMASQASAEKRTQ T0338 209 :TDGKHWWE 1volA 272 :KEIGDIAG T0338 222 :VTLELLDELTHEF 1volA 280 :VADVTIRQSYRLI Number of specific fragments extracted= 8 number of extra gaps= 1 total=186 Number of alignments=25 # 1volA read from 1volA/merged-good-all-a2m # found chain 1volA in template set Warning: unaligning (T0338)C181 because of BadResidue code BAD_PEPTIDE in next template residue (1volA)P246 Warning: unaligning (T0338)L182 because of BadResidue code BAD_PEPTIDE at template residue (1volA)P246 T0338 34 :AANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHAC 1volA 117 :AFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRIS T0338 123 :TRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLH 1volA 188 :KKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVE T0338 178 :TTF 1volA 242 :LDL T0338 183 :QYKPTVIACVCIHLACKWSNWEIP 1volA 247 :GRSPISVAAAAIYMASQASAEKRT T0338 221 :TVTLELLDELTHEF 1volA 279 :GVADVTIRQSYRLI Number of specific fragments extracted= 5 number of extra gaps= 1 total=191 Number of alignments=26 # 1volA read from 1volA/merged-good-all-a2m # found chain 1volA in template set Warning: unaligning (T0338)C181 because of BadResidue code BAD_PEPTIDE in next template residue (1volA)P246 Warning: unaligning (T0338)L182 because of BadResidue code BAD_PEPTIDE at template residue (1volA)P246 T0338 34 :AANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLE 1volA 117 :AFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGVPRTFK T0338 100 :VAHA 1volA 179 :EICA T0338 118 :AYLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKDLAQTSYFMATNSLH 1volA 183 :VSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIARKAVE T0338 178 :TTF 1volA 242 :LDL T0338 183 :QYKPTVIACVCIHLACKWSNWEIPVS 1volA 247 :GRSPISVAAAAIYMASQASAEKRTQK T0338 215 :WEYVDPTVTLELLDELTHEF 1volA 273 :EIGDIAGVADVTIRQSYRLI Number of specific fragments extracted= 6 number of extra gaps= 1 total=197 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vin/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vin expands to /projects/compbio/data/pdb/1vin.pdb.gz 1vin:Warning: there is no chain 1vin will retry with 1vinA # T0338 read from 1vin/merged-good-all-a2m # 1vin read from 1vin/merged-good-all-a2m # adding 1vin to template set # found chain 1vin in template set Warning: unaligning (T0338)S2 because first residue in template chain is (1vin)D181 Warning: unaligning (T0338)R158 because of BadResidue code BAD_PEPTIDE at template residue (1vin)P324 T0338 3 :SRWFFTREQLENTPSR 1vin 182 :IHTYLREMEVKCKPKV T0338 19 :RCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 1vin 199 :YMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEE T0338 103 :ACLHPLEPLLDTKCDAY 1vin 270 :IYPPEVAEFVYITDDTY T0338 122 :QTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLV 1vin 287 :TKKQVLRMEHLVLKVLAFDLAAPTINQFLTQYFLHQ T0338 159 :ASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWE 1vin 325 :ANCKVESLAMFLGELSLIDADPYLKYLPSVIAAAAFHLALYTVTGQ T0338 206 :PVSTDGKHWWE 1vin 371 :SWPESLVQKTG T0338 222 :VTLELLDELTHEFLQILEKTPNRLKKIRNWRANQ 1vin 382 :YTLETLKPCLLDLHQTYLRAPQHAQQSIREKYKN Number of specific fragments extracted= 7 number of extra gaps= 1 total=204 Number of alignments=28 # 1vin read from 1vin/merged-good-all-a2m # found chain 1vin in template set Warning: unaligning (T0338)R158 because of BadResidue code BAD_PEPTIDE in next template residue (1vin)P324 T0338 3 :SRWFFTREQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 1vin 183 :HTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEE T0338 103 :ACLHPLEPLLDTKCDAYL 1vin 270 :IYPPEVAEFVYITDDTYT T0338 123 :TRELVILETIMLQTLGFEITIEHPHTDVVKCTQLV 1vin 288 :KKQVLRMEHLVLKVLAFDLAAPTINQFLTQYFLHQ T0338 159 :ASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNW 1vin 325 :ANCKVESLAMFLGELSLIDADPYLKYLPSVIAAAAFHLALYTVTG T0338 206 :PVSTDGKHWWE 1vin 370 :QSWPESLVQKT T0338 221 :TVTLELLDELTHEFLQILEKTPNRLKKIRNWRANQ 1vin 381 :GYTLETLKPCLLDLHQTYLRAPQHAQQSIREKYKN Number of specific fragments extracted= 6 number of extra gaps= 1 total=210 Number of alignments=29 # 1vin read from 1vin/merged-good-all-a2m # found chain 1vin in template set Warning: unaligning (T0338)R158 because of BadResidue code BAD_PEPTIDE at template residue (1vin)P324 T0338 2 :SSRWFFTREQLENTPSRRC 1vin 182 :IHTYLREMEVKCKPKVGYM T0338 21 :GVEAD 1vin 205 :DITNS T0338 30 :CRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHA 1vin 210 :MRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITD T0338 119 :YLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLV 1vin 284 :DTYTKKQVLRMEHLVLKVLAFDLAAPTINQFLTQYFLHQ T0338 159 :ASKDLAQTSYFMATNSLHLTTFCLQYKPTVIACVCIHLACKWSNWEIPVS 1vin 325 :ANCKVESLAMFLGELSLIDADPYLKYLPSVIAAAAFHLALYTVTGQSWPE T0338 215 :WEYVDPTVTLELLDELTHEFLQILEKTPN 1vin 375 :SLVQKTGYTLETLKPCLLDLHQTYLRAPQ Number of specific fragments extracted= 6 number of extra gaps= 1 total=216 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c5nB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0338/2c5nB/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0338/2c5nB/merged-good-all-a2m.gz for input Trying 2c5nB/merged-good-all-a2m Error: Couldn't open file 2c5nB/merged-good-all-a2m or 2c5nB/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cchB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cchB expands to /projects/compbio/data/pdb/2cch.pdb.gz 2cchB:Skipped atom 2639, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 2641, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 2643, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 2645, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 2647, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 2649, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3086, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3088, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3090, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3092, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3094, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3096, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3737, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3739, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3741, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3743, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3745, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3747, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3774, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3776, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3778, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3780, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3782, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3784, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3799, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3801, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3803, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3805, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3807, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3809, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3811, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3813, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3917, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3919, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3921, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3923, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3925, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3927, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3929, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3931, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3982, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3984, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3986, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3988, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3990, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3992, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3994, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 3996, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4096, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4098, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4100, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4102, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4104, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4106, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4108, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4110, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4112, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4275, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4277, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4279, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4281, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4283, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4285, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4287, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4289, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4496, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4498, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4500, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4502, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4504, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4506, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4594, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4596, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4598, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4600, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4602, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4604, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4606, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4608, because occupancy 0.500 <= existing 0.500 in 2cchB Skipped atom 4610, because occupancy 0.500 <= existing 0.500 in 2cchB # T0338 read from 2cchB/merged-good-all-a2m # 2cchB read from 2cchB/merged-good-all-a2m # adding 2cchB to template set # found chain 2cchB in template set Warning: unaligning (T0338)F180 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cchB)Y347 Warning: unaligning (T0338)C181 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cchB)Y347 T0338 2 :SSRWFFTREQLENTPSR 2cchB 181 :DIHTYLREMEVKCKPKV T0338 19 :RCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 2cchB 199 :YMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEE T0338 103 :ACLHPLEPLLDTKCDAY 2cchB 270 :IYPPEVAEFVYITDDTY T0338 122 :QTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVR 2cchB 287 :TKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQ T0338 159 :ASKDLAQTSYFMATNSLHLTT 2cchB 325 :ANCKVESLAMFLGELSLIDAD T0338 182 :LQYKPTVIACVCIHLACKWSNWE 2cchB 348 :LKYLPSVIAGAAFHLALYTVTGQ T0338 206 :PVSTDGKHWWE 2cchB 371 :SWPESLIRKTG T0338 222 :VTLELLDELTHEFLQILEKTPNRLKKIRNWRANQ 2cchB 382 :YTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKN Number of specific fragments extracted= 8 number of extra gaps= 1 total=224 Number of alignments=31 # 2cchB read from 2cchB/merged-good-all-a2m # found chain 2cchB in template set Warning: unaligning (T0338)F180 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cchB)Y347 Warning: unaligning (T0338)C181 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cchB)Y347 T0338 3 :SRWFFTREQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 2cchB 183 :HTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEE T0338 103 :ACLHPLEPLLDTKCDAYL 2cchB 270 :IYPPEVAEFVYITDDTYT T0338 123 :TRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVR 2cchB 288 :KKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQ T0338 159 :ASKDLAQTSYFMATNSLHLTT 2cchB 325 :ANCKVESLAMFLGELSLIDAD T0338 182 :LQYKPTVIACVCIHLACKWSNW 2cchB 348 :LKYLPSVIAGAAFHLALYTVTG T0338 206 :PVSTDGKHWWE 2cchB 370 :QSWPESLIRKT T0338 221 :TVTLELLDELTHEFLQILEKTPNRLKKIRNWRANQ 2cchB 381 :GYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKN Number of specific fragments extracted= 7 number of extra gaps= 1 total=231 Number of alignments=32 # 2cchB read from 2cchB/merged-good-all-a2m # found chain 2cchB in template set Warning: unaligning (T0338)F180 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cchB)Y347 Warning: unaligning (T0338)C181 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cchB)Y347 T0338 4 :RWFFTREQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHA 2cchB 184 :TYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITD T0338 119 :YLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLV 2cchB 284 :DTYTKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQ T0338 158 :RASKDLAQTSYFMATNSLHLTT 2cchB 324 :PANCKVESLAMFLGELSLIDAD T0338 182 :LQYKPTVIACVCIHLACKWSNWEIPVS 2cchB 348 :LKYLPSVIAGAAFHLALYTVTGQSWPE T0338 215 :WEYVDPTVTLELLDELTHEFLQILEKTPN 2cchB 375 :SLIRKTGYTLESLKPCLMDLHQTYLKAPQ Number of specific fragments extracted= 5 number of extra gaps= 1 total=236 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e9hB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0338/1e9hB/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0338/1e9hB/merged-good-all-a2m.gz for input Trying 1e9hB/merged-good-all-a2m Error: Couldn't open file 1e9hB/merged-good-all-a2m or 1e9hB/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bu2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bu2A expands to /projects/compbio/data/pdb/1bu2.pdb.gz 1bu2A:# T0338 read from 1bu2A/merged-good-all-a2m # 1bu2A read from 1bu2A/merged-good-all-a2m # adding 1bu2A to template set # found chain 1bu2A in template set T0338 7 :FTREQLENTPSR 1bu2A 26 :NLKLRELLLPKF T0338 19 :RCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 1bu2A 40 :LWEIQTEVTVDNRTILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRT T0338 103 :ACLHPLEPLLDTKCDAY 1bu2A 111 :VKPMTVSKLTYLSCDCF T0338 122 :QTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRAS 1bu2A 128 :TNLELINQEKDILEALKWDTEAVLATDFLIPLCNALKIP T0338 161 :KDLAQTSYFMATNSLH 1bu2A 171 :PQLYEAASTTICKALI T0338 178 :TTFCLQYKPTVIACVCIHLACKWSN 1bu2A 187 :QPNIALLSPGLICAGGLLTTIETDN T0338 203 :WEIPVSTDGKHWWEYVD 1bu2A 213 :NCRPWTCYLEDLSSILN T0338 226 :LLDELTHEFLQILEKTPNRL 1bu2A 230 :FSTNTVRTVKDQVSEAFSLY Number of specific fragments extracted= 8 number of extra gaps= 0 total=244 Number of alignments=34 # 1bu2A read from 1bu2A/merged-good-all-a2m # found chain 1bu2A in template set T0338 3 :SRWFFTREQLENTPSRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 1bu2A 24 :LNNLKLRELLLPKFTSLWEIQTEVTVDNRTILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRT T0338 103 :ACLHPLEPLLDTKCDAYL 1bu2A 111 :VKPMTVSKLTYLSCDCFT T0338 123 :TRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1bu2A 129 :NLELINQEKDILEALKWDTEAVLATDFLIPLCNALKIPED T0338 163 :LAQTSYFMATNSLH 1bu2A 173 :LYEAASTTICKALI T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIP 1bu2A 187 :QPNIALLSPGLICAGGLLTTIETDNTNCR T0338 207 :VSTDGK 1bu2A 223 :DLSSIL T0338 225 :ELLDELTHEFLQILEKTPNR 1bu2A 229 :NFSTNTVRTVKDQVSEAFSL Number of specific fragments extracted= 7 number of extra gaps= 0 total=251 Number of alignments=35 # 1bu2A read from 1bu2A/merged-good-all-a2m # found chain 1bu2A in template set T0338 23 :EAD 1bu2A 48 :TVD T0338 30 :CRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHA 1bu2A 51 :NRTILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSC T0338 119 :YLQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLV 1bu2A 125 :DCFTNLELINQEKDILEALKWDTEAVLATDFLIPLCNAL T0338 158 :RASKDLAQTSYFMATNSLH 1bu2A 168 :DLWPQLYEAASTTICKALI T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWE 1bu2A 187 :QPNIALLSPGLICAGGLLTTIETDNTN T0338 210 :DGKHWWEYVDPTVTLELLDELTHEFLQILEKTPNRL 1bu2A 214 :CRPWTCYLEDLSSILNFSTNTVRTVKDQVSEAFSLY Number of specific fragments extracted= 6 number of extra gaps= 0 total=257 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g9xB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0338/2g9xB/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0338/2g9xB/merged-good-all-a2m.gz for input Trying 2g9xB/merged-good-all-a2m Error: Couldn't open file 2g9xB/merged-good-all-a2m or 2g9xB/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g3nC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g3nC expands to /projects/compbio/data/pdb/1g3n.pdb.gz 1g3nC:# T0338 read from 1g3nC/merged-good-all-a2m # 1g3nC read from 1g3nC/merged-good-all-a2m # adding 1g3nC to template set # found chain 1g3nC in template set Warning: unaligning (T0338)S17 because of BadResidue code BAD_PEPTIDE in next template residue (1g3nC)D36 Warning: unaligning (T0338)R18 because of BadResidue code BAD_PEPTIDE at template residue (1g3nC)D36 Warning: unaligning (T0338)V207 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1g3nC)G219 T0338 3 :SRWFFTREQLENTP 1g3nC 21 :IFYNILEIEPRFLT T0338 19 :RC 1g3nC 37 :SV T0338 23 :EADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 1g3nC 43 :QQSLTSHMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRS T0338 103 :ACLHPLEPLLDTKCDAY 1g3nC 110 :LTPISTSSLCYAAADSF T0338 122 :QTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1g3nC 127 :SRQELIDQEKELLEKLAWRTEAVLATDVTSFLLLKLVGGSQ T0338 163 :LAQTSYFMATNSLH 1g3nC 172 :WHHEVNTLITKALV T0338 178 :TTFCLQYKPTVIACVCIHLAC 1g3nC 186 :DPLTGSLPASIISAAGCALLV T0338 205 :IP 1g3nC 211 :IP T0338 208 :STDGKHWWE 1g3nC 221 :VPQLASILG T0338 222 :VTLELLDELTHEFLQILEKTP 1g3nC 230 :CDVSVLQAAVEQILTSVSDFD Number of specific fragments extracted= 10 number of extra gaps= 1 total=267 Number of alignments=37 # 1g3nC read from 1g3nC/merged-good-all-a2m # found chain 1g3nC in template set Warning: unaligning (T0338)T15 because of BadResidue code BAD_PEPTIDE in next template residue (1g3nC)D36 Warning: unaligning (T0338)P16 because of BadResidue code BAD_PEPTIDE at template residue (1g3nC)D36 T0338 3 :SRWFFTRE 1g3nC 22 :FYNILEIE T0338 11 :QLEN 1g3nC 31 :RFLT T0338 17 :SRRCGVEADKELSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQ 1g3nC 37 :SVFGTFQQSLTSHMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSL T0338 91 :ARKLEHVIKVAHAC 1g3nC 112 :PISTSSLCYAAADS T0338 119 :YL 1g3nC 126 :FS T0338 123 :TRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1g3nC 128 :RQELIDQEKELLEKLAWRTEAVLATDVTSFLLLKLVGGSQ T0338 163 :LAQTSYFMATNSLH 1g3nC 172 :WHHEVNTLITKALV T0338 178 :TTFCLQYKPTVIACVCIHLA 1g3nC 186 :DPLTGSLPASIISAAGCALL T0338 205 :IPVST 1g3nC 206 :VPANV T0338 212 :K 1g3nC 211 :I T0338 221 :TVTLELLDELTHEFLQILEKTP 1g3nC 229 :GCDVSVLQAAVEQILTSVSDFD Number of specific fragments extracted= 11 number of extra gaps= 1 total=278 Number of alignments=38 # 1g3nC read from 1g3nC/merged-good-all-a2m # found chain 1g3nC in template set Warning: unaligning (T0338)G211 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1g3nC)G219 T0338 28 :LSCRQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEE 1g3nC 48 :SHMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRS T0338 90 :QARKLEHVIKVAHA 1g3nC 111 :TPISTSSLCYAAAD T0338 120 :LQQTRELVILETIMLQTLGFEITIEHPHTDVVKCTQLVRASKD 1g3nC 125 :SFSRQELIDQEKELLEKLAWRTEAVLATDVTSFLLLKLVGGSQ T0338 163 :LAQTSYFMATNSLH 1g3nC 172 :WHHEVNTLITKALV T0338 178 :TTFCLQYKPTVIACVCIHLA 1g3nC 186 :DPLTGSLPASIISAAGCALL T0338 205 :IPVSTD 1g3nC 206 :VPANVI T0338 212 :KHWWEYVDPTVTLELLDELTHEFLQILEKTP 1g3nC 220 :VVPQLASILGCDVSVLQAAVEQILTSVSDFD Number of specific fragments extracted= 7 number of extra gaps= 0 total=285 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aisB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aisB expands to /projects/compbio/data/pdb/1ais.pdb.gz 1aisB:# T0338 read from 1aisB/merged-good-all-a2m # 1aisB read from 1aisB/merged-good-all-a2m # adding 1aisB to template set # found chain 1aisB in template set T0338 31 :RQQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVE 1aisB 1109 :LAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLL T0338 103 :ACLHPLEPLLDT 1aisB 1167 :KVPRTLDEIADI T0338 117 :DAY 1aisB 1179 :ARV T0338 122 :QTRELVILETIMLQTLGFE 1aisB 1182 :DKKEIGRSYRFIARNLNLT T0338 144 :EHPHTDVVKCTQLVRASKDLAQTSYFMATNSLH 1aisB 1206 :VKPTDYVNKFADELGLSEKVRRRAIEILDEAYK T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIPV 1aisB 1239 :RGLTSGKSPAGLVAAALYIASLLEGEKRTQ T0338 209 :TDGKHWWE 1aisB 1269 :REVAEVAR T0338 222 :VTLELLDELTHEFLQILE 1aisB 1277 :VTEVTVRNRYKELVEKLK Number of specific fragments extracted= 8 number of extra gaps= 0 total=293 Number of alignments=40 # 1aisB read from 1aisB/merged-good-all-a2m # found chain 1aisB in template set T0338 32 :QQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAHAC 1aisB 1110 :AFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVD T0338 123 :TRELVILETIMLQTLGFE 1aisB 1183 :KKEIGRSYRFIARNLNLT T0338 144 :EHPHTDVVKCTQLVRASKDLAQTSYFMATNSLH 1aisB 1206 :VKPTDYVNKFADELGLSEKVRRRAIEILDEAYK T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIP 1aisB 1239 :RGLTSGKSPAGLVAAALYIASLLEGEKRT T0338 221 :TVTLELLDELTHEFLQIL 1aisB 1276 :RVTEVTVRNRYKELVEKL Number of specific fragments extracted= 5 number of extra gaps= 0 total=298 Number of alignments=41 # 1aisB read from 1aisB/merged-good-all-a2m # found chain 1aisB in template set T0338 32 :QQAANLIQEMGQRLNVSQLTINTAIVYMHRFYMHHSFTKFNKNIISSTALFLAAKVEEQARKLEHVIKVAH 1aisB 1110 :AFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIAR T0338 121 :QQTRELVILETIMLQTLGFE 1aisB 1181 :VDKKEIGRSYRFIARNLNLT T0338 141 :ITI 1aisB 1204 :LFV T0338 145 :HPHTDVVKCTQLVRASKDLAQTSYFMATNSLH 1aisB 1207 :KPTDYVNKFADELGLSEKVRRRAIEILDEAYK T0338 178 :TTFCLQYKPTVIACVCIHLACKWSNWEIPVS 1aisB 1239 :RGLTSGKSPAGLVAAALYIASLLEGEKRTQR T0338 215 :WEYVDPTVTLELLDELTHEFLQIL 1aisB 1270 :EVAEVARVTEVTVRNRYKELVEKL Number of specific fragments extracted= 6 number of extra gaps= 0 total=304 Number of alignments=42 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 42 Done printing distance constraints # command: