# 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/T0289/ # command:# Making conformation for sequence T0289 numbered 1 through 312 Created new target T0289 from T0289.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0289/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0289//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0289/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0289//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0289/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0289/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0289/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yw4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yw4A expands to /projects/compbio/data/pdb/1yw4.pdb.gz 1yw4A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0289 read from 1yw4A/merged-good-all-a2m # 1yw4A read from 1yw4A/merged-good-all-a2m # adding 1yw4A to template set # found chain 1yw4A in template set Warning: unaligning (T0289)N132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yw4A)R170 Warning: unaligning (T0289)F261 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yw4A)A301 Warning: unaligning (T0289)P270 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yw4A)A301 T0289 8 :EPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVHRA 1yw4A 44 :RGADSVLLSCGVHGNETAPIEVVDGMLTDIAAGQLA # choosing archetypes in rotamer library T0289 44 :GLEVKPFITNPRAVEKCTRYIDCDLNRVFDLENLSKEMS 1yw4A 81 :NCRLLVMFANLDAIRQGVRYGNYDMNRLFNGAHARHPEL T0289 87 :YEVRRAQEINHLF 1yw4A 120 :PESVRAAELETLA T0289 100 :GPKNSD 1yw4A 135 :FFAGAR T0289 107 :AYDVVFDLHNT 1yw4A 141 :ARKLHYDLHTA T0289 118 :TSNMGCTLILEDSR 1yw4A 153 :RGSVFEKFAIYPFL T0289 133 :DFLIQMFHYIK 1yw4A 171 :THKREQLAWLQ T0289 146 :MAPLPCSVYL 1yw4A 182 :RCGIEAVLLH T0289 156 :IEHPSLKYATTRSIAKYPVGIEVGPQ 1yw4A 193 :QPANTFSYFTSQYCEADAFTLELGKA T0289 182 :PHGVLRADILDQMRRMLKHALD 1yw4A 220 :PFGQNDLSRFSGIDGALRGLLS T0289 209 :NEGKEFPPC 1yw4A 242 :NPQANVPDL T0289 218 :AIDVYKIMEKVDYP 1yw4A 254 :KLPLFRAKYDLVKH T0289 242 :IHP 1yw4A 275 :LAD T0289 247 :QDQDWKPLHPGDPV 1yw4A 278 :SVENFTLLPDGMLI T0289 271 :LGGDCTVYP 1yw4A 302 :TGGEERILF Number of specific fragments extracted= 15 number of extra gaps= 0 total=15 Number of alignments=1 # 1yw4A read from 1yw4A/merged-good-all-a2m # found chain 1yw4A in template set Warning: unaligning (T0289)N132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yw4A)R170 Warning: unaligning (T0289)S235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yw4A)F271 Warning: unaligning (T0289)V238 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yw4A)F271 Warning: unaligning (T0289)F261 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yw4A)A301 Warning: unaligning (T0289)P270 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yw4A)A301 T0289 8 :EPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1yw4A 44 :RGADSVLLSCGVHGNETAPIEVVDGMLTDIAAGQ T0289 42 :RAGLEVKPFITNPRAVEKCTRYIDCDLNRVFDLENLSKEMS 1yw4A 79 :ALNCRLLVMFANLDAIRQGVRYGNYDMNRLFNGAHARHPEL T0289 87 :YEVRRAQEINHLFGPKNSD 1yw4A 120 :PESVRAAELETLAAEFFAG T0289 106 :DAYDVVFDLHNT 1yw4A 140 :RARKLHYDLHTA T0289 118 :TSNMGCTLILED 1yw4A 153 :RGSVFEKFAIYP T0289 133 :DFLIQMFHYIKTC 1yw4A 171 :THKREQLAWLQRC T0289 148 :PLPCSVYLIEHP 1yw4A 184 :GIEAVLLHTQPA T0289 160 :SLKYATTRSIAKYPVGIEVGPQ 1yw4A 197 :TFSYFTSQYCEADAFTLELGKA T0289 182 :PHGVLRADILDQMRRMLKHALDFI 1yw4A 220 :PFGQNDLSRFSGIDGALRGLLSNP T0289 209 :NEG 1yw4A 244 :QAN T0289 212 :KEFPPCAIDVYKIMEKVD 1yw4A 248 :PDLDEDKLPLFRAKYDLV T0289 233 :NE 1yw4A 266 :KH T0289 239 :A 1yw4A 272 :K T0289 243 :H 1yw4A 273 :L T0289 245 :NLQDQ 1yw4A 274 :NLADS T0289 250 :DWKPLHPGDPV 1yw4A 281 :NFTLLPDGMLI T0289 271 :LGGDC 1yw4A 302 :TGGEE T0289 278 :YPVFVNEAAYYEKKEAFAKTTKL 1yw4A 307 :RILFPNPAVKPGLRAGIVVEPAR Number of specific fragments extracted= 18 number of extra gaps= 0 total=33 Number of alignments=2 # 1yw4A read from 1yw4A/merged-good-all-a2m # found chain 1yw4A in template set Warning: unaligning (T0289)R131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yw4A)R170 Warning: unaligning (T0289)D133 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yw4A)R170 Warning: unaligning (T0289)D237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yw4A)F271 Warning: unaligning (T0289)A240 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yw4A)F271 Warning: unaligning (T0289)F261 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yw4A)A301 Warning: unaligning (T0289)P270 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yw4A)A301 T0289 8 :EPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVHR 1yw4A 44 :RGADSVLLSCGVHGNETAPIEVVDGMLTDIAAGQL T0289 43 :AGLEVKPFITNPRAVEKCTRYIDCDLNRVFDLENLSKEMSE 1yw4A 80 :LNCRLLVMFANLDAIRQGVRYGNYDMNRLFNGAHARHPELP T0289 85 :LPYEVRRAQEINHLFGPKN 1yw4A 121 :ESVRAAELETLAAEFFAGA T0289 106 :DAYDVVFDLHNTT 1yw4A 140 :RARKLHYDLHTAI T0289 119 :SNMGCTLILEDS 1yw4A 155 :SVFEKFAIYPFL T0289 134 :FLIQMFHYIKTCMAPLPCSVYLIEHPSLKYATTRSIAKYPVGIEVGPQ 1yw4A 171 :THKREQLAWLQRCGIEAVLLHTQPANTFSYFTSQYCEADAFTLELGKA T0289 182 :PHGVLRADILDQMRRMLKHALD 1yw4A 220 :PFGQNDLSRFSGIDGALRGLLS T0289 209 :NEGKEFPPCA 1yw4A 242 :NPQANVPDLD T0289 219 :IDVYKIMEKVD 1yw4A 255 :LPLFRAKYDLV T0289 235 :SG 1yw4A 266 :KH T0289 241 :VIHPNLQDQDWKPLHPGDPV 1yw4A 272 :KLNLADSVENFTLLPDGMLI T0289 271 :LGGDCTVYPVFVNE 1yw4A 302 :TGGEERILFPNPAV Number of specific fragments extracted= 12 number of extra gaps= 0 total=45 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z5rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z5rA expands to /projects/compbio/data/pdb/1z5r.pdb.gz 1z5rA:# T0289 read from 1z5rA/merged-good-all-a2m # 1z5rA read from 1z5rA/merged-good-all-a2m # adding 1z5rA to template set # found chain 1z5rA in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1z5rA)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1z5rA)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1z5rA)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1z5rA)Y206 Warning: unaligning (T0289)P180 because of BadResidue code BAD_PEPTIDE at template residue (1z5rA)D273 T0289 3 :SCVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1z5rA 52 :VGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTY T0289 42 :RAGLEVKPF 1z5rA 100 :LNKLDFYVL T0289 51 :ITNPRAVEKC 1z5rA 110 :VLNIDGYIYT T0289 61 :T 1z5rA 129 :T T0289 66 :CDLNRVFDL 1z5rA 141 :TDPNRNFDA T0289 75 :ENLSKEMS 1z5rA 167 :GSAAESEK T0289 88 :EVR 1z5rA 175 :ETK T0289 91 :RAQEINHLF 1z5rA 179 :LADFIRNNL T0289 106 :DAYDVVFDLH 1z5rA 187A:SSIKAYLTIH T0289 118 :TSNMGC 1z5rA 199 :SQMILY T0289 126 :ILEDSRNDFLIQMFHYIKTCM 1z5rA 207 :SYDYKLPENNAELNNLAKAAV T0289 147 :APLPCSVYL 1z5rA 234 :YGTKYTYGP T0289 156 :IEHPSLKYATTRSIAKY 1z5rA 248 :YPAAGGSDDWAYDQGIK T0289 173 :PVGIEV 1z5rA 266 :SFTFEL T0289 181 :QP 1z5rA 274 :KG T0289 183 :HGVLRADILDQMRRMLKHALDFI 1z5rA 278 :GFILPESQIQATCEETMLAIKYV T0289 206 :QRFNEG 1z5rA 302 :NYVLGH Number of specific fragments extracted= 17 number of extra gaps= 3 total=62 Number of alignments=4 # 1z5rA read from 1z5rA/merged-good-all-a2m # found chain 1z5rA in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1z5rA)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1z5rA)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1z5rA)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1z5rA)Y206 Warning: unaligning (T0289)G179 because of BadResidue code BAD_PEPTIDE in next template residue (1z5rA)D273 Warning: unaligning (T0289)P180 because of BadResidue code BAD_PEPTIDE at template residue (1z5rA)D273 T0289 4 :CVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1z5rA 53 :GKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTY T0289 42 :RAGLEVKPF 1z5rA 100 :LNKLDFYVL T0289 51 :ITNPRAVEKC 1z5rA 110 :VLNIDGYIYT T0289 61 :TRYI 1z5rA 126 :WRKT T0289 66 :C 1z5rA 140 :G T0289 67 :DLNRVFDLENLSKEMS 1z5rA 142 :DPNRNFDAGWCTTGAS T0289 83 :EDLPYEVRRAQEINHLFG 1z5rA 170 :AESEKETKALADFIRNNL T0289 106 :DAYDVVFDLH 1z5rA 187A:SSIKAYLTIH T0289 118 :TSNMGC 1z5rA 199 :SQMILY T0289 126 :ILEDSRNDFLI 1z5rA 207 :SYDYKLPENNA T0289 137 :QMFHYIKTCM 1z5rA 225 :AAVKELATLY T0289 148 :PLPCSVYL 1z5rA 235 :GTKYTYGP T0289 156 :IEHPSLKYATTRSIAK 1z5rA 248 :YPAAGGSDDWAYDQGI T0289 172 :YPVGIEV 1z5rA 265 :YSFTFEL T0289 181 :Q 1z5rA 274 :K T0289 182 :PHG 1z5rA 276 :RYG T0289 185 :VLRADILDQMRRMLKHALDFI 1z5rA 280 :ILPESQIQATCEETMLAIKYV T0289 206 :QRF 1z5rA 302 :NYV Number of specific fragments extracted= 18 number of extra gaps= 3 total=80 Number of alignments=5 # 1z5rA read from 1z5rA/merged-good-all-a2m # found chain 1z5rA in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1z5rA)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1z5rA)Y198 Warning: unaligning (T0289)E128 because of BadResidue code BAD_PEPTIDE in next template residue (1z5rA)Y206 Warning: unaligning (T0289)D129 because of BadResidue code BAD_PEPTIDE at template residue (1z5rA)Y206 Warning: unaligning (T0289)G179 because of BadResidue code BAD_PEPTIDE in next template residue (1z5rA)D273 Warning: unaligning (T0289)P180 because of BadResidue code BAD_PEPTIDE at template residue (1z5rA)D273 T0289 5 :VAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1z5rA 54 :KPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTY T0289 44 :G 1z5rA 91 :G T0289 45 :LEVKPFITNPRAVEKCT 1z5rA 104 :DFYVLPVLNIDGYIYTW T0289 62 :RYI 1z5rA 124 :RMW T0289 65 :DCDLNRVFDLENLSKEMSED 1z5rA 140 :GTDPNRNFDAGWCTTGASTD T0289 91 :RAQEINHLFGPKN 1z5rA 174 :KETKALADFIRNN T0289 105 :DDAYDVVFDLH 1z5rA 187 :LSSIKAYLTIH T0289 118 :T 1z5rA 199 :S T0289 124 :TLIL 1z5rA 201 :MILY T0289 130 :SRND 1z5rA 207 :SYDY T0289 134 :FLIQMFHYIKTCMA 1z5rA 222 :LAKAAVKELATLYG T0289 149 :LPCS 1z5rA 236 :TKYT T0289 160 :SLKYATTRSIAKYPVGIEV 1z5rA 253 :GSDDWAYDQGIKYSFTFEL T0289 181 :Q 1z5rA 274 :K T0289 182 :PHGVLRADILDQMRRMLKHALDFIQRF 1z5rA 277 :YGFILPESQIQATCEETMLAIKYVTNY Number of specific fragments extracted= 15 number of extra gaps= 3 total=95 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yw6A/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/T0289/1yw6A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0289/1yw6A/merged-good-all-a2m.gz for input Trying 1yw6A/merged-good-all-a2m Error: Couldn't open file 1yw6A/merged-good-all-a2m or 1yw6A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c1cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c1cA expands to /projects/compbio/data/pdb/2c1c.pdb.gz 2c1cA:# T0289 read from 2c1cA/merged-good-all-a2m # 2c1cA read from 2c1cA/merged-good-all-a2m # adding 2c1cA to template set # found chain 2c1cA in template set Warning: unaligning (T0289)N116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c1cA)F198 Warning: unaligning (T0289)T117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c1cA)F198 Warning: unaligning (T0289)T124 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c1cA)W206 Warning: unaligning (T0289)L125 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c1cA)W206 T0289 6 :AEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 2c1cA 56B:EDENKPVIFIDGGIHAREWISPPSVTWAIHKLVEDV T0289 42 :RAGLEVKPF 2c1cA 100 :LEKFDWILL T0289 51 :ITNPRAVEKC 2c1cA 110 :VVNPDGYKYT T0289 65 :DCDLNRVFDL 2c1cA 140 :GADGNRNFDF T0289 75 :E 2c1cA 167 :G T0289 81 :MSEDLPYEVRRAQEINHLF 2c1cA 168 :TSAFSEVETRVVRDILHEH T0289 104 :SD 2c1cA 187 :LA T0289 107 :AYDVVFDLH 2c1cA 188A:RMALYLTMH T0289 118 :TSNMGC 2c1cA 199 :GSMILY T0289 126 :ILEDSRNDFLIQMFHYIKTCM 2c1cA 207 :GHDGSLSQNALGLHTVGVAMA T0289 147 :AP 2c1cA 236 :PN T0289 149 :LPCSVYL 2c1cA 236C:PPYTVGN T0289 156 :IEHPSLKYATTRSIAKY 2c1cA 248 :YYIAGSSEDYAHSIGVP T0289 173 :PVGIEVGPQPHG 2c1cA 266 :SYTYELPGLSSG T0289 185 :VLRADILDQMRRMLKHALDFI 2c1cA 280 :HLPPQYIEQVCRETWEGIVVG Number of specific fragments extracted= 15 number of extra gaps= 2 total=110 Number of alignments=7 # 2c1cA read from 2c1cA/merged-good-all-a2m # found chain 2c1cA in template set Warning: unaligning (T0289)N116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c1cA)F198 Warning: unaligning (T0289)T117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c1cA)F198 Warning: unaligning (T0289)T124 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c1cA)W206 Warning: unaligning (T0289)L125 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c1cA)W206 T0289 7 :EEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 2c1cA 57 :DENKPVIFIDGGIHAREWISPPSVTWAIHKLVEDV T0289 42 :RAGLEVKPF 2c1cA 100 :LEKFDWILL T0289 51 :ITNPRAVEKC 2c1cA 110 :VVNPDGYKYT T0289 61 :TRYI 2c1cA 126 :WRKT T0289 65 :D 2c1cA 131 :S T0289 66 :C 2c1cA 140 :G T0289 67 :DLNRVFDLENLSKEMS 2c1cA 142 :DGNRNFDFVWNSIGTS T0289 83 :EDLPYEVRRAQEINHLFG 2c1cA 170 :AFSEVETRVVRDILHEHL T0289 106 :DAYDVVFDLH 2c1cA 188 :ARMALYLTMH T0289 118 :TSNMGC 2c1cA 199 :GSMILY T0289 126 :ILEDSRNDFLI 2c1cA 207 :GHDGSLSQNAL T0289 138 :MFHYIKTCMAPL 2c1cA 222 :VGVAMASVIQSN T0289 150 :PCSVYL 2c1cA 237 :PYTVGN T0289 156 :IEHPSLKYATTRSIAK 2c1cA 248 :YYIAGSSEDYAHSIGV T0289 172 :YPVGIEVGPQPHG 2c1cA 265 :LSYTYELPGLSSG T0289 185 :VLRADILDQMRRMLKHALDFI 2c1cA 280 :HLPPQYIEQVCRETWEGIVVG Number of specific fragments extracted= 16 number of extra gaps= 2 total=126 Number of alignments=8 # 2c1cA read from 2c1cA/merged-good-all-a2m # found chain 2c1cA in template set Warning: unaligning (T0289)N116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c1cA)F198 Warning: unaligning (T0289)T117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c1cA)F198 Warning: unaligning (T0289)E128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c1cA)W206 Warning: unaligning (T0289)D129 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c1cA)W206 T0289 8 :EPIKKIAIFGGTHGNE 2c1cA 58 :ENKPVIFIDGGIHARE T0289 24 :LTGVFLVTHWLKNGAEVHR 2c1cA 77 :PSVTWAIHKLVEDVTENDL T0289 43 :AGLEVKPF 2c1cA 101 :EKFDWILL T0289 51 :ITNPRAVEKCT 2c1cA 110 :VVNPDGYKYTF T0289 62 :RYI 2c1cA 124 :RFW T0289 65 :DCDLNRVFDLENL 2c1cA 140 :GADGNRNFDFVWN T0289 78 :SKEMSED 2c1cA 157 :SNSPCSD T0289 87 :YEVRRAQEINHLF 2c1cA 174 :VETRVVRDILHEH T0289 105 :DDAYDVVFDLH 2c1cA 187 :LARMALYLTMH T0289 118 :T 2c1cA 199 :G T0289 123 :CTLIL 2c1cA 200 :SMILY T0289 130 :SRNDFL 2c1cA 207 :GHDGSL T0289 136 :IQMFHYIKTCMAPL 2c1cA 224 :VAMASVIQSNALPN T0289 150 :PCS 2c1cA 237 :PYT T0289 170 :AKYPVGIEVGPQPHG 2c1cA 263 :VPLSYTYELPGLSSG T0289 185 :VLRADILDQMRRMLKHALDFIQRF 2c1cA 284 :QYIEQVCRETWEGIVVGARRAGDL Number of specific fragments extracted= 16 number of extra gaps= 2 total=142 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kwmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kwmA expands to /projects/compbio/data/pdb/1kwm.pdb.gz 1kwmA:Skipped atom 268, because occupancy 0.47 <= existing 0.530 in 1kwmA Skipped atom 270, because occupancy 0.470 <= existing 0.530 in 1kwmA Skipped atom 272, because occupancy 0.470 <= existing 0.530 in 1kwmA WARNING: atom 790 has residue number 4 < previous residue 95A in 1kwmA Skipped atom 1086, because occupancy 0.330 <= existing 0.670 in 1kwmA Skipped atom 1088, because occupancy 0.330 <= existing 0.670 in 1kwmA Skipped atom 1090, because occupancy 0.330 <= existing 0.670 in 1kwmA Skipped atom 1311, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1313, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1315, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1317, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1319, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1321, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1961, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1963, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1965, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1967, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1969, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1971, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1973, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 2225, because occupancy 0.350 <= existing 0.650 in 1kwmA Skipped atom 2227, because occupancy 0.350 <= existing 0.650 in 1kwmA Skipped atom 2229, because occupancy 0.350 <= existing 0.650 in 1kwmA Skipped atom 2231, because occupancy 0.350 <= existing 0.650 in 1kwmA Skipped atom 2315, because occupancy 0.340 <= existing 0.660 in 1kwmA Skipped atom 2317, because occupancy 0.340 <= existing 0.660 in 1kwmA # T0289 read from 1kwmA/merged-good-all-a2m # 1kwmA read from 1kwmA/merged-good-all-a2m # adding 1kwmA to template set # found chain 1kwmA in template set Warning: unaligning (T0289)L45 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1kwmA)D104 Warning: unaligning (T0289)E46 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1kwmA)D104 Warning: unaligning (T0289)L68 because of BadResidue code BAD_PEPTIDE in next template residue (1kwmA)N144 Warning: unaligning (T0289)N69 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)N144 Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1kwmA)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)Y198 Warning: unaligning (T0289)T118 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)S199 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1kwmA)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)Y206 T0289 3 :SCVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1kwmA 52 :VGKAGQNKPAIFMDCGFHAREWISPAFCQWFVREAVRTY T0289 42 :RAG 1kwmA 100 :LNK T0289 47 :VKPF 1kwmA 105 :FYVL T0289 51 :ITNPRAVEKC 1kwmA 110 :VLNIDGYIYT T0289 64 :I 1kwmA 126 :W T0289 65 :DCD 1kwmA 140 :GTD T0289 70 :RVFDL 1kwmA 145 :RNFDA T0289 75 :ENLSKEMS 1kwmA 167 :GPAAESEK T0289 88 :EVR 1kwmA 175 :ETK T0289 91 :RAQEINHLF 1kwmA 179 :LADFIRNKL T0289 106 :DAYDVVFDLH 1kwmA 187A:SSIKAYLTIH T0289 119 :SNMGC 1kwmA 200 :QMMIY T0289 126 :ILEDSRNDFLIQMFHYIKTCM 1kwmA 207 :SYAYKLGENNAELNALAKATV T0289 147 :APLPCSVYL 1kwmA 234 :HGTKYTYGP T0289 156 :IEHPSLKYATTRSIAKY 1kwmA 248 :YPAAGGSDDWAYDQGIR T0289 173 :PVGIEV 1kwmA 266 :SFTFEL T0289 179 :G 1kwmA 275 :G T0289 182 :PHG 1kwmA 276 :RYG T0289 186 :LRADILDQMRRMLKHALDFI 1kwmA 281 :LPESQIRATCEETFLAIKYV T0289 206 :QRFNE 1kwmA 302 :SYVLE Number of specific fragments extracted= 20 number of extra gaps= 4 total=162 Number of alignments=10 # 1kwmA read from 1kwmA/merged-good-all-a2m # found chain 1kwmA in template set Warning: unaligning (T0289)L45 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1kwmA)D104 Warning: unaligning (T0289)E46 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1kwmA)D104 Warning: unaligning (T0289)L68 because of BadResidue code BAD_PEPTIDE in next template residue (1kwmA)N144 Warning: unaligning (T0289)N69 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)N144 Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1kwmA)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)Y198 Warning: unaligning (T0289)T118 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)S199 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1kwmA)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)Y206 Warning: unaligning (T0289)G179 because of BadResidue code BAD_PEPTIDE in next template residue (1kwmA)D273 Warning: unaligning (T0289)P180 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)D273 T0289 4 :CVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1kwmA 53 :GKAGQNKPAIFMDCGFHAREWISPAFCQWFVREAVRTY T0289 42 :RAG 1kwmA 100 :LNK T0289 47 :VKPF 1kwmA 105 :FYVL T0289 51 :ITNPRAVEKC 1kwmA 110 :VLNIDGYIYT T0289 61 :TRYI 1kwmA 126 :WRKT T0289 66 :C 1kwmA 140 :G T0289 67 :D 1kwmA 142 :D T0289 70 :RVFDLENLSKEMS 1kwmA 145 :RNFDAGWCEIGAS T0289 83 :EDLPYEVRRAQEINHLFG 1kwmA 170 :AESEKETKALADFIRNKL T0289 106 :DAYDVVFDLH 1kwmA 187A:SSIKAYLTIH T0289 119 :SNMGC 1kwmA 200 :QMMIY T0289 126 :ILEDSRNDFLI 1kwmA 207 :SYAYKLGENNA T0289 137 :QMFHYIKTCMA 1kwmA 221 :ALAKATVKELA T0289 148 :PLPCSVYL 1kwmA 235 :GTKYTYGP T0289 156 :IEHPSLKYATTRSIAK 1kwmA 248 :YPAAGGSDDWAYDQGI T0289 172 :YPVGIEV 1kwmA 265 :YSFTFEL T0289 181 :Q 1kwmA 274 :T T0289 182 :PHG 1kwmA 276 :RYG T0289 185 :VLRADILDQMRRMLKHALDFI 1kwmA 280 :LLPESQIRATCEETFLAIKYV T0289 206 :QR 1kwmA 302 :SY Number of specific fragments extracted= 20 number of extra gaps= 5 total=182 Number of alignments=11 # 1kwmA read from 1kwmA/merged-good-all-a2m # found chain 1kwmA in template set Warning: unaligning (T0289)L45 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1kwmA)D104 Warning: unaligning (T0289)E46 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1kwmA)D104 Warning: unaligning (T0289)L68 because of BadResidue code BAD_PEPTIDE in next template residue (1kwmA)N144 Warning: unaligning (T0289)N69 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)N144 Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1kwmA)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)Y198 Warning: unaligning (T0289)T118 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)S199 Warning: unaligning (T0289)E128 because of BadResidue code BAD_PEPTIDE in next template residue (1kwmA)Y206 Warning: unaligning (T0289)D129 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)Y206 Warning: unaligning (T0289)G179 because of BadResidue code BAD_PEPTIDE in next template residue (1kwmA)D273 Warning: unaligning (T0289)P180 because of BadResidue code BAD_PEPTIDE at template residue (1kwmA)D273 T0289 5 :VAEEPIKKIAIFGGTHGNELTGV 1kwmA 54 :KAGQNKPAIFMDCGFHAREWISP T0289 28 :FLVTHWLKNGAEVHR 1kwmA 81 :WFVREAVRTYGREIQ T0289 43 :AG 1kwmA 101 :NK T0289 47 :VKPFITNPRAVEKCT 1kwmA 106 :YVLPVLNIDGYIYTW T0289 62 :RYI 1kwmA 124 :RFW T0289 65 :DCD 1kwmA 140 :GTD T0289 70 :RVFDLENL 1kwmA 145 :RNFDAGWC T0289 78 :SKE 1kwmA 158 :RNP T0289 81 :MSEDL 1kwmA 169 :AAESE T0289 91 :RAQEINHLFGPKN 1kwmA 174 :KETKALADFIRNK T0289 105 :DDAYDVVFDLH 1kwmA 187 :LSSIKAYLTIH T0289 124 :TLIL 1kwmA 201 :MMIY T0289 130 :S 1kwmA 207 :S T0289 131 :RNDFLIQMFHYIKTCM 1kwmA 215 :NNAELNALAKATVKEL T0289 147 :APLPCS 1kwmA 234 :HGTKYT T0289 164 :ATTRSIAKYPVGIEV 1kwmA 257 :WAYDQGIRYSFTFEL T0289 181 :Q 1kwmA 274 :T T0289 182 :PHGVL 1kwmA 276 :RYGFL T0289 188 :ADILDQMRRMLKHALDFI 1kwmA 287 :RATCEETFLAIKYVASYV Number of specific fragments extracted= 19 number of extra gaps= 5 total=201 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h8lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h8lA expands to /projects/compbio/data/pdb/1h8l.pdb.gz 1h8lA:# T0289 read from 1h8lA/merged-good-all-a2m # 1h8lA read from 1h8lA/merged-good-all-a2m # adding 1h8lA to template set # found chain 1h8lA in template set Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1h8lA)F191 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1h8lA)F191 T0289 3 :SCVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1h8lA 57 :PGIHEAGEPEFKYIGNMHGNEVVGRELLLNLIEYLCKNF T0289 42 :RAGLEVKPF 1h8lA 105 :VQSTRIHIM T0289 51 :ITNPRAVEKC 1h8lA 115 :SMNPDGYEKS T0289 61 :TRYI 1h8lA 134 :GRNN T0289 65 :DCDLNRVF 1h8lA 140 :NYDLNRNF T0289 75 :ENLSKEMSEDLPYEV 1h8lA 148 :PDQFFQVTDPPQPET T0289 93 :QEINHLF 1h8lA 163 :LAVMSWL T0289 104 :SDDAYDVVFDLHNTTSNMGC 1h8lA 170 :KTYPFVLSANLHGGSLVVNY T0289 126 :ILE 1h8lA 192 :DDD T0289 129 :DSRNDFLIQMFHYIKTCM 1h8lA 200 :IYSKSPDDAVFQQLALSY T0289 147 :APLPCSV 1h8lA 239 :FPHGITN T0289 156 :IEHPSLKYATTRSIAKYPVGIEVGPQPHGVLR 1h8lA 251 :NVPGGMQDWNYLNTNCFEVTIELGCVKYPKAE T0289 188 :ADILDQMRRMLKHALDFIQRF 1h8lA 285 :PKYWEQNRRSLLQFIKQVHRG T0289 211 :GKEFPPCAIDVYKIME 1h8lA 313 :ATDGRGILNATISVAD T0289 227 :KVDYPRNESGDVAAVIHP 1h8lA 330 :NHPVTTYKDGDYWRLLVQ T0289 252 :KPLH 1h8lA 348 :GTYK T0289 260 :VFVSLDGK 1h8lA 352 :VTASARGY T0289 268 :VIPLGGDCTVYPVF 1h8lA 365 :TVEVDSKGGVQVNF Number of specific fragments extracted= 18 number of extra gaps= 1 total=219 Number of alignments=13 # 1h8lA read from 1h8lA/merged-good-all-a2m # found chain 1h8lA in template set Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1h8lA)F191 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1h8lA)F191 T0289 5 :VAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1h8lA 59 :IHEAGEPEFKYIGNMHGNEVVGRELLLNLIEYLCKNF T0289 42 :RAGLEVKPF 1h8lA 105 :VQSTRIHIM T0289 51 :ITNPRAVEKC 1h8lA 115 :SMNPDGYEKS T0289 61 :TRYI 1h8lA 134 :GRNN T0289 65 :DC 1h8lA 139 :NN T0289 67 :DLNRVFDLENLSKEMS 1h8lA 142 :DLNRNFPDQFFQVTDP T0289 87 :YEVRRAQEINHL 1h8lA 160 :PETLAVMSWLKT T0289 106 :DAYDVVFDLHNTTSNMGC 1h8lA 172 :YPFVLSANLHGGSLVVNY T0289 126 :ILED 1h8lA 192 :DDDE T0289 130 :SRNDFLIQMFHYIKTCMAPL 1h8lA 201 :YSKSPDDAVFQQLALSYSKE T0289 150 :PCSVY 1h8lA 241 :HGITN T0289 155 :LIEHPSLKYATTRSIAKYPVGIEVGPQ 1h8lA 250 :YNVPGGMQDWNYLNTNCFEVTIELGCV T0289 184 :GVLR 1h8lA 277 :KYPK T0289 188 :ADILDQMRRMLKHALDFIQR 1h8lA 285 :PKYWEQNRRSLLQFIKQVHR T0289 219 :I 1h8lA 305 :G T0289 238 :VAAVIHPNLQDQDW 1h8lA 306 :IWGFVLDATDGRGI T0289 256 :PGD 1h8lA 320 :LNA T0289 261 :FVSLDGK 1h8lA 323 :TISVADI T0289 268 :VIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIRST 1h8lA 334 :TTYKDGDYWRLLVQGTYKVTASARGYDPVTKTVEVDSKGGVQV Number of specific fragments extracted= 19 number of extra gaps= 1 total=238 Number of alignments=14 # 1h8lA read from 1h8lA/merged-good-all-a2m # found chain 1h8lA in template set Warning: unaligning (T0289)D129 because of BadResidue code BAD_PEPTIDE in next template residue (1h8lA)F191 Warning: unaligning (T0289)S130 because of BadResidue code BAD_PEPTIDE at template residue (1h8lA)F191 T0289 6 :AEEPIKKIAIFGGTHGNELTGVFLVTHWL 1h8lA 60 :HEAGEPEFKYIGNMHGNEVVGRELLLNLI T0289 35 :KNGAEVHR 1h8lA 96 :GTDPEVTD T0289 43 :AGLEVKPFITNPRAVEK 1h8lA 107 :STRIHIMPSMNPDGYEK T0289 65 :DCDLNRVFDLE 1h8lA 140 :NYDLNRNFPDQ T0289 79 :KEMSEDLPYEVRRAQEINHLF 1h8lA 152 :FQVTDPPQPETLAVMSWLKTY T0289 107 :AYDVVFDLHNT 1h8lA 173 :PFVLSANLHGG T0289 123 :CTLILE 1h8lA 184 :SLVVNY T0289 131 :R 1h8lA 192 :D T0289 132 :ND 1h8lA 194 :DE T0289 134 :FLIQMFHYIKTC 1h8lA 205 :PDDAVFQQLALS T0289 164 :ATTRSIAKYPVGIEVGPQ 1h8lA 259 :WNYLNTNCFEVTIELGCV T0289 182 :PHGVLRADILDQMRRMLKHALDFIQRF 1h8lA 279 :PKAEELPKYWEQNRRSLLQFIKQVHRG T0289 209 :NEGKEFPPCAIDVYKIMEKVD 1h8lA 314 :TDGRGILNATISVADINHPVT T0289 233 :NESGDVAAVIHPNL 1h8lA 335 :TYKDGDYWRLLVQG T0289 253 :PL 1h8lA 349 :TY T0289 259 :PVFVSLDG 1h8lA 351 :KVTASARG T0289 267 :KVIPLGGDCTVYPVF 1h8lA 364 :KTVEVDSKGGVQVNF Number of specific fragments extracted= 17 number of extra gaps= 1 total=255 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qmuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qmuA expands to /projects/compbio/data/pdb/1qmu.pdb.gz 1qmuA:# T0289 read from 1qmuA/merged-good-all-a2m # 1qmuA read from 1qmuA/merged-good-all-a2m # adding 1qmuA to template set # found chain 1qmuA in template set Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1qmuA)F191 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1qmuA)F191 T0289 4 :CVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1qmuA 58 :GIHEAGEPEFKYIGNMHGNEVVGRELLLNLIEYLCKNF T0289 42 :RAGLEVKPF 1qmuA 105 :VQSTRIHIM T0289 51 :ITNPRAVEKC 1qmuA 115 :SMNPDGYEKS T0289 61 :TRYI 1qmuA 134 :GRNN T0289 65 :DCDLNRVF 1qmuA 140 :NYDLNRNF T0289 75 :ENLSKEMSEDLPYEV 1qmuA 148 :PDQFFQVTDPPQPET T0289 93 :QEINHLF 1qmuA 163 :LAVMSWL T0289 104 :SDDAYDVVFDLHNTTSNMGC 1qmuA 170 :KTYPFVLSANLHGGSLVVNY T0289 126 :ILE 1qmuA 192 :DDD T0289 129 :DSRNDFLIQMFHYIKTCM 1qmuA 200 :IYSKSPDDAVFQQLALSY T0289 147 :APLPCSV 1qmuA 239 :FPHGITN T0289 156 :IEHPSLKYATTRSIAKYPVGIEVGPQPHGVLR 1qmuA 251 :NVPGGMQDWNYLNTNCFEVTIELGCVKYPKAE T0289 188 :ADILDQMRRMLKHALDFIQRF 1qmuA 285 :PKYWEQNRRSLLQFIKQVHRG T0289 209 :NEGKEF 1qmuA 314 :TDGRGI T0289 218 :AIDVYKIME 1qmuA 320 :LNATISVAD T0289 227 :KVDYPRNESGDVAAVIHP 1qmuA 330 :NHPVTTYKDGDYWRLLVQ T0289 252 :KPLH 1qmuA 348 :GTYK T0289 260 :VFVSLDGK 1qmuA 352 :VTASARGY T0289 268 :VIPLGGDCTVYPVF 1qmuA 365 :TVEVDSKGGVQVNF Number of specific fragments extracted= 19 number of extra gaps= 1 total=274 Number of alignments=16 # 1qmuA read from 1qmuA/merged-good-all-a2m # found chain 1qmuA in template set Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1qmuA)F191 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1qmuA)F191 T0289 5 :VAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1qmuA 59 :IHEAGEPEFKYIGNMHGNEVVGRELLLNLIEYLCKNF T0289 42 :RAGLEVKPF 1qmuA 105 :VQSTRIHIM T0289 51 :ITNPRAVEKC 1qmuA 115 :SMNPDGYEKS T0289 61 :TRYI 1qmuA 134 :GRNN T0289 65 :DC 1qmuA 139 :NN T0289 67 :DLNRVFDLENLSKEMS 1qmuA 142 :DLNRNFPDQFFQVTDP T0289 87 :YEVRRAQEINHL 1qmuA 160 :PETLAVMSWLKT T0289 106 :DAYDVVFDLHNTTSNMGC 1qmuA 172 :YPFVLSANLHGGSLVVNY T0289 126 :ILED 1qmuA 192 :DDDE T0289 130 :SRNDFLIQMFHYIKTCMAPL 1qmuA 201 :YSKSPDDAVFQQLALSYSKE T0289 160 :SLKYATTRSIAKYPVGIEVGPQ 1qmuA 255 :GMQDWNYLNTNCFEVTIELGCV T0289 185 :VLR 1qmuA 278 :YPK T0289 188 :ADILDQMRRMLKHALDFIQ 1qmuA 285 :PKYWEQNRRSLLQFIKQVH T0289 218 :AIDVYKIMEKVDY 1qmuA 304 :RGIWGFVLDATDG T0289 232 :RNESG 1qmuA 317 :RGILN T0289 238 :VAAVIHP 1qmuA 322 :ATISVAD T0289 263 :SLDGKVIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIRST 1qmuA 329 :INHPVTTYKDGDYWRLLVQGTYKVTASARGYDPVTKTVEVDSKGGVQV Number of specific fragments extracted= 17 number of extra gaps= 1 total=291 Number of alignments=17 # 1qmuA read from 1qmuA/merged-good-all-a2m # found chain 1qmuA in template set Warning: unaligning (T0289)E128 because of BadResidue code BAD_PEPTIDE in next template residue (1qmuA)F191 Warning: unaligning (T0289)D129 because of BadResidue code BAD_PEPTIDE at template residue (1qmuA)F191 T0289 6 :AEEPIKKIAIFGGTHGNELTGVFLVTHWLKNG 1qmuA 60 :HEAGEPEFKYIGNMHGNEVVGRELLLNLIEYL T0289 38 :AEVHR 1qmuA 99 :PEVTD T0289 43 :AGLEV 1qmuA 106 :QSTRI T0289 48 :KPFITNPRAVEK 1qmuA 112 :IMPSMNPDGYEK T0289 65 :DCDLNRVFDLEN 1qmuA 140 :NYDLNRNFPDQF T0289 79 :KEMSEDLPYEVRRAQEINHLF 1qmuA 152 :FQVTDPPQPETLAVMSWLKTY T0289 107 :AYDVVFDLHNTT 1qmuA 173 :PFVLSANLHGGS T0289 123 :CTLIL 1qmuA 185 :LVVNY T0289 130 :SRND 1qmuA 192 :DDDE T0289 134 :FLIQMFHYIKTC 1qmuA 205 :PDDAVFQQLALS T0289 165 :TTRSIAKYPVGIEVGPQ 1qmuA 260 :NYLNTNCFEVTIELGCV T0289 182 :PHGVLRADILDQMRRMLKHALDFIQRF 1qmuA 279 :PKAEELPKYWEQNRRSLLQFIKQVHRG T0289 209 :NEGKEFPPCAIDVYKIMEKVD 1qmuA 314 :TDGRGILNATISVADINHPVT T0289 233 :NESGDVAAVIHPN 1qmuA 335 :TYKDGDYWRLLVQ T0289 258 :DPVFVSLDG 1qmuA 350 :YKVTASARG T0289 267 :KVIPLGGDCTVYPVF 1qmuA 364 :KTVEVDSKGGVQVNF Number of specific fragments extracted= 16 number of extra gaps= 1 total=307 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pca/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/T0289/1pca/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0289/1pca/merged-good-all-a2m.gz for input Trying 1pca/merged-good-all-a2m Error: Couldn't open file 1pca/merged-good-all-a2m or 1pca/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bo9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bo9A expands to /projects/compbio/data/pdb/2bo9.pdb.gz 2bo9A:Skipped atom 26, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 310, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 2bo9A Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 2bo9A # T0289 read from 2bo9A/merged-good-all-a2m # 2bo9A read from 2bo9A/merged-good-all-a2m # adding 2bo9A to template set # found chain 2bo9A in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (2bo9A)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (2bo9A)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (2bo9A)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (2bo9A)Y206 Warning: unaligning (T0289)K212 because last residue in template chain is (2bo9A)L308 T0289 5 :VAEE 2bo9A 54 :TGKG T0289 9 :PIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 2bo9A 58 :RRPAVWLNAGIHSREWISQATAIWTARKIVSDY T0289 42 :RAGLEVKPF 2bo9A 100 :LEKMDIFLL T0289 51 :ITNPRAVEKC 2bo9A 110 :VANPDGYVYT T0289 65 :DCDLNRVFDL 2bo9A 140 :GADPNRNWNA T0289 75 :ENLSKE 2bo9A 168 :PHANSE T0289 87 :YEVRRAQEINHLF 2bo9A 174 :VEVKSVVDFIQKH T0289 106 :DAYDVVFDLH 2bo9A 187 :GNFKGFIDLH T0289 118 :TSNMGC 2bo9A 199 :SQLLMY T0289 126 :ILEDSRNDFLIQMFHYIKTCM 2bo9A 207 :GYSVKKAPDAEELDKVARLAA T0289 147 :APLPCSVY 2bo9A 236 :TEYQVGPT T0289 156 :IEHPSLKYATTRSIAKY 2bo9A 248 :YPASGSSIDWAYDNGIK T0289 173 :PVGIEV 2bo9A 266 :AFTFEL T0289 179 :GPQ 2bo9A 275 :GTY T0289 183 :HGVLRADILDQMRRMLKHALDFI 2bo9A 278 :GFLLPANQIIPTAEETWLGLKTI T0289 206 :QRFNEG 2bo9A 302 :EHVRDN Number of specific fragments extracted= 16 number of extra gaps= 2 total=323 Number of alignments=19 # 2bo9A read from 2bo9A/merged-good-all-a2m # found chain 2bo9A in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (2bo9A)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (2bo9A)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (2bo9A)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (2bo9A)Y206 T0289 6 :AEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 2bo9A 55A:KGVRRPAVWLNAGIHSREWISQATAIWTARKIVSDY T0289 42 :RAGLEVKPF 2bo9A 100 :LEKMDIFLL T0289 51 :ITNPRAVEKC 2bo9A 110 :VANPDGYVYT T0289 61 :TRYI 2bo9A 126 :WRKT T0289 66 :C 2bo9A 140 :G T0289 67 :DLNRVFDLENLSKEMS 2bo9A 142 :DPNRNWNASFAGKGAS T0289 83 :EDLPYEVRRAQEINHLF 2bo9A 170 :ANSEVEVKSVVDFIQKH T0289 106 :DAYDVVFDLH 2bo9A 187 :GNFKGFIDLH T0289 118 :TSNMGC 2bo9A 199 :SQLLMY T0289 126 :ILEDSRNDFLIQM 2bo9A 207 :GYSVKKAPDAEEL T0289 139 :FHYIKTCMA 2bo9A 223 :ARLAAKALA T0289 148 :PLPCSVYL 2bo9A 235 :GTEYQVGP T0289 156 :IEHPSLKYATTRSIAK 2bo9A 248 :YPASGSSIDWAYDNGI T0289 172 :YPVGIEV 2bo9A 265 :FAFTFEL T0289 179 :GPQPH 2bo9A 275 :GTYGF T0289 185 :VLR 2bo9A 280 :LLP T0289 188 :ADILDQMRRMLKHALDFIQ 2bo9A 287 :IPTAEETWLGLKTIMEHVR Number of specific fragments extracted= 17 number of extra gaps= 2 total=340 Number of alignments=20 # 2bo9A read from 2bo9A/merged-good-all-a2m # found chain 2bo9A in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (2bo9A)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (2bo9A)Y198 Warning: unaligning (T0289)E128 because of BadResidue code BAD_PEPTIDE in next template residue (2bo9A)Y206 Warning: unaligning (T0289)D129 because of BadResidue code BAD_PEPTIDE at template residue (2bo9A)Y206 Warning: unaligning (T0289)G179 because of BadResidue code BAD_PEPTIDE in next template residue (2bo9A)D273 Warning: unaligning (T0289)P180 because of BadResidue code BAD_PEPTIDE at template residue (2bo9A)D273 T0289 5 :VAEEPIKKIAIFGGTHGNEL 2bo9A 55 :GKGVRRPAVWLNAGIHSREW T0289 25 :TGVFLVTHWLKNGAEVHR 2bo9A 78 :TAIWTARKIVSDYQRDPA T0289 43 :AGLE 2bo9A 101 :EKMD T0289 47 :VKPFITNPRAVEKCT 2bo9A 106 :FLLPVANPDGYVYTQ T0289 62 :RYI 2bo9A 124 :RLW T0289 65 :DCDLNRVFDLENLSKEMSED 2bo9A 140 :GADPNRNWNASFAGKGASDN T0289 85 :LPYEVRRAQEINHLF 2bo9A 172 :SEVEVKSVVDFIQKH T0289 106 :DAYDVVFDLH 2bo9A 187 :GNFKGFIDLH T0289 118 :T 2bo9A 199 :S T0289 124 :TLIL 2bo9A 201 :LLMY T0289 130 :SRND 2bo9A 207 :GYSV T0289 134 :FLIQMFHYIKTCMA 2bo9A 222 :VARLAAKALASVSG T0289 149 :LPCS 2bo9A 236 :TEYQ T0289 165 :TTRSIAKYPVGIEV 2bo9A 258 :AYDNGIKFAFTFEL T0289 181 :Q 2bo9A 274 :T T0289 182 :PHGVLR 2bo9A 277 :YGFLLP T0289 188 :ADILDQMRRMLKHALDFI 2bo9A 287 :IPTAEETWLGLKTIMEHV Number of specific fragments extracted= 17 number of extra gaps= 3 total=357 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g9dA/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/T0289/2g9dA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0289/2g9dA/merged-good-all-a2m.gz for input Trying 2g9dA/merged-good-all-a2m Error: Couldn't open file 2g9dA/merged-good-all-a2m or 2g9dA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cbx/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/T0289/1cbx/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0289/1cbx/merged-good-all-a2m.gz for input Trying 1cbx/merged-good-all-a2m Error: Couldn't open file 1cbx/merged-good-all-a2m or 1cbx/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2boaA/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/T0289/2boaA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0289/2boaA/merged-good-all-a2m.gz for input Trying 2boaA/merged-good-all-a2m Error: Couldn't open file 2boaA/merged-good-all-a2m or 2boaA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bavA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bavA expands to /projects/compbio/data/pdb/1bav.pdb.gz 1bavA:# T0289 read from 1bavA/merged-good-all-a2m # 1bavA read from 1bavA/merged-good-all-a2m # adding 1bavA to template set # found chain 1bavA in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1bavA)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1bavA)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1bavA)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1bavA)Y206 T0289 4 :CVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1bavA 53 :STGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTENY T0289 42 :RAGLEVKPF 1bavA 100 :LDSMDIFLE T0289 51 :ITNPRAVEKC 1bavA 110 :VTNPNGFAFT T0289 64 :I 1bavA 129 :T T0289 65 :DCDLNRVFDL 1bavA 140 :GVDANRNWDA T0289 75 :ENLSKEMS 1bavA 167 :GKYANSEV T0289 88 :EV 1bavA 175 :EV T0289 93 :QEINHLF 1bavA 177 :KSIVDFV T0289 102 :KNSD 1bavA 184 :KNHG T0289 107 :AYDVVFDLH 1bavA 188 :NFKAFLSIH T0289 118 :TSNMGC 1bavA 199 :SQLLLY T0289 126 :ILEDSRNDFLIQMFHYIKTCM 1bavA 207 :GYTTQSIPDKTELNQVAKSAV T0289 147 :APLPCSVYL 1bavA 234 :YGTSYKYGS T0289 156 :IEHPSLKYATTRSIAKY 1bavA 248 :YQASGGSIDWSYNQGIK T0289 173 :PVGIEV 1bavA 266 :SFTFEL T0289 180 :PQPHGVLRADILDQMRRMLKHALDFI 1bavA 275 :GRYGFLLPASQIIPTAQETWLGVLTI T0289 206 :QR 1bavA 302 :EH Number of specific fragments extracted= 17 number of extra gaps= 2 total=374 Number of alignments=22 # 1bavA read from 1bavA/merged-good-all-a2m # found chain 1bavA in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1bavA)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1bavA)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1bavA)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1bavA)Y206 T0289 5 :VAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1bavA 54 :TGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTENY T0289 42 :RAGLEVKPF 1bavA 100 :LDSMDIFLE T0289 51 :ITNPRAVEKC 1bavA 110 :VTNPNGFAFT T0289 61 :TRYI 1bavA 126 :WRKT T0289 65 :D 1bavA 131 :S T0289 66 :C 1bavA 140 :G T0289 67 :DLNRVFDLENLSKEMS 1bavA 142 :DANRNWDAGFGKAGAS T0289 83 :EDLPYEVRRAQEINHLF 1bavA 170 :ANSEVEVKSIVDFVKNH T0289 106 :DAYDVVFDLH 1bavA 187 :GNFKAFLSIH T0289 118 :TSNMGC 1bavA 199 :SQLLLY T0289 126 :ILEDSRNDFLI 1bavA 207 :GYTTQSIPDKT T0289 137 :QMFHYIKTCM 1bavA 225 :SAVAALKSLY T0289 148 :PLPCSVYL 1bavA 235 :GTSYKYGS T0289 156 :IEHPSLKYATTRSIAK 1bavA 248 :YQASGGSIDWSYNQGI T0289 172 :YPVGIEV 1bavA 265 :YSFTFEL T0289 179 :GPQPHG 1bavA 275 :GRYGFL T0289 186 :LR 1bavA 281 :LP T0289 188 :ADILDQMRRMLKHALDFI 1bavA 287 :IPTAQETWLGVLTIMEHT Number of specific fragments extracted= 18 number of extra gaps= 2 total=392 Number of alignments=23 # 1bavA read from 1bavA/merged-good-all-a2m # found chain 1bavA in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1bavA)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1bavA)Y198 Warning: unaligning (T0289)E128 because of BadResidue code BAD_PEPTIDE in next template residue (1bavA)Y206 Warning: unaligning (T0289)D129 because of BadResidue code BAD_PEPTIDE at template residue (1bavA)Y206 Warning: unaligning (T0289)G179 because of BadResidue code BAD_PEPTIDE in next template residue (1bavA)D273 Warning: unaligning (T0289)P180 because of BadResidue code BAD_PEPTIDE at template residue (1bavA)D273 T0289 4 :CVAEEPIKKIAIFGGTHGNEL 1bavA 53 :STGGSNRPAIWIDLGIHSREW T0289 25 :TGVFLVTHWLKNGAEVHR 1bavA 78 :TGVWFAKKFTENYGQNPS T0289 43 :AGLE 1bavA 101 :DSMD T0289 47 :VKPFITNPRAVEKCT 1bavA 106 :FLEIVTNPNGFAFTH T0289 62 :RYI 1bavA 124 :RLW T0289 65 :DCDLNRVFDLEN 1bavA 140 :GVDANRNWDAGF T0289 77 :LSKEMSED 1bavA 157 :SSSPCSET T0289 85 :LPYEVRRAQEINHLF 1bavA 172 :SEVEVKSIVDFVKNH T0289 106 :DAYDVVFDLH 1bavA 187 :GNFKAFLSIH T0289 118 :T 1bavA 199 :S T0289 123 :CTLIL 1bavA 200 :QLLLY T0289 130 :SRNDFLIQMFHYIKTCM 1bavA 214 :PDKTELNQVAKSAVAAL T0289 147 :APLPCS 1bavA 234 :YGTSYK T0289 164 :ATTRSIAKYPVGIEV 1bavA 257 :WSYNQGIKYSFTFEL T0289 181 :Q 1bavA 274 :T T0289 182 :PHGVLR 1bavA 277 :YGFLLP T0289 188 :ADILDQMRRMLKHALDFI 1bavA 287 :IPTAQETWLGVLTIMEHT Number of specific fragments extracted= 17 number of extra gaps= 3 total=409 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 5cpa/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/T0289/5cpa/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0289/5cpa/merged-good-all-a2m.gz for input Trying 5cpa/merged-good-all-a2m Error: Couldn't open file 5cpa/merged-good-all-a2m or 5cpa/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zliA/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/T0289/1zliA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0289/1zliA/merged-good-all-a2m.gz for input Trying 1zliA/merged-good-all-a2m Error: Couldn't open file 1zliA/merged-good-all-a2m or 1zliA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c0pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0289 read from 1c0pA/merged-good-all-a2m # 1c0pA read from 1c0pA/merged-good-all-a2m # found chain 1c0pA in training set Warning: unaligning (T0289)I10 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)K1005 Warning: unaligning (T0289)K11 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)K1005 Warning: unaligning (T0289)L135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1c0pA)L1104 Warning: unaligning (T0289)I136 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1c0pA)L1104 Warning: unaligning (T0289)P159 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1163 Warning: unaligning (T0289)S160 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1163 Warning: unaligning (T0289)C217 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1271 Warning: unaligning (T0289)A218 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1271 T0289 6 :AEEP 1c0pA 1000 :MMHS T0289 12 :KIAIFGGT 1c0pA 1006 :RVVVLGSG T0289 24 :LTGVFLVTHWLK 1c0pA 1014 :VIGLSSALILAR T0289 43 :AGLEVKPFITN 1c0pA 1026 :KGYSVHILARD T0289 72 :FDL 1c0pA 1037 :LPE T0289 77 :LSKEMSEDLPYEVR 1c0pA 1056 :TPFMTLTDGPRQAK T0289 91 :RAQEINHLF 1c0pA 1074 :TFKKWVELV T0289 101 :PKNSD 1c0pA 1083 :PTGHA T0289 121 :MGCTLIL 1c0pA 1091 :KGTRRFA T0289 130 :SRNDF 1c0pA 1098 :QNEDG T0289 137 :QMF 1c0pA 1105 :GHW T0289 140 :HYIKTCM 1c0pA 1144 :QYLAREL T0289 147 :APLPCSVY 1c0pA 1153 :LGATFERR T0289 158 :H 1c0pA 1161 :T T0289 161 :LKYAT 1c0pA 1164 :SLEQA T0289 170 :AKYPVGIEVG 1c0pA 1219 :ASPAYIIPRP T0289 183 :HGVLRADILDQMRRMLKHA 1c0pA 1244 :DLSVNPETVQRILKHCLRL T0289 211 :GKEFPP 1c0pA 1264 :PTISSD T0289 219 :IDVYKIMEKVDYP 1c0pA 1272 :IEGIEVLRHNVGL T0289 252 :KPLHPGDPVFVS 1c0pA 1285 :RPARRGGPRVEA T0289 267 :KVIPLG 1c0pA 1297 :ERIVLP T0289 275 :CTVYPVFVNEAAY 1c0pA 1326 :TLVHAYGFSSAGY Number of specific fragments extracted= 22 number of extra gaps= 4 total=431 Number of alignments=25 # 1c0pA read from 1c0pA/merged-good-all-a2m # found chain 1c0pA in training set Warning: unaligning (T0289)I10 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)K1005 Warning: unaligning (T0289)K11 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)K1005 Warning: unaligning (T0289)S78 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)A1053 Warning: unaligning (T0289)K79 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)A1053 Warning: unaligning (T0289)L135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1c0pA)L1104 Warning: unaligning (T0289)I136 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1c0pA)L1104 Warning: unaligning (T0289)H158 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1163 Warning: unaligning (T0289)P159 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1163 Warning: unaligning (T0289)G179 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)G1236 Warning: unaligning (T0289)F214 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1271 Warning: unaligning (T0289)P215 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1271 T0289 7 :EEP 1c0pA 1001 :MHS T0289 12 :KIAIFGGT 1c0pA 1006 :RVVVLGSG T0289 24 :LTGVFLVTHWLK 1c0pA 1014 :VIGLSSALILAR T0289 43 :AGLEVKPFITN 1c0pA 1026 :KGYSVHILARD T0289 64 :I 1c0pA 1037 :L T0289 65 :D 1c0pA 1039 :E T0289 69 :NRVFDLENL 1c0pA 1043 :SQTFASPWA T0289 80 :EMS 1c0pA 1054 :NWT T0289 83 :EDLPYEVRRAQEINHLFGPKNSD 1c0pA 1062 :TDGPRQAKWEESTFKKWVELVPT T0289 117 :TTSNMGCTLILEDSRNDF 1c0pA 1085 :GHAMWLKGTRRFAQNEDG T0289 137 :QMFHYIKTCMAPLPCSVYLIE 1c0pA 1141 :KYCQYLARELQKLGATFERRT T0289 169 :IAKYPVGIEV 1c0pA 1218 :PASPAYIIPR T0289 180 :PQ 1c0pA 1237 :TY T0289 182 :PHG 1c0pA 1242 :DWD T0289 185 :VLRADILDQMRRM 1c0pA 1246 :SVNPETVQRILKH T0289 201 :ALDFIQRFNEG 1c0pA 1259 :CLRLDPTISSD T0289 216 :PCAIDVYKIME 1c0pA 1272 :IEGIEVLRHNV T0289 228 :VDYPRNESG 1c0pA 1283 :GLRPARRGG T0289 269 :IP 1c0pA 1293 :RV T0289 296 :KTTKLTLNAKS 1c0pA 1295 :EAERIVLPLDR Number of specific fragments extracted= 20 number of extra gaps= 6 total=451 Number of alignments=26 # 1c0pA read from 1c0pA/merged-good-all-a2m # found chain 1c0pA in training set Warning: unaligning (T0289)I10 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)K1005 Warning: unaligning (T0289)K11 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)K1005 Warning: unaligning (T0289)F134 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1c0pA)L1104 Warning: unaligning (T0289)L135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1c0pA)L1104 Warning: unaligning (T0289)K171 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1230 Warning: unaligning (T0289)Y172 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)G1230 Warning: unaligning (T0289)E177 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1236 Warning: unaligning (T0289)V178 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)G1236 Warning: unaligning (T0289)K212 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1271 Warning: unaligning (T0289)E213 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1271 T0289 6 :AEEP 1c0pA 1000 :MMHS T0289 12 :KIAIFGGT 1c0pA 1006 :RVVVLGSG T0289 24 :LTGVFLVTHWLK 1c0pA 1014 :VIGLSSALILAR T0289 43 :AGLEVKPFITN 1c0pA 1026 :KGYSVHILARD T0289 71 :VFDLENL 1c0pA 1045 :TFASPWA T0289 79 :KEMSEDLPYEVRRAQEINHLFGPKNSDDAYDVV 1c0pA 1058 :FMTLTDGPRQAKWEESTFKKWVELVPTGHAMWL T0289 122 :GCTLILEDSRND 1c0pA 1091 :KGTRRFAQNEDG T0289 136 :IQM 1c0pA 1105 :GHW T0289 153 :VYLIEHPSLKYATTRSIA 1c0pA 1211 :CTMDSSDPASPAYIIPRP T0289 173 :PVGI 1c0pA 1231 :EVIC T0289 179 :GPQ 1c0pA 1237 :TYG T0289 182 :PHGVLRADILDQMRRM 1c0pA 1243 :WDLSVNPETVQRILKH T0289 201 :ALDFIQRFNEG 1c0pA 1259 :CLRLDPTISSD T0289 214 :FPPCAIDVYKIM 1c0pA 1272 :IEGIEVLRHNVG T0289 296 :KTTKLTLNAK 1c0pA 1295 :EAERIVLPLD Number of specific fragments extracted= 15 number of extra gaps= 5 total=466 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1obr/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1obr expands to /projects/compbio/data/pdb/1obr.pdb.gz 1obr:Warning: there is no chain 1obr will retry with 1obrA # T0289 read from 1obr/merged-good-all-a2m # 1obr read from 1obr/merged-good-all-a2m # adding 1obr to template set # found chain 1obr in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1obr)Y206 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1obr)Y206 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1obr)Y214 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1obr)Y214 T0289 6 :AEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1obr 55 :TDENEPEVLYTALHHAREHLTVEMALYTLDLFTQNY T0289 42 :RAGLEVKPF 1obr 100 :VNNREIYIV T0289 51 :ITNPRAVEKC 1obr 110 :NINPDGGEYD T0289 61 :TRYI 1obr 128 :WRKN T0289 66 :CDLNRVFDL 1obr 143 :TDLNRNYGY T0289 86 :P 1obr 172 :S T0289 87 :YEV 1obr 177 :PET T0289 93 :QEINHLF 1obr 180 :AAMRDFI T0289 100 :GPKNSDDAYDVVFDLH 1obr 189 :RVVGGKQQIKTLITFH T0289 118 :TSNMGC 1obr 207 :SELILY T0289 126 :ILEDSRN 1obr 215 :GYTYTDV T0289 133 :DFLIQMFHYIKTCM 1obr 224 :DMTQDDFNVFKTMA T0289 147 :APLPCSVYL 1obr 244 :NGYTPQQAS T0289 156 :IEHP 1obr 255 :YITD T0289 160 :SLKYATTRSIAKYPVGIEVGPQP 1obr 260 :DMTDWAYGQHKIFAFTFEMYPTS T0289 183 :HGVLR 1obr 286 :GFYPP T0289 188 :ADILDQMRRMLKHALDFI 1obr 295 :GRETSRNKEAVLYVAEKA T0289 206 :QRFNEG 1obr 316 :YSVIGK Number of specific fragments extracted= 18 number of extra gaps= 2 total=484 Number of alignments=28 # 1obr read from 1obr/merged-good-all-a2m # found chain 1obr in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1obr)Y206 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1obr)Y206 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1obr)Y214 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1obr)Y214 T0289 5 :VAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1obr 54 :GTDENEPEVLYTALHHAREHLTVEMALYTLDLFTQNY T0289 42 :RAGLEVKPF 1obr 100 :VNNREIYIV T0289 51 :ITNPRAVEKC 1obr 110 :NINPDGGEYD T0289 61 :TRYI 1obr 128 :WRKN T0289 66 :C 1obr 142 :G T0289 67 :DLNRVFDLENLSKEMS 1obr 144 :DLNRNYGYKWGCCGGS T0289 83 :EDLPYEVRRAQEINHLFGPKNS 1obr 173 :AFSAPETAAMRDFINSRVVGGK T0289 106 :DAYDVVFDLH 1obr 195 :QQIKTLITFH T0289 118 :TSNMGC 1obr 207 :SELILY T0289 126 :ILED 1obr 215 :GYTY T0289 130 :SRNDFLIQMFHYIKTCMA 1obr 224 :DMTQDDFNVFKTMANTMA T0289 148 :PLPCSV 1obr 245 :GYTPQQ T0289 155 :LIEHPSLKYATTRSIAKYPVGIEVGPQPHG 1obr 255 :YITDGDMTDWAYGQHKIFAFTFEMYPTSYN T0289 185 :VLR 1obr 288 :YPP T0289 188 :ADILDQMRRMLKHALD 1obr 295 :GRETSRNKEAVLYVAE Number of specific fragments extracted= 15 number of extra gaps= 2 total=499 Number of alignments=29 # 1obr read from 1obr/merged-good-all-a2m # found chain 1obr in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1obr)Y206 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1obr)Y206 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1obr)Y214 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1obr)Y214 T0289 6 :AEEPIKKIAIFGGTHGNEL 1obr 55 :TDENEPEVLYTALHHAREH T0289 25 :TGVFLVTHWLKNGAEVHR 1obr 78 :MALYTLDLFTQNYNLDSR T0289 43 :AGLEV 1obr 101 :NNREI T0289 48 :KPFITNPRAVEK 1obr 107 :IVFNINPDGGEY T0289 65 :DCDLNRVFDLENL 1obr 142 :GTDLNRNYGYKWG T0289 78 :SKEMSEDL 1obr 161 :GSPSSETY T0289 87 :YEVRRAQEINHLFGPKN 1obr 177 :PETAAMRDFINSRVVGG T0289 105 :DDAYDVVFDLH 1obr 194 :KQQIKTLITFH T0289 118 :TSNMGC 1obr 207 :SELILY T0289 126 :ILEDSRN 1obr 215 :GYTYTDV T0289 133 :D 1obr 228 :D T0289 134 :FLIQMFHYIKTCMAPLPCS 1obr 232 :VFKTMANTMAQTNGYTPQQ T0289 164 :ATTRSIAKYPVGIEVGPQ 1obr 264 :WAYGQHKIFAFTFEMYPT T0289 182 :PHGVLR 1obr 284 :NPGFYP T0289 188 :ADILDQMRRMLKHALDFIQRFN 1obr 295 :GRETSRNKEAVLYVAEKADCPY Number of specific fragments extracted= 15 number of extra gaps= 2 total=514 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cpb/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/T0289/1cpb/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0289/1cpb/merged-good-all-a2m.gz for input Trying 1cpb/merged-good-all-a2m Error: Couldn't open file 1cpb/merged-good-all-a2m or 1cpb/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bcoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bcoA expands to /projects/compbio/data/pdb/2bco.pdb.gz 2bcoA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0289 read from 2bcoA/merged-good-all-a2m # 2bcoA read from 2bcoA/merged-good-all-a2m # adding 2bcoA to template set # found chain 2bcoA in template set T0289 2 :TSCVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 2bcoA 45 :IPENPTQETKNIIISCGIHGDETAPMELVDSIIKDIESGF T0289 42 :RAG 2bcoA 87 :VDA T0289 46 :EVKPFITNPRAVEKCTRYIDCDLNRVFD 2bcoA 90 :RCLFIIAHPESTLAHTRFLEENLNRLFD T0289 77 :LSKEMSE 2bcoA 118 :EKEHEPT T0289 87 :YEVRRAQEINHLF 2bcoA 125 :KELAIADTLKLLV T0289 100 :GPKNSDDAYDVVFDLHNT 2bcoA 140 :FYQDTEPKTRWHLDLHCA T0289 118 :TSNMGCTLILE 2bcoA 159 :RGSKHYTFAVS T0289 129 :DSRNDFLIQMFHYIK 2bcoA 172 :TRHPVRSKALVDFLD T0289 146 :MAPLPCSVYL 2bcoA 187 :SAHIEAVLLS T0289 156 :IEHPSLKYATTRSIAKYPVGIEVGPQ 2bcoA 198 :SPSSTFSWYSAENYSAQALTMELGRV T0289 182 :PHGVLRADILDQMRRMLKHALD 2bcoA 225 :RIGENALDRLTAFDLALRNLIA T0289 211 :GKEFP 2bcoA 247 :EAQPE T0289 216 :PCAIDVYKIMEKVDYP 2bcoA 254 :SKPCIKYRVSRTIVRL T0289 235 :SGDVAAVIHPNL 2bcoA 270 :HDDFDFMFDDNV T0289 249 :QDWKPLHPGDPVFVSLD 2bcoA 282 :ENFTSFVHGEVFGHDGD T0289 266 :GKVIPLGGDCTVYPVF 2bcoA 300 :PLMAKNDNEAIVFPNR Number of specific fragments extracted= 16 number of extra gaps= 0 total=530 Number of alignments=31 # 2bcoA read from 2bcoA/merged-good-all-a2m # found chain 2bcoA in template set Warning: unaligning (T0289)T310 because last residue in template chain is (2bcoA)D342 T0289 4 :CVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 2bcoA 47 :ENPTQETKNIIISCGIHGDETAPMELVDSIIKDIESGF T0289 42 :RA 2bcoA 87 :VD T0289 45 :LEVKPFITNPRAVEKCTRYIDCDLNRVFDLENLSKE 2bcoA 89 :ARCLFIIAHPESTLAHTRFLEENLNRLFDEKEHEPT T0289 87 :YEVRRAQEINHLFGPKNSD 2bcoA 125 :KELAIADTLKLLVRDFYQD T0289 106 :DAYDVVFDLHNT 2bcoA 146 :PKTRWHLDLHCA T0289 118 :TSNMGCTLILED 2bcoA 159 :RGSKHYTFAVSP T0289 130 :SRNDFLIQMFHYIKTC 2bcoA 173 :RHPVRSKALVDFLDSA T0289 148 :PLPCSVYLIEHP 2bcoA 189 :HIEAVLLSNSPS T0289 160 :SLKYATTRSIAKYPVGIEVGPQ 2bcoA 202 :TFSWYSAENYSAQALTMELGRV T0289 182 :PHGVLRADILDQMRRMLKHAL 2bcoA 225 :RIGENALDRLTAFDLALRNLI T0289 208 :FNEGKEFPPCAIDVYKIMEKV 2bcoA 246 :AEAQPEHLSKPCIKYRVSRTI T0289 232 :RNESGDVAAVIHPNLQD 2bcoA 267 :VRLHDDFDFMFDDNVEN T0289 251 :WKPLHPGD 2bcoA 284 :FTSFVHGE T0289 260 :VFVSLDGKVIPLGGDCT 2bcoA 292 :VFGHDGDKPLMAKNDNE T0289 278 :YPVFVNEAAYYEKKEAFAKTTKLTLNAKS 2bcoA 309 :AIVFPNRHVAIGQRAALMVCEVKTRFEEG T0289 307 :IRS 2bcoA 339 :LVY Number of specific fragments extracted= 16 number of extra gaps= 0 total=546 Number of alignments=32 # 2bcoA read from 2bcoA/merged-good-all-a2m # found chain 2bcoA in template set T0289 3 :SCVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVHR 2bcoA 46 :PENPTQETKNIIISCGIHGDETAPMELVDSIIKDIESGFQ T0289 43 :AGLEVKPFITNPRAVEKCTRYIDCDLNRVFD 2bcoA 87 :VDARCLFIIAHPESTLAHTRFLEENLNRLFD T0289 78 :SKEMSEDLPYEVRRAQEINHLFGPKNSDDAYDVVFDLHNTT 2bcoA 118 :EKEHEPTKELAIADTLKLLVRDFYQDTEPKTRWHLDLHCAI T0289 119 :SNMGCTLILEDSRNDFLIQMFHYIKTCMAPLPCSVYLIEHPSLKYATTRSIAKYPVGIEVGPQ 2bcoA 161 :SKHYTFAVSPKTRHPVRSKALVDFLDSAHIEAVLLSNSPSSTFSWYSAENYSAQALTMELGRV T0289 182 :PHGVLRADILDQMRRMLKHALDFIQRFN 2bcoA 225 :RIGENALDRLTAFDLALRNLIAEAQPEH T0289 215 :PPCAIDVYKIMEKVD 2bcoA 253 :LSKPCIKYRVSRTIV T0289 235 :SGDVAAVIHPNLQDQDWKPLHPGDPVFVSLDGKVIPLGGDCTVYPVFVNEA 2bcoA 268 :RLHDDFDFMFDDNVENFTSFVHGEVFGHDGDKPLMAKNDNEAIVFPNRHVA Number of specific fragments extracted= 7 number of extra gaps= 0 total=553 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uwyA/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/T0289/1uwyA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0289/1uwyA/merged-good-all-a2m.gz for input Trying 1uwyA/merged-good-all-a2m Error: Couldn't open file 1uwyA/merged-good-all-a2m or 1uwyA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pytB/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/T0289/1pytB/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0289/1pytB/merged-good-all-a2m.gz for input Trying 1pytB/merged-good-all-a2m Error: Couldn't open file 1pytB/merged-good-all-a2m or 1pytB/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yme/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yme expands to /projects/compbio/data/pdb/1yme.pdb.gz 1yme:Warning: there is no chain 1yme will retry with 1ymeA # T0289 read from 1yme/merged-good-all-a2m # 1yme read from 1yme/merged-good-all-a2m # adding 1yme to template set # found chain 1yme in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1yme)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1yme)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1yme)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1yme)Y206 T0289 4 :CVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1yme 53 :STGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDY T0289 42 :RAGLEVKPF 1yme 100 :LDSMDIFLE T0289 51 :ITNPRAVEKC 1yme 110 :VTNPDGFAFT T0289 64 :I 1yme 129 :T T0289 65 :DCDLNRVFDL 1yme 140 :GVDANRNWDA T0289 75 :ENLSKEM 1yme 167 :GKYANSE T0289 87 :YEV 1yme 174 :VEV T0289 93 :QEINHLF 1yme 177 :KSIVDFV T0289 102 :KNSD 1yme 184 :KDHG T0289 107 :AYDVVFDLH 1yme 188 :NFKAFLSIH T0289 118 :TSNMGC 1yme 199 :SQLLLY T0289 126 :ILEDSRNDFLIQMFHYIKTCM 1yme 207 :GYTTQSIPDKTELNQVAKSAV T0289 147 :APLPCSVYL 1yme 234 :YGTSYKYGS T0289 156 :IEHPSLKYATTRSIAKY 1yme 248 :YQASGGSIDWSYNQGIK T0289 173 :PVGIEV 1yme 266 :SFTFEL T0289 179 :GPQ 1yme 275 :GRY T0289 183 :HGVLRADILDQMRRMLKH 1yme 278 :GFLLPASQIIPTAQETWL T0289 201 :ALDFIQRFNE 1yme 297 :VLTIMEHTVN Number of specific fragments extracted= 18 number of extra gaps= 2 total=571 Number of alignments=34 # 1yme read from 1yme/merged-good-all-a2m # found chain 1yme in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1yme)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1yme)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1yme)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1yme)Y206 T0289 5 :VAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1yme 54 :TGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDY T0289 42 :RAGLEVKPF 1yme 100 :LDSMDIFLE T0289 51 :ITNPRAVEKC 1yme 110 :VTNPDGFAFT T0289 61 :TRYI 1yme 126 :WRKT T0289 65 :D 1yme 131 :S T0289 66 :C 1yme 140 :G T0289 67 :DLNRVFDLENLSKEMS 1yme 142 :DANRNWDAGFGKAGAS T0289 83 :EDLPYEVRRAQEINHLF 1yme 170 :ANSEVEVKSIVDFVKDH T0289 106 :DAYDVVFDLH 1yme 187 :GNFKAFLSIH T0289 118 :TSNMGC 1yme 199 :SQLLLY T0289 126 :ILEDSRNDFLI 1yme 207 :GYTTQSIPDKT T0289 137 :QMFHYIKTCM 1yme 225 :SAVAALKSLY T0289 148 :PLPCSVYL 1yme 235 :GTSYKYGS T0289 156 :IEHPSLKYATTRSIAK 1yme 248 :YQASGGSIDWSYNQGI T0289 172 :YPVGIEV 1yme 265 :YSFTFEL T0289 179 :GPQPHGVLRADI 1yme 275 :GRYGFLLPASQI T0289 191 :LDQMRRMLKHALDFI 1yme 290 :AQETWLGVLTIMEHT Number of specific fragments extracted= 17 number of extra gaps= 2 total=588 Number of alignments=35 # 1yme read from 1yme/merged-good-all-a2m # found chain 1yme in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1yme)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1yme)Y198 Warning: unaligning (T0289)E128 because of BadResidue code BAD_PEPTIDE in next template residue (1yme)Y206 Warning: unaligning (T0289)D129 because of BadResidue code BAD_PEPTIDE at template residue (1yme)Y206 Warning: unaligning (T0289)G179 because of BadResidue code BAD_PEPTIDE in next template residue (1yme)D273 Warning: unaligning (T0289)P180 because of BadResidue code BAD_PEPTIDE at template residue (1yme)D273 T0289 5 :VAEEPIKKIAIFGGTHGNEL 1yme 54 :TGGSNRPAIWIDLGIHSREW T0289 25 :TGVFLVTHWLKNGAEVHR 1yme 78 :TGVWFAKKFTEDYGQDPS T0289 43 :AGLE 1yme 101 :DSMD T0289 47 :VKPFITNPRAVEKCT 1yme 106 :FLEIVTNPDGFAFTH T0289 62 :RYI 1yme 124 :RLW T0289 65 :DCDLNRVFDLEN 1yme 140 :GVDANRNWDAGF T0289 77 :LSKEMSEDL 1yme 157 :SSSPCSETY T0289 87 :YEVRRAQEINHLF 1yme 174 :VEVKSIVDFVKDH T0289 106 :DAYDVVFDLH 1yme 187 :GNFKAFLSIH T0289 118 :T 1yme 199 :S T0289 123 :CTLIL 1yme 200 :QLLLY T0289 130 :SRNDFLIQMFHYIKTCM 1yme 214 :PDKTELNQVAKSAVAAL T0289 147 :APLPCS 1yme 234 :YGTSYK T0289 163 :YATTRSIAKYPVGIEV 1yme 256 :DWSYNQGIKYSFTFEL T0289 181 :Q 1yme 274 :T T0289 182 :PHG 1yme 276 :RYG T0289 185 :VLR 1yme 280 :LLP T0289 188 :ADILDQMRRMLKHALDFI 1yme 287 :IPTAQETWLGVLTIMEHT Number of specific fragments extracted= 18 number of extra gaps= 3 total=606 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aye/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aye expands to /projects/compbio/data/pdb/1aye.pdb.gz 1aye:Warning: there is no chain 1aye will retry with 1ayeA WARNING: atom 767 has residue number 1 < previous residue 99A in 1aye # T0289 read from 1aye/merged-good-all-a2m # 1aye read from 1aye/merged-good-all-a2m # adding 1aye to template set # found chain 1aye in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1aye)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1aye)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1aye)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1aye)Y206 T0289 5 :VAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1aye 53 :STGGDKPAIWLDAGIHAREWVTQATALWTANKIVSDY T0289 42 :RAGLEVKPF 1aye 100 :LDALDIFLL T0289 51 :ITNPRAVEKC 1aye 110 :VTNPDGYVFS T0289 61 :TRYI 1aye 126 :WRKT T0289 65 :DCDLNRVFDL 1aye 140 :GVDPNRNWDA T0289 76 :NLSKEM 1aye 168 :PSANSE T0289 87 :YEV 1aye 174 :VEV T0289 93 :QEINHLF 1aye 177 :KSIVDFI T0289 102 :KNSD 1aye 184 :KSHG T0289 107 :AYDVVFDLH 1aye 188 :KVKAFIILH T0289 118 :TSNMGC 1aye 199 :SQLLMF T0289 126 :ILEDSRNDFLIQMFHYIKTCM 1aye 207 :GYKCTKLDDFDELSEVAQKAA T0289 147 :APLPCSVYL 1aye 234 :HGTKYKVGP T0289 156 :IEHPSLKYATTRSIAKY 1aye 248 :YQASGGSIDWSYDYGIK T0289 173 :PVGIEV 1aye 266 :SFAFEL T0289 179 :GP 1aye 275 :GR T0289 182 :PHGVLR 1aye 277 :YGFLLP T0289 188 :ADILDQMRRMLKHALDFIQ 1aye 287 :LPTAEETWLGLKAIMEHVR Number of specific fragments extracted= 18 number of extra gaps= 2 total=624 Number of alignments=37 # 1aye read from 1aye/merged-good-all-a2m # found chain 1aye in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1aye)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1aye)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1aye)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1aye)Y206 T0289 5 :VAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1aye 53 :STGGDKPAIWLDAGIHAREWVTQATALWTANKIVSDY T0289 42 :RAGLEVKPF 1aye 100 :LDALDIFLL T0289 51 :ITNPRAVEKC 1aye 110 :VTNPDGYVFS T0289 61 :TRYI 1aye 126 :WRKT T0289 66 :C 1aye 140 :G T0289 67 :DLNRVFDLENLSKEMS 1aye 142 :DPNRNWDAGFGGPGAS T0289 83 :EDLPYEVRRAQEINHLF 1aye 170 :ANSEVEVKSIVDFIKSH T0289 106 :DAYDVVFDLH 1aye 187 :GKVKAFIILH T0289 118 :TSNMGC 1aye 199 :SQLLMF T0289 126 :ILEDSRNDFLIQM 1aye 207 :GYKCTKLDDFDEL T0289 139 :FHYIKTCMA 1aye 223 :AQKAAQSLR T0289 148 :PLPCSVYL 1aye 235 :GTKYKVGP T0289 156 :IEHPSLKYATTRSIAK 1aye 248 :YQASGGSIDWSYDYGI T0289 172 :YPVGIEV 1aye 265 :YSFAFEL T0289 179 :GPQPHG 1aye 275 :GRYGFL T0289 186 :LR 1aye 281 :LP T0289 188 :ADILDQMRRMLKHALDFIQRF 1aye 287 :LPTAEETWLGLKAIMEHVRDH Number of specific fragments extracted= 17 number of extra gaps= 2 total=641 Number of alignments=38 # 1aye read from 1aye/merged-good-all-a2m # found chain 1aye in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1aye)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1aye)Y198 Warning: unaligning (T0289)E128 because of BadResidue code BAD_PEPTIDE in next template residue (1aye)Y206 Warning: unaligning (T0289)D129 because of BadResidue code BAD_PEPTIDE at template residue (1aye)Y206 Warning: unaligning (T0289)G179 because of BadResidue code BAD_PEPTIDE in next template residue (1aye)D273 Warning: unaligning (T0289)P180 because of BadResidue code BAD_PEPTIDE at template residue (1aye)D273 T0289 5 :VAEEPIKKIAIFGGTHGNEL 1aye 53 :STGGDKPAIWLDAGIHAREW T0289 25 :TGVFLVTHWLKNGAEVHR 1aye 78 :TALWTANKIVSDYGKDPS T0289 43 :AGLEVKPFITNPRAVEKCT 1aye 102 :ALDIFLLPVTNPDGYVFSQ T0289 62 :RYI 1aye 124 :RMW T0289 65 :DCDLNRVFDLENLSKE 1aye 140 :GVDPNRNWDAGFGGPG T0289 81 :MSEDLPYEVRRAQEINHLF 1aye 168 :PSANSEVEVKSIVDFIKSH T0289 106 :DAYDVVFDLH 1aye 187 :GKVKAFIILH T0289 118 :T 1aye 199 :S T0289 124 :TLIL 1aye 201 :LLMF T0289 130 :SRND 1aye 207 :GYKC T0289 134 :FLIQMFHYIKTCMA 1aye 222 :VAQKAAQSLRSLHG T0289 149 :LPCS 1aye 236 :TKYK T0289 164 :ATTRSIAKYPVGIEV 1aye 257 :WSYDYGIKYSFAFEL T0289 181 :Q 1aye 274 :T T0289 182 :PHGVL 1aye 276 :RYGFL T0289 188 :ADILDQMRRMLKHALDFIQRF 1aye 287 :LPTAEETWLGLKAIMEHVRDH Number of specific fragments extracted= 16 number of extra gaps= 3 total=657 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jqgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jqgA expands to /projects/compbio/data/pdb/1jqg.pdb.gz 1jqgA:WARNING: atom 739 has residue number 1 < previous residue 100P in 1jqgA # T0289 read from 1jqgA/merged-good-all-a2m # 1jqgA read from 1jqgA/merged-good-all-a2m # adding 1jqgA to template set # found chain 1jqgA in template set Warning: unaligning (T0289)N116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1jqgA)F198 Warning: unaligning (T0289)T117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1jqgA)F198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1jqgA)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1jqgA)Y206 T0289 6 :AEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1jqgA 55C:QDASKPVVMMQSLLHCREWVTLPATLYAIHKLVIDV T0289 42 :RAGLEVKPF 1jqgA 100 :INNIDWIIL T0289 51 :ITNPRAVEKC 1jqgA 110 :VANPDGYVHT T0289 61 :TRYI 1jqgA 126 :WRKN T0289 65 :DCDLNRVFDL 1jqgA 140 :GVDLNRNFGM T0289 75 :ENLSKEMS 1jqgA 167 :GRSAFSEP T0289 88 :EVRRAQEINHLF 1jqgA 175 :ESSVIRDIIAEH T0289 104 :SD 1jqgA 186A:RN T0289 107 :AYDVVFDLH 1jqgA 188 :RMALYLDIH T0289 118 :TSNMGC 1jqgA 199 :GSMILY T0289 126 :IL 1jqgA 207 :GN T0289 129 :DSRNDFLIQMF 1jqgA 210 :GVLPSNALQLH T0289 143 :KTCM 1jqgA 224 :VQMA T0289 147 :APLPCSV 1jqgA 236 :KDYIVGN T0289 154 :YLIEHPSLKYATTRSIAKYPVGIEVGPQP 1jqgA 247 :LYAASGGASDYAMQAAAPFSYTYELPAYR T0289 183 :HGVLRADILDQMRRMLKHALDFI 1jqgA 278 :GFLVDPDFIEQAGFETWEGIKVG T0289 206 :QRFNE 1jqgA 302 :RAAAA Number of specific fragments extracted= 17 number of extra gaps= 2 total=674 Number of alignments=40 # 1jqgA read from 1jqgA/merged-good-all-a2m # found chain 1jqgA in template set Warning: unaligning (T0289)N116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1jqgA)F198 Warning: unaligning (T0289)T117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1jqgA)F198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1jqgA)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1jqgA)Y206 T0289 6 :AEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1jqgA 55C:QDASKPVVMMQSLLHCREWVTLPATLYAIHKLVIDV T0289 42 :RAGLEVKPF 1jqgA 100 :INNIDWIIL T0289 51 :ITNPRAVEKC 1jqgA 110 :VANPDGYVHT T0289 61 :TRYID 1jqgA 126 :WRKNR T0289 66 :C 1jqgA 140 :G T0289 67 :DLNRVFDLENLSKEMS 1jqgA 142 :DLNRNFGMNWGTASSS T0289 83 :EDLPYEVRRAQEINHLFG 1jqgA 170 :AFSEPESSVIRDIIAEHR T0289 106 :DAYDVVFDLH 1jqgA 187 :NRMALYLDIH T0289 118 :TSNMGC 1jqgA 199 :GSMILY T0289 126 :I 1jqgA 207 :G T0289 128 :EDSRNDFLIQM 1jqgA 209 :NGVLPSNALQL T0289 139 :FHYIKTCMAPL 1jqgA 223 :GVQMAQAIDRV T0289 150 :PCSVY 1jqgA 237 :DYIVG T0289 155 :LIEHPSLKYATTRSIAKYPVGIEVGPQPHG 1jqgA 248 :YAASGGASDYAMQAAAPFSYTYELPAYRNS T0289 185 :VLRADILDQMRRMLKHALDFI 1jqgA 280 :LVDPDFIEQAGFETWEGIKVG Number of specific fragments extracted= 15 number of extra gaps= 2 total=689 Number of alignments=41 # 1jqgA read from 1jqgA/merged-good-all-a2m # found chain 1jqgA in template set Warning: unaligning (T0289)N116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1jqgA)F198 Warning: unaligning (T0289)T117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1jqgA)F198 T0289 9 :PIKKIAIFGGTHGNE 1jqgA 58 :SKPVVMMQSLLHCRE T0289 24 :LTGVFLVTHWLKNGAEVHR 1jqgA 77 :PATLYAIHKLVIDVTESDL T0289 43 :AGLEVK 1jqgA 101 :NNIDWI T0289 49 :PFITNPRAVEKCT 1jqgA 108 :LPVANPDGYVHTF T0289 62 :RYI 1jqgA 124 :RYW T0289 65 :DCDLNRVFDLENLSKEMSE 1jqgA 140 :GVDLNRNFGMNWGTASSSS T0289 87 :YEVRRAQEINHLF 1jqgA 174 :PESSVIRDIIAEH T0289 105 :DDAYDVVFDLH 1jqgA 186A:RNRMALYLDIH T0289 118 :TS 1jqgA 199 :GS T0289 124 :TLIL 1jqgA 201 :MILY T0289 128 :EDSRNDFLIQMFHYIKTCMAP 1jqgA 212 :LPSNALQLHLIGVQMAQAIDR T0289 149 :LPCS 1jqgA 236 :KDYI T0289 153 :VYLIEHPSLKYATTRSIAKYPVGIEVGPQPHGVLR 1jqgA 246 :VLYAASGGASDYAMQAAAPFSYTYELPAYRNSVWF T0289 188 :ADILDQMRRMLKHALDFI 1jqgA 287 :EQAGFETWEGIKVGARAA Number of specific fragments extracted= 14 number of extra gaps= 1 total=703 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d3cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d3cA expands to /projects/compbio/data/pdb/1d3c.pdb.gz 1d3cA:# T0289 read from 1d3cA/merged-good-all-a2m # 1d3cA read from 1d3cA/merged-good-all-a2m # adding 1d3cA to template set # found chain 1d3cA in template set T0289 30 :VTHWLKNGAEVHRAG 1d3cA 54 :WQGIINKINDGYLTG T0289 45 :LEVKPF 1d3cA 71 :VTAIWI T0289 51 :I 1d3cA 78 :Q T0289 70 :RVFDL 1d3cA 82 :NIYSI T0289 75 :ENLSKEMS 1d3cA 109 :NPAYGTIA T0289 88 :EV 1d3cA 117 :DF T0289 93 :QEINHLF 1d3cA 119 :QNLIAAA T0289 104 :SDDAYDVVFDLH 1d3cA 126 :HAKNIKVIIDFA T0289 121 :MGCTLILEDSRNDFLIQMF 1d3cA 138 :PNHTSPASSDQPSFAENGR T0289 140 :HYIKTCM 1d3cA 213 :DAIKMWL T0289 147 :APLPCSVYL 1d3cA 221 :LGIDGIRMN T0289 160 :SL 1d3cA 230 :AV T0289 170 :AKYPVGIEVGPQPHGVLRADILDQMRR 1d3cA 249 :YKPVFTFGQWFLGVNEVSPENHKFANE T0289 199 :KHALDFIQRFNEGKE 1d3cA 283 :FRFAQKVRQVFRDNT T0289 218 :AIDVYKIME 1d3cA 538 :GADITSWED T0289 227 :KVDYPRNESGDVAAVIHPNLQD 1d3cA 550 :KVKIPAVAGGNYNIKVANAAGT T0289 249 :QDWKPLHPGDPVFV 1d3cA 577 :DNFEVLSGDQVSVR T0289 263 :SLDGKVIPLGGDCTVYP 1d3cA 592 :VVNNATTALGQNVYLTG Number of specific fragments extracted= 18 number of extra gaps= 0 total=721 Number of alignments=43 # 1d3cA read from 1d3cA/merged-good-all-a2m # found chain 1d3cA in template set T0289 30 :VTHWLKNGAEVHRAGL 1d3cA 54 :WQGIINKINDGYLTGM T0289 46 :EVKPF 1d3cA 72 :TAIWI T0289 53 :NP 1d3cA 78 :QP T0289 66 :CDLNRVF 1d3cA 99 :GYWARDF T0289 73 :DLENLSKE 1d3cA 108 :TNPAYGTI T0289 87 :YEV 1d3cA 116 :ADF T0289 93 :QEINHLFGP 1d3cA 119 :QNLIAAAHA T0289 106 :DAYDVVFDLH 1d3cA 128 :KNIKVIIDFA T0289 121 :MGCTLILEDSRNDFLI 1d3cA 138 :PNHTSPASSDQPSFAE T0289 137 :QMFHYIKTC 1d3cA 213 :DAIKMWLDL T0289 148 :PLPCSVYLIEHP 1d3cA 222 :GIDGIRMNAVKH T0289 161 :L 1d3cA 240 :K T0289 169 :IAKYPVGIEVGPQPHGVLRADILDQMRR 1d3cA 248 :NYKPVFTFGQWFLGVNEVSPENHKFANE T0289 199 :KHALDFI 1d3cA 283 :FRFAQKV T0289 206 :QRFNEG 1d3cA 291 :QVFRDN T0289 212 :KEFPPCAIDVYKIM 1d3cA 628 :QVVYQYPNWYYDVS T0289 232 :RNESGDVAAV 1d3cA 642 :VPAGKTIEFK T0289 260 :VFVSLDGKVIPLGGDCT 1d3cA 652 :FLKKQGSTVTWEGGSNH T0289 299 :KLTLNAKSIRS 1d3cA 669 :TFTAPSSGTAT Number of specific fragments extracted= 19 number of extra gaps= 0 total=740 Number of alignments=44 # 1d3cA read from 1d3cA/merged-good-all-a2m # found chain 1d3cA in template set T0289 91 :RAQEINHLFGPK 1d3cA 117 :DFQNLIAAAHAK T0289 107 :AYDVVFDL 1d3cA 129 :NIKVIIDF T0289 120 :NMGCTLILEDSRNDFLIQ 1d3cA 137 :APNHTSPASSDQPSFAEN T0289 149 :LPCS 1d3cA 155 :GRLY T0289 153 :VYLIEHPSLKY 1d3cA 175 :FHHNGGTDFST T0289 165 :TTRSIAKY 1d3cA 186 :TENGIYKN T0289 184 :GVLRADILDQMRRMLKHALDF 1d3cA 201 :NHNNSTVDVYLKDAIKMWLDL Number of specific fragments extracted= 7 number of extra gaps= 0 total=747 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m4lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0289 read from 1m4lA/merged-good-all-a2m # 1m4lA read from 1m4lA/merged-good-all-a2m # found chain 1m4lA in training set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1m4lA)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1m4lA)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1m4lA)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1m4lA)Y206 T0289 4 :CVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1m4lA 53 :STGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDY T0289 42 :RAGLEVKPF 1m4lA 100 :LDSMDIFLE T0289 51 :ITNPRAVEKC 1m4lA 110 :VTNPDGFAFT T0289 64 :I 1m4lA 129 :T T0289 65 :DCDLNRVFDL 1m4lA 140 :GVDANRNWDA T0289 75 :ENLSKEM 1m4lA 167 :GKYANSE T0289 87 :YEV 1m4lA 174 :VEV T0289 93 :QEINHLF 1m4lA 177 :KSIVDFV T0289 102 :KNSD 1m4lA 184 :KDHG T0289 107 :AYDVVFDLH 1m4lA 188 :NFKAFLSIH T0289 118 :TSNMGC 1m4lA 199 :SQLLLY T0289 126 :ILEDSRNDFLIQMFHYIKTCM 1m4lA 207 :GYTTQSIPDKTELNQVAKSAV T0289 147 :APLPCSVYL 1m4lA 234 :YGTSYKYGS T0289 156 :IEHPSLKYATTRSIAKY 1m4lA 248 :YQASGGSIDWSYNQGIK T0289 173 :PVGIEV 1m4lA 266 :SFTFEL T0289 179 :GPQPH 1m4lA 275 :GRYGF T0289 185 :VLR 1m4lA 280 :LLP T0289 188 :ADILDQMRRMLKHALDFI 1m4lA 287 :IPTAQETWLGVLTIMEHT Number of specific fragments extracted= 18 number of extra gaps= 2 total=765 Number of alignments=46 # 1m4lA read from 1m4lA/merged-good-all-a2m # found chain 1m4lA in training set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1m4lA)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1m4lA)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (1m4lA)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (1m4lA)Y206 T0289 5 :VAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1m4lA 54 :TGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDY T0289 42 :RAGLEVKPF 1m4lA 100 :LDSMDIFLE T0289 51 :ITNPRAVEKC 1m4lA 110 :VTNPDGFAFT T0289 61 :TRYI 1m4lA 126 :WRKT T0289 65 :D 1m4lA 131 :S T0289 66 :C 1m4lA 140 :G T0289 67 :DLNRVFDLENLSKEMS 1m4lA 142 :DANRNWDAGFGKAGAS T0289 83 :EDLPYEVRRAQEINHLF 1m4lA 170 :ANSEVEVKSIVDFVKDH T0289 106 :DAYDVVFDLH 1m4lA 187 :GNFKAFLSIH T0289 118 :TSNMGC 1m4lA 199 :SQLLLY T0289 126 :ILEDSRNDFLI 1m4lA 207 :GYTTQSIPDKT T0289 137 :QMFHYIKTCM 1m4lA 225 :SAVAALKSLY T0289 148 :PLPCSVYL 1m4lA 235 :GTSYKYGS T0289 156 :IEHPSLKYATTRSIAK 1m4lA 248 :YQASGGSIDWSYNQGI T0289 172 :YPVGIEV 1m4lA 265 :YSFTFEL T0289 179 :GPQPHGVLRADI 1m4lA 275 :GRYGFLLPASQI T0289 191 :LDQMRRMLKHALDFI 1m4lA 290 :AQETWLGVLTIMEHT Number of specific fragments extracted= 17 number of extra gaps= 2 total=782 Number of alignments=47 # 1m4lA read from 1m4lA/merged-good-all-a2m # found chain 1m4lA in training set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (1m4lA)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (1m4lA)Y198 Warning: unaligning (T0289)E128 because of BadResidue code BAD_PEPTIDE in next template residue (1m4lA)Y206 Warning: unaligning (T0289)D129 because of BadResidue code BAD_PEPTIDE at template residue (1m4lA)Y206 Warning: unaligning (T0289)G179 because of BadResidue code BAD_PEPTIDE in next template residue (1m4lA)D273 Warning: unaligning (T0289)P180 because of BadResidue code BAD_PEPTIDE at template residue (1m4lA)D273 T0289 4 :CVAEEPIKKIAIFGGTHGNEL 1m4lA 53 :STGGSNRPAIWIDLGIHSREW T0289 25 :TGVFLVTHWLKNGAEVHR 1m4lA 78 :TGVWFAKKFTEDYGQDPS T0289 43 :AGLE 1m4lA 101 :DSMD T0289 47 :VKPFITNPRAVEKCT 1m4lA 106 :FLEIVTNPDGFAFTH T0289 62 :RYI 1m4lA 124 :RLW T0289 65 :DCDLNRVFDLEN 1m4lA 140 :GVDANRNWDAGF T0289 77 :LSKEMSEDL 1m4lA 157 :SSSPCSETY T0289 87 :YEVRRAQEINHLF 1m4lA 174 :VEVKSIVDFVKDH T0289 106 :DAYDVVFDLH 1m4lA 187 :GNFKAFLSIH T0289 118 :T 1m4lA 199 :S T0289 124 :TLIL 1m4lA 201 :LLLY T0289 130 :SRNDFLIQMFHYIKTCM 1m4lA 214 :PDKTELNQVAKSAVAAL T0289 147 :APLPCS 1m4lA 234 :YGTSYK T0289 163 :YATTRSIAKYPVGIEV 1m4lA 256 :DWSYNQGIKYSFTFEL T0289 181 :Q 1m4lA 274 :T T0289 182 :PHGVL 1m4lA 276 :RYGFL T0289 188 :ADILDQMRRMLKHALDFI 1m4lA 287 :IPTAQETWLGVLTIMEHT Number of specific fragments extracted= 17 number of extra gaps= 3 total=799 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dtdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dtdA expands to /projects/compbio/data/pdb/1dtd.pdb.gz 1dtdA:# T0289 read from 1dtdA/merged-good-all-a2m # 1dtdA read from 1dtdA/merged-good-all-a2m # adding 1dtdA to template set # found chain 1dtdA in template set Warning: unaligning (T0289)N116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dtdA)Y554 Warning: unaligning (T0289)T117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dtdA)Y554 Warning: unaligning (T0289)T124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dtdA)Y562 Warning: unaligning (T0289)L125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dtdA)Y562 Warning: unaligning (T0289)I176 because of BadResidue code BAD_PEPTIDE in next template residue (1dtdA)E626 Warning: unaligning (T0289)E177 because of BadResidue code BAD_PEPTIDE at template residue (1dtdA)E626 T0289 5 :VAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1dtdA 409 :STGGDKPAIWLDAGIHAREWVTQATALWTANKIVSDY T0289 42 :RAGLEVKPF 1dtdA 455 :LDALDIFLL T0289 51 :ITNPRAVEKC 1dtdA 465 :VTNPDGYVFS T0289 65 :DCDLNRVFDL 1dtdA 496 :GVDPNRNWDA T0289 75 :ENLS 1dtdA 524 :PSAN T0289 85 :LPYEV 1dtdA 528 :SEVEV T0289 93 :QEINHLF 1dtdA 533 :KSIVDFI T0289 102 :KNSD 1dtdA 540 :KSHG T0289 107 :AYDVVFDLH 1dtdA 544 :KVKAFIILH T0289 118 :TSNMGC 1dtdA 555 :SQLLMF T0289 126 :ILEDSRNDFLIQMFHYIKTCM 1dtdA 563 :GYKCTKLDDFDELSEVAQKAA T0289 147 :APLPCSVY 1dtdA 592 :TKYKVGPI T0289 156 :IEHPSLKYATTRSIAKY 1dtdA 604 :YQASGGSIDWSYDYGIK T0289 173 :PVG 1dtdA 622 :SFA T0289 178 :V 1dtdA 627 :L T0289 180 :PQPHGVLRADILDQMRRMLKHALDFI 1dtdA 631 :GRYGFLLPARQILPTAEETWLGLKAI T0289 206 :QRFN 1dtdA 658 :EHVR Number of specific fragments extracted= 17 number of extra gaps= 3 total=816 Number of alignments=49 # 1dtdA read from 1dtdA/merged-good-all-a2m # found chain 1dtdA in template set Warning: unaligning (T0289)N116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dtdA)Y554 Warning: unaligning (T0289)T117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dtdA)Y554 Warning: unaligning (T0289)T124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dtdA)Y562 Warning: unaligning (T0289)L125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dtdA)Y562 Warning: unaligning (T0289)I176 because of BadResidue code BAD_PEPTIDE in next template residue (1dtdA)E626 Warning: unaligning (T0289)E177 because of BadResidue code BAD_PEPTIDE at template residue (1dtdA)E626 T0289 4 :CVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 1dtdA 408 :FSTGGDKPAIWLDAGIHAREWVTQATALWTANKIVSDY T0289 42 :RAGLEVKPF 1dtdA 455 :LDALDIFLL T0289 51 :ITNPRAVEKC 1dtdA 465 :VTNPDGYVFS T0289 61 :TRYI 1dtdA 481 :WRKT T0289 66 :C 1dtdA 496 :G T0289 67 :DLNRVFDLENLSKEMS 1dtdA 498 :DPNRNWDAGFGGPGAS T0289 83 :EDLPYEVRRAQEINHLF 1dtdA 526 :ANSEVEVKSIVDFIKSH T0289 106 :DAYDVVFDLH 1dtdA 543 :GKVKAFIILH T0289 118 :TSNMGC 1dtdA 555 :SQLLMF T0289 126 :ILEDSRNDFLI 1dtdA 563 :GYKCTKLDDFD T0289 137 :QMFHYIKTCMA 1dtdA 577 :EVAQKAAQSLS T0289 148 :PLPCSVYL 1dtdA 591 :GTKYKVGP T0289 156 :IEHPSLKYATTRSIAK 1dtdA 604 :YQASGGSIDWSYDYGI T0289 172 :YPVG 1dtdA 621 :YSFA T0289 178 :V 1dtdA 627 :L T0289 179 :GPQPHG 1dtdA 631 :GRYGFL T0289 186 :LR 1dtdA 637 :LP T0289 188 :ADILDQMRRMLKHALDFIQR 1dtdA 643 :LPTAEETWLGLKAIMEHVRD Number of specific fragments extracted= 18 number of extra gaps= 3 total=834 Number of alignments=50 # 1dtdA read from 1dtdA/merged-good-all-a2m # found chain 1dtdA in template set Warning: unaligning (T0289)N116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dtdA)Y554 Warning: unaligning (T0289)T117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dtdA)Y554 Warning: unaligning (T0289)E128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dtdA)Y562 Warning: unaligning (T0289)D129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dtdA)Y562 Warning: unaligning (T0289)I176 because of BadResidue code BAD_PEPTIDE in next template residue (1dtdA)E626 Warning: unaligning (T0289)E177 because of BadResidue code BAD_PEPTIDE at template residue (1dtdA)E626 Warning: unaligning (T0289)G179 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dtdA)D629 Warning: unaligning (T0289)P180 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dtdA)D629 T0289 5 :VAEEPIKKIAIFGGTHGNEL 1dtdA 409 :STGGDKPAIWLDAGIHAREW T0289 25 :TGVFLVTHWLKNGAEVHR 1dtdA 433 :TALWTANKIVSDYGKDPS T0289 43 :AGLE 1dtdA 456 :DALD T0289 47 :VKPFITNPRAVEKCT 1dtdA 461 :FLLPVTNPDGYVFSQ T0289 65 :DCDLNRVFDLENLSKE 1dtdA 496 :GVDPNRNWDAGFGGPG T0289 81 :MSEDLPYEVRRAQEINHLF 1dtdA 524 :PSANSEVEVKSIVDFIKSH T0289 106 :DAYDVVFDLH 1dtdA 543 :GKVKAFIILH T0289 118 :T 1dtdA 555 :S T0289 123 :CTLIL 1dtdA 556 :QLLMF T0289 130 :SRND 1dtdA 563 :GYKC T0289 134 :FLIQMFHYIKTCMAPLPCS 1dtdA 578 :VAQKAAQSLSRLHGTKYKV T0289 164 :ATTRSIAKYPVG 1dtdA 613 :WSYDYGIKYSFA T0289 178 :V 1dtdA 627 :L T0289 181 :Q 1dtdA 630 :T T0289 182 :PHGVL 1dtdA 632 :RYGFL T0289 187 :R 1dtdA 638 :P T0289 188 :ADILDQMRRMLKHALDFIQRF 1dtdA 643 :LPTAEETWLGLKAIMEHVRDH Number of specific fragments extracted= 17 number of extra gaps= 4 total=851 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ctc/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ctc expands to /projects/compbio/data/pdb/2ctc.pdb.gz 2ctc:Warning: there is no chain 2ctc will retry with 2ctcA # T0289 read from 2ctc/merged-good-all-a2m # 2ctc read from 2ctc/merged-good-all-a2m # adding 2ctc to template set # found chain 2ctc in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (2ctc)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (2ctc)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (2ctc)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (2ctc)Y206 T0289 4 :CVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 2ctc 53 :STGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDY T0289 42 :RAGLEVKPF 2ctc 100 :LDSMDIFLE T0289 51 :ITNPRAVEKC 2ctc 110 :VTNPDGFAFT T0289 61 :T 2ctc 129 :T T0289 65 :DCDLNRVFDL 2ctc 140 :GVDANRNWDA T0289 75 :ENLSKEMS 2ctc 167 :GKYANSEV T0289 88 :EV 2ctc 175 :EV T0289 93 :QEINHLF 2ctc 177 :KSIVDFV T0289 102 :KNSD 2ctc 184 :KDHG T0289 107 :AYDVVFDLH 2ctc 188 :NFKAFLSIH T0289 118 :TSNMGC 2ctc 199 :SQLLLY T0289 126 :ILEDSRNDFLIQMFHYIKTCM 2ctc 207 :GYTTQSIPDKTELNQVAKSAV T0289 147 :APLPCSVYL 2ctc 234 :YGTSYKYGS T0289 156 :IEHPSLKYATTRSIAKY 2ctc 248 :YQASGGSIDWSYNQGIK T0289 173 :PVGIEV 2ctc 266 :SFTFEL T0289 179 :GPQ 2ctc 275 :GRY T0289 183 :HGVLR 2ctc 278 :GFLLP T0289 188 :ADILDQMRRMLKHALDFI 2ctc 287 :IPTAQETWLGVLTIMEHT Number of specific fragments extracted= 18 number of extra gaps= 2 total=869 Number of alignments=52 # 2ctc read from 2ctc/merged-good-all-a2m # found chain 2ctc in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (2ctc)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (2ctc)Y198 Warning: unaligning (T0289)T124 because of BadResidue code BAD_PEPTIDE in next template residue (2ctc)Y206 Warning: unaligning (T0289)L125 because of BadResidue code BAD_PEPTIDE at template residue (2ctc)Y206 T0289 5 :VAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVH 2ctc 54 :TGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDY T0289 42 :RAGLEVKPF 2ctc 100 :LDSMDIFLE T0289 51 :ITNPRAVEKC 2ctc 110 :VTNPDGFAFT T0289 61 :TRYI 2ctc 126 :WRKT T0289 66 :C 2ctc 140 :G T0289 67 :DLNRVFDLENLSKEMS 2ctc 142 :DANRNWDAGFGKAGAS T0289 83 :EDLPYEVRRAQEINHLF 2ctc 170 :ANSEVEVKSIVDFVKDH T0289 106 :DAYDVVFDLH 2ctc 187 :GNFKAFLSIH T0289 118 :TSNMGC 2ctc 199 :SQLLLY T0289 126 :ILEDSRNDFLI 2ctc 207 :GYTTQSIPDKT T0289 137 :QMFHYIKTCM 2ctc 225 :SAVEALKSLY T0289 148 :PLPCSVYL 2ctc 235 :GTSYKYGS T0289 156 :IEHPSLKYATTRSIAK 2ctc 248 :YQASGGSIDWSYNQGI T0289 172 :YPVGIEV 2ctc 265 :YSFTFEL T0289 179 :GPQPHGVLRADI 2ctc 275 :GRYGFLLPASQI T0289 191 :LDQMRRMLKHALDFI 2ctc 290 :AQETWLGVLTIMEHT Number of specific fragments extracted= 16 number of extra gaps= 2 total=885 Number of alignments=53 # 2ctc read from 2ctc/merged-good-all-a2m # found chain 2ctc in template set Warning: unaligning (T0289)N116 because of BadResidue code BAD_PEPTIDE in next template residue (2ctc)Y198 Warning: unaligning (T0289)T117 because of BadResidue code BAD_PEPTIDE at template residue (2ctc)Y198 Warning: unaligning (T0289)E128 because of BadResidue code BAD_PEPTIDE in next template residue (2ctc)Y206 Warning: unaligning (T0289)D129 because of BadResidue code BAD_PEPTIDE at template residue (2ctc)Y206 Warning: unaligning (T0289)G179 because of BadResidue code BAD_PEPTIDE in next template residue (2ctc)D273 Warning: unaligning (T0289)P180 because of BadResidue code BAD_PEPTIDE at template residue (2ctc)D273 T0289 4 :CVAEEPIKKIAIFGGTHGNEL 2ctc 53 :STGGSNRPAIWIDLGIHSREW T0289 25 :TGVFLVTHWLKNGAEVHR 2ctc 78 :TGVWFAKKFTEDYGQDPS T0289 43 :AGLE 2ctc 101 :DSMD T0289 47 :VKPFITNPRAVEKCT 2ctc 106 :FLEIVTNPDGFAFTH T0289 62 :RYI 2ctc 124 :RLW T0289 65 :DCDLNRVFDLENLSKE 2ctc 140 :GVDANRNWDAGFGKAG T0289 81 :MSEDLPYEVRRAQEINHLF 2ctc 168 :KYANSEVEVKSIVDFVKDH T0289 106 :DAYDVVFDLH 2ctc 187 :GNFKAFLSIH T0289 118 :T 2ctc 199 :S T0289 123 :CTLIL 2ctc 200 :QLLLY T0289 130 :SRNDFLIQMFHYIKTCM 2ctc 214 :PDKTELNQVAKSAVEAL T0289 147 :APLPCS 2ctc 234 :YGTSYK T0289 164 :ATTRSIAKYPVGIEV 2ctc 257 :WSYNQGIKYSFTFEL T0289 181 :Q 2ctc 274 :T T0289 182 :PHGVL 2ctc 276 :RYGFL T0289 187 :R 2ctc 282 :P T0289 188 :ADILDQMRRMLKHALDFI 2ctc 287 :IPTAQETWLGVLTIMEHT Number of specific fragments extracted= 17 number of extra gaps= 3 total=902 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xovA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xovA expands to /projects/compbio/data/pdb/1xov.pdb.gz 1xovA:# T0289 read from 1xovA/merged-good-all-a2m # 1xovA read from 1xovA/merged-good-all-a2m # adding 1xovA to template set # found chain 1xovA in template set Warning: unaligning (T0289)P9 because first residue in template chain is (1xovA)A0 Warning: unaligning (T0289)S119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xovA)G85 Warning: unaligning (T0289)N120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xovA)G85 T0289 10 :IKKIAIFGG 1xovA 1 :MSNYSMSRG T0289 21 :GNE 1xovA 16 :GAE T0289 24 :LTGVFLVTHWLKNGAEVH 1xovA 21 :LSEIKEAEKVLNAASDEL T0289 42 :RAGLEVKPF 1xovA 40 :REGHNVKTF T0289 77 :LSKEMS 1xovA 50 :DRTSTT T0289 88 :EVRRAQEINHLF 1xovA 56 :QSANLNKIVNWH T0289 104 :SDDAYDVVFDLH 1xovA 68 :NANPADVHISVH T0289 116 :NTT 1xovA 81 :NAG T0289 121 :MGCTLIL 1xovA 86 :TGVEVWY T0289 129 :DSRNDFLIQMFHYIKTCM 1xovA 93 :YAGDEKGRKLAVEISAKM T0289 147 :APLPCSVYLIEHP 1xovA 114 :LGLPNRGAKATKD T0289 163 :YATTRSIAKYPVGIEVGPQPH 1xovA 127 :LRFLNSTKGTAVLLEVCFVDR T0289 192 :DQMRRML 1xovA 148 :KEDANAI T0289 199 :KHALDFIQR 1xovA 161 :DKLGIAIAE T0289 208 :FNEGKEFP 1xovA 171 :LTGKTVAA T0289 216 :PC 1xovA 180 :NP T0289 218 :AIDVYKI 1xovA 250 :GRIKVRI T0289 233 :NESGDVAAVIHP 1xovA 257 :KSAKDLRIPVWN T0289 245 :NLQDQDWKPLHPGDPVFVSLDGK 1xovA 271 :KLNSGKIKWYSPGTKLSWYDNKK T0289 268 :VIPLGG 1xovA 297 :ELWYEK T0289 274 :DCTVYPVFV 1xovA 304 :GWYYTANYF Number of specific fragments extracted= 21 number of extra gaps= 1 total=923 Number of alignments=55 # 1xovA read from 1xovA/merged-good-all-a2m # found chain 1xovA in template set Warning: unaligning (T0289)P9 because first residue in template chain is (1xovA)A0 Warning: unaligning (T0289)S119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xovA)G85 Warning: unaligning (T0289)N120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xovA)G85 Warning: unaligning (T0289)K212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xovA)N243 Warning: unaligning (T0289)E213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xovA)G244 T0289 10 :IKKIAIFGG 1xovA 1 :MSNYSMSRG T0289 21 :GNE 1xovA 16 :GAE T0289 24 :LTGVFLVTHWLKNGAEVH 1xovA 21 :LSEIKEAEKVLNAASDEL T0289 42 :RAGLEVKPF 1xovA 40 :REGHNVKTF T0289 51 :I 1xovA 50 :D T0289 75 :ENLSK 1xovA 51 :RTSTT T0289 88 :EVRRAQEINHLFGP 1xovA 56 :QSANLNKIVNWHNA T0289 106 :DAYDVVFDLH 1xovA 70 :NPADVHISVH T0289 116 :NTT 1xovA 81 :NAG T0289 121 :MGCTLILE 1xovA 86 :TGVEVWYY T0289 130 :SRNDFLIQMFHYIKTCMA 1xovA 94 :AGDEKGRKLAVEISAKMA T0289 148 :PLPCSVYLIEHP 1xovA 115 :GLPNRGAKATKD T0289 163 :YATTRSIAKYPVGIEVGPQP 1xovA 127 :LRFLNSTKGTAVLLEVCFVD T0289 187 :RADILDQM 1xovA 147 :RKEDANAI T0289 195 :R 1xovA 160 :Y T0289 199 :KHALDFI 1xovA 161 :DKLGIAI T0289 206 :QRFNEG 1xovA 169 :EGLTGK T0289 214 :FPPCAIDV 1xovA 245 :KKDAKGRI T0289 224 :IME 1xovA 253 :KVR T0289 232 :RNESGDVAAVIHP 1xovA 256 :IKSAKDLRIPVWN T0289 245 :NLQDQDWKPLHPGDPVFVSL 1xovA 271 :KLNSGKIKWYSPGTKLSWYD T0289 265 :DGKVIPLGGDCTVYPV 1xovA 294 :GYLELWYEKDGWYYTA Number of specific fragments extracted= 22 number of extra gaps= 2 total=945 Number of alignments=56 # 1xovA read from 1xovA/merged-good-all-a2m # found chain 1xovA in template set Warning: unaligning (T0289)P9 because first residue in template chain is (1xovA)A0 Warning: unaligning (T0289)S119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xovA)G85 Warning: unaligning (T0289)N120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xovA)G85 Warning: unaligning (T0289)D229 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xovA)M194 Warning: unaligning (T0289)S309 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xovA)N243 T0289 10 :IKKIAIFGG 1xovA 1 :MSNYSMSRG T0289 24 :LTGVFLVTHWLKNGAEVHR 1xovA 21 :LSEIKEAEKVLNAASDELK T0289 43 :AGLEVKPFIT 1xovA 41 :EGHNVKTFID T0289 78 :S 1xovA 51 :R T0289 81 :MSEDLPYEVRRAQEINHL 1xovA 52 :TSTTQSANLNKIVNWHNA T0289 106 :DAYDVVFDLHNTT 1xovA 70 :NPADVHISVHLNA T0289 121 :MGCTLILEDSRNDFLIQMFHYIKT 1xovA 86 :TGVEVWYYAGDEKGRKLAVEISAK T0289 145 :CMAPLPCSVYLIE 1xovA 113 :ALGLPNRGAKATK T0289 162 :KYATTRSIAKYPVGIEVGPQ 1xovA 126 :DLRFLNSTKGTAVLLEVCFV T0289 186 :LRADILDQM 1xovA 146 :DRKEDANAI T0289 197 :MLKHALDFIQRFNEGKEF 1xovA 159 :MYDKLGIAIAEGLTGKTV T0289 215 :PPCAIDVYKIMEKV 1xovA 179 :KNPNRHSGAVVDSV T0289 230 :YPRNESGDVAAVIHPNLQ 1xovA 196 :SKMDFKSSPIKMYKAGSS T0289 259 :PVFVSLDGKV 1xovA 214 :LLVYEHNKYW T0289 269 :IPLGG 1xovA 226 :AYIND T0289 298 :TKLTLNAKSIR 1xovA 231 :KLCYIYKSFCI Number of specific fragments extracted= 16 number of extra gaps= 3 total=961 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nsa/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/T0289/1nsa/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0289/1nsa/merged-good-all-a2m.gz for input Trying 1nsa/merged-good-all-a2m Error: Couldn't open file 1nsa/merged-good-all-a2m or 1nsa/merged-good-all-a2m.gz for input # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 57 Adding 3319 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: -589.7481, CN propb: -589.7481 weights: 0.2728 constraints: 946 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 946 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 946 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 2373 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 2373 # 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 3319 # command: