parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0320/ # command:# Making conformation for sequence T0320 numbered 1 through 306 Created new target T0320 from T0320.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0320/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0320//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0320/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0320//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0320/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0320/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0320/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wy5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wy5A expands to /projects/compbio/data/pdb/1wy5.pdb.gz 1wy5A:# T0320 read from 1wy5A/merged-good-all-a2m # 1wy5A read from 1wy5A/merged-good-all-a2m # adding 1wy5A to template set # found chain 1wy5A in template set T0320 35 :RLTRKYLLSEIFVRWS 1wy5A 4 :ESRVIRKVLALQNDEK # choosing archetypes in rotamer library T0320 51 :PLNGEISFSYNGGKDCQVLLLLYLSC 1wy5A 22 :SGERRVLIAFSGGVDSVVLTDVLLKL T0320 78 :W 1wy5A 49 :N T0320 79 :EY 1wy5A 55 :EV T0320 81 :FFIKAQNSQFDFEFQSFPMQRLPTVFIDQEETFPT 1wy5A 59 :AHFNHMLRESAERDEEFCKEFAKERNMKIFVGKED T0320 120 :VLETSERY 1wy5A 94 :VRAFAKEN T0320 128 :CLSLYESQRQSGA 1wy5A 104 :SLEEAGRFLRYKF T0320 148 :FRDFIKIY 1wy5A 117 :LKEILESE T0320 157 :ETEAIVIGIRH 1wy5A 125 :GFDCIATAHHL T0320 172 :GEALKPIQRT 1wy5A 154 :GLIGFLPKEE T0320 189 :MRLQPLLHWDLTNIWSFLLYSNEPICGLY 1wy5A 164 :VIRRPLYYVKRSEIEEYAKFKGLRWVEDE T0320 249 :WEIIHAFGKDAEGER 1wy5A 280 :YEKVELVRSLLEKGG T0320 266 :AINTSPISVVDKER 1wy5A 295 :EVNLGKGKVLKRKE Number of specific fragments extracted= 13 number of extra gaps= 0 total=13 Number of alignments=1 # 1wy5A read from 1wy5A/merged-good-all-a2m # found chain 1wy5A in template set Warning: unaligning (T0320)K282 because last residue in template chain is (1wy5A)L311 T0320 22 :QKSQIIASTQEAIR 1wy5A 3 :PESRVIRKVLALQN T0320 48 :R 1wy5A 17 :D T0320 49 :WSPLNGEISFSYNGGKDCQVLLLLYLSCLWEYFFIK 1wy5A 20 :IFSGERRVLIAFSGGVDSVVLTDVLLKLKNYFSLKE T0320 102 :LPTVFIDQEE 1wy5A 56 :VALAHFNHML T0320 112 :TFPTLENFVLETSERYCLSLYE 1wy5A 68 :SAERDEEFCKEFAKERNMKIFV T0320 134 :SQRQSGA 1wy5A 91 :KEDVRAF T0320 141 :SVNMAD 1wy5A 102 :RMSLEE T0320 148 :FRDFIKIY 1wy5A 117 :LKEILESE T0320 157 :ETEAIVIGIRHTD 1wy5A 125 :GFDCIATAHHLND T0320 171 :FGEALKPIQRTD 1wy5A 138 :LLETSLLFFTRG T0320 187 :DF 1wy5A 150 :TG T0320 189 :MRLQPLLHWDLTNIWSFLLYSNEPICGLYG 1wy5A 164 :VIRRPLYYVKRSEIEEYAKFKGLRWVEDET T0320 221 :FT 1wy5A 277 :EK T0320 248 :EWEIIHAFGKDAEG 1wy5A 279 :DYEKVELVRSLLEK T0320 264 :SSAINTSPISVVDKERFS 1wy5A 293 :GGEVNLGKGKVLKRKERW Number of specific fragments extracted= 15 number of extra gaps= 0 total=28 Number of alignments=2 # 1wy5A read from 1wy5A/merged-good-all-a2m # found chain 1wy5A in template set T0320 22 :QKSQIIASTQEAIRLT 1wy5A 3 :PESRVIRKVLALQNDE T0320 48 :RWSPLNGEISFSYNGGKDCQVLLLLYLSCLWE 1wy5A 19 :KIFSGERRVLIAFSGGVDSVVLTDVLLKLKNY T0320 80 :YFFIKAQNSQFD 1wy5A 55 :EVALAHFNHMLR T0320 100 :QRLPT 1wy5A 67 :ESAER T0320 116 :LENFVLETSERYCLSL 1wy5A 72 :DEEFCKEFAKERNMKI T0320 142 :VNMADAFRDFI 1wy5A 88 :FVGKEDVRAFA T0320 153 :KIYPETEAIVIGIR 1wy5A 121 :LESEGFDCIATAHH T0320 180 :RTDSN 1wy5A 160 :PKEEV T0320 190 :RLQPLLHWDLTNIWSFLLYSNEPIC 1wy5A 165 :IRRPLYYVKRSEIEEYAKFKGLRWV Number of specific fragments extracted= 9 number of extra gaps= 0 total=37 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q15A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1q15A expands to /projects/compbio/data/pdb/1q15.pdb.gz 1q15A:# T0320 read from 1q15A/merged-good-all-a2m # 1q15A read from 1q15A/merged-good-all-a2m # adding 1q15A to template set # found chain 1q15A in template set Warning: unaligning (T0320)R303 because last residue in template chain is (1q15A)K501 T0320 11 :YEIT 1q15A 198 :VESR T0320 15 :NSYLH 1q15A 204 :TTPAS T0320 20 :IDQKSQIIAST 1q15A 212 :LALPREPLLAL T0320 38 :RKYLLSEIFVRWSPLNGEISFSYNGGKDCQVLLLLYLSCLWEYFFIKAQN 1q15A 223 :IDRYLNAPLEDLAPRFDTVGIPLSGGLDSSLVTALASRHFKKLNTYSIGT T0320 89 :QFD 1q15A 273 :ELS T0320 93 :EFQSFPMQRLPTVFIDQEETFPTLENFVLETSERYCLS 1q15A 276 :NEFEFSQQVADALGTHHQMKILSETEVINGIIESIYYN T0320 148 :FRDFIK 1q15A 330 :VYRQAQ T0320 156 :PETEAIVIGIRHT 1q15A 336 :GQVSCMLTGYGSD T0320 183 :SNW 1q15A 352 :GGI T0320 186 :PDFMRLQPLLH 1q15A 389 :YGIDIRHPFWS T0320 200 :TNIWSFLLY 1q15A 400 :HSLISLCHA T0320 213 :ICGLY 1q15A 409 :LHPDY T0320 218 :GKGFTS 1q15A 485 :RLSITD T0320 293 :LVDDTLERAG 1q15A 491 :VTPSQLKDLI Number of specific fragments extracted= 14 number of extra gaps= 0 total=51 Number of alignments=4 # 1q15A read from 1q15A/merged-good-all-a2m # found chain 1q15A in template set T0320 13 :ITNS 1q15A 207 :ASNQ T0320 19 :HIDQKSQI 1q15A 211 :LLALPREP T0320 34 :IRLTRKYLLSEIFVRWSPLNGEISFSYNGGKDCQVLLLLYLSCLWE 1q15A 219 :LLALIDRYLNAPLEDLAPRFDTVGIPLSGGLDSSLVTALASRHFKK T0320 102 :LPTVFIDQEETF 1q15A 265 :LNTYSIGTELSN T0320 116 :LENFVLETSERYCLSLYE 1q15A 277 :EFEFSQQVADALGTHHQM T0320 146 :DA 1q15A 299 :ET T0320 148 :FRDFIKIY 1q15A 327 :LFNVYRQA T0320 156 :PETEAIVIG 1q15A 336 :GQVSCMLTG T0320 171 :FGEALKPIQRTDS 1q15A 345 :YGSDLLFGGILKP T0320 187 :DF 1q15A 358 :GA T0320 189 :MRLQPLLH 1q15A 392 :DIRHPFWS T0320 201 :NIWSFLLYSNEPICGL 1q15A 401 :SLISLCHALHPDYKIF T0320 248 :EWEII 1q15A 452 :VNQAF T0320 253 :HAFGKDAEGE 1q15A 458 :NVLGSTVDNY Number of specific fragments extracted= 14 number of extra gaps= 0 total=65 Number of alignments=5 # 1q15A read from 1q15A/merged-good-all-a2m # found chain 1q15A in template set T0320 23 :KSQIIASTQEAIRLTRKY 1q15A 216 :REPLLALIDRYLNAPLED T0320 49 :WSPLNGEISFSYNGGKDCQVLLLLYLSCLWE 1q15A 234 :LAPRFDTVGIPLSGGLDSSLVTALASRHFKK T0320 81 :FFIKAQNSQFDFE 1q15A 265 :LNTYSIGTELSNE T0320 117 :ENFVLETSERYCLSLYE 1q15A 278 :FEFSQQVADALGTHHQM T0320 141 :SVNMADAFRDFI 1q15A 295 :KILSETEVINGI T0320 153 :KIYPETEAIVIG 1q15A 333 :QAQGQVSCMLTG Number of specific fragments extracted= 6 number of extra gaps= 0 total=71 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m1zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m1zA expands to /projects/compbio/data/pdb/1m1z.pdb.gz 1m1zA:# T0320 read from 1m1zA/merged-good-all-a2m # 1m1zA read from 1m1zA/merged-good-all-a2m # adding 1m1zA to template set # found chain 1m1zA in template set Warning: unaligning (T0320)H235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1m1zA)S454 Warning: unaligning (T0320)H246 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1m1zA)S454 Warning: unaligning (T0320)F247 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m1zA)S455 Warning: unaligning (T0320)E248 because of BadResidue code BAD_PEPTIDE at template residue (1m1zA)F456 Warning: unaligning (T0320)A259 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1m1zA)A473 T0320 9 :MCYEITNSYLHIDQKSQ 1m1zA 204 :THRTWTPGLSRRILPEG T0320 33 :AIRLTRKYLLSEIFVRWSPLNGEISFSYNGGKDCQVLLLLYLSC 1m1zA 221 :EAVAAVRAALEKAVAQRVTPGDTPLVVLSGGIDSSGVAACAHRA T0320 77 :LW 1m1zA 266 :GE T0320 79 :EYFFIKAQN 1m1zA 269 :DTVSMGTDT T0320 91 :D 1m1zA 278 :S T0320 93 :EFQSFPMQRLPTVFIDQEETFPT 1m1zA 279 :NEFREARAVVDHLRTRHREITIP T0320 116 :LENFVLETSE 1m1zA 320 :DPDIIEYLLP T0320 148 :FRDFIKIYP 1m1zA 330 :LTALYRALD T0320 157 :ETEAIVIGI 1m1zA 340 :PERRILTGY T0320 166 :RHTDPF 1m1zA 358 :HREDRL T0320 183 :SNW 1m1zA 375 :ATF T0320 186 :PDFMRLQPLLH 1m1zA 391 :AGHWTTHPYWD T0320 201 :NIWSFLLYS 1m1zA 403 :EVLDLLVSL T0320 213 :ICGLY 1m1zA 412 :EAGLK T0320 234 :P 1m1zA 442 :P T0320 249 :WEIIHAFGKD 1m1zA 457 :SRLLLDHGVA Number of specific fragments extracted= 16 number of extra gaps= 0 total=87 Number of alignments=7 # 1m1zA read from 1m1zA/merged-good-all-a2m # found chain 1m1zA in template set T0320 18 :LHIDQKSQIIASTQEAIRLTRKYL 1m1zA 214 :RRILPEGEAVAAVRAALEKAVAQR T0320 50 :SPLNGEISFSYNGGKDCQVLLLLYLSCLWE 1m1zA 238 :VTPGDTPLVVLSGGIDSSGVAACAHRAAGE T0320 102 :LPTVFIDQEE 1m1zA 268 :LDTVSMGTDT T0320 114 :PTLENFVLETSERYCLSLYESQR 1m1zA 278 :SNEFREARAVVDHLRTRHREITI T0320 144 :MADA 1m1zA 301 :PTTE T0320 148 :FRDFIKIY 1m1zA 330 :LTALYRAL T0320 157 :ETE 1m1zA 338 :DGP T0320 160 :AIVIGI 1m1zA 343 :RILTGY T0320 166 :RHTD 1m1zA 358 :HRED T0320 171 :FGEALKPIQRTD 1m1zA 362 :RLPALDTVLAHD T0320 183 :SNWPDF 1m1zA 375 :ATFDGL T0320 189 :MRLQPLLH 1m1zA 394 :WTTHPYWD T0320 200 :TNIWSFLLYSNEP 1m1zA 402 :REVLDLLVSLEAG T0320 216 :LYG 1m1zA 415 :LKR Number of specific fragments extracted= 14 number of extra gaps= 0 total=101 Number of alignments=8 # 1m1zA read from 1m1zA/merged-good-all-a2m # found chain 1m1zA in template set T0320 31 :QEAIRLTRKYLLSEIFVR 1m1zA 220 :GEAVAAVRAALEKAVAQR T0320 50 :SPLNGEISFSYNGGKDCQVLLLLYLSCLWE 1m1zA 238 :VTPGDTPLVVLSGGIDSSGVAACAHRAAGE T0320 81 :FFIKAQNSQFDFE 1m1zA 268 :LDTVSMGTDTSNE T0320 117 :ENFVLETSERYC 1m1zA 281 :FREARAVVDHLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=105 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kqpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0320 read from 1kqpA/merged-good-all-a2m # 1kqpA read from 1kqpA/merged-good-all-a2m # found chain 1kqpA in training set Warning: unaligning (T0320)Y132 because of BadResidue code BAD_PEPTIDE in next template residue (1kqpA)D124 Warning: unaligning (T0320)E133 because of BadResidue code BAD_PEPTIDE at template residue (1kqpA)D124 T0320 22 :QKSQIIAST 1kqpA 2 :MQEKIMREL T0320 31 :QEAIRLTRKYLLSEIFVRW 1kqpA 18 :PKQEIEDRVNFLKQYVKKT T0320 53 :N 1kqpA 37 :G T0320 54 :GEISFSYNGGKDCQVLLLLYLSCLW 1kqpA 39 :KGFVLGISGGQDSTLAGRLAQLAVE T0320 79 :EYFFIKAQN 1kqpA 73 :QFIAVRLPH T0320 89 :QFD 1kqpA 82 :GTQ T0320 93 :EFQSFPMQRLPTVFI 1kqpA 85 :QDEDDAQLALKFIKP T0320 108 :DQEETFPT 1kqpA 101 :KSWKFDIK T0320 118 :NFVLETSERYCLSL 1kqpA 109 :STVSAFSDQYQQET T0320 134 :SQRQ 1kqpA 125 :QLTD T0320 145 :ADAFRDFIKIY 1kqpA 140 :MIAQYAIGGQE T0320 157 :ET 1kqpA 151 :GL T0320 161 :IVIGIRH 1kqpA 153 :LVLGTDH T0320 169 :DPFGEALK 1kqpA 162 :EAVTGFFT T0320 183 :SNWPDFMRLQPLLHWDLTNIWSFLLYSNEPI 1kqpA 170 :KYGDGGADLLPLTGLTKRQGRTLLKELGAPE T0320 215 :G 1kqpA 206 :E T0320 236 :LRKDSNNPALHFEWEIIHAFGKD 1kqpA 207 :PTADLLDEKPQQSDETELGISYD T0320 259 :AEGERS 1kqpA 236 :EGKEVS T0320 296 :DTLERA 1kqpA 242 :AKVSEA Number of specific fragments extracted= 19 number of extra gaps= 1 total=124 Number of alignments=10 # 1kqpA read from 1kqpA/merged-good-all-a2m # found chain 1kqpA in training set Warning: unaligning (T0320)S141 because of BadResidue code BAD_PEPTIDE in next template residue (1kqpA)D124 Warning: unaligning (T0320)V142 because of BadResidue code BAD_PEPTIDE at template residue (1kqpA)D124 T0320 23 :KSQIIAST 1kqpA 3 :QEKIMREL T0320 34 :IRLTRKYLLSEIFVRWSPLNG 1kqpA 18 :PKQEIEDRVNFLKQYVKKTGA T0320 55 :EISFSYNGGKDCQVLLLLY 1kqpA 40 :GFVLGISGGQDSTLAGRLA T0320 74 :LSCLWE 1kqpA 66 :REEGGD T0320 102 :LPTVFIDQEETFPTLENFVLETSERYCL 1kqpA 72 :AQFIAVRLPHGTQQDEDDAQLALKFIKP T0320 130 :SLYE 1kqpA 101 :KSWK T0320 143 :NMADA 1kqpA 125 :QLTDF T0320 148 :FRDFIKIY 1kqpA 143 :QYAIGGQE T0320 157 :ETE 1kqpA 151 :GLL T0320 162 :VIGI 1kqpA 154 :VLGT T0320 169 :DPFGEALKPIQRTDSN 1kqpA 158 :DHAAEAVTGFFTKYGD T0320 187 :DFMRLQPLLHWDLTNIWSFLLYSNEPI 1kqpA 174 :GGADLLPLTGLTKRQGRTLLKELGAPE T0320 215 :GLYG 1kqpA 210 :DLLD T0320 239 :DSNNPAL 1kqpA 238 :KEVSAKV T0320 248 :EWEI 1kqpA 245 :SEAL T0320 253 :HAFGKDAEGERSSAINTSP 1kqpA 250 :KRYSMTEHKRQVPASMFDD Number of specific fragments extracted= 16 number of extra gaps= 1 total=140 Number of alignments=11 # 1kqpA read from 1kqpA/merged-good-all-a2m # found chain 1kqpA in training set Warning: unaligning (T0320)G139 because of BadResidue code BAD_PEPTIDE in next template residue (1kqpA)D124 Warning: unaligning (T0320)A140 because of BadResidue code BAD_PEPTIDE at template residue (1kqpA)D124 T0320 30 :TQEAIRLTRKYLLSEIFVR 1kqpA 18 :PKQEIEDRVNFLKQYVKKT T0320 52 :LNGEISFSYNGGKDCQVLLLLYLSCLWE 1kqpA 37 :GAKGFVLGISGGQDSTLAGRLAQLAVES T0320 80 :YFFIKAQNSQFDFEFQSFPMQRLPTVFIDQEETFPTLENFVLETSERYCLS 1kqpA 71 :DAQFIAVRLPHGTQQDEDDAQLALKFIKPDKSWKFDIKSTVSAFSDQYQQE T0320 138 :S 1kqpA 122 :T T0320 141 :SVNMADAFRDFI 1kqpA 125 :QLTDFNKGNVKA T0320 157 :ETEA 1kqpA 151 :GLLV T0320 180 :RTDSNWPDFMRLQPLLHWDLTNIWSFLLYSNEP 1kqpA 167 :FFTKYGDGGADLLPLTGLTKRQGRTLLKELGAP Number of specific fragments extracted= 7 number of extra gaps= 1 total=147 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1korA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1korA expands to /projects/compbio/data/pdb/1kor.pdb.gz 1korA:# T0320 read from 1korA/merged-good-all-a2m # 1korA read from 1korA/merged-good-all-a2m # adding 1korA to template set # found chain 1korA in template set Warning: unaligning (T0320)G54 because first residue in template chain is (1korA)M1 Warning: unaligning (T0320)C214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1korA)P171 T0320 55 :EISFSYNGGKDCQVLLLLYLSC 1korA 2 :KIVLAYSGGLDTSIILKWLKET T0320 77 :LWEYFFIKAQN 1korA 25 :RAEVIAFTADI T0320 89 :QFD 1korA 36 :GQG T0320 93 :EFQSFPMQRLPTVFI 1korA 39 :EEVEEAREKALRTGA T0320 108 :DQEETFPT 1korA 55 :KAIALDLK T0320 117 :ENFVLETSERYCL 1korA 63 :EEFVRDFVFPMMR T0320 146 :DAFRDFIKIY 1korA 97 :KHLVRIAEEE T0320 157 :ETEAIVIGIR 1korA 107 :GAEAIAHGAT T0320 183 :SNW 1korA 117 :GKG T0320 186 :PDFMRLQPLLHW 1korA 134 :PDIKVIAPWREW T0320 198 :DLTNIWSFLLYSNEPI 1korA 149 :GRKEMIAYAEAHGIPV Number of specific fragments extracted= 11 number of extra gaps= 0 total=158 Number of alignments=13 # 1korA read from 1korA/merged-good-all-a2m # found chain 1korA in template set Warning: unaligning (T0320)C214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1korA)P171 T0320 55 :EISFSYNGGKDCQVLLLLYLSC 1korA 2 :KIVLAYSGGLDTSIILKWLKET T0320 77 :LWE 1korA 25 :RAE T0320 102 :LPTVFIDQEE 1korA 28 :VIAFTADIGQ T0320 114 :PTLENFVLETSERYCL 1korA 38 :GEEVEEAREKALRTGA T0320 130 :SLYESQR 1korA 55 :KAIALDL T0320 145 :ADA 1korA 62 :KEE T0320 148 :FRDFIKIY 1korA 99 :LVRIAEEE T0320 157 :ETEAIVIGI 1korA 107 :GAEAIAHGA T0320 166 :RHTD 1korA 118 :KGND T0320 171 :FGEALKPIQRTDS 1korA 122 :QVRFELTAYALKP T0320 187 :DFMRLQPLLHW 1korA 135 :DIKVIAPWREW T0320 198 :DLTNIWSFLLYSNEPI 1korA 149 :GRKEMIAYAEAHGIPV Number of specific fragments extracted= 12 number of extra gaps= 0 total=170 Number of alignments=14 # 1korA read from 1korA/merged-good-all-a2m # found chain 1korA in template set Warning: unaligning (T0320)C214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1korA)P171 Warning: unaligning (T0320)G220 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1korA)P171 T0320 55 :EISFSYNGGKDCQVLLLLYLSCLWEYFFIKAQNSQFDF 1korA 2 :KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGE T0320 116 :LENFVLETSERYCLSLYESQRQ 1korA 40 :EVEEAREKALRTGASKAIALDL T0320 145 :ADAFR 1korA 62 :KEEFV T0320 154 :I 1korA 105 :E T0320 156 :PETEAIVIGIRHTDPFGEA 1korA 106 :EGAEAIAHGATGKGNDQVR T0320 185 :WPDFMRLQPLLHWD 1korA 133 :KPDIKVIAPWREWS T0320 199 :LTNIWSFLLYSNEPI 1korA 150 :RKEMIAYAEAHGIPV T0320 221 :FTSIGGINN 1korA 172 :YSMDANLLH T0320 234 :PHLRKDSNNPALHF 1korA 186 :GVLEDPWAEPPKGM T0320 259 :AEGERSSA 1korA 200 :FRMTQDPE Number of specific fragments extracted= 10 number of extra gaps= 0 total=180 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xngA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xngA expands to /projects/compbio/data/pdb/1xng.pdb.gz 1xngA:# T0320 read from 1xngA/merged-good-all-a2m # 1xngA read from 1xngA/merged-good-all-a2m # adding 1xngA to template set # found chain 1xngA in template set T0320 23 :KS 1xngA 5 :YQ T0320 33 :AIRLTRKYLLSEIFVR 1xngA 7 :KLIVYLCDFLEKEVQK T0320 52 :LN 1xngA 23 :RG T0320 54 :GEISFSYNGGKDCQVLLLLYLSCLW 1xngA 26 :KKVVYGLSGGLDSAVVGVLCQKVFK T0320 79 :EYFFIKAQNSQFDFEFQSFPMQRLPTVFIDQEETFPT 1xngA 52 :NAHALLMPSSVSMPENKTDALNLCEKFSIPYTEYSIA T0320 122 :ETSERYCLSLYESQRQ 1xngA 89 :PYDAIFSSHFKDASLT T0320 138 :SGASVNM 1xngA 107 :GNFCARL T0320 145 :ADAFRDFIKIY 1xngA 115 :MAFLYDYSLKS T0320 157 :ETEAI 1xngA 126 :DSLVI T0320 164 :GIRH 1xngA 131 :GTSN T0320 179 :QRTD 1xngA 141 :GYGT T0320 183 :SN 1xngA 146 :FG T0320 187 :DFMR 1xngA 148 :DLAC T0320 191 :LQPLLHWDLTNIWSFLLYSNE 1xngA 153 :INPIGELFKTEVYELARRLNI T0320 212 :PICGLY 1xngA 181 :PPSADL T0320 245 :LHFEWEIIHAFGKDAEGERS 1xngA 200 :YSVIDPLLKDIEALFQTKPI T0320 294 :VDDTLERA 1xngA 220 :DTETLAQL Number of specific fragments extracted= 17 number of extra gaps= 0 total=197 Number of alignments=16 # 1xngA read from 1xngA/merged-good-all-a2m # found chain 1xngA in template set Warning: unaligning (T0320)A28 because first residue in template chain is (1xngA)K3 Warning: unaligning (T0320)E278 because last residue in template chain is (1xngA)F257 T0320 29 :STQEAIRLTRKYLL 1xngA 4 :DYQKLIVYLCDFLE T0320 47 :VRWSPLNG 1xngA 18 :KEVQKRGF T0320 55 :EISFSYNGGKDCQVLLLLYLSCLWEY 1xngA 27 :KVVYGLSGGLDSAVVGVLCQKVFKEN T0320 102 :LPTVFIDQEETFPTLENFVLETSERYCLSLYE 1xngA 53 :AHALLMPSSVSMPENKTDALNLCEKFSIPYTE T0320 138 :SGA 1xngA 85 :YSI T0320 141 :SVNMAD 1xngA 99 :KDASLT T0320 148 :FRDFIKIY 1xngA 118 :LYDYSLKS T0320 157 :ETEAI 1xngA 126 :DSLVI T0320 164 :GIRH 1xngA 131 :GTSN T0320 171 :FGEALKPIQRTDS 1xngA 135 :KSERMLGYGTLFG T0320 187 :DF 1xngA 148 :DL T0320 189 :MRLQPLLHWDLTNIWSFLLYSNE 1xngA 151 :CAINPIGELFKTEVYELARRLNI T0320 212 :PICGLYG 1xngA 181 :PPSADLF T0320 219 :KGF 1xngA 227 :LGY T0320 248 :EWEII 1xngA 230 :DEILV T0320 253 :HAFGK 1xngA 239 :SRIQK T0320 265 :SAINTSPISVVDK 1xngA 244 :NAFKLELPAIAKR Number of specific fragments extracted= 17 number of extra gaps= 0 total=214 Number of alignments=17 # 1xngA read from 1xngA/merged-good-all-a2m # found chain 1xngA in template set T0320 25 :QIIASTQEAIRLTRKYLLS 1xngA 4 :DYQKLIVYLCDFLEKEVQK T0320 51 :PLNGEISFSYNGGKDCQVLLLLYLSCLWEYFFIKAQNSQFDFEFQSFPMQRLPTVFIDQEETFPTLENFVLETSERYCLSLYESQRQ 1xngA 23 :RGFKKVVYGLSGGLDSAVVGVLCQKVFKENAHALLMPSSVSMPENKTDALNLCEKFSIPYTEYSIAPYDAIFSSHFKDASLTRKGNF T0320 140 :ASVNMADAFRDFIKIYP 1xngA 110 :CARLRMAFLYDYSLKSD T0320 158 :TEA 1xngA 127 :SLV T0320 163 :I 1xngA 130 :I T0320 180 :RTDSNWPDFMRLQPLLHWDLTNIWSFLLYSNEP 1xngA 142 :YGTLFGDLACAINPIGELFKTEVYELARRLNIP Number of specific fragments extracted= 6 number of extra gaps= 0 total=220 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ve1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ve1A expands to /projects/compbio/data/pdb/1ve1.pdb.gz 1ve1A:# T0320 read from 1ve1A/merged-good-all-a2m # 1ve1A read from 1ve1A/merged-good-all-a2m # adding 1ve1A to template set # found chain 1ve1A in template set T0320 38 :RKYLLSEIFVRWS 1ve1A 44 :AWYMIKDAEERGI T0320 51 :PLN 1ve1A 58 :RPG T0320 54 :GEISFSYNGGKDCQVLLLLYLSCLWEYFFIKAQ 1ve1A 62 :GQVIVEPTSGNTGIGLAMIAASRGYRLILTMPA T0320 93 :EFQSFPMQRLPTVFIDQEETFPT 1ve1A 95 :QMSEERKRVLKAFGAELVLTDPE T0320 116 :LENFVLETSERY 1ve1A 120 :MLAAREEALRLK T0320 129 :LSLYESQRQSGASVNMAD 1ve1A 132 :EELGAFMPDQFKNPANVR T0320 147 :A 1ve1A 154 :T T0320 148 :FRDFIKIYP 1ve1A 156 :GPELYEALE T0320 157 :ETEAIVIGIRHT 1ve1A 166 :RIDAFVYGSGTG T0320 183 :SNWPDFMR 1ve1A 189 :ERIPHVKV T0320 191 :LQPLL 1ve1A 199 :VEPAR T0320 213 :ICGLY 1ve1A 204 :SNVLS T0320 218 :GKGF 1ve1A 214 :QHGF T0320 224 :IGGINNSLP 1ve1A 218 :QGMGPGFIP T0320 260 :EGE 1ve1A 227 :ENL T0320 283 :YHDNYYPGWYLVDDTLERA 1ve1A 230 :DLSLLDGVIQVWEEDAFPL Number of specific fragments extracted= 16 number of extra gaps= 0 total=236 Number of alignments=19 # 1ve1A read from 1ve1A/merged-good-all-a2m # found chain 1ve1A in template set T0320 40 :YLLSEIFVR 1ve1A 46 :YMIKDAEER T0320 49 :WSPLNG 1ve1A 56 :ILRPGS T0320 55 :EISFSYNGGKDCQVLLLLYLSCLWE 1ve1A 63 :QVIVEPTSGNTGIGLAMIAASRGYR T0320 102 :LPT 1ve1A 88 :LIL T0320 107 :IDQ 1ve1A 91 :TMP T0320 114 :PTLENFVLETSERYCLSLYESQRQSGA 1ve1A 94 :AQMSEERKRVLKAFGAELVLTDPERRM T0320 141 :SVNMADA 1ve1A 135 :GAFMPDQ T0320 148 :FRDFIKIYPETEAIVIGIRHTDPFGEALKP 1ve1A 184 :GRYLKERIPHVKVIAVEPARSNVLSGGKMG T0320 189 :MRLQ 1ve1A 236 :GVIQ T0320 197 :WDLTNIWSFLLYS 1ve1A 240 :VWEEDAFPLARRL Number of specific fragments extracted= 10 number of extra gaps= 0 total=246 Number of alignments=20 # 1ve1A read from 1ve1A/merged-good-all-a2m # found chain 1ve1A in template set T0320 43 :SEIFV 1ve1A 50 :DAEER T0320 48 :RWSPLNGEISFSYNGGKDCQVLLLLYLSCL 1ve1A 56 :ILRPGSGQVIVEPTSGNTGIGLAMIAASRG T0320 81 :FFIKAQNS 1ve1A 86 :YRLILTMP T0320 114 :PTLENFVLETSERYCLSLYESQR 1ve1A 94 :AQMSEERKRVLKAFGAELVLTDP T0320 138 :SGASVNMADAFRDFI 1ve1A 117 :ERRMLAAREEALRLK T0320 153 :KIYPETEAIVIGIRHTDPFGEAL 1ve1A 189 :ERIPHVKVIAVEPARSNVLSGGK T0320 180 :RTDSNW 1ve1A 228 :NLDLSL T0320 191 :LQPLLHWDLTNIWSFLLY 1ve1A 234 :LDGVIQVWEEDAFPLARR Number of specific fragments extracted= 8 number of extra gaps= 0 total=254 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t1gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0320 read from 1t1gA/merged-good-all-a2m # 1t1gA read from 1t1gA/merged-good-all-a2m # found chain 1t1gA in training set Warning: unaligning (T0320)G220 because of BadResidue code BAD_PEPTIDE in next template residue (1t1gA)Y331 Warning: unaligning (T0320)F221 because of BadResidue code BAD_PEPTIDE at template residue (1t1gA)Y331 T0320 71 :LLYLSC 1t1gA 10 :DVAQAY T0320 77 :LW 1t1gA 17 :FP T0320 79 :EYFFIKAQN 1t1gA 27 :CIAIIALGG T0320 89 :QFD 1t1gA 36 :GYD T0320 93 :EF 1t1gA 39 :ET T0320 97 :FPMQRLPTVFI 1t1gA 41 :SLAQYFASLGV T0320 108 :DQEETFPT 1t1gA 55 :QVVSVSVD T0320 131 :LYESQRQ 1t1gA 63 :GATNQPT T0320 138 :SGA 1t1gA 72 :PNG T0320 145 :ADAFRDFIKI 1t1gA 145 :NRAFLDAAAL T0320 157 :ETEAIVIGIRHT 1t1gA 155 :GVTVLAAAGDSG T0320 169 :DP 1t1gA 171 :EQ T0320 183 :SNW 1t1gA 173 :DGL T0320 186 :PDFMRLQP 1t1gA 200 :GRIERETV T0320 212 :PICGLY 1t1gA 226 :PLPSWQ T0320 218 :GK 1t1gA 328 :AR T0320 222 :T 1t1gA 332 :Q T0320 223 :SIGGINNSL 1t1gA 334 :GPGWDPCTG Number of specific fragments extracted= 18 number of extra gaps= 1 total=272 Number of alignments=22 # 1t1gA read from 1t1gA/merged-good-all-a2m # found chain 1t1gA in training set Warning: unaligning (T0320)G220 because of BadResidue code BAD_PEPTIDE in next template residue (1t1gA)Y331 Warning: unaligning (T0320)F221 because of BadResidue code BAD_PEPTIDE at template residue (1t1gA)Y331 T0320 72 :LYLSC 1t1gA 11 :VAQAY T0320 77 :LWEY 1t1gA 17 :FPEG T0320 97 :FPMQRLPTVFIDQEETFPTLE 1t1gA 21 :LDGQGQCIAIIALGGGYDETS T0320 120 :VLETSERYCL 1t1gA 42 :LAQYFASLGV T0320 130 :SLYE 1t1gA 55 :QVVS T0320 137 :QSGA 1t1gA 62 :DGAT T0320 141 :SVNMADA 1t1gA 71 :DPNGPDG T0320 148 :FRDFIKI 1t1gA 148 :FLDAAAL T0320 157 :ETEAIVIGI 1t1gA 155 :GVTVLAAAG T0320 169 :DPFGEALKP 1t1gA 164 :DSGSTDGEQ T0320 178 :IQRTDSN 1t1gA 194 :RLVASAG T0320 187 :D 1t1gA 201 :R T0320 189 :MRLQPLLH 1t1gA 222 :SRIFPLPS T0320 216 :LYG 1t1gA 230 :WQE T0320 219 :K 1t1gA 329 :R T0320 222 :T 1t1gA 332 :Q T0320 223 :SIGGINNSL 1t1gA 334 :GPGWDPCTG Number of specific fragments extracted= 17 number of extra gaps= 1 total=289 Number of alignments=23 # 1t1gA read from 1t1gA/merged-good-all-a2m # found chain 1t1gA in training set T0320 63 :GKDCQVLLLL 1t1gA 74 :GPDGEVELDI T0320 73 :YLSCLWE 1t1gA 86 :AGALAPG T0320 81 :FFIKAQ 1t1gA 93 :AKIAVY T0320 112 :TFPTLENFVLETSE 1t1gA 99 :FAPNTDAGFLNAIT Number of specific fragments extracted= 4 number of extra gaps= 0 total=293 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ni5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ni5A expands to /projects/compbio/data/pdb/1ni5.pdb.gz 1ni5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0320 read from 1ni5A/merged-good-all-a2m # 1ni5A read from 1ni5A/merged-good-all-a2m # adding 1ni5A to template set # found chain 1ni5A in template set T0320 38 :RKYLLSEIFVRW 1ni5A 1 :MTLTLNRQLLTS T0320 54 :GEISFSYNGGKDCQVLLLLYLSC 1ni5A 13 :RQILVAFSGGLDSTVLLHQLVQW T0320 78 :W 1ni5A 37 :T T0320 79 :EYFFIKAQNSQFDFEFQSFPMQRLPTVFIDQEETFPT 1ni5A 45 :RAIHVHHGLSANADAWVTHCENVCQQWQVPLVVERVQ T0320 138 :SGASVNMADA 1ni5A 87 :LGIEAQARQA T0320 148 :FRDFIKIYPETEAIVIGIRHTDPFGEALKPIQRTD 1ni5A 98 :YQAFARTLLPGEVLVTAQHLDDQCETFLLALKRGS T0320 183 :SNW 1ni5A 135 :AGL T0320 186 :PDFMRLQPLLHWDLTNIWSFLLYSNEPICGLY 1ni5A 147 :AGTRLIRPLLARTRGELVQWARQYDLRWIEDE T0320 218 :GKGFTS 1ni5A 266 :NAPMPS T0320 249 :WEIIHAFGKDAEGERSSA 1ni5A 272 :RDALVRIWQEVALAREDA T0320 267 :INTSPISVVDKER 1ni5A 302 :RYQSQLWWIKSVT T0320 280 :FSKYHDNYYPGWYLVD 1ni5A 319 :NIVPWQTWLQPLELPA Number of specific fragments extracted= 12 number of extra gaps= 0 total=305 Number of alignments=25 # 1ni5A read from 1ni5A/merged-good-all-a2m # found chain 1ni5A in template set T0320 41 :LLSEIFVRWSP 1ni5A 1 :MTLTLNRQLLT T0320 53 :NGEISFSYNGGKDCQVLLLLYLSCLWEYF 1ni5A 12 :SRQILVAFSGGLDSTVLLHQLVQWRTENP T0320 82 :FI 1ni5A 42 :VA T0320 102 :LPTVFIDQEE 1ni5A 44 :LRAIHVHHGL T0320 112 :TFPTLENFVLETSERYCLSLYESQRQSGA 1ni5A 56 :NADAWVTHCENVCQQWQVPLVVERVQLAQ T0320 141 :SVNMADA 1ni5A 86 :GLGIEAQ T0320 148 :FRDF 1ni5A 97 :RYQA T0320 152 :IKIYPETEAIVIGIRHTD 1ni5A 102 :ARTLLPGEVLVTAQHLDD T0320 171 :FGEALKPIQRTDSNWPDF 1ni5A 120 :QCETFLLALKRGSGPAGL T0320 189 :MRLQPLLHWDLTNIWSFLLYSNEPICGLYG 1ni5A 150 :RLIRPLLARTRGELVQWARQYDLRWIEDES Number of specific fragments extracted= 10 number of extra gaps= 0 total=315 Number of alignments=26 # 1ni5A read from 1ni5A/merged-good-all-a2m # found chain 1ni5A in template set T0320 43 :SEIFVRWSPLNGEISFSYNGGKDCQVLLLLYLSCLWE 1ni5A 2 :TLTLNRQLLTSRQILVAFSGGLDSTVLLHQLVQWRTE T0320 80 :YFFIKAQNSQFDFE 1ni5A 43 :ALRAIHVHHGLSAN T0320 95 :QSFPMQ 1ni5A 57 :ADAWVT T0320 119 :FVLETSERYCLSLYESQRQSGAS 1ni5A 63 :HCENVCQQWQVPLVVERVQLAQE T0320 142 :VNMADAFRDFI 1ni5A 91 :AQARQARYQAF T0320 153 :KIYPETEAIVIGI 1ni5A 103 :RTLLPGEVLVTAQ T0320 166 :RHTDPFGEALKPIQRTD 1ni5A 130 :RGSGPAGLSAMAEVSEF T0320 186 :PDFMRLQPLLHWDLTNIWSFLLYSNEP 1ni5A 147 :AGTRLIRPLLARTRGELVQWARQYDLR T0320 259 :AEGERSSAINTSPISVVDKERFSK 1ni5A 174 :WIEDESNQDDSYDRNFLRLRVVPL Number of specific fragments extracted= 9 number of extra gaps= 0 total=324 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jmvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jmvA expands to /projects/compbio/data/pdb/1jmv.pdb.gz 1jmvA:# T0320 read from 1jmvA/merged-good-all-a2m # 1jmvA read from 1jmvA/merged-good-all-a2m # adding 1jmvA to template set # found chain 1jmvA in template set T0320 54 :GEISFSYNGGKDCQVLLL 1jmvA 3 :KHILVAVDLSEESPILLK T0320 72 :LYLSCLW 1jmvA 25 :IAKRHDA T0320 79 :EYFFIKAQNS 1jmvA 34 :SIIHVDVNFS T0320 89 :QFDFEFQSFPMQRLPTVFIDQ 1jmvA 60 :RISTETQKALLDLAESVDYPI T0320 110 :EETFPT 1jmvA 84 :LSGSGD T0320 124 :SERY 1jmvA 90 :LGQV T0320 148 :FRDFIKIY 1jmvA 94 :LSDAIEQY T0320 157 :ETEAIVIGIRHTD 1jmvA 102 :DVDLLVTGHHQDF Number of specific fragments extracted= 8 number of extra gaps= 0 total=332 Number of alignments=28 # 1jmvA read from 1jmvA/merged-good-all-a2m # found chain 1jmvA in template set T0320 53 :NGEISFSYNGGKDCQVLLLLYLSCLWEYFFI 1jmvA 2 :YKHILVAVDLSEESPILLKKAVGIAKRHDAK T0320 102 :LPTVFIDQE 1jmvA 33 :LSIIHVDVN T0320 111 :ETFPTLENFVLETSERYCLSLYE 1jmvA 60 :RISTETQKALLDLAESVDYPISE T0320 134 :S 1jmvA 88 :G T0320 144 :MADA 1jmvA 89 :DLGQ T0320 148 :FRDFIKIY 1jmvA 94 :LSDAIEQY T0320 157 :ETEAIVIGIRHTD 1jmvA 102 :DVDLLVTGHHQDF T0320 171 :FGEA 1jmvA 115 :WSKL Number of specific fragments extracted= 8 number of extra gaps= 0 total=340 Number of alignments=29 # 1jmvA read from 1jmvA/merged-good-all-a2m # found chain 1jmvA in template set T0320 53 :NGEISFSYNGGKDCQVLLLLYLSCLWE 1jmvA 2 :YKHILVAVDLSEESPILLKKAVGIAKR T0320 80 :YFFIKAQN 1jmvA 32 :KLSIIHVD T0320 90 :FD 1jmvA 40 :VN T0320 98 :PMQRLPTVFI 1jmvA 42 :FSDLYTGLID T0320 108 :DQEETFPTLENFVLETSERYCLSLYE 1jmvA 57 :MQDRISTETQKALLDLAESVDYPISE T0320 142 :VNMADAFRDFIKIYPETEAIVIGIRHTDPFGEA 1jmvA 87 :SGDLGQVLSDAIEQYDVDLLVTGHHQDFWSKLM T0320 175 :LKPI 1jmvA 125 :VMNT T0320 185 :WPDFMRLQPL 1jmvA 129 :IKIDMLVVPL Number of specific fragments extracted= 8 number of extra gaps= 0 total=348 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zvkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zvkA expands to /projects/compbio/data/pdb/1zvk.pdb.gz 1zvkA:# T0320 read from 1zvkA/merged-good-all-a2m # 1zvkA read from 1zvkA/merged-good-all-a2m # adding 1zvkA to template set # found chain 1zvkA in template set Warning: unaligning (T0320)F171 because of BadResidue code BAD_PEPTIDE in next template residue (1zvkA)G174 Warning: unaligning (T0320)G172 because of BadResidue code BAD_PEPTIDE at template residue (1zvkA)G174 Warning: unaligning (T0320)G220 because of BadResidue code BAD_PEPTIDE in next template residue (1zvkA)Y331 Warning: unaligning (T0320)F221 because of BadResidue code BAD_PEPTIDE at template residue (1zvkA)Y331 T0320 71 :LLYLSC 1zvkA 10 :DVAQAY T0320 77 :LW 1zvkA 17 :FP T0320 79 :EYFFIKAQN 1zvkA 27 :CIAIIELGG T0320 89 :QFD 1zvkA 36 :GYD T0320 95 :QSFPMQRLPTVFI 1zvkA 39 :EASLAQYFASLGV T0320 108 :DQEETFPT 1zvkA 55 :QVVSVSVD T0320 126 :RY 1zvkA 63 :GA T0320 130 :SLYESQRQSG 1zvkA 65 :SNQPTGDPSG T0320 145 :ADAFRDFIKI 1zvkA 145 :NRAFLDAAAL T0320 157 :ETEAIVIGIRHT 1zvkA 155 :GVTVLAAAGNSG T0320 169 :DP 1zvkA 171 :EQ T0320 173 :EALKPIQRTDSNW 1zvkA 175 :LYHVDFPAASPYV T0320 218 :GK 1zvkA 328 :AQ T0320 222 :T 1zvkA 332 :Q T0320 223 :SIGGINNSL 1zvkA 334 :GPGWDPCTG Number of specific fragments extracted= 15 number of extra gaps= 2 total=363 Number of alignments=31 # 1zvkA read from 1zvkA/merged-good-all-a2m # found chain 1zvkA in template set Warning: unaligning (T0320)G220 because of BadResidue code BAD_PEPTIDE in next template residue (1zvkA)Y331 Warning: unaligning (T0320)F221 because of BadResidue code BAD_PEPTIDE at template residue (1zvkA)Y331 T0320 72 :LYLSC 1zvkA 11 :VAQAY T0320 77 :LWEY 1zvkA 17 :FPEG T0320 97 :FPMQRLPTVFIDQEETFPT 1zvkA 21 :LDGQGQCIAIIELGGGYDE T0320 118 :NFVLETSERYCL 1zvkA 40 :ASLAQYFASLGV T0320 130 :SLYESQRQSGA 1zvkA 55 :QVVSVSVDGAS T0320 141 :SVNMADA 1zvkA 68 :PTGDPSG T0320 148 :FRDFIKI 1zvkA 148 :FLDAAAL T0320 157 :ETEAIVIGIRHT 1zvkA 155 :GVTVLAAAGNSG T0320 172 :GEALKP 1zvkA 167 :STDGEQ T0320 178 :IQRTDS 1zvkA 194 :RLVASG T0320 187 :DF 1zvkA 200 :GR T0320 219 :K 1zvkA 329 :Q T0320 222 :T 1zvkA 332 :Q T0320 223 :SIGGINNS 1zvkA 334 :GPGWDPCT Number of specific fragments extracted= 14 number of extra gaps= 1 total=377 Number of alignments=32 # 1zvkA read from 1zvkA/merged-good-all-a2m # found chain 1zvkA in template set T0320 82 :FIKAQNSQF 1zvkA 27 :CIAIIELGG T0320 196 :HWDLTNIWSFLLYSNEPICGLY 1zvkA 36 :GYDEASLAQYFASLGVPAPQVV T0320 222 :TSIGGINN 1zvkA 59 :VSVDGASN Number of specific fragments extracted= 3 number of extra gaps= 0 total=380 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vb5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vb5A expands to /projects/compbio/data/pdb/1vb5.pdb.gz 1vb5A:# T0320 read from 1vb5A/merged-good-all-a2m # 1vb5A read from 1vb5A/merged-good-all-a2m # adding 1vb5A to template set # found chain 1vb5A in template set T0320 15 :NSYLHIDQKSQIIASTQEAIRLTRKYLLSEIFVRWSP 1vb5A 73 :PVTNRRDILKSRALEFLRRMEEAKRELASIGAQLIDD T0320 54 :GEISFSYNGGKDCQVLLLLYLSCLW 1vb5A 110 :GDVIITHSFSSTVLEIIRTAKERKK T0320 79 :EYFFIKAQNS 1vb5A 137 :KVILTESSPD T0320 93 :EFQSFPMQRLPTVFIDQEETFPT 1vb5A 147 :YEGLHLARELEFSGIEFEVITDA T0320 129 :L 1vb5A 170 :Q T0320 148 :FRDFIK 1vb5A 171 :MGLFCR T0320 157 :ETEAIVIG 1vb5A 177 :EASIAIVG T0320 165 :I 1vb5A 188 :I T0320 173 :EALKPIQRT 1vb5A 189 :TKDGYVVNK T0320 183 :SN 1vb5A 198 :AG T0320 199 :LTNIWSFLLYSNEPI 1vb5A 200 :TYLLALACHENAIPF T0320 214 :CGLYGKGFTSIGGINNSLP 1vb5A 219 :ETYKFHPTLKSGDVMLMER T0320 234 :PHLRKDSNNPAL 1vb5A 238 :DLIRGNVRIRNV T0320 279 :RFSKYHDNYYPGW 1vb5A 250 :LFDVTPWKYVRGI Number of specific fragments extracted= 14 number of extra gaps= 0 total=394 Number of alignments=34 # 1vb5A read from 1vb5A/merged-good-all-a2m # found chain 1vb5A in template set T0320 13 :ITNSYLHIDQKSQIIASTQEAIRLTRKYLL 1vb5A 71 :FIPVTNRRDILKSRALEFLRRMEEAKRELA T0320 44 :EIFVRWSPLN 1vb5A 101 :SIGAQLIDDG T0320 55 :EISFSYNGGKDCQVLLLLYLSCLWE 1vb5A 111 :DVIITHSFSSTVLEIIRTAKERKKR T0320 102 :LPTVFIDQEE 1vb5A 136 :FKVILTESSP T0320 114 :PTLENFVLETSERYCLSLYE 1vb5A 146 :DYEGLHLARELEFSGIEFEV T0320 134 :SQRQ 1vb5A 167 :TDAQ T0320 148 :FRDFIK 1vb5A 171 :MGLFCR T0320 157 :ETEAIVIGI 1vb5A 177 :EASIAIVGA T0320 166 :RHTD 1vb5A 189 :TKDG T0320 177 :PIQRTDS 1vb5A 193 :YVVNKAG T0320 199 :LTNIWSFLLYSNEPI 1vb5A 200 :TYLLALACHENAIPF T0320 214 :CGLYGKGFT 1vb5A 219 :ETYKFHPTL T0320 232 :PNPH 1vb5A 228 :KSGD T0320 261 :GERSSAINTSPISVVDKERFSKYHDNYYPGWYL 1vb5A 232 :VMLMERDLIRGNVRIRNVLFDVTPWKYVRGIIT Number of specific fragments extracted= 14 number of extra gaps= 0 total=408 Number of alignments=35 # 1vb5A read from 1vb5A/merged-good-all-a2m # found chain 1vb5A in template set T0320 21 :DQKSQIIASTQEAIRLTRKYLLSEIFVRWS 1vb5A 76 :NRRDILKSRALEFLRRMEEAKRELASIGAQ T0320 51 :PLNGEISFSYNGGK 1vb5A 107 :IDDGDVIITHSFSS T0320 68 :VLLLLYLSCLWE 1vb5A 121 :TVLEIIRTAKER T0320 80 :YFFIKAQNSQFD 1vb5A 135 :RFKVILTESSPD T0320 115 :TLENFVLETSERYCLSLYESQRQ 1vb5A 147 :YEGLHLARELEFSGIEFEVITDA T0320 150 :DFIKIYPETEAIVIGI 1vb5A 170 :QMGLFCREASIAIVGA Number of specific fragments extracted= 6 number of extra gaps= 0 total=414 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z7wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z7wA expands to /projects/compbio/data/pdb/1z7w.pdb.gz 1z7wA:# T0320 read from 1z7wA/merged-good-all-a2m # 1z7wA read from 1z7wA/merged-good-all-a2m # adding 1z7wA to template set # found chain 1z7wA in template set T0320 41 :LLSEIFVRWS 1z7wA 53 :MISDAEKKGL T0320 51 :PLNGEISFSYNGGKDCQVLLLLYLSCLWEYFFIKAQN 1z7wA 64 :KPGESVLIEPTSGNTGVGLAFTAAAKGYKLIITMPAS T0320 89 :QF 1z7wA 101 :MS T0320 96 :SFPMQRLPTVFIDQEETFPT 1z7wA 103 :TERRIILLAFGVELVLTDPA T0320 118 :NFVLETSERY 1z7wA 123 :KGMKGAIAKA T0320 129 :LSLYESQR 1z7wA 133 :EEILAKTP T0320 138 :SGASVNM 1z7wA 141 :NGYMLQQ T0320 148 :FRDFIKIYPETEAIVIGI 1z7wA 190 :GKYLKEQNANVKLYGVEP T0320 171 :FGE 1z7wA 208 :VES T0320 174 :ALKPIQRTD 1z7wA 212 :ILSGGKPGP T0320 186 :PDFMRLQ 1z7wA 238 :DLIDEVV T0320 196 :HWDLTNIWSFLL 1z7wA 245 :QVSSDESIDMAR T0320 208 :YSNE 1z7wA 261 :KEGL T0320 212 :PICGLY 1z7wA 297 :SFGERY T0320 243 :PALHFEWEIIHAFGK 1z7wA 303 :LSTVLFDATRKEAEA Number of specific fragments extracted= 15 number of extra gaps= 0 total=429 Number of alignments=37 # 1z7wA read from 1z7wA/merged-good-all-a2m # found chain 1z7wA in template set T0320 40 :YLLSEIFVR 1z7wA 52 :SMISDAEKK T0320 49 :WSPLNGEISFSYNGGKDCQVLLLLYLSCLWE 1z7wA 62 :LIKPGESVLIEPTSGNTGVGLAFTAAAKGYK T0320 104 :TVFIDQEETFPT 1z7wA 93 :LIITMPASMSTE T0320 120 :VLETSERYCLSLYESQRQS 1z7wA 105 :RRIILLAFGVELVLTDPAK T0320 144 :MADA 1z7wA 124 :GMKG T0320 148 :FRDFIKIYP 1z7wA 132 :AEEILAKTP T0320 157 :ETEAIVIGIRHTDPFGEALKPIQRTDSNW 1z7wA 172 :KIDGFVSGIGTGGTITGAGKYLKEQNANV T0320 189 :MRLQ 1z7wA 242 :EVVQ T0320 197 :WDLTNIWSFLL 1z7wA 246 :VSSDESIDMAR T0320 208 :YSNE 1z7wA 261 :KEGL T0320 212 :P 1z7wA 297 :S T0320 238 :KDSNNPALHFEWEIIHAFG 1z7wA 298 :FGERYLSTVLFDATRKEAE Number of specific fragments extracted= 12 number of extra gaps= 0 total=441 Number of alignments=38 # 1z7wA read from 1z7wA/merged-good-all-a2m # found chain 1z7wA in template set T0320 40 :YLLSEIFVR 1z7wA 52 :SMISDAEKK T0320 49 :WSPLNGEISFSYNGGKDCQVLLLLYLSCL 1z7wA 62 :LIKPGESVLIEPTSGNTGVGLAFTAAAKG T0320 81 :FFIKAQNS 1z7wA 91 :YKLIITMP T0320 114 :PTLENFVLETSERYCLSLYESQRQ 1z7wA 99 :ASMSTERRIILLAFGVELVLTDPA T0320 139 :GASVNMADAFRDFIKIYPE 1z7wA 123 :KGMKGAIAKAEEILAKTPN T0320 158 :TEAIVIGIRH 1z7wA 173 :IDGFVSGIGT Number of specific fragments extracted= 6 number of extra gaps= 0 total=447 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zunA/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/T0320/1zunA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0320/1zunA/merged-good-all-a2m.gz for input Trying 1zunA/merged-good-all-a2m Error: Couldn't open file 1zunA/merged-good-all-a2m or 1zunA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sur/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sur expands to /projects/compbio/data/pdb/1sur.pdb.gz 1sur:Warning: there is no chain 1sur will retry with 1surA # T0320 read from 1sur/merged-good-all-a2m # 1sur read from 1sur/merged-good-all-a2m # adding 1sur to template set # found chain 1sur in template set Warning: unaligning (T0320)N228 because last residue in template chain is (1sur)H215 T0320 17 :YLHIDQKSQIIASTQEAIR 1sur 10 :ELPKVDRILALAETNAELE T0320 36 :LTRKYLLSEIFVRWS 1sur 30 :LDAEGRVAWALDNLP T0320 54 :GEISFSYNGGKDCQVLLLLYLSCLW 1sur 45 :GEYVLSSSFGIQAAVSLHLVNQIRP T0320 79 :EYFFIKAQN 1sur 72 :PVILTDTGY T0320 89 :QFD 1sur 81 :LFP T0320 93 :EFQSFPMQRLPTVFIDQEETFPT 1sur 84 :ETYRFIDELTDKLKLNLKVYRAT T0320 116 :LENFVLET 1sur 109 :AAWQEARY T0320 124 :SERYCLSLYES 1sur 119 :LWEQGVEGIEK T0320 138 :SGASVNMAD 1sur 130 :YNDINKVEP T0320 148 :FRDFIKIY 1sur 139 :MNRALKEL T0320 157 :ETEAIVIGIRHTDPFGEALKPIQRTDS 1sur 147 :NAQTWFAGLRREQSGSRANLPVLAIQR T0320 187 :DFMRLQPLLHWDLTNIWSFLLYSNEPICGLYGKGFTSIGGI 1sur 174 :GVFKVLPIIDWDNRTIYQYLQKHGLKYHPLWDEGYLSVGDT Number of specific fragments extracted= 12 number of extra gaps= 0 total=459 Number of alignments=40 # 1sur read from 1sur/merged-good-all-a2m # found chain 1sur in template set Warning: unaligning (T0320)N228 because last residue in template chain is (1sur)H215 T0320 21 :DQKSQIIASTQEAIRLTRKYLLSEIFVRWSPLNG 1sur 11 :LPKVDRILALAETNAELEKLDAEGRVAWALDNLP T0320 55 :EISFSYNGGKDCQVLLLLYLSCLWE 1sur 46 :EYVLSSSFGIQAAVSLHLVNQIRPD T0320 102 :LPTVFIDQEETFPTLENFVLETSERYCLSLYESQRQSGA 1sur 71 :IPVILTDTGYLFPETYRFIDELTDKLKLNLKVYRATESA T0320 141 :SVNMADA 1sur 116 :YGKLWEQ T0320 148 :FRDFIKIY 1sur 139 :MNRALKEL T0320 157 :ETEAIVIGIRHTDPFGEALKPIQRTDS 1sur 147 :NAQTWFAGLRREQSGSRANLPVLAIQR T0320 187 :DFMRLQPLLHWDLTNIWSFLLYSNEPICGLYGKGFTSIGGI 1sur 174 :GVFKVLPIIDWDNRTIYQYLQKHGLKYHPLWDEGYLSVGDT Number of specific fragments extracted= 7 number of extra gaps= 0 total=466 Number of alignments=41 # 1sur read from 1sur/merged-good-all-a2m # found chain 1sur in template set Warning: unaligning (T0320)N228 because last residue in template chain is (1sur)H215 T0320 23 :KSQIIASTQEAIRLTRKY 1sur 13 :KVDRILALAETNAELEKL T0320 41 :LLSEIFVRWSPLNGEISFSYNGGKDCQVLLLLYLSCLWE 1sur 32 :AEGRVAWALDNLPGEYVLSSSFGIQAAVSLHLVNQIRPD T0320 81 :FFIKAQNSQFDFEFQSFPMQRLPTVFIDQEETFPTLENFVLETSERYCLSLYESQRQSGASVNMADAFRDFIKIYPETEAIVIGIRHTDPFGEALKPIQRTD 1sur 71 :IPVILTDTGYLFPETYRFIDELTDKLKLNLKVYRATESAAWQEARYGKLWEQGVEGIEKYNDINKVEPMNRALKELNAQTWFAGLRREQSGSRANLPVLAIQ T0320 186 :PDFMRLQPLLHWDLTNIWSFLLYSNEPICGLYGKGFTSIGGI 1sur 173 :RGVFKVLPIIDWDNRTIYQYLQKHGLKYHPLWDEGYLSVGDT Number of specific fragments extracted= 4 number of extra gaps= 0 total=470 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gpmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gpmA expands to /projects/compbio/data/pdb/1gpm.pdb.gz 1gpmA:# T0320 read from 1gpmA/merged-good-all-a2m # 1gpmA read from 1gpmA/merged-good-all-a2m # adding 1gpmA to template set # found chain 1gpmA in template set Warning: unaligning (T0320)D187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gpmA)K369 T0320 2 :QLSKAAEMCYEITNSYLHIDQKSQIIASTQ 1gpmA 173 :KRFYGVQFHPEVTHTRQGMRMLERFVRDIC T0320 32 :EAIRLTRKYLLSEIFV 1gpmA 211 :AKIIDDAVARIREQVG T0320 53 :NGEISFSYNGGKDCQVLLLLYLSC 1gpmA 227 :DDKVILGLSGGVDSSVTAMLLHRA T0320 77 :LW 1gpmA 252 :GK T0320 79 :EYFFIKAQN 1gpmA 256 :TCVFVDNGL T0320 89 :QFDFEFQSFPMQRLPTVFIDQEETFPT 1gpmA 265 :LRLNEAEQVLDMFGDHFGLNIVHVPAE T0320 117 :ENFVLETSERYCLSLYESQRQ 1gpmA 292 :DRFLSALAGENDPEAKRKIIG T0320 143 :NMADAFRDFIKIYPETEAIVIGIRH 1gpmA 314 :VFVEVFDEEALKLEDVKWLAQGTIY T0320 169 :DPF 1gpmA 343 :ESA T0320 188 :FMRLQPLLHWDLTNIWSFLLYSNEPICGLYGKGFTSIGGINNSLP 1gpmA 370 :MGLVEPLKELFKDEVRKIGLELGLPYDMLYRHPFPGPGLGVRVLG T0320 244 :ALHFE 1gpmA 415 :EVKKE T0320 249 :WEIIHA 1gpmA 421 :CDLLRR T0320 255 :FGKDAEGERSSAINTSPISVVDKERFSKYHDNYYPGWYL 1gpmA 432 :IEELRKADLYDKVSQAFTVFLPVRSVGVMGDGRKYDWVV Number of specific fragments extracted= 13 number of extra gaps= 0 total=483 Number of alignments=43 # 1gpmA read from 1gpmA/merged-good-all-a2m # found chain 1gpmA in template set Warning: unaligning (T0320)K176 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gpmA)K369 T0320 18 :LHIDQKSQIIAST 1gpmA 189 :QGMRMLERFVRDI T0320 38 :RKYLLSEIFVRWSPLNG 1gpmA 210 :PAKIIDDAVARIREQVG T0320 55 :EISFSYNGGKDCQVLLLLYLSCLWEY 1gpmA 229 :KVILGLSGGVDSSVTAMLLHRAIGKN T0320 102 :LPTVFIDQEETFPTLENFVLETS 1gpmA 255 :LTCVFVDNGLLRLNEAEQVLDMF T0320 125 :ERYCLSLYESQRQSGA 1gpmA 279 :DHFGLNIVHVPAEDRF T0320 141 :SVNMADA 1gpmA 300 :GENDPEA T0320 148 :FRDFIKIYPETEAIVIGIRHTD 1gpmA 319 :FDEEALKLEDVKWLAQGTIYPD T0320 171 :FGEAL 1gpmA 341 :VIESA T0320 189 :MRLQPLLHWDLTNIWSFLLYSNEPICGLYGKGFTSIG 1gpmA 371 :GLVEPLKELFKDEVRKIGLELGLPYDMLYRHPFPGPG T0320 226 :GINNSLPN 1gpmA 409 :GVRVLGEV T0320 242 :NPAL 1gpmA 417 :KKEY T0320 252 :I 1gpmA 421 :C T0320 253 :HAFGKDAE 1gpmA 433 :EELRKADL T0320 266 :AINTSPISVVDKERFSKYHDNYYPGWYLV 1gpmA 441 :YDKVSQAFTVFLPVRSVGVMGDGRKYDWV Number of specific fragments extracted= 14 number of extra gaps= 0 total=497 Number of alignments=44 # 1gpmA read from 1gpmA/merged-good-all-a2m # found chain 1gpmA in template set Warning: unaligning (T0320)K176 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gpmA)K369 Warning: unaligning (T0320)D187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gpmA)K369 T0320 31 :QEAIRLTRKYLLSEI 1gpmA 211 :AKIIDDAVARIREQV T0320 52 :LNGEISFSYNGGKDCQVLLLLYLSCLWEYFFIKAQNSQFDF 1gpmA 226 :GDDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLR T0320 93 :EFQSFPMQRLPTVFIDQEETFPTLENFVL 1gpmA 268 :NEAEQVLDMFGDHFGLNIVHVPAEDRFLS T0320 122 :ETSERYCLSL 1gpmA 305 :EAKRKIIGRV T0320 144 :MADAFRDFIKIYPETEAIVIGIRHTDPF 1gpmA 315 :FVEVFDEEALKLEDVKWLAQGTIYPDVI T0320 173 :EAL 1gpmA 343 :ESA T0320 188 :FMRLQPLLHWDLTNIWSFLLYSNEPICGL 1gpmA 370 :MGLVEPLKELFKDEVRKIGLELGLPYDML T0320 227 :INNSLPNPHLRKDSNNPALHFEWEIIHAF 1gpmA 399 :YRHPFPGPGLGVRVLGEVKKEYCDLLRRA T0320 273 :SVVDKERFSKY 1gpmA 428 :DAIFIEELRKA T0320 284 :HDNYYPGWYL 1gpmA 441 :YDKVSQAFTV Number of specific fragments extracted= 10 number of extra gaps= 0 total=507 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ct9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ct9A expands to /projects/compbio/data/pdb/1ct9.pdb.gz 1ct9A:# T0320 read from 1ct9A/merged-good-all-a2m # 1ct9A read from 1ct9A/merged-good-all-a2m # adding 1ct9A to template set # found chain 1ct9A in template set Warning: unaligning (T0320)L77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ct9A)L267 T0320 17 :YLHIDQKSQ 1ct9A 201 :VKDNVTDKN T0320 37 :TRKYLLSEIFVRWS 1ct9A 210 :ELRQALEDSVKSHL T0320 54 :GEISFSYNGGKDCQVLLLLYLSC 1ct9A 227 :VPYGVLLSGGLDSSIISAITKKY T0320 81 :FFIKAQN 1ct9A 268 :HSFAVGL T0320 89 :QFD 1ct9A 275 :PGS T0320 93 :EFQSFPMQRLPTVFIDQEETFPTLENFVLETSERYCL 1ct9A 278 :PDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYH T0320 131 :L 1ct9A 315 :I T0320 145 :AD 1ct9A 324 :RA T0320 147 :AFRDFIKIY 1ct9A 331 :LMSRKIKAM T0320 157 :ETEAIVIGIRHTD 1ct9A 340 :GIKMVLSGEGSDE T0320 174 :ALKPIQRTD 1ct9A 354 :FGGYLYFHK T0320 183 :SN 1ct9A 364 :PN T0320 200 :TNIWSFLLY 1ct9A 371 :EETVRKLLA T0320 213 :ICG 1ct9A 380 :LHM T0320 217 :Y 1ct9A 383 :Y T0320 236 :LRKDSNNPALHFE 1ct9A 447 :RQKEQFSDGVGYS T0320 249 :WEIIHAFGKDA 1ct9A 461 :IDTLKEVAAQQ T0320 293 :LVDDTLE 1ct9A 472 :VSDQQLE Number of specific fragments extracted= 18 number of extra gaps= 0 total=525 Number of alignments=46 # 1ct9A read from 1ct9A/merged-good-all-a2m # found chain 1ct9A in template set Warning: unaligning (T0320)L77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ct9A)L267 Warning: unaligning (T0320)L102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ct9A)L267 T0320 11 :YEITNSYLHIDQKSQIIA 1ct9A 185 :GEIRSYYHRDWFDYDAVK T0320 29 :STQEAIRLTRKYLL 1ct9A 210 :ELRQALEDSVKSHL T0320 53 :NG 1ct9A 224 :MS T0320 55 :EISFSYNGGKDCQVLLLLYLSC 1ct9A 228 :PYGVLLSGGLDSSIISAITKKY T0320 103 :PTVFIDQEE 1ct9A 268 :HSFAVGLPG T0320 114 :PTLENFVLETSERYCLSLYESQR 1ct9A 277 :SPDLKAAQEVANHLGTVHHEIHF T0320 144 :MADA 1ct9A 300 :TVQE T0320 148 :FRDFIKIY 1ct9A 332 :MSRKIKAM T0320 157 :ETEAIVIGIRHTDPFGEALKP 1ct9A 340 :GIKMVLSGEGSDEVFGGYLYF T0320 183 :SNWPDF 1ct9A 361 :HKAPNA T0320 199 :LTNIWSFLLY 1ct9A 370 :HEETVRKLLA T0320 214 :CGLYG 1ct9A 380 :LHMYD Number of specific fragments extracted= 12 number of extra gaps= 0 total=537 Number of alignments=47 # 1ct9A read from 1ct9A/merged-good-all-a2m # found chain 1ct9A in template set Warning: unaligning (T0320)L77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ct9A)L267 Warning: unaligning (T0320)F81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ct9A)L267 T0320 14 :TNSYLHIDQKSQIIASTQEAIRLTRKYLLS 1ct9A 192 :HRDWFDYDAVKDNVTDKNELRQALEDSVKS T0320 49 :WSPLNGEISFSYNGGKDCQVLLLLYLSC 1ct9A 222 :HLMSDVPYGVLLSGGLDSSIISAITKKY T0320 82 :FIKAQNSQF 1ct9A 268 :HSFAVGLPG T0320 92 :F 1ct9A 277 :S T0320 115 :TLENFVLETSERYCLSLYESQRQ 1ct9A 278 :PDLKAAQEVANHLGTVHHEIHFT T0320 145 :ADAFRDFI 1ct9A 301 :VQEGLDAI T0320 155 :YPETEAIVIG 1ct9A 338 :AMGIKMVLSG Number of specific fragments extracted= 7 number of extra gaps= 0 total=544 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vp8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0320 read from 1vp8A/merged-good-all-a2m # 1vp8A read from 1vp8A/merged-good-all-a2m # found chain 1vp8A in training set Warning: unaligning (T0320)N15 because first residue in template chain is (1vp8A)H0 Warning: unaligning (T0320)K23 because of BadResidue code BAD_PEPTIDE in next template residue (1vp8A)R13 Warning: unaligning (T0320)S24 because of BadResidue code BAD_PEPTIDE at template residue (1vp8A)R13 T0320 16 :SYLHI 1vp8A 1 :MEKKI T0320 21 :DQ 1vp8A 10 :KP T0320 25 :QIIASTQEAIRLTRKYL 1vp8A 14 :ENTEETLRLAVERAKEL T0320 53 :N 1vp8A 31 :G T0320 54 :GEISFSYNGGK 1vp8A 33 :KHLVVASSYGD T0320 69 :LLLLYLSCLW 1vp8A 44 :TAMKALEMAE T0320 79 :EYFFIKAQNS 1vp8A 56 :EVVVVTYHTG T0320 90 :FDFEFQ 1vp8A 66 :FVREGE T0320 96 :SFPMQRLPTVFIDQEETFPT 1vp8A 76 :PEVEEELRKRGAKIVRQSHI T0320 116 :LENFVLETSERYCL 1vp8A 113 :TEAIAEALRSLFGH T0320 148 :FRDF 1vp8A 127 :GLKV Number of specific fragments extracted= 11 number of extra gaps= 1 total=555 Number of alignments=49 # 1vp8A read from 1vp8A/merged-good-all-a2m # found chain 1vp8A in training set Warning: unaligning (T0320)K23 because of BadResidue code BAD_PEPTIDE in next template residue (1vp8A)R13 Warning: unaligning (T0320)S24 because of BadResidue code BAD_PEPTIDE at template residue (1vp8A)R13 T0320 16 :SYLHIDQ 1vp8A 5 :IVYFNKP T0320 25 :QIIASTQE 1vp8A 14 :ENTEETLR T0320 44 :EIFVRWSPLNGEISFSYNGGKD 1vp8A 22 :LAVERAKELGIKHLVVASSYGD T0320 69 :LLLLYLSCLWE 1vp8A 44 :TAMKALEMAEG T0320 102 :LPTVFIDQE 1vp8A 55 :LEVVVVTYH T0320 111 :ETFPTLENFVLE 1vp8A 73 :TMPPEVEEELRK T0320 128 :CLSLYE 1vp8A 86 :GAKIVR T0320 134 :SQRQSGA 1vp8A 93 :SHILSGL T0320 141 :SVNMADA 1vp8A 107 :LGGVSRT T0320 148 :FRDFIKIY 1vp8A 134 :ITIMAADS T0320 157 :ETE 1vp8A 142 :GAI T0320 160 :AIVIGIRH 1vp8A 149 :VVAVGGRS Number of specific fragments extracted= 12 number of extra gaps= 1 total=567 Number of alignments=50 # 1vp8A read from 1vp8A/merged-good-all-a2m # found chain 1vp8A in training set T0320 29 :STQEAIRLTRKYLLSE 1vp8A 15 :NTEETLRLAVERAKEL T0320 52 :LNGEISFSYNGGKDCQ 1vp8A 31 :GIKHLVVASSYGDTAM T0320 72 :LYLSCLWE 1vp8A 47 :KALEMAEG T0320 81 :FFIKAQNSQFDFEFQSFP 1vp8A 55 :LEVVVVTYHTGFVREGEN T0320 112 :T 1vp8A 73 :T T0320 116 :LENFVLETSERYCLSLYESQRQ 1vp8A 74 :MPPEVEEELRKRGAKIVRQSHI Number of specific fragments extracted= 6 number of extra gaps= 0 total=573 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gt91/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gt91 expands to /projects/compbio/data/pdb/1gt9.pdb.gz 1gt91:Skipped atom 85, because occupancy 0.5 <= existing 0.500 in 1gt91 Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 89, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 91, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 93, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 95, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 99, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 686, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1015, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1041, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1053, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1057, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1059, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1063, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1065, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1067, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1203, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1205, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1207, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1209, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1211, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1213, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1413, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1415, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1417, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1419, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1421, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1423, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1425, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1427, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1429, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1431, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1433, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1640, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1642, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1644, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1646, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1648, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1650, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1652, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1781, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1783, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1785, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1787, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1789, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1791, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1793, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1795, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1797, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1799, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1801, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1803, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1805, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1807, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1809, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1811, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1813, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1815, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1817, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1819, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1821, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1829, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1833, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 1835, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 2029, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 2031, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 2033, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 2035, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 2037, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 2039, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 2041, because occupancy 0.500 <= existing 0.500 in 1gt91 Skipped atom 2043, because occupancy 0.500 <= existing 0.500 in 1gt91 # T0320 read from 1gt91/merged-good-all-a2m # 1gt91 read from 1gt91/merged-good-all-a2m # adding 1gt91 to template set # found chain 1gt91 in template set Warning: unaligning (T0320)G220 because of BadResidue code BAD_PEPTIDE in next template residue (1gt91)Y331 Warning: unaligning (T0320)F221 because of BadResidue code BAD_PEPTIDE at template residue (1gt91)Y331 T0320 71 :LLYLSC 1gt91 10 :DVAQAY T0320 77 :LW 1gt91 17 :FP T0320 79 :EYFFIKAQN 1gt91 27 :CIAIIELGG T0320 89 :QFD 1gt91 36 :GYD T0320 93 :EF 1gt91 39 :ET T0320 97 :FPMQRLPTVFI 1gt91 41 :SLAQYFASLGV T0320 108 :DQEETFPT 1gt91 55 :QVVSVSVD T0320 131 :LYESQRQ 1gt91 63 :GATNQPT T0320 138 :SGA 1gt91 72 :PNG T0320 145 :ADAFRDFIKI 1gt91 145 :NRAFLDAAAL T0320 157 :ETEAIVIGIRHT 1gt91 155 :GVTVLAAAGDSG T0320 169 :DPF 1gt91 171 :EQD T0320 184 :NW 1gt91 174 :GL T0320 186 :PDFMRLQP 1gt91 200 :GRIERETV T0320 212 :PICGLY 1gt91 226 :PLPSWQ T0320 218 :GK 1gt91 328 :AR T0320 222 :T 1gt91 332 :Q T0320 223 :SIGGINNSL 1gt91 334 :GPGWDPCTG Number of specific fragments extracted= 18 number of extra gaps= 1 total=591 Number of alignments=52 # 1gt91 read from 1gt91/merged-good-all-a2m # found chain 1gt91 in template set Warning: unaligning (T0320)G220 because of BadResidue code BAD_PEPTIDE in next template residue (1gt91)Y331 Warning: unaligning (T0320)F221 because of BadResidue code BAD_PEPTIDE at template residue (1gt91)Y331 T0320 71 :LLYLSC 1gt91 10 :DVAQAY T0320 77 :LWE 1gt91 17 :FPE T0320 96 :SFPMQRLPTVFIDQEETFPTLE 1gt91 20 :GLDGQGQCIAIIELGGGYDETS T0320 120 :VLETSERYCL 1gt91 42 :LAQYFASLGV T0320 130 :SLYE 1gt91 55 :QVVS T0320 137 :QSGA 1gt91 62 :DGAT T0320 141 :SVNMADA 1gt91 71 :DPNGPDG T0320 148 :FRDFIKI 1gt91 148 :FLDAAAL T0320 157 :ETEAIVIGI 1gt91 155 :GVTVLAAAG T0320 169 :DPFGEALKP 1gt91 164 :DSGSTDGEQ T0320 178 :IQRTDSN 1gt91 194 :RLVASAG T0320 187 :D 1gt91 201 :R T0320 189 :MRLQPL 1gt91 222 :SRIFPL T0320 214 :CGLYG 1gt91 228 :PSWQE T0320 222 :T 1gt91 332 :Q T0320 223 :SIGGINNS 1gt91 334 :GPGWDPCT Number of specific fragments extracted= 16 number of extra gaps= 1 total=607 Number of alignments=53 # 1gt91 read from 1gt91/merged-good-all-a2m # found chain 1gt91 in template set T0320 63 :GKDCQVLLLL 1gt91 74 :GPDGEVELDI T0320 73 :YLSCLWE 1gt91 86 :AGALAPG T0320 81 :FFIKAQ 1gt91 93 :AKIAVY T0320 112 :TFPTLENFVLETSERYCLS 1gt91 99 :FAPNTDAGFLNAITTAVHD T0320 138 :SGAS 1gt91 118 :PTHK T0320 142 :VNMADAFRDFIK 1gt91 142 :AAMNRAFLDAAA T0320 156 :PETEAIVIG 1gt91 154 :LGVTVLAAA Number of specific fragments extracted= 7 number of extra gaps= 0 total=614 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ru8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ru8A expands to /projects/compbio/data/pdb/1ru8.pdb.gz 1ru8A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0320 read from 1ru8A/merged-good-all-a2m # 1ru8A read from 1ru8A/merged-good-all-a2m # adding 1ru8A to template set # found chain 1ru8A in template set Warning: unaligning (T0320)F90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ru8A)T49 Warning: unaligning (T0320)F92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ru8A)T49 Warning: unaligning (T0320)G164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ru8A)A100 Warning: unaligning (T0320)I165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ru8A)A100 T0320 53 :NGEISFSYNGGKDCQVLLLLYLSCLWEY 1ru8A 4 :LADVAVLYSGGKDSNYALYWAIKNRFSV T0320 81 :FFIKAQNS 1ru8A 35 :VTMVSENE T0320 89 :Q 1ru8A 46 :M T0320 93 :EFQSFPMQRLPTVFIDQEETFPT 1ru8A 50 :INANLTDLQARALGIPLVKGFTQ T0320 116 :LENFVLE 1ru8A 75 :KEKEVED T0320 148 :FRDFIKIY 1ru8A 82 :LKRVLSGL T0320 157 :ETEAIVI 1ru8A 90 :KIQGIVA T0320 168 :TDPF 1ru8A 101 :SKYQ T0320 187 :DFMRLQPLLHWDLTNIWSFLLYSNEPI 1ru8A 116 :GLEVYTPAWGRDAKEYMRELLNLGFKI T0320 234 :PHLRKDSNNPALHFEWEIIHAF 1ru8A 148 :SAYGLDESWLGRILDESALEEL T0320 256 :GKDAEGERSSAINTSPISVV 1ru8A 171 :TLNEKYKVHVAGEGGEFETF T0320 276 :DKERFSKYHDNYYPGWYL 1ru8A 204 :DKAKKVWEPCTSSGKLII Number of specific fragments extracted= 12 number of extra gaps= 1 total=626 Number of alignments=55 # 1ru8A read from 1ru8A/merged-good-all-a2m # found chain 1ru8A in template set Warning: unaligning (T0320)T112 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ru8A)T49 Warning: unaligning (T0320)P114 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ru8A)T49 Warning: unaligning (T0320)G164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ru8A)A100 Warning: unaligning (T0320)I165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ru8A)A100 T0320 53 :NGEISFSYNGGKDCQVLLLLYLSCLWE 1ru8A 4 :LADVAVLYSGGKDSNYALYWAIKNRFS T0320 102 :LP 1ru8A 31 :VK T0320 104 :TVFIDQE 1ru8A 34 :LVTMVSE T0320 118 :NFVLETSERYCLSLYESQRQSG 1ru8A 53 :NLTDLQARALGIPLVKGFTQGE T0320 141 :SVNMADAFRDFIKIY 1ru8A 75 :KEKEVEDLKRVLSGL T0320 157 :ETEAIVI 1ru8A 90 :KIQGIVA T0320 168 :TDPFGEALKPIQRTD 1ru8A 101 :SKYQRKRIEKVAKEL T0320 187 :DFMRLQPLLHWDLTNIWSFLLYSNEPI 1ru8A 116 :GLEVYTPAWGRDAKEYMRELLNLGFKI T0320 214 :CGLYGKGFTSI 1ru8A 147 :VSAYGLDESWL T0320 238 :KDSNNPALHFEWEII 1ru8A 158 :GRILDESALEELITL T0320 253 :HAFGKDAEG 1ru8A 174 :EKYKVHVAG T0320 262 :ERSSAINTSPISVV 1ru8A 196 :LFKYKIVVDKAKKV T0320 277 :KE 1ru8A 212 :PC Number of specific fragments extracted= 13 number of extra gaps= 1 total=639 Number of alignments=56 # 1ru8A read from 1ru8A/merged-good-all-a2m # found chain 1ru8A in template set Warning: unaligning (T0320)L52 because first residue in template chain is (1ru8A)G3 Warning: unaligning (T0320)S96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ru8A)T49 Warning: unaligning (T0320)P98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ru8A)T49 Warning: unaligning (T0320)G164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ru8A)A100 Warning: unaligning (T0320)I165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ru8A)A100 T0320 53 :NGEISFSYNGGKDCQVLLLLYLSCLWEYFFIKAQNSQFDFEFQ 1ru8A 4 :LADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEESYM T0320 99 :M 1ru8A 50 :I T0320 116 :LENFVLETSERYCLSLY 1ru8A 51 :NANLTDLQARALGIPLV T0320 133 :ESQRQSGA 1ru8A 70 :FTQGEKEK T0320 144 :MADAFRDFIKIY 1ru8A 78 :EVEDLKRVLSGL T0320 157 :ETEAIVI 1ru8A 90 :KIQGIVA T0320 168 :TDPFGEA 1ru8A 101 :SKYQRKR T0320 175 :L 1ru8A 114 :E T0320 186 :PDFMRLQPLLHWDLTNIWSFLLYSNEPI 1ru8A 115 :LGLEVYTPAWGRDAKEYMRELLNLGFKI Number of specific fragments extracted= 9 number of extra gaps= 1 total=648 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1izcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0320 read from 1izcA/merged-good-all-a2m # 1izcA read from 1izcA/merged-good-all-a2m # found chain 1izcA in training set T0320 42 :LSEIFVRWS 1izcA 28 :LRQALKDAM T0320 51 :PL 1izcA 38 :DP T0320 54 :GEISFSYNGGKDCQVLLLLYLSCLWEYFFIKAQNSQFDFEFQ 1izcA 40 :SKTLMGVAHGIPSTFVTKVLAATKPDFVWIDVEHGMFNRLEL T0320 96 :SFPMQRLPTV 1izcA 83 :DAIHAAQHHS T0320 106 :FIDQEETFPT 1izcA 94 :GRSLVIVRVP T0320 116 :LENFVLETSERYCLS 1izcA 128 :TVEEVREFVKEMYYG T0320 134 :SQRQSGASVNM 1izcA 143 :PIGRRSFSPWT T0320 145 :ADAFRDFIKIY 1izcA 236 :MTKFSTAAQRN T0320 157 :ETE 1izcA 247 :GVP T0320 161 :IVIGIRHTDPFG 1izcA 250 :IFGGALSVDMVP Number of specific fragments extracted= 10 number of extra gaps= 0 total=658 Number of alignments=58 # 1izcA read from 1izcA/merged-good-all-a2m # found chain 1izcA in training set T0320 42 :LSEIFVRWSPLNGEISFSYNGGKDCQVLLLLYLSC 1izcA 28 :LRQALKDAMADPSKTLMGVAHGIPSTFVTKVLAAT T0320 102 :LPTVFIDQEE 1izcA 64 :PDFVWIDVEH T0320 112 :TFPTLENFVLETSERYCLSLYE 1izcA 77 :NRLELHDAIHAAQHHSEGRSLV T0320 148 :FRDFIKIY 1izcA 239 :FSTAAQRN T0320 157 :ETE 1izcA 247 :GVP T0320 161 :IVIGIRHTD 1izcA 250 :IFGGALSVD T0320 171 :FGE 1izcA 259 :MVP Number of specific fragments extracted= 7 number of extra gaps= 0 total=665 Number of alignments=59 # 1izcA read from 1izcA/merged-good-all-a2m # found chain 1izcA in training set Warning: unaligning (T0320)N53 because last residue in template chain is (1izcA)G300 T0320 29 :STQEAIRLTRKYLLSEIFVRWSPL 1izcA 276 :DVWGLSRLVHGSLAQARASAKQFA Number of specific fragments extracted= 1 number of extra gaps= 0 total=666 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0320 read from 1ek6A/merged-good-all-a2m # 1ek6A read from 1ek6A/merged-good-all-a2m # found chain 1ek6A in training set T0320 53 :NGEISFSYNGGKDCQVLLLLYLSCLW 1ek6A 2 :AEKVLVTGGAGYIGSHTVLELLEAGY T0320 79 :EYFFIKAQN 1ek6A 29 :PVVIDNFHN T0320 88 :SQFDFEFQSFPMQRLPTVFIDQEETFPT 1ek6A 39 :FRGGGSLPESLRRVQELTGRSVEFEEMD T0320 116 :LENFVLETSERY 1ek6A 69 :DQGALQRLFKKY T0320 129 :L 1ek6A 81 :S T0320 141 :SVNM 1ek6A 82 :FMAV T0320 145 :AD 1ek6A 166 :EM T0320 148 :FRDFIKIYPETEAIV 1ek6A 168 :IRDLCQADKTWNAVL T0320 163 :IGIRHT 1ek6A 189 :TGAHAS T0320 169 :DPF 1ek6A 202 :QGI T0320 172 :GE 1ek6A 218 :GR T0320 186 :PDFMR 1ek6A 260 :EQCGC T0320 191 :LQPLLH 1ek6A 266 :IYNLGT T0320 197 :WDLTNIWSFLLYS 1ek6A 275 :YSVLQMVQAMEKA T0320 210 :NEPIC 1ek6A 291 :KIPYK T0320 280 :FSKYHDNYYPGWYLVDDTLERAGRIK 1ek6A 296 :VVARREGDVAACYANPSLAQEELGWT Number of specific fragments extracted= 16 number of extra gaps= 0 total=682 Number of alignments=61 # 1ek6A read from 1ek6A/merged-good-all-a2m # found chain 1ek6A in training set T0320 53 :NGEISFSYNGGKDCQVLLLLYLSCL 1ek6A 2 :AEKVLVTGGAGYIGSHTVLELLEAG T0320 102 :LPTVFIDQE 1ek6A 27 :YLPVVIDNF T0320 111 :ETFPTLENFVLETSERY 1ek6A 99 :QKPLDYYRVNLTGTIQL T0320 128 :CL 1ek6A 123 :GV T0320 130 :SLYE 1ek6A 126 :NLVF T0320 134 :SQRQSGA 1ek6A 137 :GNPQYLP T0320 141 :SVNMADA 1ek6A 152 :GCTNPYG T0320 148 :FRDFIKIYPETEAIV 1ek6A 168 :IRDLCQADKTWNAVL T0320 163 :IGIRHTDPFGEALKP 1ek6A 189 :TGAHASGCIGEDPQG T0320 178 :IQRTDSNWPDF 1ek6A 225 :VFGNDYDTEDG T0320 189 :MRLQPLLH 1ek6A 264 :CRIYNLGT T0320 197 :WDLTNIWSFLLYS 1ek6A 275 :YSVLQMVQAMEKA T0320 210 :NEPI 1ek6A 291 :KIPY T0320 215 :GLYG 1ek6A 296 :VVAR T0320 223 :SIG 1ek6A 300 :REG T0320 226 :GINNSLP 1ek6A 304 :VAACYAN T0320 249 :WEII 1ek6A 311 :PSLA T0320 253 :HAFGKD 1ek6A 316 :EELGWT Number of specific fragments extracted= 18 number of extra gaps= 0 total=700 Number of alignments=62 # 1ek6A read from 1ek6A/merged-good-all-a2m # found chain 1ek6A in training set T0320 23 :KSQIIASTQEAIRLTRKYLLSEIFVRWSPLNGEISFSYN 1ek6A 94 :VGESVQKPLDYYRVNLTGTIQLLEIMKAHGVKNLVFSSS T0320 96 :SFPMQRLPTVFIDQEETFPTLENFVLETSERYCL 1ek6A 133 :ATVYGNPQYLPLDEAHPTGGCTNPYGKSKFFIEE T0320 147 :AFRDFIKIYPETEAIVIG 1ek6A 167 :MIRDLCQADKTWNAVLLR Number of specific fragments extracted= 3 number of extra gaps= 0 total=703 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d13A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2d13A expands to /projects/compbio/data/pdb/2d13.pdb.gz 2d13A:# T0320 read from 2d13A/merged-good-all-a2m # 2d13A read from 2d13A/merged-good-all-a2m # adding 2d13A to template set # found chain 2d13A in template set Warning: unaligning (T0320)F90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 Warning: unaligning (T0320)P114 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 T0320 53 :NGEISFSYNGGKDCQVLLLLYLSCLWEY 2d13A 4 :LADVAVLYSGGKDSNYALYWALKSGLRV T0320 81 :FFIKAQN 2d13A 33 :YLVSMVS T0320 89 :Q 2d13A 40 :E T0320 96 :SFPMQRLPTVFIDQEETF 2d13A 53 :ELTSLQARALGIPIIKGF T0320 116 :LENFVLE 2d13A 75 :KEKEVED T0320 148 :FRDFIKIY 2d13A 82 :LKNVLEGL T0320 157 :ETEAIVIGIRHT 2d13A 90 :KVDGIVAGALAS T0320 169 :DPFGEAL 2d13A 109 :ENVAREL T0320 187 :DFMRLQPLLHWDLTNIWSFLLYSNE 2d13A 116 :GLKVYTPAWEKDPYQYMLEIIKLGF T0320 212 :PICGLY 2d13A 151 :GLNESW T0320 224 :IGGIN 2d13A 157 :LGREL T0320 248 :EWEIIHAFGKD 2d13A 162 :NYKNLEELKKL T0320 259 :AEGERSSAINTSPI 2d13A 174 :EKYGIHIAGEGGEF Number of specific fragments extracted= 13 number of extra gaps= 0 total=716 Number of alignments=64 # 2d13A read from 2d13A/merged-good-all-a2m # found chain 2d13A in template set Warning: unaligning (T0320)L116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)N51 Warning: unaligning (T0320)R136 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 Warning: unaligning (T0320)G139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)E74 T0320 53 :NGEISFSYNGGKDCQVLLLLYLSCLWE 2d13A 4 :LADVAVLYSGGKDSNYALYWALKSGLR T0320 102 :LP 2d13A 31 :VR T0320 104 :TVFIDQE 2d13A 34 :LVSMVSE T0320 117 :ENFVLETSERYCLSLYESQ 2d13A 52 :VELTSLQARALGIPIIKGF T0320 141 :SVNMADAFRDFIKIY 2d13A 75 :KEKEVEDLKNVLEGL T0320 157 :ETEAIVIGIRHTDPFGEALKP 2d13A 90 :KVDGIVAGALASRYQKERIEN T0320 187 :DFMRLQPLLHWDLTNIWSFLLYSNEPI 2d13A 116 :GLKVYTPAWEKDPYQYMLEIIKLGFKV T0320 214 :CGLYGK 2d13A 147 :VSAYGL T0320 233 :NPHLRKDSNNPALHFEWEII 2d13A 153 :NESWLGRELNYKNLEELKKL T0320 253 :HAFGKDAEG 2d13A 174 :EKYGIHIAG T0320 262 :ERSSAINTSPISVV 2d13A 196 :FFKAKIVIDDAEKF T0320 284 :HDNYYPGWYL 2d13A 210 :WDGLSGKFII Number of specific fragments extracted= 12 number of extra gaps= 0 total=728 Number of alignments=65 # 2d13A read from 2d13A/merged-good-all-a2m # found chain 2d13A in template set Warning: unaligning (T0320)P51 because first residue in template chain is (2d13A)V2 Warning: unaligning (T0320)F90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 Warning: unaligning (T0320)L116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)N51 Warning: unaligning (T0320)S134 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 Warning: unaligning (T0320)Q137 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)E74 T0320 52 :LNGEISFSYNGGKDCQVLLLLYLSCLWEYFFIKAQNSQ 2d13A 3 :GLADVAVLYSGGKDSNYALYWALKSGLRVRYLVSMVSE T0320 117 :ENFVLETSERYCLSLY 2d13A 52 :VELTSLQARALGIPII T0320 133 :E 2d13A 70 :F T0320 138 :SGA 2d13A 75 :KEK T0320 144 :MADAFRDFIKIY 2d13A 78 :EVEDLKNVLEGL T0320 157 :ETEAIVIGIRHTDPFG 2d13A 90 :KVDGIVAGALASRYQK T0320 200 :TNIWSFLLYSNEPI 2d13A 106 :ERIENVARELGLKV Number of specific fragments extracted= 7 number of extra gaps= 0 total=735 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vl2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0320 read from 1vl2A/merged-good-all-a2m # 1vl2A read from 1vl2A/merged-good-all-a2m # found chain 1vl2A in training set Warning: unaligning (T0320)S50 because first residue in template chain is (1vl2A)K2 Warning: unaligning (T0320)W197 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl2A)T156 Warning: unaligning (T0320)T200 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl2A)T156 Warning: unaligning (T0320)S223 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl2A)G379 Warning: unaligning (T0320)N242 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl2A)G379 T0320 54 :GEISFSYNGGKDCQVLLLLYLSCLWEYFFIKAQN 1vl2A 3 :EKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANV T0320 89 :QFD 1vl2A 37 :GQK T0320 93 :EFQSFPMQRLPTVFI 1vl2A 40 :DDFVAIKEKALKTGA T0320 108 :DQEETFPT 1vl2A 56 :KVYVEDLR T0320 121 :LETSERYCLSLY 1vl2A 64 :REFVTDYIFTAL T0320 145 :AD 1vl2A 98 :KR T0320 148 :FRDFIKIY 1vl2A 100 :QVEIAEKE T0320 157 :ETEAIVIGIRH 1vl2A 108 :GAQYVAHGATG T0320 183 :SNW 1vl2A 119 :KGN T0320 186 :PDFMRLQPLLH 1vl2A 135 :PNLKVISPWKD T0320 201 :NIWSFLLYSNEPICGLY 1vl2A 157 :DLINYAMEKGIPIKVSK T0320 219 :KGFT 1vl2A 366 :SLYN T0320 243 :PALHFEWEIIHAFGKD 1vl2A 380 :GFDATDSKGFINIHAL Number of specific fragments extracted= 13 number of extra gaps= 0 total=748 Number of alignments=67 # 1vl2A read from 1vl2A/merged-good-all-a2m # found chain 1vl2A in training set Warning: unaligning (T0320)G54 because first residue in template chain is (1vl2A)K2 Warning: unaligning (T0320)W197 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl2A)T156 Warning: unaligning (T0320)T200 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl2A)T156 Warning: unaligning (T0320)G220 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl2A)G379 Warning: unaligning (T0320)S240 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl2A)G379 T0320 55 :EISFSYNGGKDCQVLLLLYLSCLWE 1vl2A 4 :KVVLAYSGGLDTSVILKWLCEKGFD T0320 102 :LPTVFIDQEE 1vl2A 29 :VIAYVANVGQ T0320 114 :PTLENFVLETSERYCL 1vl2A 39 :KDDFVAIKEKALKTGA T0320 130 :SLYESQR 1vl2A 56 :KVYVEDL T0320 145 :ADA 1vl2A 63 :RRE T0320 148 :FRDFIKIY 1vl2A 100 :QVEIAEKE T0320 157 :ETEAIVIGI 1vl2A 108 :GAQYVAHGA T0320 166 :RHTD 1vl2A 119 :KGND T0320 171 :FGEALKPIQRTDS 1vl2A 123 :QVRFELTYAALNP T0320 187 :DFMRLQPLLH 1vl2A 136 :NLKVISPWKD T0320 201 :NIWSFLLYSNEPI 1vl2A 157 :DLINYAMEKGIPI T0320 214 :CGLY 1vl2A 171 :VSKK T0320 219 :K 1vl2A 369 :N T0320 241 :NNPALHFEWEII 1vl2A 380 :GFDATDSKGFIN Number of specific fragments extracted= 14 number of extra gaps= 0 total=762 Number of alignments=68 # 1vl2A read from 1vl2A/merged-good-all-a2m # found chain 1vl2A in training set Warning: unaligning (T0320)N53 because first residue in template chain is (1vl2A)K2 Warning: unaligning (T0320)Q179 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl2A)T156 Warning: unaligning (T0320)T200 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl2A)T156 T0320 54 :GEISFSYNGGKDCQVLLLLYLSCLWE 1vl2A 3 :EKVVLAYSGGLDTSVILKWLCEKGFD T0320 81 :FFIKAQNSQFDFE 1vl2A 29 :VIAYVANVGQKDD T0320 117 :ENFVLETSERYCLSLYESQRQ 1vl2A 42 :FVAIKEKALKTGASKVYVEDL T0320 145 :ADAFRDFI 1vl2A 63 :RREFVTDY T0320 153 :KIYPETEAI 1vl2A 132 :ALNPNLKVI T0320 168 :TDPFGEAL 1vl2A 144 :KDPEFLAK T0320 178 :I 1vl2A 152 :F T0320 201 :NIWSFLLYSNEPI 1vl2A 157 :DLINYAMEKGIPI Number of specific fragments extracted= 8 number of extra gaps= 0 total=770 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c5sA/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/T0320/2c5sA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0320/2c5sA/merged-good-all-a2m.gz for input Trying 2c5sA/merged-good-all-a2m Error: Couldn't open file 2c5sA/merged-good-all-a2m or 2c5sA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ih8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ih8A expands to /projects/compbio/data/pdb/1ih8.pdb.gz 1ih8A:# T0320 read from 1ih8A/merged-good-all-a2m # 1ih8A read from 1ih8A/merged-good-all-a2m # adding 1ih8A to template set # found chain 1ih8A in template set T0320 25 :QIIAST 1ih8A 5 :KIMREL T0320 31 :QEAIRLTRKYLLSEIFVRW 1ih8A 18 :PKQEIEDRVNFLKQYVKKT T0320 53 :N 1ih8A 37 :G T0320 54 :GEISFSYNGGKDCQVLLLLYLSCLW 1ih8A 39 :KGFVLGISGGQDSTLAGRLAQLAVE T0320 79 :EYFFIKAQN 1ih8A 73 :QFIAVRLPH T0320 89 :QFD 1ih8A 82 :GTQ T0320 93 :EFQSFPMQRLPTVFI 1ih8A 85 :QDEDDAQLALKFIKP T0320 108 :DQEETFPT 1ih8A 101 :KSWKFDIK T0320 118 :NFVLETSERYCLSLYESQRQ 1ih8A 109 :STVSAFSDQYQQETGDQLTD T0320 145 :ADAFRDFIKIY 1ih8A 140 :MIAQYAIGGQE T0320 157 :ET 1ih8A 151 :GL T0320 161 :IVIGIRH 1ih8A 153 :LVLGTDH T0320 171 :FGEALK 1ih8A 164 :VTGFFT T0320 186 :PDFMRLQPLLHWDLTNIWSFLLYSNEPIC 1ih8A 173 :DGGADLLPLTGLTKRQGRTLLKELGAPER T0320 216 :LYGKGFTS 1ih8A 202 :LYLKEPTA T0320 239 :DSNNPALHFEWEIIHAFGKD 1ih8A 210 :DLLDEKPQQSDETELGISYD T0320 259 :AEGER 1ih8A 236 :EGKEV T0320 295 :DDTLERA 1ih8A 241 :SAKVSEA Number of specific fragments extracted= 18 number of extra gaps= 0 total=788 Number of alignments=70 # 1ih8A read from 1ih8A/merged-good-all-a2m # found chain 1ih8A in template set T0320 25 :QIIAST 1ih8A 5 :KIMREL T0320 34 :IRLTRKYLLSEIFVRWSPLNG 1ih8A 18 :PKQEIEDRVNFLKQYVKKTGA T0320 55 :EISFSYNGGKDCQVLLLLY 1ih8A 40 :GFVLGISGGQDSTLAGRLA T0320 74 :LSCLWE 1ih8A 66 :REEGGD T0320 102 :LPTVFIDQEETFPTLENFVLETSERYCL 1ih8A 72 :AQFIAVRLPHGTQQDEDDAQLALKFIKP T0320 130 :SLYE 1ih8A 101 :KSWK T0320 141 :SVNMADA 1ih8A 125 :QLTDFNK T0320 148 :FRDFIKIY 1ih8A 143 :QYAIGGQE T0320 157 :ETE 1ih8A 151 :GLL T0320 162 :VIGI 1ih8A 154 :VLGT T0320 169 :DPFGEALKPIQRTDSN 1ih8A 158 :DHAAEAVTGFFTKYGD T0320 187 :DFMRLQPLLHWDLTNIWSFLLYSNEPICGLYGKGFTSI 1ih8A 174 :GGADLLPLTGLTKRQGRTLLKELGAPERLYLKEPTADL T0320 238 :KDS 1ih8A 212 :LDE T0320 241 :NNPAL 1ih8A 240 :VSAKV T0320 248 :EWEI 1ih8A 245 :SEAL T0320 253 :HAFGKDAEGERSSAINTSP 1ih8A 250 :KRYSMTEHKRQVPASMFDD Number of specific fragments extracted= 16 number of extra gaps= 0 total=804 Number of alignments=71 # 1ih8A read from 1ih8A/merged-good-all-a2m # found chain 1ih8A in template set T0320 30 :TQEAIRLTRKYLLSEIFVR 1ih8A 18 :PKQEIEDRVNFLKQYVKKT T0320 52 :LNGEISFSYNGGKDCQVLLLLYLSCLWE 1ih8A 37 :GAKGFVLGISGGQDSTLAGRLAQLAVES T0320 80 :YFFIKAQNSQFDFEFQSFPMQRLPTVFIDQEETFPTLENFVLETSERYCLS 1ih8A 71 :DAQFIAVRLPHGTQQDEDDAQLALKFIKPDKSWKFDIKSTVSAFSDQYQQE T0320 138 :SGASVNMADAFRDFI 1ih8A 122 :TGDQLTDFNKGNVKA T0320 157 :ETE 1ih8A 151 :GLL T0320 180 :RTDSNWPDFMRLQPLLHWDLTNIWSFLLYSNEPI 1ih8A 167 :FFTKYGDGGADLLPLTGLTKRQGRTLLKELGAPE T0320 215 :GLYGKGFT 1ih8A 201 :RLYLKEPT T0320 231 :LPNPHL 1ih8A 209 :ADLLDE T0320 237 :RKDSNNPALHFEWEIIHAFGKDAE 1ih8A 237 :GKEVSAKVSEALEKRYSMTEHKRQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=813 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wxiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wxiA expands to /projects/compbio/data/pdb/1wxi.pdb.gz 1wxiA:# T0320 read from 1wxiA/merged-good-all-a2m # 1wxiA read from 1wxiA/merged-good-all-a2m # adding 1wxiA to template set # found chain 1wxiA in template set Warning: unaligning (T0320)D21 because first residue in template chain is (1wxiA)T2 T0320 22 :QKSQIIAST 1wxiA 3 :LQQQIIKAL T0320 31 :QEAIRLTRKYLLSEIFVRW 1wxiA 19 :AEEEIRRSVDFLKSYLQTY T0320 52 :LN 1wxiA 38 :PF T0320 54 :GEISFSYNGGKDCQVLLLLYLSCLW 1wxiA 41 :KSLVLGISGGQDSTLAGKLCQMAIN T0320 79 :EYFFIKAQN 1wxiA 77 :QFIAVRLPY T0320 89 :QFD 1wxiA 86 :GVQ T0320 93 :EFQSFPMQRLPTVFI 1wxiA 89 :ADEQDCQDAIAFIQP T0320 108 :DQEETFPT 1wxiA 105 :RVLTVNIK T0320 118 :NFVLETSERYCLSLYESQR 1wxiA 113 :GAVLASEQALREAGIELSD T0320 144 :M 1wxiA 132 :F T0320 145 :ADAFRDFIKIY 1wxiA 143 :MKAQYSIAGMT T0320 159 :EAIVIG 1wxiA 154 :SGVVVG T0320 165 :IRHTDPFGEALK 1wxiA 161 :DHAAEAITGFFT T0320 183 :SNWPDFMRLQPLLHWDLTNIWSFLLYSNEPICGLY 1wxiA 173 :KYGDGGTDINPLYRLNKRQGKQLLAALACPEHLYK T0320 219 :KGFT 1wxiA 241 :KNVP T0320 242 :NPALHFEWEIIHAFGKDAEGERSSA 1wxiA 245 :QQVARTIENWYLKTEHKRRPPITVF Number of specific fragments extracted= 16 number of extra gaps= 0 total=829 Number of alignments=73 # 1wxiA read from 1wxiA/merged-good-all-a2m # found chain 1wxiA in template set T0320 25 :QIIAST 1wxiA 6 :QIIKAL T0320 34 :IRLTRKYLLSEIFVRWSPLNG 1wxiA 19 :AEEEIRRSVDFLKSYLQTYPF T0320 55 :EISFSYNGGKDCQVLLLLYLSCLWEYFFIKAQNS 1wxiA 42 :SLVLGISGGQDSTLAGKLCQMAINELRLETGNES T0320 102 :LPTVFIDQEETFPTLENFVLETSERYCL 1wxiA 76 :LQFIAVRLPYGVQADEQDCQDAIAFIQP T0320 130 :SLYESQRQSGA 1wxiA 105 :RVLTVNIKGAV T0320 141 :SVNMADA 1wxiA 126 :GIELSDF T0320 148 :FRDFIKIY 1wxiA 146 :QYSIAGMT T0320 159 :EAIVIGI 1wxiA 154 :SGVVVGT T0320 169 :DPFGEALKPIQRTDSN 1wxiA 161 :DHAAEAITGFFTKYGD T0320 187 :DFMRLQPLLHWDLTNIWSFLLYSNEPICGLYG 1wxiA 177 :GGTDINPLYRLNKRQGKQLLAALACPEHLYKK T0320 219 :KGF 1wxiA 263 :RPP T0320 238 :KDSNNPAL 1wxiA 266 :ITVFDDFW Number of specific fragments extracted= 12 number of extra gaps= 0 total=841 Number of alignments=74 # 1wxiA read from 1wxiA/merged-good-all-a2m # found chain 1wxiA in template set Warning: unaligning (T0320)G220 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wxiA)D223 Warning: unaligning (T0320)L236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wxiA)D223 T0320 26 :IIASTQEAIRLTRKYLLS 1wxiA 19 :AEEEIRRSVDFLKSYLQT T0320 50 :SPLNGEISFSYNGGKDCQVLLLLYLSCLWE 1wxiA 37 :YPFIKSLVLGISGGQDSTLAGKLCQMAINE T0320 80 :YFFIKAQNSQFDFEFQSFPMQRLPTVFIDQEETFPTLENFVLETSERYCLSLYESQRQ 1wxiA 75 :SLQFIAVRLPYGVQADEQDCQDAIAFIQPDRVLTVNIKGAVLASEQALREAGIELSDF T0320 142 :VNMADAFRDFIKIYP 1wxiA 140 :RERMKAQYSIAGMTS T0320 160 :AIVIGI 1wxiA 155 :GVVVGT T0320 169 :DPFGEALKPIQ 1wxiA 161 :DHAAEAITGFF T0320 182 :DSNWPDFMRLQPLLHWDLTNIWSFLLYSNEPI 1wxiA 172 :TKYGDGGTDINPLYRLNKRQGKQLLAALACPE T0320 215 :GLYGK 1wxiA 204 :HLYKK T0320 237 :RKDSNNPALHFEWEIIHAFGKDAEGERSSAI 1wxiA 240 :GKNVPQQVARTIENWYLKTEHKRRPPITVFD Number of specific fragments extracted= 9 number of extra gaps= 0 total=850 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k92A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0320 read from 1k92A/merged-good-all-a2m # 1k92A read from 1k92A/merged-good-all-a2m # found chain 1k92A in training set Warning: unaligning (T0320)A266 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1k92A)A431 Warning: unaligning (T0320)I267 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1k92A)A431 Warning: unaligning (T0320)N268 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1k92A)A432 Warning: unaligning (T0320)F280 because last residue in template chain is (1k92A)K444 T0320 52 :LNGEISFSYNGGKDCQVLLLLYLSCLW 1k92A 9 :VGQRIGIAFSGGLDTSAALLWMRQKGA T0320 79 :EYFFIKAQN 1k92A 38 :YAYTANLGQ T0320 89 :QFD 1k92A 47 :PDE T0320 93 :EFQSFPMQRLPTVFI 1k92A 50 :EDYDAIPRRAMEYGA T0320 108 :DQEETFPT 1k92A 66 :NARLIDCR T0320 121 :LETSERY 1k92A 74 :KQLVAEG T0320 129 :LSL 1k92A 81 :IAA T0320 145 :AD 1k92A 111 :TM T0320 148 :FRDFIKIY 1k92A 113 :LVAAMKED T0320 157 :ETEAIVIGIRH 1k92A 121 :GVNIWGDGSTY T0320 183 :SNW 1k92A 132 :KGN T0320 186 :PDFMRLQPLLH 1k92A 148 :AELQIYKPWLD T0320 197 :W 1k92A 165 :L T0320 198 :DLTNIWSFLLYSNEPICGLY 1k92A 167 :GRHEMSEFMIACGFDYKMSV T0320 225 :GGINNSLPNPHLRKDSNNPALHFE 1k92A 378 :NLTYKPERLTMEKGDSVFSPDDRI T0320 249 :WEIIHAF 1k92A 412 :TDTREKL T0320 256 :GKDAEGERSS 1k92A 420 :GYAKTGLLSS T0320 269 :TSPISVVDKER 1k92A 433 :SGVPQVENLEN Number of specific fragments extracted= 18 number of extra gaps= 1 total=868 Number of alignments=76 # 1k92A read from 1k92A/merged-good-all-a2m # found chain 1k92A in training set Warning: unaligning (T0320)G261 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1k92A)A431 Warning: unaligning (T0320)E262 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1k92A)A431 Warning: unaligning (T0320)R263 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1k92A)A432 T0320 52 :LNGEISFSYNGGKDCQVLLLLYLSCLWE 1k92A 9 :VGQRIGIAFSGGLDTSAALLWMRQKGAV T0320 102 :LPTVFIDQEETFPTLENFVLETSERYCL 1k92A 37 :PYAYTANLGQPDEEDYDAIPRRAMEYGA T0320 130 :SLYESQ 1k92A 66 :NARLID T0320 144 :MADA 1k92A 72 :CRKQ T0320 148 :FRDFIKIY 1k92A 113 :LVAAMKED T0320 157 :ETEAIVIGIRHTDPFGEALKP 1k92A 121 :GVNIWGDGSTYKGNDIERFYR T0320 178 :IQRTDS 1k92A 143 :GLLTNA T0320 187 :DFMRLQPLLH 1k92A 149 :ELQIYKPWLD T0320 197 :W 1k92A 165 :L T0320 198 :DLTNIWSFLLYSNEPICGLYG 1k92A 167 :GRHEMSEFMIACGFDYKMSVE T0320 219 :KGFTSIG 1k92A 367 :NDYSILN T0320 226 :GINNSLPNPHLRKDS 1k92A 376 :SENLTYKPERLTMEK T0320 246 :HFEWEII 1k92A 405 :TMRNLDI T0320 253 :HAF 1k92A 417 :KLF T0320 256 :GKDAE 1k92A 425 :GLLSS T0320 264 :SSAINTSP 1k92A 433 :SGVPQVEN T0320 277 :K 1k92A 441 :L Number of specific fragments extracted= 17 number of extra gaps= 1 total=885 Number of alignments=77 # 1k92A read from 1k92A/merged-good-all-a2m # found chain 1k92A in training set T0320 51 :PLNGEISFSYNGGKDCQVLLLLYLSCLWE 1k92A 8 :PVGQRIGIAFSGGLDTSAALLWMRQKGAV T0320 81 :FFIKAQNSQF 1k92A 37 :PYAYTANLGQ T0320 93 :EFQ 1k92A 47 :PDE T0320 115 :TLENFVLETSERYCLSLYESQRQ 1k92A 50 :EDYDAIPRRAMEYGAENARLIDC T0320 145 :ADAFR 1k92A 73 :RKQLV T0320 154 :IYPETEAIVIGIRHTDPFGEA 1k92A 118 :KEDGVNIWGDGSTYKGNDIER T0320 182 :D 1k92A 147 :N T0320 186 :PDFMRLQPLLH 1k92A 148 :AELQIYKPWLD T0320 198 :DLTNIWSFLLYSNEPI 1k92A 167 :GRHEMSEFMIACGFDY Number of specific fragments extracted= 9 number of extra gaps= 0 total=894 Number of alignments=78 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 78 Done printing distance constraints # command: