# 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/T0310/ # command:# Making conformation for sequence T0310 numbered 1 through 425 Created new target T0310 from T0310.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0310/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0310//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0310/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0310//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0310/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0310/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0310/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qi1A/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/T0310/1qi1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0310/1qi1A/merged-good-all-a2m.gz for input Trying 1qi1A/merged-good-all-a2m Error: Couldn't open file 1qi1A/merged-good-all-a2m or 1qi1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k75A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1k75A expands to /projects/compbio/data/pdb/1k75.pdb.gz 1k75A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1791, because occupancy 0.5 <= existing 0.500 in 1k75A Skipped atom 2010, because occupancy 0.500 <= existing 0.500 in 1k75A Skipped atom 2012, because occupancy 0.500 <= existing 0.500 in 1k75A Skipped atom 2014, because occupancy 0.500 <= existing 0.500 in 1k75A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2034, because occupancy 0.500 <= existing 0.500 in 1k75A Skipped atom 2036, because occupancy 0.500 <= existing 0.500 in 1k75A Skipped atom 2038, because occupancy 0.500 <= existing 0.500 in 1k75A Skipped atom 2040, because occupancy 0.500 <= existing 0.500 in 1k75A Skipped atom 2042, because occupancy 0.500 <= existing 0.500 in 1k75A Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in 1k75A Skipped atom 2532, because occupancy 0.500 <= existing 0.500 in 1k75A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0310 read from 1k75A/merged-good-all-a2m # 1k75A read from 1k75A/merged-good-all-a2m # adding 1k75A to template set # found chain 1k75A in template set T0310 16 :LATLEPEQRAEI 1k75A 9 :WNSCTAEQQRQL # choosing archetypes in rotamer library T0310 28 :IHHLADLLTDQRDEILLAN 1k75A 36 :VNDILDNVKARGDEALREY T0310 47 :KKDLEEAEGRLAAPLLKR 1k75A 70 :AEEIAAASERLSDELKQA T0310 72 :LNSLAIGLRQIAAS 1k75A 88 :MAVAVKNIETFHTA T0310 87 :QDSVGRVLRR 1k75A 102 :QKLPPVDVET T0310 100 :AKNLELEQVTVPIGVLLVIFE 1k75A 112 :QPGVRCQQVTRPVASVGLYIP T0310 121 :SRPDCL 1k75A 135 :SAPLFS T0310 127 :PQVAALAIASGN 1k75A 143 :LMLATPASIAGC T0310 139 :GLLLKGGKEAAHSNRILH 1k75A 157 :VVLCSPPPIADEILYAAQ T0310 161 :EA 1k75A 175 :LC T0310 167 :GVKEAVQL 1k75A 177 :GVQDVFNV T0310 177 :TR 1k75A 185 :GG T0310 182 :ELDKMIDLIIPRGS 1k75A 198 :ESVPKVDKIFGPGN T0310 196 :SQLVRDIQKAAKGIPVMGHSEGIC 1k75A 215 :TEAKRQVSQRLDGAAIDMPAGPSE T0310 221 :MYVDSEASVDKVTRLVRDS 1k75A 241 :VIADSGATPDFVASDLLSQ T0310 240 :KCEYPAA 1k75A 262 :HGPDSQV T0310 252 :TLLIHRD 1k75A 269 :ILLTPAA T0310 263 :PLFDQIIDMLRVEQVKIHA 1k75A 276 :DMARRVAEAVERQLAELPR T0310 292 :VKSLRTEYGDLELC 1k75A 295 :AETARQALNASRLI T0310 308 :VVDNVQDAIDHIHKYGSSH 1k75A 309 :VTKDLAQCVEISNQYGPEH T0310 328 :DVIVTEDENTA 1k75A 328 :LIIQTRNAREL T0310 346 :DSACVFW 1k75A 344 :SAGSVFL Number of specific fragments extracted= 22 number of extra gaps= 0 total=22 Number of alignments=1 # 1k75A read from 1k75A/merged-good-all-a2m # found chain 1k75A in template set Warning: unaligning (T0310)L50 because of BadResidue code BAD_PEPTIDE in next template residue (1k75A)D59 Warning: unaligning (T0310)E51 because of BadResidue code BAD_PEPTIDE at template residue (1k75A)D59 Warning: unaligning (T0310)E52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1k75A)K60 T0310 16 :LATLEPEQRAEI 1k75A 9 :WNSCTAEQQRQL T0310 28 :IHHLADLLTDQRDEILLANKKD 1k75A 36 :VNDILDNVKARGDEALREYSAK T0310 53 :AE 1k75A 61 :TT T0310 55 :G 1k75A 64 :T T0310 56 :RLAAPLLKRLSL 1k75A 67 :KVSAEEIAAASE T0310 68 :STSKLNSLAIGLRQIAAS 1k75A 84 :LKQAMAVAVKNIETFHTA T0310 90 :VGRVLRRTRIAKNLELEQVTVPIGVLLVIFE 1k75A 102 :QKLPPVDVETQPGVRCQQVTRPVASVGLYIP T0310 121 :SRPDCLPQVAAL 1k75A 134 :GSAPLFSTVLML T0310 133 :AIASGN 1k75A 149 :ASIAGC T0310 139 :GLLLKGGKEAAHSNRILH 1k75A 157 :VVLCSPPPIADEILYAAQ T0310 165 :IHGVKEAVQL 1k75A 175 :LCGVQDVFNV T0310 177 :TR 1k75A 185 :GG T0310 179 :EE 1k75A 188 :QA T0310 184 :DKMIDLIIPRGS 1k75A 200 :VPKVDKIFGPGN T0310 196 :SQLVRDIQKAAKGIPV 1k75A 215 :TEAKRQVSQRLDGAAI T0310 212 :MGHSEGICHMYVDSEASVDKVT 1k75A 232 :MPAGPSEVLVIADSGATPDFVA T0310 234 :RLVRDSKCEYPAAC 1k75A 255 :DLLSQAEHGPDSQV T0310 252 :TLLIHRD 1k75A 269 :ILLTPAA T0310 263 :PLFDQIIDMLRVEQVKIHA 1k75A 276 :DMARRVAEAVERQLAELPR T0310 292 :VKSLRTEYGDLE 1k75A 295 :AETARQALNASR T0310 306 :IEVVDNVQDAIDHIHKYGSSH 1k75A 307 :LIVTKDLAQCVEISNQYGPEH T0310 328 :DVIVTEDENTA 1k75A 328 :LIIQTRNAREL T0310 344 :HV 1k75A 341 :SI T0310 346 :DSACVFWN 1k75A 344 :SAGSVFLG T0310 354 :ASTRFSDG 1k75A 367 :HVLPTYGY Number of specific fragments extracted= 25 number of extra gaps= 1 total=47 Number of alignments=2 # 1k75A read from 1k75A/merged-good-all-a2m # found chain 1k75A in template set Warning: unaligning (T0310)L57 because of BadResidue code BAD_PEPTIDE in next template residue (1k75A)D59 T0310 16 :LATLEPEQRAEI 1k75A 9 :WNSCTAEQQRQL T0310 33 :DLLTDQRDEILLANKKDLEEAEGR 1k75A 34 :RTVNDILDNVKARGDEALREYSAK T0310 58 :AAPLLKRLS 1k75A 69 :SAEEIAAAS T0310 67 :LSTSKLNSLAIGLRQIAASSQDSVGRVLRRTRIAKNLELEQVTVPIGVLLVIFESRPDCLPQV 1k75A 79 :RLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGLYIPGGSAPLFST T0310 130 :AALAIASGN 1k75A 146 :ATPASIAGC T0310 139 :GLLLKGGKEAAHSNRILH 1k75A 157 :VVLCSPPPIADEILYAAQ T0310 165 :IHGVKEAVQLVN 1k75A 175 :LCGVQDVFNVGG T0310 177 :TREEVELDKMIDLIIPRGSS 1k75A 193 :LAFGTESVPKVDKIFGPGNA T0310 197 :QLVRDIQK 1k75A 216 :EAKRQVSQ T0310 206 :AKGIPVMGHSEGICH 1k75A 224 :RLDGAAIDMPAGPSE T0310 221 :MYVDSEASVDKVTRLVRD 1k75A 241 :VIADSGATPDFVASDLLS T0310 239 :SKCEYPAAC 1k75A 261 :EHGPDSQVI T0310 253 :LLIH 1k75A 270 :LLTP T0310 260 :LRTPLFDQIIDMLRVEQV 1k75A 274 :AADMARRVAEAVERQLAE T0310 289 :LTFVKSLRTEYGDLELC 1k75A 292 :LPRAETARQALNASRLI T0310 308 :VVDNVQDAIDHIHKYGSSH 1k75A 309 :VTKDLAQCVEISNQYGPEH T0310 328 :DVIVTEDENTA 1k75A 328 :LIIQTRNAREL T0310 346 :DSACVFWNASTRFSDGYRFGLGAEVGISTSRIHARGPVGLEGLLTTKWL 1k75A 344 :SAGSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRMTV Number of specific fragments extracted= 18 number of extra gaps= 1 total=65 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bxsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bxsA expands to /projects/compbio/data/pdb/1bxs.pdb.gz 1bxsA:# T0310 read from 1bxsA/merged-good-all-a2m # 1bxsA read from 1bxsA/merged-good-all-a2m # adding 1bxsA to template set # found chain 1bxsA in template set T0310 2 :VEQQGEMARSGGR 1bxsA 59 :VDKAVKAARQAFQ T0310 15 :MLATLEPEQRAEIIHHLADLLTDQRDEILL 1bxsA 75 :PWRTMDASERGRLLNKLADLIERDRLLLAT T0310 50 :LEEAEGR 1bxsA 105 :MEAMNGG T0310 59 :APLLKR 1bxsA 112 :KLFSNA T0310 68 :STSKLNSLAIGLRQIAASSQDSVGRVLRR 1bxsA 118 :YLMDLGGCIKTLRYCAGWADKIQGRTIPM T0310 100 :AKNLELEQVTVPIGVLLVIFE 1bxsA 147 :DGNFFTYTRSEPVGVCGQIIP T0310 121 :SRP 1bxsA 169 :NFP T0310 124 :DCLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1bxsA 173 :LMFLWKIGPALSCGNTVVVKPAEQTPLTALHMGSLIKEA T0310 167 :GV 1bxsA 212 :GF T0310 169 :KEAVQLVNTR 1bxsA 215 :PGVVNIVPGY T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKAA 1bxsA 230 :AAISSHMDVDKVAFTGSTEVGKLIKEAA T0310 207 :KGIPVMGHSEGICHMYVDSEASVDKVTRLVRDS 1bxsA 261 :NLKRVSLELGGKSPCIVFADADLDNAVEFAHQG T0310 240 :KCEYPAACNALETLLIHRDLLRT 1bxsA 295 :FYHQGQCCIAASRLFVEESIYDE T0310 264 :LFDQIIDMLRVEQVKIHAGPK 1bxsA 318 :FVRRSVERAKKYVLGNPLTPG T0310 285 :FASYLTFV 1bxsA 341 :QGPQIDKE T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFSDGYRFGLGAEVGISTSR 1bxsA 394 :RIAKEEIFGPVQQIMKFKSLDDVIKRANNTFYGLSAGIFTNDIDKAITVSSALQSGTVWVNCYSVVSAQCPFGGFKMSGNGREL T0310 381 :GPVGLEGLLTTKWLLRGKDHV 1bxsA 478 :GEYGFHEYTEVKTVTIKISQK Number of specific fragments extracted= 17 number of extra gaps= 0 total=82 Number of alignments=4 # 1bxsA read from 1bxsA/merged-good-all-a2m # found chain 1bxsA in template set T0310 2 :VEQQGEMARSGGR 1bxsA 59 :VDKAVKAARQAFQ T0310 15 :MLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1bxsA 75 :PWRTMDASERGRLLNKLADLIERDRLLLATMEAMNGGKL T0310 65 :LSLST 1bxsA 114 :FSNAY T0310 70 :SKLNSLAIGLRQIAASSQDSVGRVLRR 1bxsA 120 :MDLGGCIKTLRYCAGWADKIQGRTIPM T0310 100 :AKNLELEQVTVPIGVLLVIFESRPDCLPQVAAL 1bxsA 147 :DGNFFTYTRSEPVGVCGQIIPWNFPLLMFLWKI T0310 133 :AIASGNGLLLKGGKEAAHSNRILHLLTQEA 1bxsA 182 :ALSCGNTVVVKPAEQTPLTALHMGSLIKEA T0310 167 :GV 1bxsA 212 :GF T0310 169 :KEAVQLVNT 1bxsA 215 :PGVVNIVPG T0310 178 :R 1bxsA 225 :G T0310 179 :EEVEL 1bxsA 227 :TAGAA T0310 184 :DKMIDLIIPRGSSQLVRDIQKAA 1bxsA 235 :HMDVDKVAFTGSTEVGKLIKEAA T0310 207 :KGIPV 1bxsA 261 :NLKRV T0310 212 :MGHS 1bxsA 267 :LELG T0310 217 :GICHMYVDSEASVDKVT 1bxsA 271 :GKSPCIVFADADLDNAV T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLR 1bxsA 289 :FAHQGVFYHQGQCCIAASRLFVEESIYD T0310 263 :PLFDQIIDMLRVEQVKIHAGPK 1bxsA 317 :EFVRRSVERAKKYVLGNPLTPG T0310 285 :FASYLTF 1bxsA 341 :QGPQIDK T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWN 1bxsA 393 :MRIAKEEIFGPVQQIMKFKSLDDVIKRANNTFYGLSAGIFTNDIDKAITVSSALQSGTVWVN T0310 354 :ASTRFSDGYRFGLGAEVG 1bxsA 461 :AQCPFGGFKMSGNGRELG T0310 372 :ISTSRIHARGPVGLEGLL 1bxsA 480 :YGFHEYTEVKTVTIKISQ Number of specific fragments extracted= 20 number of extra gaps= 0 total=102 Number of alignments=5 # 1bxsA read from 1bxsA/merged-good-all-a2m # found chain 1bxsA in template set T0310 2 :VEQQGEMARSGGR 1bxsA 59 :VDKAVKAARQAFQ T0310 15 :MLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLE 1bxsA 75 :PWRTMDASERGRLLNKLADLIERDRLLLATMEAMNGG T0310 57 :LAAPLLK 1bxsA 112 :KLFSNAY T0310 70 :SKLNSLAIGLRQIAASSQDSV 1bxsA 119 :LMDLGGCIKTLRYCAGWADKI T0310 93 :VLRRTRIAKNLELEQVTVPIGVLLVIFESRPDCLPQV 1bxsA 140 :QGRTIPMDGNFFTYTRSEPVGVCGQIIPWNFPLLMFL T0310 130 :AALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1bxsA 179 :IGPALSCGNTVVVKPAEQTPLTALHMGSLIKEA T0310 167 :GVKEAVQLVN 1bxsA 212 :GFPPGVVNIV T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQK 1bxsA 228 :AGAAISSHMDVDKVAFTGSTEVGKLIKE T0310 205 :AAKGIPVMGHSEGICHMYVDSEASVDKVTRLVRDSKC 1bxsA 259 :KSNLKRVSLELGGKSPCIVFADADLDNAVEFAHQGVF T0310 242 :EYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQV 1bxsA 297 :HQGQCCIAASRLFVEESIYDEFVRRSVERAKKYVLG T0310 278 :KIHAGPKFASYLTFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTR 1bxsA 379 :YFIQPTVFSDVTDDMRIAKEEIFGPVQQIMKFKSLDDVIKRANNTFYGLSAGIFTNDIDKAITVSSALQSGTVWVNCYSV T0310 360 :DGYRFGLGAEVGISTSRIH 1bxsA 459 :VSAQCPFGGFKMSGNGREL T0310 381 :GPVGLEGLLTTKWLLRG 1bxsA 478 :GEYGFHEYTEVKTVTIK Number of specific fragments extracted= 13 number of extra gaps= 0 total=115 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cw3A/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/T0310/1cw3A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0310/1cw3A/merged-good-all-a2m.gz for input Trying 1cw3A/merged-good-all-a2m Error: Couldn't open file 1cw3A/merged-good-all-a2m or 1cw3A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ag8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ag8A expands to /projects/compbio/data/pdb/1ag8.pdb.gz 1ag8A:# T0310 read from 1ag8A/merged-good-all-a2m # 1ag8A read from 1ag8A/merged-good-all-a2m # adding 1ag8A to template set # found chain 1ag8A in template set T0310 2 :VEQQGEMARSGGR 1ag8A 59 :VDRAVKAARAAFQ T0310 15 :MLATLEPEQRAEIIHHLADLLTDQRDEILL 1ag8A 75 :PWRRMDASERGRLLNRLADLIERDRTYLAA T0310 50 :LEEAEGR 1ag8A 105 :LETLDNG T0310 59 :APLLKR 1ag8A 112 :KPYIIS T0310 68 :STSKLNSLAIGLRQIAASSQDSVGRVLRR 1ag8A 118 :YLVDLDMVLKCLRYYAGWADKYHGKTIPI T0310 100 :AKNLELEQVTVPIGVLLVIFE 1ag8A 147 :DGDYFSYTRHEPVGVCGQIIP T0310 121 :SRP 1ag8A 169 :NFP T0310 124 :DCLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1ag8A 173 :LMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEA T0310 167 :GV 1ag8A 212 :GF T0310 169 :KEAVQLVNTR 1ag8A 215 :PGVVNVIPGF T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKAA 1ag8A 230 :AAIASHEDVDKVAFTGSTEVGHLIQVAA T0310 207 :KGIPVMGHSEGICHMYVDSEASVDKVTRLVRDS 1ag8A 261 :NLKRVTLEIGGKSPNIIMSDADMDWAVEQAHFA T0310 240 :KCEYPAACNALETLLIHRDLLRT 1ag8A 295 :FFNQGQCCCAGSRTFVQEDIYAE T0310 264 :LFDQIIDMLRVEQVKIHAGPK 1ag8A 318 :FVERSVARAKSRVVGNPFDSR T0310 285 :FASYLTFV 1ag8A 341 :QGPQVDET T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFSDGYRFGLGAEVGISTSR 1ag8A 394 :TIAKEEIFGPVMQILKFKSMEEVVGRANNSKYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKLSGSGREL T0310 381 :GPVGLEGLLTTKWLLRGKDHV 1ag8A 478 :GEYGLQAYTEVKTVTVRVPQK Number of specific fragments extracted= 17 number of extra gaps= 0 total=132 Number of alignments=7 # 1ag8A read from 1ag8A/merged-good-all-a2m # found chain 1ag8A in template set T0310 2 :VEQQGEMARSGGR 1ag8A 59 :VDRAVKAARAAFQ T0310 15 :MLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1ag8A 75 :PWRRMDASERGRLLNRLADLIERDRTYLAALETLDNGKP T0310 65 :LSLST 1ag8A 114 :YIISY T0310 70 :SKLNSLAIGLRQIAASSQDSVGRVLRR 1ag8A 120 :VDLDMVLKCLRYYAGWADKYHGKTIPI T0310 100 :AKNLELEQVTVPIGVLLVIFESRPDCLPQVAAL 1ag8A 147 :DGDYFSYTRHEPVGVCGQIIPWNFPLLMQAWKL T0310 133 :AIASGNGLLLKGGKEAAHSNRILHLLTQEA 1ag8A 182 :ALATGNVVVMKVAEQTPLTALYVANLIKEA T0310 167 :GV 1ag8A 212 :GF T0310 169 :KEAVQLVNT 1ag8A 215 :PGVVNVIPG T0310 178 :R 1ag8A 225 :G T0310 179 :EEVEL 1ag8A 227 :TAGAA T0310 184 :DKMIDLIIPRGSSQLVRDIQKAA 1ag8A 235 :HEDVDKVAFTGSTEVGHLIQVAA T0310 207 :KGIPV 1ag8A 261 :NLKRV T0310 212 :MGHS 1ag8A 267 :LEIG T0310 217 :GICHMYVDSEASVDKVT 1ag8A 271 :GKSPNIIMSDADMDWAV T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLR 1ag8A 289 :QAHFALFFNQGQCCCAGSRTFVQEDIYA T0310 263 :PLFDQIIDMLRVEQVKIHAGPK 1ag8A 317 :EFVERSVARAKSRVVGNPFDSR T0310 285 :FASYLTF 1ag8A 341 :QGPQVDE T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWN 1ag8A 393 :MTIAKEEIFGPVMQILKFKSMEEVVGRANNSKYGLAAAVFTKDLDKANYLSQALQAGTVWVN T0310 354 :ASTRFSDGYRFGLGAEVG 1ag8A 461 :AQSPFGGYKLSGSGRELG T0310 372 :ISTSRIHARGPVGLEGLL 1ag8A 480 :YGLQAYTEVKTVTVRVPQ Number of specific fragments extracted= 20 number of extra gaps= 0 total=152 Number of alignments=8 # 1ag8A read from 1ag8A/merged-good-all-a2m # found chain 1ag8A in template set T0310 2 :VEQQGEMARSGGR 1ag8A 59 :VDRAVKAARAAFQ T0310 15 :MLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDL 1ag8A 75 :PWRRMDASERGRLLNRLADLIERDRTYLAALETLDN T0310 57 :LAAPLLKRL 1ag8A 112 :KPYIISYLV T0310 72 :LNSLAIGLRQIAASSQDS 1ag8A 121 :DLDMVLKCLRYYAGWADK T0310 92 :RVLRRTRIAKNLELEQVTVPIGVLLVIFESRPDCLPQV 1ag8A 139 :YHGKTIPIDGDYFSYTRHEPVGVCGQIIPWNFPLLMQA T0310 130 :AALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1ag8A 179 :LGPALATGNVVVMKVAEQTPLTALYVANLIKEA T0310 167 :GVKEAVQLVN 1ag8A 212 :GFPPGVVNVI T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQK 1ag8A 228 :AGAAIASHEDVDKVAFTGSTEVGHLIQV T0310 205 :AAKGIPVMGHSEGICHMYVDSEASVDKVTRLVRDS 1ag8A 259 :KSNLKRVTLEIGGKSPNIIMSDADMDWAVEQAHFA T0310 240 :KCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQV 1ag8A 295 :FFNQGQCCCAGSRTFVQEDIYAEFVERSVARAKSRVVG T0310 278 :KIHAGPKFASYLTFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTR 1ag8A 379 :YFIQPTVFGDLQDGMTIAKEEIFGPVMQILKFKSMEEVVGRANNSKYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDV T0310 360 :DGYRFGLGAEVGISTSRIH 1ag8A 459 :FGAQSPFGGYKLSGSGREL T0310 381 :GPVGLEGLLTTKWLLRGK 1ag8A 478 :GEYGLQAYTEVKTVTVRV Number of specific fragments extracted= 13 number of extra gaps= 0 total=165 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bjkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bjkA expands to /projects/compbio/data/pdb/2bjk.pdb.gz 2bjkA:Skipped atom 202, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 204, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 206, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 208, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 341, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 343, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 858, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 860, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 862, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 864, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 2273, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 2275, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 2277, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 2279, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 2281, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 2283, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 2285, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 2303, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2305, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2307, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2309, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2311, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2313, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2315, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2317, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2319, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2321, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2323, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2325, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2327, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2329, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2331, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2560, because occupancy 0.300 <= existing 0.700 in 2bjkA Skipped atom 2956, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 3415, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 3417, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 3419, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 3421, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 3684, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 3686, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 3688, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 3690, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 3692, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 4000, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 4002, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 4004, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 4006, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 4008, because occupancy 0.500 <= existing 0.500 in 2bjkA Skipped atom 4010, because occupancy 0.500 <= existing 0.500 in 2bjkA # T0310 read from 2bjkA/merged-good-all-a2m # 2bjkA read from 2bjkA/merged-good-all-a2m # adding 2bjkA to template set # found chain 2bjkA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILL 2bjkA 76 :AEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEA T0310 50 :LEEAEGR 2bjkA 119 :TLVYEVG T0310 59 :APLLK 2bjkA 126 :KNWVE T0310 68 :STSKLNSLAIGLRQIAASSQDSVGRVLRRTR 2bjkA 131 :ASADVAEAIDFIEYYARAALRYRYPAVEVVP T0310 100 :AKNLELEQVTVPIGVLLVIFE 2bjkA 162 :YPGEDNESFYVPLGAGVVIAP T0310 121 :SRPDCL 2bjkA 184 :NFPVAI T0310 127 :PQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 2bjkA 191 :TGMIVGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEA T0310 167 :GV 2bjkA 227 :GF T0310 169 :KEAVQLVNTR 2bjkA 230 :PGVVNFLPGV T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKAA 2bjkA 245 :AYLVEHPRIRFINFTGSLEVGLKIYEAA T0310 207 :KGIPVMGHSEGICHMYVDSEASVDKVT 2bjkA 281 :WFKRAYVETGGKDAIIVDETADFDLAA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRT 2bjkA 309 :GVVVSAYGFQGQKCSAASRLILTQGAYEP T0310 264 :LFDQIIDMLRVEQVKIHA 2bjkA 338 :VLERVLKRAERLSVGPAE T0310 282 :GPKFASYLTFV 2bjkA 357 :NPDLGPVVSAE T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFS 2bjkA 412 :RIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGA T0310 360 :DGYRFGLGAEVGIS 2bjkA 481 :GVQPFGGFKLSGTN T0310 381 :GPVGLEGLLTT 2bjkA 495 :AKTGALDYLRL Number of specific fragments extracted= 17 number of extra gaps= 0 total=182 Number of alignments=10 # 2bjkA read from 2bjkA/merged-good-all-a2m # found chain 2bjkA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 2bjkA 76 :AEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKN T0310 65 :LSLSTSKLNSLAIGLRQIAASSQDSVGRVLRR 2bjkA 128 :WVEASADVAEAIDFIEYYARAALRYRYPAVEV T0310 98 :RIAKNLELEQVTVPIGVLLVIFESRPDCLPQVAAL 2bjkA 160 :VPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMI T0310 133 :AIASGNGLLLKGGKEAAHSNRILHLLTQEA 2bjkA 197 :PVAVGNTVIAKPAEDAVVVGAKVFEIFHEA T0310 167 :GV 2bjkA 227 :GF T0310 169 :KEAVQLVNT 2bjkA 230 :PGVVNFLPG T0310 178 :R 2bjkA 240 :G T0310 179 :EEVEL 2bjkA 242 :EVGAY T0310 184 :DKMIDLIIPRGSSQLVRDIQKAA 2bjkA 250 :HPRIRFINFTGSLEVGLKIYEAA T0310 207 :KGIPV 2bjkA 281 :WFKRA T0310 212 :MGHS 2bjkA 287 :VETG T0310 217 :GICHMYVDSEASVDKVT 2bjkA 291 :GKDAIIVDETADFDLAA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLR 2bjkA 309 :GVVVSAYGFQGQKCSAASRLILTQGAYE T0310 263 :PLFDQIIDMLRVEQVKIH 2bjkA 337 :PVLERVLKRAERLSVGPA T0310 281 :AGPKFASYLTF 2bjkA 356 :ENPDLGPVVSA T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWN 2bjkA 411 :ARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFN T0310 354 :ASTRFSDGYRFGLGAEVG 2bjkA 481 :GVQPFGGFKLSGTNAKTG T0310 372 :ISTSRIHARG 2bjkA 501 :DYLRLFLEMK Number of specific fragments extracted= 18 number of extra gaps= 0 total=200 Number of alignments=11 # 2bjkA read from 2bjkA/merged-good-all-a2m # found chain 2bjkA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDL 2bjkA 76 :AEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEV T0310 62 :LKRLSLSTSKLNSLAIGLRQIAASSQDSVGRVL 2bjkA 128 :WVEASADVAEAIDFIEYYARAALRYRYPAVEVV T0310 99 :IAKNLELEQVTVPIGVLLVIFESRPDCLPQV 2bjkA 161 :PYPGEDNESFYVPLGAGVVIAPWNFPVAIFT T0310 130 :AALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 2bjkA 194 :IVGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEA T0310 167 :GVKEAVQLVN 2bjkA 227 :GFPPGVVNFL T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQK 2bjkA 243 :VGAYLVEHPRIRFINFTGSLEVGLKIYE T0310 205 :AAKGIPVMGHSEGICHMYVDSEASVDKVT 2bjkA 279 :QTWFKRAYVETGGKDAIIVDETADFDLAA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQV 2bjkA 309 :GVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVG T0310 278 :KIHAGPKFASYLTFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFSDGYRFGLGAEVGISTSRIH 2bjkA 397 :YFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKT T0310 380 :RGPVGLEGLLTTKW 2bjkA 498 :GALDYLRLFLEMKA Number of specific fragments extracted= 10 number of extra gaps= 0 total=210 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zumA/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/T0310/1zumA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0310/1zumA/merged-good-all-a2m.gz for input Trying 1zumA/merged-good-all-a2m Error: Couldn't open file 1zumA/merged-good-all-a2m or 1zumA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1euhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1euhA expands to /projects/compbio/data/pdb/1euh.pdb.gz 1euhA:# T0310 read from 1euhA/merged-good-all-a2m # 1euhA read from 1euhA/merged-good-all-a2m # adding 1euhA to template set # found chain 1euhA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLE 1euhA 42 :VDYVYASAKKAQPAWRALSYIERAAYLHKVADILMRDKEKIGAILSKEVA T0310 57 :LAAPLLK 1euhA 93 :GYKSAVS T0310 71 :KLNSLAIGLRQIAASSQDSVGRVLRRTRIAK 1euhA 100 :EVVRTAEIINYAAEEGLRMEGEVLEGGSFEA T0310 102 :NLELEQVTVPIGVLLVIFE 1euhA 134 :KKIAVVRREPVGLVLAISP T0310 121 :SRPDCL 1euhA 154 :NYPVNL T0310 127 :PQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1euhA 161 :GSKIAPALIAGNVIAFKPPTQGSISGLLLAEAFAEA T0310 167 :GV 1euhA 197 :GL T0310 169 :KEAVQLVNTR 1euhA 200 :AGVFNTITGR T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKAAKGIPVMGHSEGICHMYVDSEASVDKVT 1euhA 215 :DYIVEHQAVNFINFTGSTGIGERIGKMAGMRPIMLELGGKDSAIVLEDADLELTA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRT 1euhA 271 :NIIAGAFGYSGQRCTAVKRVLVMESVADE T0310 264 :LFDQIIDMLRVEQVKIHAGPK 1euhA 300 :LVEKIREKVLALTIGNPEDDA T0310 285 :FASYLTFV 1euhA 322 :ITPLIDTK T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFS 1euhA 372 :RLAWEEPFGPVLPIIRVTSVEEAIEISNKSEYGLQASIFTNDFPRAFGIAEQLEVGTVHINNKTQRG T0310 360 :DGYRFGLGAEVGISTSR 1euhA 440 :DNFPFLGAKKSGAGIQG T0310 381 :GPVGLEGLLTTKWLLRGK 1euhA 457 :VKYSIEAMTTVKSVVFDI Number of specific fragments extracted= 15 number of extra gaps= 0 total=225 Number of alignments=13 # 1euhA read from 1euhA/merged-good-all-a2m # found chain 1euhA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1euhA 42 :VDYVYASAKKAQPAWRALSYIERAAYLHKVADILMRDKEKIGAILSKEVAKG T0310 65 :LSLSTSKLNSLAIGLRQIAASSQDSVGRVLRRTR 1euhA 94 :YKSAVSEVVRTAEIINYAAEEGLRMEGEVLEGGS T0310 99 :IAKNLELEQVTVPIGVLLVIFESRPDCLPQVAAL 1euhA 131 :ASKKKIAVVRREPVGLVLAISPFNYPVNLAGSKI T0310 133 :AIASGNGLLLKGGKEAAHSNRILHLLTQEA 1euhA 167 :ALIAGNVIAFKPPTQGSISGLLLAEAFAEA T0310 167 :GV 1euhA 197 :GL T0310 169 :KEAVQLVNT 1euhA 200 :AGVFNTITG T0310 179 :EEVEL 1euhA 212 :EIGDY T0310 184 :DKMIDLIIPRGSSQLVRDIQKAAKGIPV 1euhA 220 :HQAVNFINFTGSTGIGERIGKMAGMRPI T0310 212 :MGHS 1euhA 249 :LELG T0310 217 :GICHMYVDSEASVDKVT 1euhA 253 :GKDSAIVLEDADLELTA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLR 1euhA 271 :NIIAGAFGYSGQRCTAVKRVLVMESVAD T0310 263 :PLFDQIIDMLRVEQVKIHAGPK 1euhA 299 :ELVEKIREKVLALTIGNPEDDA T0310 285 :FASYLTF 1euhA 322 :ITPLIDT T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWN 1euhA 371 :MRLAWEEPFGPVLPIIRVTSVEEAIEISNKSEYGLQASIFTNDFPRAFGIAEQLEVGTVHIN T0310 354 :ASTRFSDGYRFGLGAEVG 1euhA 440 :DNFPFLGAKKSGAGIQGV T0310 372 :ISTSRIHARGPVGLEG 1euhA 459 :YSIEAMTTVKSVVFDI Number of specific fragments extracted= 16 number of extra gaps= 0 total=241 Number of alignments=14 # 1euhA read from 1euhA/merged-good-all-a2m # found chain 1euhA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEAEGRL 1euhA 42 :VDYVYASAKKAQPAWRALSYIERAAYLHKVADILMRDKEKIGAILSKEVAKGYKSA T0310 59 :APLL 1euhA 98 :VSEV T0310 70 :SKLNSLAIGLRQIAASSQ 1euhA 102 :VRTAEIINYAAEEGLRME T0310 91 :GRVLRRTRI 1euhA 120 :GEVLEGGSF T0310 100 :AKNLELEQVTVPIGVLLVIFESRPDCLPQV 1euhA 132 :SKKKIAVVRREPVGLVLAISPFNYPVNLAG T0310 130 :AALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1euhA 164 :IAPALIAGNVIAFKPPTQGSISGLLLAEAFAEA T0310 167 :GVKEAVQLVN 1euhA 197 :GLPAGVFNTI T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQKAAKGIPVMGHSEGICHMYVDSEASVDKVT 1euhA 213 :IGDYIVEHQAVNFINFTGSTGIGERIGKMAGMRPIMLELGGKDSAIVLEDADLELTA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQV 1euhA 271 :NIIAGAFGYSGQRCTAVKRVLVMESVADELVEKIREKVLALTIG T0310 278 :KIHAGPKFASYLTFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTR 1euhA 357 :NLICPILFDKVTTDMRLAWEEPFGPVLPIIRVTSVEEAIEISNKSEYGLQASIFTNDFPRAFGIAEQLEVGTVHINNKTQ T0310 359 :SDGYRFGLGAEVGISTSRIH 1euhA 437 :RGTDNFPFLGAKKSGAGIQG T0310 381 :GPVGLEGLLTTKWLLR 1euhA 457 :VKYSIEAMTTVKSVVF Number of specific fragments extracted= 12 number of extra gaps= 0 total=253 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ky8A/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/T0310/1ky8A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0310/1ky8A/merged-good-all-a2m.gz for input Trying 1ky8A/merged-good-all-a2m Error: Couldn't open file 1ky8A/merged-good-all-a2m or 1ky8A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ez0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ez0A expands to /projects/compbio/data/pdb/1ez0.pdb.gz 1ez0A:# T0310 read from 1ez0A/merged-good-all-a2m # 1ez0A read from 1ez0A/merged-good-all-a2m # adding 1ez0A to template set # found chain 1ez0A in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILL 1ez0A 32 :VNQAATAAAKVARDFRRLNNSKRASLLRTIASELEARSDDIIA T0310 50 :LEEAEGRLAAPLLK 1ez0A 75 :RAHLETALPEVRLT T0310 70 :SKLNSLAIGLRQIAASSQ 1ez0A 89 :GEIARTANQLRLFADVVN T0310 88 :DSVGRVLRRT 1ez0A 109 :SYHQAILDTP T0310 100 :AKNL 1ez0A 119 :NPTR T0310 104 :ELEQVTVPIGVLLVIFE 1ez0A 129 :DIRRQQIALGPVAVFGA T0310 121 :SRP 1ez0A 147 :NFP T0310 124 :DCL 1ez0A 151 :AFS T0310 127 :PQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGV 1ez0A 156 :GGDTASALAAGCPVIVKGHTAHPGTSQIVAECIEQALKQEQL T0310 169 :KEAVQLVNTR 1ez0A 199 :QAIFTLLQGN T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKAA 1ez0A 214 :QALVSHPEIKAVGFTGSVGGGRALFNLA T0310 207 :KGIPVMGHSEGICHMYVDSEA 1ez0A 246 :EPIPFYGELGAINPTFIFPSA T0310 230 :DKVTRLVRDSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQ 1ez0A 272 :DLADQFVASMTMGCGQFCTKPGVVFALNTPETQAFIETAQSLIRQQS T0310 286 :AS 1ez0A 320 :ST T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTE 1ez0A 372 :PAWEEEIFGPQSLIVVCENVADMLSLSEMLAGSLTATIHAT T0310 334 :DENTAEFFLQHVD 1ez0A 415 :DYPQVSQLIPRLE T0310 347 :SACVFWNASTRFS 1ez0A 430 :AGRLVFNGWPTGV T0310 360 :DGYRFGLGAEVGISTS 1ez0A 446 :YAMVHGGPYPASTHSA T0310 377 :IHARGPVGLEGLLTTKWLLRGKDHVVSDFSEHGS 1ez0A 462 :STSVGAEAIHRWLRPVAYQALPESLLPDSLKAEN Number of specific fragments extracted= 19 number of extra gaps= 0 total=272 Number of alignments=16 # 1ez0A read from 1ez0A/merged-good-all-a2m # found chain 1ez0A in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1ez0A 32 :VNQAATAAAKVARDFRRLNNSKRASLLRTIASELEARSDDIIARAHLETALP T0310 65 :LSLSTSKLNSLAIGLRQIAASSQD 1ez0A 84 :EVRLTGEIARTANQLRLFADVVNS T0310 89 :SVGRVLRR 1ez0A 110 :YHQAILDT T0310 99 :IAKNL 1ez0A 118 :PNPTR T0310 104 :ELEQVTVPIGVLLVIFESRPDCLP 1ez0A 129 :DIRRQQIALGPVAVFGASNFPLAF T0310 128 :QVAAL 1ez0A 156 :GGDTA T0310 133 :AIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGV 1ez0A 162 :ALAAGCPVIVKGHTAHPGTSQIVAECIEQALKQEQL T0310 169 :KEAVQLVNT 1ez0A 199 :QAIFTLLQG T0310 178 :R 1ez0A 209 :Q T0310 179 :EEVEL 1ez0A 211 :ALGQA T0310 184 :DKMIDLIIPRGSSQLVRDIQKAA 1ez0A 219 :HPEIKAVGFTGSVGGGRALFNLA T0310 207 :KGIPV 1ez0A 246 :EPIPF T0310 212 :MGHS 1ez0A 252 :GELG T0310 217 :GICHMYVDSEA 1ez0A 256 :AINPTFIFPSA T0310 232 :VT 1ez0A 273 :LA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQ 1ez0A 276 :QFVASMTMGCGQFCTKPGVVFALNTPETQAFIETAQSLIRQQS T0310 285 :FASYLTF 1ez0A 319 :PSTLLTP T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTE 1ez0A 371 :HPAWEEEIFGPQSLIVVCENVADMLSLSEMLAGSLTATIHAT T0310 334 :DENTAEFFLQHVD 1ez0A 415 :DYPQVSQLIPRLE T0310 347 :SACVFWN 1ez0A 430 :AGRLVFN T0310 354 :ASTRFSDGYRFGLGAEVG 1ez0A 446 :YAMVHGGPYPASTHSAST T0310 372 :ISTSRIHA 1ez0A 465 :VGAEAIHR T0310 387 :GLLTTKWLLRGKDHVVSDFSEH 1ez0A 473 :WLRPVAYQALPESLLPDSLKAE T0310 409 :GSLKYLHENLP 1ez0A 497 :LEIARAVDGKA Number of specific fragments extracted= 24 number of extra gaps= 0 total=296 Number of alignments=17 # 1ez0A read from 1ez0A/merged-good-all-a2m # found chain 1ez0A in template set T0310 1 :TVEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDL 1ez0A 31 :EVNQAATAAAKVARDFRRLNNSKRASLLRTIASELEARSDDIIARAHLET T0310 57 :LAAPLLKRLS 1ez0A 82 :LPEVRLTGEI T0310 70 :SKLNSLAIGLRQIAASSQD 1ez0A 92 :ARTANQLRLFADVVNSGSY T0310 91 :GRVLRRTRIAKNL 1ez0A 111 :HQAILDTPNPTRA T0310 104 :ELEQVTVPIGVLLVIFESRPDCLPQV 1ez0A 129 :DIRRQQIALGPVAVFGASNFPLAFSA T0310 130 :AALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGVKEAVQLVN 1ez0A 159 :TASALAAGCPVIVKGHTAHPGTSQIVAECIEQALKQEQLPQAIFTLL T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQK 1ez0A 212 :LGQALVSHPEIKAVGFTGSVGGGRALFN T0310 205 :AAKGIPVMGHSEGICHMYVDSEA 1ez0A 244 :RPEPIPFYGELGAINPTFIFPSA T0310 230 :DKVTRLVRDSKCEYPAACNALETLLIHR 1ez0A 272 :DLADQFVASMTMGCGQFCTKPGVVFALN T0310 261 :RTPLFDQIIDMLRVEQV 1ez0A 300 :TPETQAFIETAQSLIRQ T0310 278 :KIHAGPKFASYL 1ez0A 347 :TFSQAESPCVAS T0310 290 :TFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTE 1ez0A 369 :RKHPAWEEEIFGPQSLIVVCENVADMLSLSEMLAGSLTATIHAT T0310 334 :DENTAEFFLQHVD 1ez0A 415 :DYPQVSQLIPRLE T0310 347 :SACVFWNASTRFSD 1ez0A 430 :AGRLVFNGWPTGVE T0310 361 :GYRFGLGAEVGIST 1ez0A 445 :GYAMVHGGPYPAST T0310 375 :SRIHARGPVGLEGLLTTKWL 1ez0A 460 :SASTSVGAEAIHRWLRPVAY T0310 403 :SDFSEHGSLKYLHENLPIPQ 1ez0A 480 :QALPESLLPDSLKAENPLEI Number of specific fragments extracted= 17 number of extra gaps= 0 total=313 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uzbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0310 read from 1uzbA/merged-good-all-a2m # 1uzbA read from 1uzbA/merged-good-all-a2m # found chain 1uzbA in training set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILL 1uzbA 76 :AEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEA T0310 50 :LEEAEGR 1uzbA 119 :TLVYEVG T0310 59 :APLLK 1uzbA 126 :KNWVE T0310 68 :STSKLNSLAIGLRQIAASSQDSVGRVLRRTR 1uzbA 131 :ASADVAEAIDFIEYYARAALRYRYPAVEVVP T0310 100 :AKNLELEQVTVPIGVLLVIFE 1uzbA 162 :YPGEDNESFYVPLGAGVVIAP T0310 121 :SRPDCL 1uzbA 184 :NFPVAI T0310 127 :PQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1uzbA 191 :TGMIVGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEA T0310 167 :GV 1uzbA 227 :GF T0310 169 :KEAVQLVNTR 1uzbA 230 :PGVVNFLPGV T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKAA 1uzbA 245 :AYLVEHPRIRFINFTGSLEVGLKIYEAA T0310 207 :KGIPVMGHSEGICHMYVDSEASVDKVT 1uzbA 281 :WFKRAYVETGGKNAIIVDETADFDLAA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRT 1uzbA 309 :GVVVSAYGFQGQKCSAASRLILTQGAYEP T0310 264 :LFDQIIDMLRVEQVKIHA 1uzbA 338 :VLERVLKRAERLSVGPAE T0310 282 :GPKFASYLTFV 1uzbA 357 :NPDLGPVVSAE T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFS 1uzbA 412 :RIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGA T0310 360 :DGYRFGLGAEVGIS 1uzbA 481 :GVQPFGGFKLSGTN T0310 381 :GPVGLEGLLTT 1uzbA 495 :AKTGALDYLRL Number of specific fragments extracted= 17 number of extra gaps= 0 total=330 Number of alignments=19 # 1uzbA read from 1uzbA/merged-good-all-a2m # found chain 1uzbA in training set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1uzbA 76 :AEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKN T0310 65 :LSLSTSKLNSLAIGLRQIAASSQDSVGRVLRRT 1uzbA 128 :WVEASADVAEAIDFIEYYARAALRYRYPAVEVV T0310 99 :IAKNLELEQVTVPIGVLLVIFESRPDCLPQVAAL 1uzbA 161 :PYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMI T0310 133 :AIASGNGLLLKGGKEAAHSNRILHLLTQEA 1uzbA 197 :PVAVGNTVIAKPAEDAVVVGAKVFEIFHEA T0310 167 :GV 1uzbA 227 :GF T0310 169 :KEAVQLVNT 1uzbA 230 :PGVVNFLPG T0310 178 :R 1uzbA 240 :G T0310 179 :EEVEL 1uzbA 242 :EVGAY T0310 184 :DKMIDLIIPRGSSQLVRDIQKAA 1uzbA 250 :HPRIRFINFTGSLEVGLKIYEAA T0310 207 :KGIPV 1uzbA 281 :WFKRA T0310 212 :MGHS 1uzbA 287 :VETG T0310 217 :GICHMYVDSEASVDKVT 1uzbA 291 :GKNAIIVDETADFDLAA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLR 1uzbA 309 :GVVVSAYGFQGQKCSAASRLILTQGAYE T0310 263 :PLFDQIIDMLRVEQVKIH 1uzbA 337 :PVLERVLKRAERLSVGPA T0310 281 :AGPKFASYLTF 1uzbA 356 :ENPDLGPVVSA T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWN 1uzbA 411 :ARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFN T0310 354 :ASTRFSDGYRFGLGAEVG 1uzbA 481 :GVQPFGGFKLSGTNAKTG T0310 372 :ISTSRIHARG 1uzbA 501 :DYLRLFLEMK Number of specific fragments extracted= 18 number of extra gaps= 0 total=348 Number of alignments=20 # 1uzbA read from 1uzbA/merged-good-all-a2m # found chain 1uzbA in training set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDL 1uzbA 76 :AEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEV T0310 62 :LKRLSLSTSKLNSLAIGLRQIAASSQDSVGRVL 1uzbA 128 :WVEASADVAEAIDFIEYYARAALRYRYPAVEVV T0310 99 :IAKNLELEQVTVPIGVLLVIFESRPDCLPQV 1uzbA 161 :PYPGEDNESFYVPLGAGVVIAPWNFPVAIFT T0310 130 :AALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1uzbA 194 :IVGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEA T0310 167 :GVKEAVQLVN 1uzbA 227 :GFPPGVVNFL T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQK 1uzbA 243 :VGAYLVEHPRIRFINFTGSLEVGLKIYE T0310 205 :AAKGIPVMGHSEGICHMYVDSEASVDKVT 1uzbA 279 :QTWFKRAYVETGGKNAIIVDETADFDLAA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQV 1uzbA 309 :GVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVG T0310 278 :KIHAGPKFASYLTFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFSDGYRFGLGAEVGISTSRIH 1uzbA 397 :YFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKT T0310 380 :RGPVGLEGLLTTKWL 1uzbA 498 :GALDYLRLFLEMKAV Number of specific fragments extracted= 10 number of extra gaps= 0 total=358 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qi6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qi6A expands to /projects/compbio/data/pdb/1qi6.pdb.gz 1qi6A:# T0310 read from 1qi6A/merged-good-all-a2m # 1qi6A read from 1qi6A/merged-good-all-a2m # adding 1qi6A to template set # found chain 1qi6A in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILL 1qi6A 42 :VDYVYASAKKAQPAWRALSYIERAAYLHKVADILMRDKEKIGA T0310 50 :LEEAEGR 1qi6A 85 :ILSKEVA T0310 57 :LAAPLLK 1qi6A 93 :GYKSAVS T0310 71 :KLNSLAIGLRQIAASSQDSVGRVLRRTRIAK 1qi6A 100 :EVVRTAEIINYAAEEGLRMEGEVLEGGSFEA T0310 102 :NLELEQVTVPIGVLLVIFE 1qi6A 134 :KKIAVVRREPVGLVLAISP T0310 121 :SRPDCL 1qi6A 154 :NYPVNL T0310 127 :PQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1qi6A 161 :GSKIAPALIAGNVIAFKPPTQGSISGLLLAEAFAEA T0310 167 :GV 1qi6A 197 :GL T0310 169 :KEAVQLVNTR 1qi6A 200 :AGVFNTITGR T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKAAKGIPVMGHSEGICHMYVDSEASVDKVT 1qi6A 215 :DYIVEHQAVNFINFTGSTGIGERIGKMAGMRPIMLELGGKDSAIVLEDADLELTA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRT 1qi6A 271 :NIIAGAFGYSGQRCTAVKRVLVMESVADE T0310 264 :LFDQIIDMLRVEQVKIHAGPK 1qi6A 300 :LVEKIREKVLALTIGNPEDDA T0310 285 :FASYLTFV 1qi6A 322 :ITPLIDTK T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFS 1qi6A 372 :RLAWEEPFGPVLPIIRVTSVEEAIEISNKSEYGLQASIFTNDFPRAFGIAEQLEVGTVHINNKTQRG T0310 360 :DGYRFGLGAEVGISTSR 1qi6A 440 :DNFPFLGAKKSGAGIQG T0310 381 :GPVGLEGLLTTKWLLRGK 1qi6A 457 :VKYSIEAMTTVKSVVFDI Number of specific fragments extracted= 16 number of extra gaps= 0 total=374 Number of alignments=22 # 1qi6A read from 1qi6A/merged-good-all-a2m # found chain 1qi6A in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1qi6A 42 :VDYVYASAKKAQPAWRALSYIERAAYLHKVADILMRDKEKIGAILSKEVAKG T0310 65 :LSLSTSKLNSLAIGLRQIAASSQDSVGRVLRRTR 1qi6A 94 :YKSAVSEVVRTAEIINYAAEEGLRMEGEVLEGGS T0310 99 :IAKNLELEQVTVPIGVLLVIFESRPDCLPQVAAL 1qi6A 131 :ASKKKIAVVRREPVGLVLAISPFNYPVNLAGSKI T0310 133 :AIASGNGLLLKGGKEAAHSNRILHLLTQEA 1qi6A 167 :ALIAGNVIAFKPPTQGSISGLLLAEAFAEA T0310 167 :GV 1qi6A 197 :GL T0310 169 :KEAVQLVNT 1qi6A 200 :AGVFNTITG T0310 178 :R 1qi6A 210 :G T0310 179 :EEVEL 1qi6A 212 :EIGDY T0310 184 :DKMIDLIIPRGSSQLVRDIQKAAKGIPV 1qi6A 220 :HQAVNFINFTGSTGIGERIGKMAGMRPI T0310 212 :MGHS 1qi6A 249 :LELG T0310 217 :GICHMYVDSEASVDKVT 1qi6A 253 :GKDSAIVLEDADLELTA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLR 1qi6A 271 :NIIAGAFGYSGQRCTAVKRVLVMESVAD T0310 263 :PLFDQIIDMLRVEQVKIHAGPK 1qi6A 299 :ELVEKIREKVLALTIGNPEDDA T0310 285 :FASYLTF 1qi6A 322 :ITPLIDT T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWN 1qi6A 371 :MRLAWEEPFGPVLPIIRVTSVEEAIEISNKSEYGLQASIFTNDFPRAFGIAEQLEVGTVHIN T0310 354 :ASTRFSDGYRFGLGAEVG 1qi6A 440 :DNFPFLGAKKSGAGIQGV T0310 372 :ISTSRIHARGPVGLEG 1qi6A 459 :YSIEAMTTVKSVVFDI Number of specific fragments extracted= 17 number of extra gaps= 0 total=391 Number of alignments=23 # 1qi6A read from 1qi6A/merged-good-all-a2m # found chain 1qi6A in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEAEG 1qi6A 42 :VDYVYASAKKAQPAWRALSYIERAAYLHKVADILMRDKEKIGAILSKEVAKGYK T0310 61 :LLK 1qi6A 96 :SAV T0310 67 :LSTSKLNSLAIGLRQIAASSQ 1qi6A 99 :SEVVRTAEIINYAAEEGLRME T0310 91 :GRVLRRTRI 1qi6A 120 :GEVLEGGSF T0310 100 :AKNLELEQVTVPIGVLLVIFESRPDCLPQV 1qi6A 132 :SKKKIAVVRREPVGLVLAISPFNYPVNLAG T0310 130 :AALAIASGNGLLLKGGKEAAHSNRILHLLTQ 1qi6A 164 :IAPALIAGNVIAFKPPTQGSISGLLLAEAFA T0310 165 :IHGVKEAVQLVN 1qi6A 195 :EAGLPAGVFNTI T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQKAAKGIPVMGHSEGICHMYVDSEASVDKVT 1qi6A 213 :IGDYIVEHQAVNFINFTGSTGIGERIGKMAGMRPIMLELGGKDSAIVLEDADLELTA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQV 1qi6A 271 :NIIAGAFGYSGQRCTAVKRVLVMESVADELVEKIREKVLALTIG T0310 278 :KIHAGPKFASYLTFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTR 1qi6A 357 :NLICPILFDKVTTDMRLAWEEPFGPVLPIIRVTSVEEAIEISNKSEYGLQASIFTNDFPRAFGIAEQLEVGTVHINNKTQ T0310 359 :SDGYRFGLGAEVGISTSRIH 1qi6A 437 :RGTDNFPFLGAKKSGAGIQG T0310 381 :GPVGLEGLLTTKWLLR 1qi6A 457 :VKYSIEAMTTVKSVVF Number of specific fragments extracted= 12 number of extra gaps= 0 total=403 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t90A/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/T0310/1t90A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0310/1t90A/merged-good-all-a2m.gz for input Trying 1t90A/merged-good-all-a2m Error: Couldn't open file 1t90A/merged-good-all-a2m or 1t90A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bi9A/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/T0310/1bi9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0310/1bi9A/merged-good-all-a2m.gz for input Trying 1bi9A/merged-good-all-a2m Error: Couldn't open file 1bi9A/merged-good-all-a2m or 1bi9A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o9jA/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/T0310/1o9jA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0310/1o9jA/merged-good-all-a2m.gz for input Trying 1o9jA/merged-good-all-a2m Error: Couldn't open file 1o9jA/merged-good-all-a2m or 1o9jA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o20A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o20A expands to /projects/compbio/data/pdb/1o20.pdb.gz 1o20A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 979, because occupancy 0.350 <= existing 0.650 in 1o20A Skipped atom 981, because occupancy 0.350 <= existing 0.650 in 1o20A Skipped atom 983, because occupancy 0.350 <= existing 0.650 in 1o20A Skipped atom 985, because occupancy 0.350 <= existing 0.650 in 1o20A Skipped atom 987, because occupancy 0.350 <= existing 0.650 in 1o20A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2477, because occupancy 0.350 <= existing 0.650 in 1o20A Skipped atom 2479, because occupancy 0.350 <= existing 0.650 in 1o20A Skipped atom 2553, because occupancy 0.350 <= existing 0.650 in 1o20A Skipped atom 2555, because occupancy 0.350 <= existing 0.650 in 1o20A Skipped atom 2557, because occupancy 0.350 <= existing 0.650 in 1o20A Skipped atom 2559, because occupancy 0.350 <= existing 0.650 in 1o20A Skipped atom 2561, because occupancy 0.350 <= existing 0.650 in 1o20A # T0310 read from 1o20A/merged-good-all-a2m # 1o20A read from 1o20A/merged-good-all-a2m # adding 1o20A to template set # found chain 1o20A in template set Warning: unaligning (T0310)E120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o20A)S123 Warning: unaligning (T0310)S121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o20A)S123 Warning: unaligning (T0310)A206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o20A)T216 Warning: unaligning (T0310)K207 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o20A)T216 Warning: unaligning (T0310)A246 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o20A)C255 Warning: unaligning (T0310)C247 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o20A)C255 T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLE 1o20A 4 :LLEKAKKVREAWDVLRNATTREKNKAIKKIAEKLDERRKEILEANRIDVE T0310 52 :EAEGRLAAPLLKRLSLSTSKLNSLAIGLRQIAA 1o20A 55 :ARERGVKESLVDRLALNDKRIDEMIKACETVIG T0310 86 :SQDSVGRVLRRTRIAKNLELEQVTVPIGVLLVIF 1o20A 88 :LKDPVGEVIDSWVREDGLRIARVRVPIGPIGIIY T0310 122 :RPDCLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGV 1o20A 124 :RPNVTVETTILALKSGNTILLRGGSDALNSNKAIVSAIREALKETEI T0310 169 :KEAVQLVNTR 1o20A 172 :ESSVEFIENT T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKA 1o20A 188 :EMIRLREYLSLVIPRGGYGLISFVRDN T0310 209 :IPVMGHSEGICHMYVDSEASVDKVTRLVRDSKCEYPA 1o20A 217 :VPVLETGVGNCHIFVDESADLKKAVPVIINAKTQRPG T0310 248 :NALETLLIHRDLLRT 1o20A 256 :NAAEKLLVHEKIAKE T0310 264 :LFDQIIDMLRVEQVKIHAG 1o20A 271 :FLPVIVEELRKHGVEVRGC T0310 283 :PKFASY 1o20A 297 :PDVVPA T0310 291 :FVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFSDGYRFGLGAEVGISTSRIHARGPVGLEGLLTTKWLLRGKDHVV 1o20A 303 :TEDDWPTEYLDLIIAIKVVKNVDEAIEHIKKYSTGHSESILTENYSNAKKFVSEIDAAAVYVNASTRFTDGGQFGFGAEIGISTQRFHARGPVGLRELTTYKFVVLGEYHVR Number of specific fragments extracted= 11 number of extra gaps= 3 total=414 Number of alignments=25 # 1o20A read from 1o20A/merged-good-all-a2m # found chain 1o20A in template set Warning: unaligning (T0310)E120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o20A)S123 Warning: unaligning (T0310)S121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o20A)S123 Warning: unaligning (T0310)A206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o20A)T216 Warning: unaligning (T0310)K207 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o20A)T216 Warning: unaligning (T0310)A246 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o20A)C255 Warning: unaligning (T0310)C247 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o20A)C255 T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEAE 1o20A 4 :LLEKAKKVREAWDVLRNATTREKNKAIKKIAEKLDERRKEILEANRIDVEKAR T0310 55 :GRLAAPLLKRLSLSTSKLNSLAIGLRQIAAS 1o20A 58 :RGVKESLVDRLALNDKRIDEMIKACETVIGL T0310 87 :QDSVGRVLRRTRIAKNLELEQVTVPIGVLLVIF 1o20A 89 :KDPVGEVIDSWVREDGLRIARVRVPIGPIGIIY T0310 122 :RPDCLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGV 1o20A 124 :RPNVTVETTILALKSGNTILLRGGSDALNSNKAIVSAIREALKETEI T0310 169 :KEAVQLVNT 1o20A 172 :ESSVEFIEN T0310 178 :R 1o20A 182 :D T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKA 1o20A 188 :EMIRLREYLSLVIPRGGYGLISFVRDN T0310 209 :IPVMGHSEGICHMYVDSEASVDKVTRLVRDSKCEYPA 1o20A 217 :VPVLETGVGNCHIFVDESADLKKAVPVIINAKTQRPG T0310 248 :NALETLLIHRDLLR 1o20A 256 :NAAEKLLVHEKIAK T0310 263 :PLFDQIIDMLRVEQVKIHAGPKFASYLTF 1o20A 270 :EFLPVIVEELRKHGVEVRGCEKTREIVPD T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFSDGYRFGLGAEVGISTSRIHARGPVGLEGLLTTKWLLRGKDHVV 1o20A 304 :EDDWPTEYLDLIIAIKVVKNVDEAIEHIKKYSTGHSESILTENYSNAKKFVSEIDAAAVYVNASTRFTDGGQFGFGAEIGISTQRFHARGPVGLRELTTYKFVVLGEYHVR Number of specific fragments extracted= 11 number of extra gaps= 3 total=425 Number of alignments=26 # 1o20A read from 1o20A/merged-good-all-a2m # found chain 1o20A in template set Warning: unaligning (T0310)E120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o20A)S123 Warning: unaligning (T0310)S121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o20A)S123 Warning: unaligning (T0310)K207 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o20A)T216 Warning: unaligning (T0310)G208 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o20A)T216 Warning: unaligning (T0310)A246 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o20A)C255 Warning: unaligning (T0310)C247 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o20A)C255 T0310 1 :TVEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEAEGRLAAPLLKRLSLSTSKLNSLAIGLRQIAASSQDSVGRVLRRTRIAKNLELEQVTVPIGVLLVIF 1o20A 3 :ELLEKAKKVREAWDVLRNATTREKNKAIKKIAEKLDERRKEILEANRIDVEKARERGVKESLVDRLALNDKRIDEMIKACETVIGLKDPVGEVIDSWVREDGLRIARVRVPIGPIGIIY T0310 122 :RPDCLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGVKEAVQLVN 1o20A 124 :RPNVTVETTILALKSGNTILLRGGSDALNSNKAIVSAIREALKETEIPESSVEFI T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQK 1o20A 186 :VLEMIRLREYLSLVIPRGGYGLISFVRD T0310 206 :A 1o20A 214 :N T0310 209 :IPVMGHSEGICHMYVDSEASVDKVTRLVRDSKCEYPA 1o20A 217 :VPVLETGVGNCHIFVDESADLKKAVPVIINAKTQRPG T0310 248 :NALETLLIHRDLLRTPLFDQIIDMLRVEQV 1o20A 256 :NAAEKLLVHEKIAKEFLPVIVEELRKHGVE T0310 286 :ASYLTFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFSDGYRFGLGAEVGISTSRIHARGPVGLEGLLTTKWLLRGKDH 1o20A 298 :DVVPATEDDWPTEYLDLIIAIKVVKNVDEAIEHIKKYSTGHSESILTENYSNAKKFVSEIDAAAVYVNASTRFTDGGQFGFGAEIGISTQRFHARGPVGLRELTTYKFVVLGEYH Number of specific fragments extracted= 7 number of extra gaps= 3 total=432 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o02A/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/T0310/1o02A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0310/1o02A/merged-good-all-a2m.gz for input Trying 1o02A/merged-good-all-a2m Error: Couldn't open file 1o02A/merged-good-all-a2m or 1o02A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ad3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ad3A expands to /projects/compbio/data/pdb/1ad3.pdb.gz 1ad3A:# T0310 read from 1ad3A/merged-good-all-a2m # 1ad3A read from 1ad3A/merged-good-all-a2m # adding 1ad3A to template set # found chain 1ad3A in template set Warning: unaligning (T0310)K412 because last residue in template chain is (1ad3A)A447 T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDL 1ad3A 3 :ISDTVKRAREAFNSGKTRSLQFRIQQLEALQRMINENLKSISGALASDL T0310 56 :RLAAPLLK 1ad3A 52 :GKNEWTSY T0310 69 :TSKLNSLAIGLRQIAASSQDSVG 1ad3A 60 :YEEVAHVLEELDTTIKELPDWAE T0310 92 :RVLRRTRIAKNLELEQVTVPIGVLLVIFE 1ad3A 84 :EPVAKTRQTQQDDLYIHSEPLGVVLVIGA T0310 121 :SRPDCL 1ad3A 114 :NYPFNL T0310 127 :PQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1ad3A 121 :IQPMVGAVAAGNAVILKPSEVSGHMADLLATLIPQY T0310 168 :V 1ad3A 157 :M T0310 169 :KEAVQLVNTR 1ad3A 159 :QNLYLVVKGG T0310 179 :EEVELD 1ad3A 173 :TELLKE T0310 186 :MIDLIIPRGSSQLVRDIQKAA 1ad3A 179 :RFDHIMYTGSTAVGKIVMAAA T0310 207 :KGIPVMGHSEGICHMYVDSEASVDKVT 1ad3A 202 :HLTPVTLELGGKSPCYVDKDCDLDVAC T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRT 1ad3A 230 :RIAWGKFMNSGQTCVAPDYILCDPSIQNQ T0310 264 :LFDQIIDMLRVEQVKIHA 1ad3A 259 :IVEKLKKSLKDFYGEDAK T0310 282 :GPKFASYLTFV 1ad3A 278 :SRDYGRIINDR T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFS 1ad3A 328 :PVMQEEIFGPVMPIVCVRSLEEAIQFINQREKPLALYVFSNNEKVIKKMIAETSSGGVTANDVIVHI T0310 360 :DGYRFGLGAEVGISTSR 1ad3A 397 :PTLPFGGVGNSGMGAYH T0310 381 :GPVGLEGLLTTKWLLRGKDHVVS 1ad3A 414 :GKKSFETFSHRRSCLVKSLLNEE T0310 404 :DFSEHGSL 1ad3A 439 :KARYPPSP Number of specific fragments extracted= 18 number of extra gaps= 0 total=450 Number of alignments=28 # 1ad3A read from 1ad3A/merged-good-all-a2m # found chain 1ad3A in template set T0310 1 :TVEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1ad3A 2 :SISDTVKRAREAFNSGKTRSLQFRIQQLEALQRMINENLKSISGALASDLGKN T0310 65 :LSLSTSK 1ad3A 55 :EWTSYYE T0310 72 :LNSLAIGLRQIAASSQDSVGRVLRRTR 1ad3A 63 :VAHVLEELDTTIKELPDWAEDEPVAKT T0310 99 :IAKNLELEQVTVPIGVLLVIFESRPDCLPQVAAL 1ad3A 91 :QTQQDDLYIHSEPLGVVLVIGAWNYPFNLTIQPM T0310 133 :AIASGNGLLLKGGKEAAHSNRILHLLTQEA 1ad3A 127 :AVAAGNAVILKPSEVSGHMADLLATLIPQY T0310 168 :V 1ad3A 157 :M T0310 169 :KEAVQLVNTR 1ad3A 159 :QNLYLVVKGG T0310 179 :EEVEL 1ad3A 171 :ETTEL T0310 184 :DKMIDLIIPRGSSQLVRDIQKAA 1ad3A 177 :KERFDHIMYTGSTAVGKIVMAAA T0310 207 :KGIPV 1ad3A 202 :HLTPV T0310 212 :MGHS 1ad3A 208 :LELG T0310 217 :GICHMYVDSEASVDKVT 1ad3A 212 :GKSPCYVDKDCDLDVAC T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLR 1ad3A 230 :RIAWGKFMNSGQTCVAPDYILCDPSIQN T0310 263 :PLFDQIIDMLRVEQVKIH 1ad3A 258 :QIVEKLKKSLKDFYGEDA T0310 281 :AGPKFASYLTF 1ad3A 277 :QSRDYGRIIND T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWN 1ad3A 327 :SPVMQEEIFGPVMPIVCVRSLEEAIQFINQREKPLALYVFSNNEKVIKKMIAETSSGGVTAN T0310 354 :ASTRFSDGYRFGLGAEVG 1ad3A 397 :PTLPFGGVGNSGMGAYHG T0310 372 :ISTSRIHARGPVGLEGLLTTK 1ad3A 416 :KSFETFSHRRSCLVKSLLNEE T0310 403 :SDFSEHGSL 1ad3A 437 :AHKARYPPS Number of specific fragments extracted= 19 number of extra gaps= 0 total=469 Number of alignments=29 # 1ad3A read from 1ad3A/merged-good-all-a2m # found chain 1ad3A in template set Warning: unaligning (T0310)Q422 because last residue in template chain is (1ad3A)A447 T0310 1 :TVEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEAEGRLAAPLLKRLSLSTSKLNSLAIGLRQ 1ad3A 2 :SISDTVKRAREAFNSGKTRSLQFRIQQLEALQRMINENLKSISGALASDLGKNEWTSYYEEVAHVLEELDTTIKELPDWAE T0310 91 :GRVLRRTRIAKNLELEQVTVPIGVLLVIFESRPDCLPQV 1ad3A 83 :DEPVAKTRQTQQDDLYIHSEPLGVVLVIGAWNYPFNLTI T0310 130 :AALAIASGNGLLLKGGKEAAHSNRILHLLTQEAL 1ad3A 124 :MVGAVAAGNAVILKPSEVSGHMADLLATLIPQYM T0310 165 :IHGVKEAVQLVN 1ad3A 158 :DQNLYLVVKGGV T0310 177 :TREE 1ad3A 172 :TTEL T0310 183 :LDKMIDLIIPRGSSQLVRDIQK 1ad3A 176 :LKERFDHIMYTGSTAVGKIVMA T0310 205 :AAKGIPVMGHSEGICHMYVDSEASVDKVT 1ad3A 200 :AKHLTPVTLELGGKSPCYVDKDCDLDVAC T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQV 1ad3A 230 :RIAWGKFMNSGQTCVAPDYILCDPSIQNQIVEKLKKSLKDFYGE T0310 278 :KIHAGPKFASYLTFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFSDGYRFGLGAEVGISTSRIH 1ad3A 313 :RYIAPTILVDVDPQSPVMQEEIFGPVMPIVCVRSLEEAIQFINQREKPLALYVFSNNEKVIKKMIAETSSGGVTANDVIVHITVPTLPFGGVGNSGMGAYH T0310 381 :GPVGLEGLLTTKWLLRG 1ad3A 414 :GKKSFETFSHRRSCLVK T0310 406 :SEHGSLKYLHENLPIP 1ad3A 431 :SLLNEEAHKARYPPSP Number of specific fragments extracted= 11 number of extra gaps= 0 total=480 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2esdA/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/T0310/2esdA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0310/2esdA/merged-good-all-a2m.gz for input Trying 2esdA/merged-good-all-a2m Error: Couldn't open file 2esdA/merged-good-all-a2m or 2esdA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uxtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1uxtA expands to /projects/compbio/data/pdb/1uxt.pdb.gz 1uxtA:# T0310 read from 1uxtA/merged-good-all-a2m # 1uxtA read from 1uxtA/merged-good-all-a2m # adding 1uxtA to template set # found chain 1uxtA in template set Warning: unaligning (T0310)G217 because of BadResidue code BAD_PEPTIDE in next template residue (1uxtA)G267 Warning: unaligning (T0310)I218 because of BadResidue code BAD_PEPTIDE at template residue (1uxtA)G267 T0310 2 :VEQQGEMARS 1uxtA 56 :VERTLDVLFK T0310 12 :GGRMLATLEPEQRAEIIHHLADLLTDQRDEILL 1uxtA 67 :GRWSARDMPGTERLAVLRKAADIIERNLDVFAE T0310 50 :LEEAEGRLAAPLLK 1uxtA 100 :VLVMNAGKPKSAAV T0310 74 :SLAIGLRQIAASSQ 1uxtA 114 :GEVKAAVDRLRLAE T0310 88 :DSVGRVLRRTRIAK 1uxtA 132 :KIGGDYIPGDWTYD T0310 102 :NLELEQVTVPIGVLLVIFE 1uxtA 148 :ETEGLVRREPLGVVAAITP T0310 121 :SRPDCL 1uxtA 168 :NYPLFD T0310 127 :PQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1uxtA 175 :VNKITYSFIYGNAVVVKPSISDPLPAAMAVKALLDA T0310 167 :GV 1uxtA 211 :GF T0310 169 :KEAVQLVNTR 1uxtA 214 :PDAIALLNLP T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKAAKGIPVMGHSE 1uxtA 228 :EKIVADDRVAAVSFTGSTEVGERVVKVGGVKQYVMELG T0310 219 :CHMYVDSEASVDKVT 1uxtA 268 :DPAIVLEDADLDLAA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRT 1uxtA 284 :KIARGIYSYAGQRCDAIKLVLAERPVYGK T0310 264 :LFDQIIDMLRVEQVKIHAGPK 1uxtA 313 :LVEEVAKRLSSLRVGDPRDPT T0310 285 :FASYLTFV 1uxtA 336 :VGPLISPS T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFSD 1uxtA 390 :VLYKREVFAPVALAVEVKDLDQAIELANGRPYGLDAAVFGRDVVKIRRAVRLLEVGAIYINDMPRHGI T0310 361 :GYRFGLGAEVGISTSRI 1uxtA 459 :YYPFGGRKKSGVFREGI T0310 382 :PVGLEGLLTTKWLLRGKDHVV 1uxtA 476 :GYAVEAVTAYKTIVFNYKGKG Number of specific fragments extracted= 18 number of extra gaps= 1 total=498 Number of alignments=31 # 1uxtA read from 1uxtA/merged-good-all-a2m # found chain 1uxtA in template set Warning: unaligning (T0310)G217 because of BadResidue code BAD_PEPTIDE in next template residue (1uxtA)G267 Warning: unaligning (T0310)I218 because of BadResidue code BAD_PEPTIDE at template residue (1uxtA)G267 T0310 2 :VEQQGEMARS 1uxtA 56 :VERTLDVLFK T0310 12 :GGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1uxtA 67 :GRWSARDMPGTERLAVLRKAADIIERNLDVFAEVLVMNAGKP T0310 65 :LSLSTSKLNSLAIGLRQ 1uxtA 109 :KSAAVGEVKAAVDRLRL T0310 86 :SQD 1uxtA 126 :AEL T0310 89 :SVGRVLRRTRIAK 1uxtA 133 :IGGDYIPGDWTYD T0310 102 :NLELEQVTVPIGVLLVIFESRPDCLPQVAAL 1uxtA 148 :ETEGLVRREPLGVVAAITPFNYPLFDAVNKI T0310 133 :AIASGNGLLLKGGKEAAHSNRILHLLTQEA 1uxtA 181 :SFIYGNAVVVKPSISDPLPAAMAVKALLDA T0310 167 :GV 1uxtA 211 :GF T0310 169 :KEAVQLVNTR 1uxtA 214 :PDAIALLNLP T0310 179 :EEVEL 1uxtA 225 :KEAEK T0310 184 :DKMIDLIIPRGSSQLVRDIQKAAKGIPV 1uxtA 233 :DDRVAAVSFTGSTEVGERVVKVGGVKQY T0310 212 :MGHS 1uxtA 262 :MELG T0310 219 :CHMYVDSEASVDKVT 1uxtA 268 :DPAIVLEDADLDLAA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLR 1uxtA 284 :KIARGIYSYAGQRCDAIKLVLAERPVYG T0310 263 :PLFDQIIDMLRVEQVKIHAGPK 1uxtA 312 :KLVEEVAKRLSSLRVGDPRDPT T0310 285 :FASYLTF 1uxtA 336 :VGPLISP T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWN 1uxtA 389 :MVLYKREVFAPVALAVEVKDLDQAIELANGRPYGLDAAVFGRDVVKIRRAVRLLEVGAIYIN T0310 354 :ASTRFSDGYRFGLGAEVG 1uxtA 458 :GYYPFGGRKKSGVFREGI T0310 372 :ISTSRIHARGPVGLEGL 1uxtA 477 :YAVEAVTAYKTIVFNYK T0310 397 :GKD 1uxtA 494 :GKG Number of specific fragments extracted= 20 number of extra gaps= 1 total=518 Number of alignments=32 # 1uxtA read from 1uxtA/merged-good-all-a2m # found chain 1uxtA in template set Warning: unaligning (T0310)G217 because of BadResidue code BAD_PEPTIDE in next template residue (1uxtA)G267 Warning: unaligning (T0310)I218 because of BadResidue code BAD_PEPTIDE at template residue (1uxtA)G267 T0310 2 :VEQQGEMARS 1uxtA 56 :VERTLDVLFK T0310 12 :GGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1uxtA 67 :GRWSARDMPGTERLAVLRKAADIIERNLDVFAEVLVMNAGKP T0310 69 :TSKLNSLAIGLRQIAASSQ 1uxtA 109 :KSAAVGEVKAAVDRLRLAE T0310 88 :DSVGR 1uxtA 131 :KKIGG T0310 95 :RRTRIAKN 1uxtA 136 :DYIPGDWT T0310 103 :LELEQVTVPIGVLLVIFESRPDCLPQV 1uxtA 149 :TEGLVRREPLGVVAAITPFNYPLFDAV T0310 130 :AALAIASGNGLLLKGGKEAAHSNRILHLLTQ 1uxtA 178 :ITYSFIYGNAVVVKPSISDPLPAAMAVKALL T0310 165 :IHGVKEAVQLVN 1uxtA 209 :DAGFPPDAIALL T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQKAAKGIPVMGHSE 1uxtA 226 :EAEKIVADDRVAAVSFTGSTEVGERVVKVGGVKQYVMELG T0310 219 :CHMYVDSEASVDKVT 1uxtA 268 :DPAIVLEDADLDLAA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQV 1uxtA 284 :KIARGIYSYAGQRCDAIKLVLAERPVYGKLVEEVAKRLSSLRVG T0310 278 :KIHAGPKFASYL 1uxtA 367 :RRLGPTYVQPTF T0310 290 :TFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTR 1uxtA 387 :KDMVLYKREVFAPVALAVEVKDLDQAIELANGRPYGLDAAVFGRDVVKIRRAVRLLEVGAIYINDMPR T0310 359 :SDGYRFGLGAEVGISTSRIH 1uxtA 455 :HGIGYYPFGGRKKSGVFREG T0310 381 :GPVGLEGLLTTKWLLR 1uxtA 475 :IGYAVEAVTAYKTIVF T0310 404 :DFSEHGS 1uxtA 491 :NYKGKGV Number of specific fragments extracted= 16 number of extra gaps= 1 total=534 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o04A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0310 read from 1o04A/merged-good-all-a2m # 1o04A read from 1o04A/merged-good-all-a2m # found chain 1o04A in training set Warning: unaligning (T0310)R92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o04A)T143 Warning: unaligning (T0310)V93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o04A)T143 Warning: unaligning (T0310)L94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o04A)I144 Warning: unaligning (T0310)L366 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o04A)Y468 Warning: unaligning (T0310)G367 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o04A)Y468 T0310 2 :VEQQGEMARSGGR 1o04A 59 :VDKAVKAARAAFQ T0310 15 :MLATLEPEQRAEIIHHLADLLTDQRDEILL 1o04A 75 :PWRRMDASHRGRLLNRLADLIERDRTYLAA T0310 50 :LEEAEGR 1o04A 105 :LETLDNG T0310 59 :APLLKR 1o04A 112 :KPYVIS T0310 68 :STSKLNSLAIGLRQIAASSQDSVG 1o04A 118 :YLVDLDMVLKCLRYYAGWADKYHG T0310 95 :RR 1o04A 145 :PI T0310 100 :AKNLELEQVTVPIGVLLVIFE 1o04A 147 :DGDFFSYTRHEPVGVCGQIIP T0310 121 :SRP 1o04A 169 :NFP T0310 124 :DCLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1o04A 173 :LMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEA T0310 167 :GV 1o04A 212 :GF T0310 169 :KEAVQLVNTR 1o04A 215 :PGVVNIVPGF T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKAA 1o04A 230 :AAIASHEDVDKVAFTGSTEIGRVIQVAA T0310 207 :KGIPVMGHSEGICHMYVDSEASVDKVT 1o04A 261 :NLKRVTLELGGKSPNIIMSDADMDWAV T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRT 1o04A 289 :QAHFALFFNQGQCSCAGSRTFVQEDIYDE T0310 264 :LFDQIIDMLRVEQVKIHAGPK 1o04A 318 :FVERSVARAKSRVVGNPFDSK T0310 285 :FASYLTFV 1o04A 341 :QGPQVDET T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFSDGYRFG 1o04A 394 :TIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFG T0310 368 :AEVGISTSR 1o04A 469 :KMSGSGREL T0310 381 :GPVGLEGLLTTKWLLRGKDHV 1o04A 478 :GEYGLQAYTEVKTVTVKVPQK Number of specific fragments extracted= 19 number of extra gaps= 2 total=553 Number of alignments=34 # 1o04A read from 1o04A/merged-good-all-a2m # found chain 1o04A in training set Warning: unaligning (T0310)R92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o04A)T143 Warning: unaligning (T0310)V93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o04A)T143 Warning: unaligning (T0310)L94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o04A)I144 Warning: unaligning (T0310)D360 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o04A)Y468 Warning: unaligning (T0310)G361 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o04A)Y468 T0310 2 :VEQQGEMARSGGR 1o04A 59 :VDKAVKAARAAFQ T0310 15 :MLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1o04A 75 :PWRRMDASHRGRLLNRLADLIERDRTYLAALETLDNGKP T0310 65 :LSLST 1o04A 114 :YVISY T0310 70 :SKLNSLAIGLRQIAASSQDSVG 1o04A 120 :VDLDMVLKCLRYYAGWADKYHG T0310 95 :RR 1o04A 145 :PI T0310 100 :AKNLELEQVTVPIGVLLVIFESRPDCLPQVAAL 1o04A 147 :DGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKL T0310 133 :AIASGNGLLLKGGKEAAHSNRILHLLTQEA 1o04A 182 :ALATGNVVVMKVAEQTPLTALYVANLIKEA T0310 167 :GV 1o04A 212 :GF T0310 169 :KEAVQLVNT 1o04A 215 :PGVVNIVPG T0310 178 :R 1o04A 225 :G T0310 179 :EEVEL 1o04A 227 :TAGAA T0310 184 :DKMIDLIIPRGSSQLVRDIQKAA 1o04A 235 :HEDVDKVAFTGSTEIGRVIQVAA T0310 207 :KGIPV 1o04A 261 :NLKRV T0310 212 :MGHS 1o04A 267 :LELG T0310 217 :GICHMYVDSEASVDKVT 1o04A 271 :GKSPNIIMSDADMDWAV T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLR 1o04A 289 :QAHFALFFNQGQCSCAGSRTFVQEDIYD T0310 263 :PLFDQIIDMLRVEQVKIHAGPK 1o04A 317 :EFVERSVARAKSRVVGNPFDSK T0310 285 :FASYLTF 1o04A 341 :QGPQVDE T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWN 1o04A 393 :MTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGTVWVN T0310 354 :ASTRFS 1o04A 461 :AQSPFG T0310 362 :YRFGLGAEVG 1o04A 469 :KMSGSGRELG T0310 372 :ISTSRIHARGPVGLEGLLT 1o04A 480 :YGLQAYTEVKTVTVKVPQK Number of specific fragments extracted= 22 number of extra gaps= 2 total=575 Number of alignments=35 # 1o04A read from 1o04A/merged-good-all-a2m # found chain 1o04A in training set Warning: unaligning (T0310)R95 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o04A)T143 Warning: unaligning (T0310)R96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o04A)T143 Warning: unaligning (T0310)T97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o04A)I144 Warning: unaligning (T0310)A368 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o04A)Y468 Warning: unaligning (T0310)E369 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o04A)Y468 T0310 2 :VEQQGEMARSGGR 1o04A 59 :VDKAVKAARAAFQ T0310 15 :MLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1o04A 75 :PWRRMDASHRGRLLNRLADLIERDRTYLAALETLDNGKP T0310 59 :APL 1o04A 114 :YVI T0310 68 :STSKLNSLAIGLRQIAASSQD 1o04A 117 :SYLVDLDMVLKCLRYYAGWAD T0310 91 :GRVL 1o04A 138 :KYHG T0310 98 :RIAKNLELEQVTVPIGVLLVIFESRPDCLPQV 1o04A 145 :PIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQA T0310 130 :AALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1o04A 179 :LGPALATGNVVVMKVAEQTPLTALYVANLIKEA T0310 167 :GVKEAVQLVN 1o04A 212 :GFPPGVVNIV T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQK 1o04A 228 :AGAAIASHEDVDKVAFTGSTEIGRVIQV T0310 205 :AAKGIPVMGHSEGICHMYVDSEASVDKVTRLVRDSKC 1o04A 259 :SSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALF T0310 242 :EYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQV 1o04A 297 :NQGQCSCAGSRTFVQEDIYDEFVERSVARAKSRVVG T0310 278 :KIHAGPKFASYLTFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTR 1o04A 379 :YFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDV T0310 360 :DGYRFGLG 1o04A 459 :FGAQSPFG T0310 370 :VGISTSRIH 1o04A 469 :KMSGSGREL T0310 381 :GPVGLEGLLTTKWLLRGK 1o04A 478 :GEYGLQAYTEVKTVTVKV Number of specific fragments extracted= 15 number of extra gaps= 2 total=590 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d4eA/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/T0310/2d4eA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0310/2d4eA/merged-good-all-a2m.gz for input Trying 2d4eA/merged-good-all-a2m Error: Couldn't open file 2d4eA/merged-good-all-a2m or 2d4eA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wndA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wndA expands to /projects/compbio/data/pdb/1wnd.pdb.gz 1wndA:# T0310 read from 1wndA/merged-good-all-a2m # 1wndA read from 1wndA/merged-good-all-a2m # adding 1wndA to template set # found chain 1wndA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILL 1wndA 41 :VDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFAE T0310 50 :LEEAEGR 1wndA 84 :LESRNCG T0310 59 :APLLKR 1wndA 91 :KPLHSA T0310 68 :STSKLNSLAIGLRQIAASSQDSVGRVLRRT 1wndA 97 :FNDEIPAIVDVFRFFAGAARCLNGLAAGEY T0310 100 :AKNLELEQVTVPIGVLLVIFE 1wndA 127 :LEGHTSMIRRDPLGVVASIAP T0310 121 :SRP 1wndA 149 :NYP T0310 124 :DCLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLT 1wndA 153 :MMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELA T0310 166 :HGV 1wndA 190 :DIF T0310 169 :KEAVQLVNTR 1wndA 194 :AGVVNILFGR T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKAA 1wndA 209 :DPLTGHPKVRMVSLTGSIATGEHIISHT T0310 207 :KGIPVMGHSEGICHMYVDSEASVDKVTRLVRDS 1wndA 239 :SIKRTHMELGGKAPVIVFDDADIEAVVEGVRTF T0310 240 :KCEYPAACNALETLLIHRDLLRT 1wndA 273 :YYNAGQDCTAACRIYAQKGIYDT T0310 264 :LFDQIIDMLRVEQVKIHAGPK 1wndA 296 :LVEKLGAAVATLKSGAPDDES T0310 285 :FASYLTFV 1wndA 319 :LGPLSSLA T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFSDGYRFGLGAEVGISTSR 1wndA 373 :AIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDM T0310 381 :GPVGLEGLLTTKWLLRG 1wndA 457 :SLYGLEDYTVVRHVMVK Number of specific fragments extracted= 16 number of extra gaps= 0 total=606 Number of alignments=37 # 1wndA read from 1wndA/merged-good-all-a2m # found chain 1wndA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1wndA 41 :VDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFAELESRNCGKP T0310 65 :LSLSTSK 1wndA 93 :LHSAFND T0310 72 :LNSLAIGLRQIAASSQDSVGRVLRR 1wndA 101 :IPAIVDVFRFFAGAARCLNGLAAGE T0310 99 :IAKNLELEQVTVPIGVLLVIFESRPDCLPQVAAL 1wndA 126 :YLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKL T0310 133 :AIASGNGLLLKGGKEAAHSNRILHLLT 1wndA 162 :ALAAGNCVVLKPSEITPLTALKLAELA T0310 167 :GV 1wndA 190 :DI T0310 169 :KEAVQLVNT 1wndA 194 :AGVVNILFG T0310 178 :R 1wndA 204 :G T0310 179 :EEVEL 1wndA 206 :TVGDP T0310 184 :DKMIDLIIPRGSSQLVRDIQKAA 1wndA 214 :HPKVRMVSLTGSIATGEHIISHT T0310 207 :KGIPV 1wndA 239 :SIKRT T0310 212 :MGHS 1wndA 245 :MELG T0310 217 :GICHMYVDSEASVDKVT 1wndA 249 :GKAPVIVFDDADIEAVV T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLR 1wndA 267 :GVRTFGYYNAGQDCTAACRIYAQKGIYD T0310 263 :PLFDQIIDMLRVEQVKIHAGPK 1wndA 295 :TLVEKLGAAVATLKSGAPDDES T0310 285 :FASYLTF 1wndA 319 :LGPLSSL T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWN 1wndA 372 :DAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVN T0310 354 :ASTRFSDGYRFGLGAEVG 1wndA 440 :SEMPHGGQKLSGYGKDMS T0310 372 :ISTSRIHARGPVGLE 1wndA 459 :YGLEDYTVVRHVMVK Number of specific fragments extracted= 19 number of extra gaps= 0 total=625 Number of alignments=38 # 1wndA read from 1wndA/merged-good-all-a2m # found chain 1wndA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEAEGRLAAP 1wndA 41 :VDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFND T0310 72 :LNSLAIGLRQIAASSQDSVG 1wndA 100 :EIPAIVDVFRFFAGAARCLN T0310 93 :VLRRTRIAKNLELEQVTVPIGVLLVIFESRPDCLPQV 1wndA 120 :GLAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAA T0310 130 :AALAIASGNGLLLKGGKEAAHSNRILHLLT 1wndA 159 :LAPALAAGNCVVLKPSEITPLTALKLAELA T0310 165 :IHGVKEAVQLVN 1wndA 189 :KDIFPAGVVNIL T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQK 1wndA 207 :VGDPLTGHPKVRMVSLTGSIATGEHIIS T0310 205 :AAKGIPVMGHSEGICHMYVDSEASVDKVTRLVRD 1wndA 237 :ASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRT T0310 239 :SKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQV 1wndA 272 :GYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSG T0310 278 :KIHAGPKFASYLTFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTR 1wndA 358 :YYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVNTHFM T0310 360 :DGYRFGLGAEVGISTSRIH 1wndA 438 :LVSEMPHGGQKLSGYGKDM T0310 381 :GPVGLEGLLTTKWLLR 1wndA 457 :SLYGLEDYTVVRHVMV Number of specific fragments extracted= 11 number of extra gaps= 0 total=636 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uxvA/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/T0310/1uxvA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0310/1uxvA/merged-good-all-a2m.gz for input Trying 1uxvA/merged-good-all-a2m Error: Couldn't open file 1uxvA/merged-good-all-a2m or 1uxvA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bpwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bpwA expands to /projects/compbio/data/pdb/1bpw.pdb.gz 1bpwA:# T0310 read from 1bpwA/merged-good-all-a2m # 1bpwA read from 1bpwA/merged-good-all-a2m # adding 1bpwA to template set # found chain 1bpwA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILL 1bpwA 60 :VDQAVQSAQAAYLKWSKMAGIERSRVMLEAARIIRERRDNIAK T0310 50 :LEEAEGR 1bpwA 103 :LEVINNG T0310 59 :APLLK 1bpwA 110 :KTITE T0310 68 :STSKLNSLAIGLRQIAASSQDSVGRVLRR 1bpwA 115 :AEYDIDAAWQCIEYYAGLAPTLSGQHIQL T0310 100 :AKNLELEQVTVPIGVLLVIFE 1bpwA 144 :PGGAFAYTRREPLGVCAGILA T0310 121 :SRPDCL 1bpwA 166 :NYPFMI T0310 127 :PQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1bpwA 173 :AWKCAPALACGNAVVFKPSPMTPVTGVILAEIFHEA T0310 167 :GV 1bpwA 209 :GV T0310 169 :KEAVQLVNTR 1bpwA 212 :VGLVNVVQGG T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKAA 1bpwA 226 :SLLCHHPNVAKVSFTGSVPTGKKVMEMS T0310 207 :KGIPVMGHSEGICHMYVDSEASVDKVTRLVRDS 1bpwA 256 :TVKHVTLELGGKSPLLIFKDCELENAVRGALMA T0310 240 :KCEYPAACNALETLLIHRDLLRT 1bpwA 290 :FLTQGQVCTNGTRVFVQREIMPQ T0310 264 :LFDQIIDMLRVEQVKIHAGPK 1bpwA 313 :FLEEVVKRTKAIVVGDPLLTE T0310 285 :FASYLTFV 1bpwA 336 :MGGLISKP T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFSDGYRFGLGAEVGISTSR 1bpwA 395 :TCVKEEIFGPVMSVLPFDTEEEVLQRANNTTFGLASGVFTRDISRAHRVAANLEAGTCYINTYSISPVEVPFGGYKMSGFGREN T0310 381 :GPVGLEGLLTTKWLLRGKDHVVS 1bpwA 479 :GQATVDYYSQLKTVIVEMGDVDS Number of specific fragments extracted= 16 number of extra gaps= 0 total=652 Number of alignments=40 # 1bpwA read from 1bpwA/merged-good-all-a2m # found chain 1bpwA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1bpwA 60 :VDQAVQSAQAAYLKWSKMAGIERSRVMLEAARIIRERRDNIAKLEVINNGKT T0310 65 :LSLSTSKLNSLAIGLRQIAASSQDSVGRVLRR 1bpwA 112 :ITEAEYDIDAAWQCIEYYAGLAPTLSGQHIQL T0310 100 :AKNLELEQVTVPIGVLLVIFESRPDCLPQVAAL 1bpwA 144 :PGGAFAYTRREPLGVCAGILAWNYPFMIAAWKC T0310 133 :AIASGNGLLLKGGKEAAHSNRILHLLTQEA 1bpwA 179 :ALACGNAVVFKPSPMTPVTGVILAEIFHEA T0310 167 :GV 1bpwA 209 :GV T0310 169 :KEAVQLVNTR 1bpwA 212 :VGLVNVVQGG T0310 179 :EEVEL 1bpwA 223 :ETGSL T0310 184 :DKMIDLIIPRGSSQLVRDIQKAA 1bpwA 231 :HPNVAKVSFTGSVPTGKKVMEMS T0310 207 :KGIPV 1bpwA 256 :TVKHV T0310 212 :MGHS 1bpwA 262 :LELG T0310 217 :GICHMYVDSEASVDKVT 1bpwA 266 :GKSPLLIFKDCELENAV T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLR 1bpwA 284 :GALMANFLTQGQVCTNGTRVFVQREIMP T0310 263 :PLFDQIIDMLRVEQVKIHAGPK 1bpwA 312 :QFLEEVVKRTKAIVVGDPLLTE T0310 285 :FASYLTF 1bpwA 336 :MGGLISK T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWN 1bpwA 394 :MTCVKEEIFGPVMSVLPFDTEEEVLQRANNTTFGLASGVFTRDISRAHRVAANLEAGTCYIN T0310 354 :ASTRFSDGYRFGLGAEVG 1bpwA 462 :VEVPFGGYKMSGFGRENG T0310 372 :ISTSRI 1bpwA 481 :ATVDYY T0310 389 :LTTKWLLRGKDHVV 1bpwA 487 :SQLKTVIVEMGDVD Number of specific fragments extracted= 18 number of extra gaps= 0 total=670 Number of alignments=41 # 1bpwA read from 1bpwA/merged-good-all-a2m # found chain 1bpwA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDL 1bpwA 60 :VDQAVQSAQAAYLKWSKMAGIERSRVMLEAARIIRERRDNIAKLEVINN T0310 65 :LSLSTSKLNSLAIGLRQIAASSQDS 1bpwA 111 :TITEAEYDIDAAWQCIEYYAGLAPT T0310 92 :RVLRRTRIAKNLELEQVTVPIGVLLVIFESRPDCLPQV 1bpwA 136 :LSGQHIQLPGGAFAYTRREPLGVCAGILAWNYPFMIAA T0310 130 :AALAIASGNGLLLKGGKEAAHSNRILHLLTQEA 1bpwA 176 :CAPALACGNAVVFKPSPMTPVTGVILAEIFHEA T0310 167 :GVKEAVQLVN 1bpwA 209 :GVPVGLVNVV T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQK 1bpwA 224 :TGSLLCHHPNVAKVSFTGSVPTGKKVME T0310 205 :AAKGIPVMGHSEGICHMYVDSEASVDKVTRLVRDSKC 1bpwA 254 :AKTVKHVTLELGGKSPLLIFKDCELENAVRGALMANF T0310 242 :EYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQV 1bpwA 292 :TQGQVCTNGTRVFVQREIMPQFLEEVVKRTKAIVVG T0310 278 :KIHAGPKFASYLTFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTR 1bpwA 380 :YFMSPCVLDNCRDDMTCVKEEIFGPVMSVLPFDTEEEVLQRANNTTFGLASGVFTRDISRAHRVAANLEAGTCYINTYSI T0310 360 :DGYRFGLGAEVGISTSRIH 1bpwA 460 :SPVEVPFGGYKMSGFGREN T0310 381 :GPVGLEGLLTTKWLLRGKD 1bpwA 479 :GQATVDYYSQLKTVIVEMG Number of specific fragments extracted= 11 number of extra gaps= 0 total=681 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a4sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a4sA expands to /projects/compbio/data/pdb/1a4s.pdb.gz 1a4sA:# T0310 read from 1a4sA/merged-good-all-a2m # 1a4sA read from 1a4sA/merged-good-all-a2m # adding 1a4sA to template set # found chain 1a4sA in template set Warning: unaligning (T0310)G144 because of BadResidue code BAD_PEPTIDE in next template residue (1a4sA)S191 Warning: unaligning (T0310)G145 because of BadResidue code BAD_PEPTIDE at template residue (1a4sA)S191 Warning: unaligning (T0310)A149 because of BadResidue code BAD_PEPTIDE in next template residue (1a4sA)V196 Warning: unaligning (T0310)H150 because of BadResidue code BAD_PEPTIDE at template residue (1a4sA)V196 Warning: unaligning (T0310)L366 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1a4sA)Y469 Warning: unaligning (T0310)G367 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1a4sA)Y469 T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILL 1a4sA 60 :VDQAVQSAQAAYLKWSKMAGIERSRVMLEAARIIRERRDNIAK T0310 50 :LEEAEGR 1a4sA 103 :LEVINNG T0310 59 :APLLK 1a4sA 110 :KTITE T0310 68 :STSKLNSLAIGLRQIAASSQDSVGRVLRR 1a4sA 115 :AEYDIDAAWQCIEYYAGLAPTLSGQHIQL T0310 100 :AKNLELEQVTVPIGVLLVIFE 1a4sA 144 :PGGAFAYTRREPLGVCAGILA T0310 121 :SRPDCL 1a4sA 166 :NYPFMI T0310 127 :PQVAALAIASGNGLLLK 1a4sA 173 :AWKCAPALACGNAVVFK T0310 146 :KEA 1a4sA 192 :PMT T0310 151 :SNRILHLLTQEA 1a4sA 197 :TGVILAEIFHEA T0310 167 :GV 1a4sA 209 :GV T0310 169 :KEAVQLVNTR 1a4sA 212 :VGLVNVVQGG T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKAA 1a4sA 226 :SLLCHHPNVAKVSFTGSVPTGKKVMEMS T0310 207 :KGIPVMGHSEGICHMYVDSEASVDKVTRLVRDS 1a4sA 256 :TVKHVTLELGGKSPLLIFKDCELENAVRGALMA T0310 240 :KCEYPAACNALETLLIHRDLLRT 1a4sA 290 :FLTQGQVCTNGTRVFVQREIMPQ T0310 264 :LFDQIIDMLRVEQVKIHAGPK 1a4sA 313 :FLEEVVKRTKAIVVGDPLLTE T0310 285 :FASYLTFV 1a4sA 336 :MGGLISKP T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTRFSDGYRFG 1a4sA 395 :TCVKEEIFGPVMSVLPFDTEEEVLQRANNTTFGLASGVFTRDISRAHRVAANLEAGTCYINTYSISPVEVPFG T0310 368 :AEVGISTSR 1a4sA 470 :KMSGFGREN T0310 381 :GPVGLEGLLTTKWLLRGKDHVVS 1a4sA 479 :GQATVDYYSQLKTVIVEMGDVDS Number of specific fragments extracted= 19 number of extra gaps= 3 total=700 Number of alignments=43 # 1a4sA read from 1a4sA/merged-good-all-a2m # found chain 1a4sA in template set Warning: unaligning (T0310)G144 because of BadResidue code BAD_PEPTIDE in next template residue (1a4sA)S191 Warning: unaligning (T0310)G145 because of BadResidue code BAD_PEPTIDE at template residue (1a4sA)S191 Warning: unaligning (T0310)A149 because of BadResidue code BAD_PEPTIDE in next template residue (1a4sA)V196 Warning: unaligning (T0310)H150 because of BadResidue code BAD_PEPTIDE at template residue (1a4sA)V196 Warning: unaligning (T0310)D360 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1a4sA)Y469 Warning: unaligning (T0310)G361 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1a4sA)Y469 T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1a4sA 60 :VDQAVQSAQAAYLKWSKMAGIERSRVMLEAARIIRERRDNIAKLEVINNGKT T0310 65 :LSLSTSKLNSLAIGLRQIAASSQDSVGRVLRR 1a4sA 112 :ITEAEYDIDAAWQCIEYYAGLAPTLSGQHIQL T0310 100 :AKNLELEQVTVPIGVLLVIFESRPDCLPQVAAL 1a4sA 144 :PGGAFAYTRREPLGVCAGILAWNYPFMIAAWKC T0310 133 :AIASGNGLLLK 1a4sA 179 :ALACGNAVVFK T0310 146 :KEA 1a4sA 192 :PMT T0310 151 :SNRILHLLTQEA 1a4sA 197 :TGVILAEIFHEA T0310 167 :GV 1a4sA 209 :GV T0310 169 :KEAVQLVNTR 1a4sA 212 :VGLVNVVQGG T0310 179 :EEVEL 1a4sA 223 :ETGSL T0310 184 :DKMIDLIIPRGSSQLVRDIQKAA 1a4sA 231 :HPNVAKVSFTGSVPTGKKVMEMS T0310 207 :KGIPV 1a4sA 256 :TVKHV T0310 212 :MGHS 1a4sA 262 :LELG T0310 217 :GICHMYVDSEASVDKVT 1a4sA 266 :GKSPLLIFKDCELENAV T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLR 1a4sA 284 :GALMANFLTQGQVCTNGTRVFVQREIMP T0310 263 :PLFDQIIDMLRVEQVKIHAGPK 1a4sA 312 :QFLEEVVKRTKAIVVGDPLLTE T0310 285 :FASYLTF 1a4sA 336 :MGGLISK T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWN 1a4sA 394 :MTCVKEEIFGPVMSVLPFDTEEEVLQRANNTTFGLASGVFTRDISRAHRVAANLEAGTCYIN T0310 354 :ASTRFS 1a4sA 462 :VEVPFG T0310 362 :YRFGLGAEVG 1a4sA 470 :KMSGFGRENG T0310 372 :ISTSRIHARGPVGLEGLLT 1a4sA 481 :ATVDYYSQLKTVIVEMGDV Number of specific fragments extracted= 20 number of extra gaps= 3 total=720 Number of alignments=44 # 1a4sA read from 1a4sA/merged-good-all-a2m # found chain 1a4sA in template set Warning: unaligning (T0310)G144 because of BadResidue code BAD_PEPTIDE in next template residue (1a4sA)S191 Warning: unaligning (T0310)G145 because of BadResidue code BAD_PEPTIDE at template residue (1a4sA)S191 Warning: unaligning (T0310)A149 because of BadResidue code BAD_PEPTIDE in next template residue (1a4sA)V196 Warning: unaligning (T0310)H150 because of BadResidue code BAD_PEPTIDE at template residue (1a4sA)V196 Warning: unaligning (T0310)A368 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1a4sA)Y469 Warning: unaligning (T0310)E369 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1a4sA)Y469 T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1a4sA 60 :VDQAVQSAQAAYLKWSKMAGIERSRVMLEAARIIRERRDNIAKLEVINNGKT T0310 66 :SLSTSKLNSLAIGLRQIAASSQDS 1a4sA 112 :ITEAEYDIDAAWQCIEYYAGLAPT T0310 92 :RVLRRTRIAKNLELEQVTVPIGVLLVIFESRPDCLPQV 1a4sA 136 :LSGQHIQLPGGAFAYTRREPLGVCAGILAWNYPFMIAA T0310 130 :AALAIASGNGLLLK 1a4sA 176 :CAPALACGNAVVFK T0310 146 :KEA 1a4sA 192 :PMT T0310 151 :SNRILHLLTQ 1a4sA 197 :TGVILAEIFH T0310 165 :IHGVKEAVQLVN 1a4sA 207 :EAGVPVGLVNVV T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQK 1a4sA 224 :TGSLLCHHPNVAKVSFTGSVPTGKKVME T0310 205 :AAKGIPVMGHSEGICHMYVDSEASVDKVTRLVRDSKC 1a4sA 254 :AKTVKHVTLELGGKSPLLIFKDCELENAVRGALMANF T0310 242 :EYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQV 1a4sA 292 :TQGQVCTNGTRVFVQREIMPQFLEEVVKRTKAIVVG T0310 278 :KIHAGPKFASYLTFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDSACVFWNASTR 1a4sA 380 :YFMSPCVLDNCRDDMTCVKEEIFGPVMSVLPFDTEEEVLQRANNTTFGLASGVFTRDISRAHRVAANLEAGTCYINTYSI T0310 360 :DGYRFGLG 1a4sA 460 :SPVEVPFG T0310 370 :VGISTSRIH 1a4sA 470 :KMSGFGREN T0310 381 :GPVGLEGLLTTKWLLRGKD 1a4sA 479 :GQATVDYYSQLKTVIVEMG Number of specific fragments extracted= 14 number of extra gaps= 3 total=734 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vluA/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/T0310/1vluA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0310/1vluA/merged-good-all-a2m.gz for input Trying 1vluA/merged-good-all-a2m Error: Couldn't open file 1vluA/merged-good-all-a2m or 1vluA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eyyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1eyyA expands to /projects/compbio/data/pdb/1eyy.pdb.gz 1eyyA:# T0310 read from 1eyyA/merged-good-all-a2m # 1eyyA read from 1eyyA/merged-good-all-a2m # adding 1eyyA to template set # found chain 1eyyA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILL 1eyyA 32 :VNQAATAAAKVARDFRRLNNSKRASLLRTIASELEARSDDIIA T0310 50 :LEEAEGRLAAPLLK 1eyyA 75 :RAHLETALPEVRLT T0310 70 :SKLNSLAIGLRQIAASSQ 1eyyA 89 :GEIARTANQLRLFADVVN T0310 88 :DSVGRVLRRT 1eyyA 109 :SYHQAILDTP T0310 100 :AKNL 1eyyA 119 :NPTR T0310 104 :ELEQVTVPIGVLLVIFE 1eyyA 129 :DIRRQQIALGPVAVFGA T0310 121 :SRP 1eyyA 147 :NFP T0310 124 :DCL 1eyyA 151 :AFS T0310 127 :PQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGV 1eyyA 156 :GGDTASALAAGCPVIVKGHTAHPGTSQIVAECIEQALKQEQL T0310 169 :KEAVQLVNTR 1eyyA 199 :QAIFTLLQGN T0310 179 :EEVELDKMIDLIIPRGSSQLVRDIQKAA 1eyyA 214 :QALVSHPEIKAVGFTGSVGGGRALFNLA T0310 207 :KGIPVMGHSEGICHMYVDSEA 1eyyA 246 :EPIPFYGELGAINPTFIFPSA T0310 230 :DKVTRLVRDSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQ 1eyyA 272 :DLADQFVASMTMGCGQFCTKPGVVFALNTPETQAFIETAQSLIRQQS T0310 277 :VK 1eyyA 320 :ST T0310 293 :KSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTE 1eyyA 372 :PAWEEEIFGPQSLIVVCENVADMLSLSEMLAGSLTATIHAT T0310 334 :DENTAEFFLQHVD 1eyyA 415 :DYPQVSQLIPRLE T0310 347 :SACVFWNASTRFS 1eyyA 430 :AGRLVFNGWPTGV T0310 360 :DGYRFGLGAEVGISTS 1eyyA 446 :YAMVHGGPYPASTHSA T0310 377 :IHARGPVGLEGLLTTKWLLRGKDHVVSDFSEHGS 1eyyA 462 :STSVGAEAIHRWLRPVAYQALPESLLPDSLKAEN Number of specific fragments extracted= 19 number of extra gaps= 0 total=753 Number of alignments=46 # 1eyyA read from 1eyyA/merged-good-all-a2m # found chain 1eyyA in template set T0310 2 :VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA 1eyyA 32 :VNQAATAAAKVARDFRRLNNSKRASLLRTIASELEARSDDIIARAHLETALP T0310 65 :LSLSTSKLNSLAIGLRQIAASSQD 1eyyA 84 :EVRLTGEIARTANQLRLFADVVNS T0310 89 :SVGRVLRR 1eyyA 110 :YHQAILDT T0310 99 :IAKNL 1eyyA 118 :PNPTR T0310 104 :ELEQVTVPIGVLLVIFESRPDCLP 1eyyA 129 :DIRRQQIALGPVAVFGASNFPLAF T0310 128 :QVAA 1eyyA 157 :GDTA T0310 133 :AIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGV 1eyyA 162 :ALAAGCPVIVKGHTAHPGTSQIVAECIEQALKQEQL T0310 169 :KEAVQLVNT 1eyyA 199 :QAIFTLLQG T0310 178 :R 1eyyA 209 :Q T0310 179 :EEVEL 1eyyA 211 :ALGQA T0310 184 :DKMIDLIIPRGSSQLVRDIQKAA 1eyyA 219 :HPEIKAVGFTGSVGGGRALFNLA T0310 207 :KGIPV 1eyyA 246 :EPIPF T0310 212 :MGHS 1eyyA 252 :GELG T0310 217 :GICHMYVDSEA 1eyyA 256 :AINPTFIFPSA T0310 232 :VT 1eyyA 273 :LA T0310 234 :RLVRDSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQ 1eyyA 276 :QFVASMTMGCGQFCTKPGVVFALNTPETQAFIETAQSLIRQQS T0310 285 :FASYLTF 1eyyA 319 :PSTLLTP T0310 292 :VKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTE 1eyyA 371 :HPAWEEEIFGPQSLIVVCENVADMLSLSEMLAGSLTATIHAT T0310 334 :DENTAEFFLQHVD 1eyyA 415 :DYPQVSQLIPRLE T0310 347 :SACVFWN 1eyyA 430 :AGRLVFN T0310 354 :ASTRFSDGYRFGLGAEVG 1eyyA 446 :YAMVHGGPYPASTHSAST T0310 372 :ISTSRIHA 1eyyA 465 :VGAEAIHR T0310 387 :GLLTTKWLLRGKDHVVSDFSEH 1eyyA 473 :WLRPVAYQALPESLLPDSLKAE T0310 409 :GSLKYLHENLP 1eyyA 497 :LEIARAVDGKA Number of specific fragments extracted= 24 number of extra gaps= 0 total=777 Number of alignments=47 # 1eyyA read from 1eyyA/merged-good-all-a2m # found chain 1eyyA in template set T0310 1 :TVEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDL 1eyyA 31 :EVNQAATAAAKVARDFRRLNNSKRASLLRTIASELEARSDDIIARAHLET T0310 57 :LAAPLLKRLSLS 1eyyA 82 :LPEVRLTGEIAR T0310 72 :LNSLAIGLRQIAASSQDS 1eyyA 94 :TANQLRLFADVVNSGSYH T0310 92 :RVLRRTRIAKN 1eyyA 112 :QAILDTPNPTR T0310 103 :LELEQVTVPIGVLLVIFESRPDCLPQV 1eyyA 128 :PDIRRQQIALGPVAVFGASNFPLAFSA T0310 130 :AALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGVKEAVQLVN 1eyyA 159 :TASALAAGCPVIVKGHTAHPGTSQIVAECIEQALKQEQLPQAIFTLL T0310 177 :TREEVELDKMIDLIIPRGSSQLVRDIQK 1eyyA 212 :LGQALVSHPEIKAVGFTGSVGGGRALFN T0310 205 :AAKGIPVMGHSEGICHMYVDSEA 1eyyA 244 :RPEPIPFYGELGAINPTFIFPSA T0310 228 :S 1eyyA 272 :D T0310 231 :K 1eyyA 273 :L T0310 233 :T 1eyyA 274 :A T0310 234 :RLVRDSKCEYPAACNALETLLIHR 1eyyA 276 :QFVASMTMGCGQFCTKPGVVFALN T0310 261 :RTPLFDQIIDMLRVEQV 1eyyA 300 :TPETQAFIETAQSLIRQ T0310 278 :KIHAGPKFASYL 1eyyA 347 :TFSQAESPCVAS T0310 290 :TFVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTE 1eyyA 369 :RKHPAWEEEIFGPQSLIVVCENVADMLSLSEMLAGSLTATIHAT T0310 334 :DENTAEFFLQHVD 1eyyA 415 :DYPQVSQLIPRLE T0310 347 :SACVFWNASTRFSD 1eyyA 430 :AGRLVFNGWPTGVE T0310 361 :GYRFGLGAEVGIST 1eyyA 445 :GYAMVHGGPYPAST T0310 375 :SRIHARGPVGLEGLLTTKWL 1eyyA 460 :SASTSVGAEAIHRWLRPVAY T0310 403 :SDFSEHGSLKYLHENLPIPQ 1eyyA 480 :QALPESLLPDSLKAENPLEI Number of specific fragments extracted= 20 number of extra gaps= 0 total=797 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kaeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0310 read from 1kaeA/merged-good-all-a2m # 1kaeA read from 1kaeA/merged-good-all-a2m # found chain 1kaeA in training set T0310 16 :LATLEPEQRAEI 1kaeA 9 :WNSCTAEQQRQL T0310 28 :IHHLADLLTDQRDEILLAN 1kaeA 36 :VNDILDNVKARGDEALREY T0310 47 :KKDLEEAEGRLAAPLLKR 1kaeA 70 :AEEIAAASERLSDELKQA T0310 72 :LNSLAIGLRQIAAS 1kaeA 88 :MAVAVKNIETFHTA T0310 87 :QDSVGRVLRR 1kaeA 102 :QKLPPVDVET T0310 100 :AKNLELEQVTVPIGVLLVIFE 1kaeA 112 :QPGVRCQQVTRPVASVGLYIP T0310 121 :SRPDCL 1kaeA 135 :SAPLFS T0310 127 :PQVAALAIASGN 1kaeA 143 :LMLATPASIAGC T0310 139 :GLLLKGGKEAAHSNRIL 1kaeA 157 :VVLCSPPPIADEILYAA T0310 160 :QEA 1kaeA 174 :QLC T0310 167 :GVKEAVQL 1kaeA 177 :GVQDVFNV T0310 177 :TR 1kaeA 185 :GG T0310 182 :ELDKMIDLIIPRGS 1kaeA 198 :ESVPKVDKIFGPGN T0310 196 :SQLVRDIQKAAKGIPVMGHSEGICH 1kaeA 215 :TEAKRQVSQRLDGAAIDMPAGPSEV T0310 221 :MYVDSEASVDKVTRLVRDS 1kaeA 241 :VIADSGATPDFVASDLLSQ T0310 240 :KCEYPAA 1kaeA 262 :HGPDSQV T0310 252 :TLLIHRD 1kaeA 269 :ILLTPAA T0310 263 :PLFDQIIDMLRVEQVKIHA 1kaeA 276 :DMARRVAEAVERQLAELPR T0310 292 :VKSLRTEYGDLELC 1kaeA 295 :AETARQALNASRLI T0310 308 :VVDNVQDAIDHIHKYGSSH 1kaeA 309 :VTKDLAQCVEISNQYGPEH T0310 328 :DVIVTEDENTA 1kaeA 328 :LIIQTRNAREL T0310 346 :DSACVFW 1kaeA 344 :SAGSVFL Number of specific fragments extracted= 22 number of extra gaps= 0 total=819 Number of alignments=49 # 1kaeA read from 1kaeA/merged-good-all-a2m # found chain 1kaeA in training set Warning: unaligning (T0310)E52 because of BadResidue code BAD_PEPTIDE in next template residue (1kaeA)T61 Warning: unaligning (T0310)A53 because of BadResidue code BAD_PEPTIDE at template residue (1kaeA)T61 T0310 16 :LATLEPEQRAEI 1kaeA 9 :WNSCTAEQQRQL T0310 28 :IHHLADLLTDQRDEILLANKKDLE 1kaeA 36 :VNDILDNVKARGDEALREYSAKFD T0310 54 :E 1kaeA 62 :T T0310 55 :G 1kaeA 64 :T T0310 56 :RLAAPLLKRLSL 1kaeA 67 :KVSAEEIAAASE T0310 68 :STSKLNSLAIGLRQIAAS 1kaeA 84 :LKQAMAVAVKNIETFHTA T0310 87 :QD 1kaeA 102 :QK T0310 92 :RVLRRTRIAKNLELEQVTVPIGVLLVIFE 1kaeA 104 :LPPVDVETQPGVRCQQVTRPVASVGLYIP T0310 121 :SRPDCLPQVAAL 1kaeA 135 :SAPLFSTVLMLA T0310 133 :AIASGN 1kaeA 149 :ASIAGC T0310 139 :GLLLKGGKEAAHSNRILH 1kaeA 157 :VVLCSPPPIADEILYAAQ T0310 165 :IHGVKEAVQL 1kaeA 175 :LCGVQDVFNV T0310 177 :TR 1kaeA 185 :GG T0310 179 :EE 1kaeA 188 :QA T0310 184 :DKMIDLIIPRGS 1kaeA 200 :VPKVDKIFGPGN T0310 196 :SQLVRDIQKAAKGIPV 1kaeA 215 :TEAKRQVSQRLDGAAI T0310 212 :MGHSEGICHMYVDSEASVDKVT 1kaeA 232 :MPAGPSEVLVIADSGATPDFVA T0310 234 :RLVRDSKCEYPAAC 1kaeA 255 :DLLSQAEHGPDSQV T0310 252 :TLLIHRD 1kaeA 269 :ILLTPAA T0310 263 :PLFDQIIDMLRVEQVKIHA 1kaeA 276 :DMARRVAEAVERQLAELPR T0310 292 :VKSLRTEYGDL 1kaeA 295 :AETARQALNAS T0310 305 :CIEVVDNVQDAIDHIHKYGSSH 1kaeA 306 :RLIVTKDLAQCVEISNQYGPEH T0310 328 :DVIVTEDENTA 1kaeA 328 :LIIQTRNAREL T0310 344 :HV 1kaeA 341 :SI T0310 346 :DSACVFWN 1kaeA 344 :SAGSVFLG T0310 354 :ASTRFS 1kaeA 367 :HVLPTY Number of specific fragments extracted= 26 number of extra gaps= 1 total=845 Number of alignments=50 # 1kaeA read from 1kaeA/merged-good-all-a2m # found chain 1kaeA in training set T0310 16 :LATLEPEQRAEI 1kaeA 9 :WNSCTAEQQRQL T0310 32 :ADLLTDQRDEILLANKKDLEEAEGRL 1kaeA 33 :TRTVNDILDNVKARGDEALREYSAKF T0310 58 :AAPLLKRLS 1kaeA 69 :SAEEIAAAS T0310 67 :LSTSKLNSLAIGLRQIAASSQDSVGRVLRRTRIAKNLELEQVTVPIGVLLVIFESRPDCLPQV 1kaeA 79 :RLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGLYIPGGSAPLFST T0310 130 :AALAIASGN 1kaeA 146 :ATPASIAGC T0310 139 :GLLLKGGKEAAHSNRILH 1kaeA 157 :VVLCSPPPIADEILYAAQ T0310 165 :IHGVKEAVQLVN 1kaeA 175 :LCGVQDVFNVGG T0310 177 :TREEVELDKMIDLIIPRGSS 1kaeA 193 :LAFGTESVPKVDKIFGPGNA T0310 197 :QLVRDIQKAAKGIPVMGHS 1kaeA 216 :EAKRQVSQRLDGAAIDMPA T0310 217 :GICH 1kaeA 235 :GPSE T0310 221 :MYVDSEASVDKVTRLVRD 1kaeA 241 :VIADSGATPDFVASDLLS T0310 239 :SKCEYPAAC 1kaeA 261 :EHGPDSQVI T0310 253 :LLIH 1kaeA 270 :LLTP T0310 260 :LRTPLFDQIIDMLRVEQ 1kaeA 274 :AADMARRVAEAVERQLA T0310 288 :YLTFVKSLRTEYGDLELC 1kaeA 291 :ELPRAETARQALNASRLI T0310 308 :VVDNVQDAIDHIHKYGSSH 1kaeA 309 :VTKDLAQCVEISNQYGPEH T0310 328 :DVIVTEDENTA 1kaeA 328 :LIIQTRNAREL T0310 346 :DSACVFWNASTRFSDGYRFGLGAEVGISTSRIHARGPVGLEGLLTTKWL 1kaeA 344 :SAGSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRMTV Number of specific fragments extracted= 18 number of extra gaps= 0 total=863 Number of alignments=51 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 51 Adding 3568 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -735.9833, CN propb: -735.9833 weights: 0.5122 constraints: 1004 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 1004 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 1004 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 2564 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 2564 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 3568 # command: