parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0333/ # command:# Making conformation for sequence T0333 numbered 1 through 376 Created new target T0333 from T0333.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0333/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0333//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0333/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0333//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0333/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0333/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0333/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c3oE/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c3oE expands to /projects/compbio/data/pdb/1c3o.pdb.gz 1c3oE:Skipped atom 23348, because occupancy 0.5 <= existing 0.500 in 1c3oE Skipped atom 23350, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 23352, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 23354, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 23356, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 25848, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 25850, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 25852, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 25854, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 25856, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 26478, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 26480, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 27205, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 27207, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 27209, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 27211, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 27213, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 27256, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 27258, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 27260, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 27262, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 27264, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 28342, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 28344, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 28346, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 28348, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 28350, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29126, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29128, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29130, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29132, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29134, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29136, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29138, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29461, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29463, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29465, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29467, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29469, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29471, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29473, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29853, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29855, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29857, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29859, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29861, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29879, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29881, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29883, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29885, because occupancy 0.500 <= existing 0.500 in 1c3oE Skipped atom 29887, because occupancy 0.500 <= existing 0.500 in 1c3oE # T0333 read from 1c3oE/merged-good-all-a2m # 1c3oE read from 1c3oE/merged-good-all-a2m # adding 1c3oE to template set # found chain 1c3oE in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1c3oE)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1c3oE)D558 T0333 2 :LFVSSPGI 1c3oE 10 :ILILGAGP # choosing archetypes in rotamer library T0333 10 :GHL 1c3oE 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1c3oE 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEHADRAAAA 1c3oE 51 :PATIMTDPEM T0333 45 :LEVVDVAP 1c3oE 61 :ADATYIEP T0333 94 :RPL 1c3oE 71 :WEV T0333 100 :TMALVDDYRPDLVVYEQGATVGLLAADRA 1c3oE 74 :VRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1c3oE 112 :GVT T0333 135 :RNQSA 1c3oE 115 :MIGAT T0333 141 :RTRGMHRSIASFLTDL 1c3oE 505 :LAGVREAEIRKLRDQY T0333 165 :PEPVATIESFPPSLL 1c3oE 521 :DLHPVYKRVDTCAAE T0333 184 :PEGWFMRWVPYGGGAV 1c3oE 536 :FATDTAYMYSTYEEEC T0333 204 :LPPV 1c3oE 553 :ANPS T0333 210 :RPEVAITMGT 1c3oE 559 :REKIMVLGGG T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1c3oE 572 :IGQGIEFDYCCVHASLALREDGYETIMVNCNPE T0333 275 :LRTCTAVVHHG 1c3oE 610 :YDTSDRLYFEP T0333 286 :GGGTVMTAIDAGIP 1c3oE 622 :TLEDVLEIVRIEKP T0333 300 :QLLAPDPRD 1c3oE 637 :GVIVQYGGQ T0333 309 :QFQHTAR 1c3oE 647 :PLKLARA T0333 318 :VSRRGIGLV 1c3oE 654 :LEAAGVPVI T0333 327 :ST 1c3oE 664 :TS T0333 334 :ADLLRRLIG 1c3oE 666 :PDAIDRAED T0333 347 :RTAAREVREE 1c3oE 675 :RERFQHAVER T0333 363 :PAETVRRIVERI 1c3oE 697 :AIEMAVEKAKEI Number of specific fragments extracted= 24 number of extra gaps= 1 total=24 Number of alignments=1 # 1c3oE read from 1c3oE/merged-good-all-a2m # found chain 1c3oE in template set T0333 2 :LFVSSPGI 1c3oE 12 :ILGAGPIV T0333 10 :GHL 1c3oE 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHADRAAAAG 1c3oE 28 :YSGAQACKALREEGYRVILVNSNPATIMTDPE T0333 45 :LEVVDVAPDYSA 1c3oE 61 :ADATYIEPIHWE T0333 99 :GTMALVDDYRPDLVVYEQGATVGLLAADRA 1c3oE 73 :VVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1c3oE 112 :GVT T0333 135 :RNQSA 1c3oE 115 :MIGAT T0333 140 :WRTRGMHRSIASFLTDLM 1c3oE 800 :TLSQEIQDVMRQQVQKLA T0333 173 :SFPPSLLL 1c3oE 878 :GVTKEVIP T0333 186 :GWFMRWVPYGGGAVLGDRLPPVP 1c3oE 886 :PYYSVKEVVLPFNKFPGVDPLLG T0333 209 :ARPEVAITM 1c3oE 941 :KHGRALLSV T0333 223 :QAFGIGAVEPIIAAAGEVDADFVL 1c3oE 950 :REGDKERVVDLAAKLLKQGFELDA T0333 250 :DLDI 1c3oE 985 :GINP T0333 254 :SPLGT 1c3oE 992 :NKVHE T0333 267 :G 1c3oE 997 :G T0333 269 :TP 1c3oE 998 :RP T0333 271 :LHTLLR 1c3oE 1001 :IQDRIK T0333 277 :TCTAVVHHG 1c3oE 1009 :EYTYIINTT T0333 286 :GGGTV 1c3oE 1019 :GRRAI T0333 308 :DQF 1c3oE 1025 :DSR T0333 313 :TAREAVSRRGIGLVS 1c3oE 1028 :VIRRSALQYKVHYDT Number of specific fragments extracted= 21 number of extra gaps= 0 total=45 Number of alignments=2 # 1c3oE read from 1c3oE/merged-good-all-a2m # found chain 1c3oE in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1c3oE)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1c3oE)D558 T0333 1 :MLFVSSPGI 1c3oE 10 :ILILGAGPI T0333 10 :GH 1c3oE 21 :GQ T0333 12 :LFPLIQLAWGFRTAGHDVLIAV 1c3oE 27 :DYSGAQACKALREEGYRVILVN T0333 34 :AEHA 1c3oE 51 :PATI T0333 45 :LEVVDVAPDY 1c3oE 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1c3oE 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GV 1c3oE 112 :GV T0333 136 :N 1c3oE 114 :T T0333 138 :SAWRTRGMHRSIAS 1c3oE 115 :MIGATADAIDKAED T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1c3oE 508 :VREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEEC T0333 204 :LPPV 1c3oE 553 :ANPS T0333 210 :RPEVAITMGTIELQAFGIGAVEPII 1c3oE 559 :REKIMVLGGGPNRIGQGIEFDYCCV T0333 235 :AAAGEVDADFVLALGD 1c3oE 587 :LALREDGYETIMVNCN T0333 251 :LDISPLGTLPR 1c3oE 604 :ETVSTDYDTSD T0333 279 :TAVVHHGGGGTVMTAIDAGIP 1c3oE 615 :RLYFEPVTLEDVLEIVRIEKP T0333 300 :QLLAP 1c3oE 637 :GVIVQ T0333 305 :DPRDQFQHTAREAVSRRGIGL 1c3oE 643 :GGQTPLKLARALEAAGVPVIG T0333 329 :SD 1c3oE 665 :SP T0333 335 :DLLRRLIGDESLRTAAREV 1c3oE 667 :DAIDRAEDRERFQHAVERL T0333 360 :LPTPAETVRRIVER 1c3oE 695 :VTAIEMAVEKAKEI Number of specific fragments extracted= 20 number of extra gaps= 1 total=65 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c3oG/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c3oG expands to /projects/compbio/data/pdb/1c3o.pdb.gz 1c3oG:Skipped atom 35834, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 35836, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 35838, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 35840, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 36529, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 36531, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 36533, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 36535, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 36537, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 36539, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 36541, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 36923, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 36925, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 36927, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 36929, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 36931, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 39048, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 39050, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 39052, because occupancy 0.500 <= existing 0.500 in 1c3oG Skipped atom 39054, because occupancy 0.500 <= existing 0.500 in 1c3oG # T0333 read from 1c3oG/merged-good-all-a2m # 1c3oG read from 1c3oG/merged-good-all-a2m # adding 1c3oG to template set # found chain 1c3oG in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1c3oG)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1c3oG)D558 T0333 2 :LFVSSPGI 1c3oG 10 :ILILGAGP T0333 10 :GHL 1c3oG 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1c3oG 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEHADRAAAA 1c3oG 51 :PATIMTDPEM T0333 45 :LEVVDVAP 1c3oG 61 :ADATYIEP T0333 94 :RPL 1c3oG 71 :WEV T0333 100 :TMALVDDYRPDLVVYEQGATVGLLAADRA 1c3oG 74 :VRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1c3oG 112 :GVT T0333 135 :RNQSA 1c3oG 115 :MIGAT T0333 141 :RTRGMHRSIASFLTDL 1c3oG 505 :LAGVREAEIRKLRDQY T0333 165 :PEPVATIESFPPSLL 1c3oG 521 :DLHPVYKRVDTCAAE T0333 183 :E 1c3oG 536 :F T0333 200 :LGDR 1c3oG 547 :YEEE T0333 204 :LPPV 1c3oG 553 :ANPS T0333 210 :RPEVAITMG 1c3oG 559 :REKIMVLGG T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1c3oG 572 :IGQGIEFDYCCVHASLALREDGYETIMVNCNPE T0333 275 :LRTCTAVVHHG 1c3oG 610 :YDTSDRLYFEP T0333 286 :GGGTVMTAIDAGIP 1c3oG 622 :TLEDVLEIVRIEKP T0333 300 :QLLAPDPRD 1c3oG 637 :GVIVQYGGQ T0333 309 :QFQHTAR 1c3oG 647 :PLKLARA T0333 318 :VSRRGIG 1c3oG 654 :LEAAGVP T0333 325 :LVST 1c3oG 662 :IGTS T0333 334 :ADLLRRLIG 1c3oG 666 :PDAIDRAED T0333 347 :RTAAREVREE 1c3oG 675 :RERFQHAVER T0333 362 :TPAETVRRIVERIS 1c3oG 696 :TAIEMAVEKAKEIG Number of specific fragments extracted= 25 number of extra gaps= 1 total=90 Number of alignments=4 # 1c3oG read from 1c3oG/merged-good-all-a2m # found chain 1c3oG in template set T0333 2 :LFVSSPGI 1c3oG 12 :ILGAGPIV T0333 10 :GHL 1c3oG 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHADRAAAAG 1c3oG 28 :YSGAQACKALREEGYRVILVNSNPATIMTDPE T0333 45 :LEVVDVAPDYSA 1c3oG 61 :ADATYIEPIHWE T0333 99 :GTMALVDDYRPDLVVYEQGATVGLLAADRA 1c3oG 73 :VVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1c3oG 112 :GVT T0333 135 :RNQSA 1c3oG 115 :MIGAT T0333 140 :WRTRGMHRSIASFLTDLM 1c3oG 800 :TLSQEIQDVMRQQVQKLA T0333 168 :VATI 1c3oG 874 :LAEQ T0333 173 :SFPPSLLL 1c3oG 878 :GVTKEVIP T0333 186 :GWFMRWVPYGGGAVLGDRLPPVP 1c3oG 886 :PYYSVKEVVLPFNKFPGVDPLLG T0333 209 :ARPEVAITM 1c3oG 941 :KHGRALLSV T0333 223 :QAFGIGAVEPIIAAAGEVDADFVLA 1c3oG 950 :REGDKERVVDLAAKLLKQGFELDAT T0333 254 :SPLG 1c3oG 982 :GEAG T0333 261 :RNVRAVGWT 1c3oG 986 :INPRLVNKV T0333 271 :LHTLLR 1c3oG 1001 :IQDRIK T0333 277 :TCTAVVHHG 1c3oG 1009 :EYTYIINTT T0333 286 :GGGT 1c3oG 1019 :GRRA T0333 308 :DQF 1c3oG 1025 :DSR T0333 313 :TAREAVSRRGIGLV 1c3oG 1028 :VIRRSALQYKVHYD Number of specific fragments extracted= 20 number of extra gaps= 0 total=110 Number of alignments=5 # 1c3oG read from 1c3oG/merged-good-all-a2m # found chain 1c3oG in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1c3oG)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1c3oG)D558 T0333 1 :MLFVSSPGI 1c3oG 10 :ILILGAGPI T0333 10 :GHL 1c3oG 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1c3oG 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEHA 1c3oG 51 :PATI T0333 40 :AAAAG 1c3oG 55 :MTDPE T0333 45 :LEVVDVAPDY 1c3oG 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1c3oG 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GV 1c3oG 112 :GV T0333 136 :NQSAW 1c3oG 114 :TMIGA T0333 142 :TRGMHRSIAS 1c3oG 119 :TADAIDKAED T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1c3oG 508 :VREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEEC T0333 204 :LPPV 1c3oG 553 :ANPS T0333 210 :RPEVAITMGTIELQAFGIGAVEPIIA 1c3oG 559 :REKIMVLGGGPNRIGQGIEFDYCCVH T0333 236 :AAGEVDADFVLALGD 1c3oG 588 :ALREDGYETIMVNCN T0333 251 :LDISPL 1c3oG 608 :TDYDTS T0333 279 :TAVVHHGGGGTVMTAIDAGIP 1c3oG 615 :RLYFEPVTLEDVLEIVRIEKP T0333 300 :QLLAP 1c3oG 637 :GVIVQ T0333 305 :DPRDQFQHTAREAVSRRGIGL 1c3oG 643 :GGQTPLKLARALEAAGVPVIG T0333 329 :SD 1c3oG 665 :SP T0333 335 :DLLRRLIGDESLRTAAREV 1c3oG 667 :DAIDRAEDRERFQHAVERL T0333 360 :LPTPAETVRRIVER 1c3oG 695 :VTAIEMAVEKAKEI Number of specific fragments extracted= 21 number of extra gaps= 1 total=131 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j0aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1j0aA expands to /projects/compbio/data/pdb/1j0a.pdb.gz 1j0aA:# T0333 read from 1j0aA/merged-good-all-a2m # 1j0aA read from 1j0aA/merged-good-all-a2m # adding 1j0aA to template set # found chain 1j0aA in template set T0333 2 :LFVSSPG 1j0aA 73 :VITVGAV T0333 11 :HLFPLIQLAWGFRTAGHDVLIAV 1j0aA 80 :HSNHAFVTGLAAKKLGLDAILVL T0333 34 :AEH 1j0aA 104 :GKE T0333 37 :ADRAAAAGLEVVDVA 1j0aA 112 :YLLDKIMGIETRVYD T0333 54 :YS 1j0aA 127 :AK T0333 81 :DLEEWGVQIAAV 1j0aA 132 :ELMKYAEEIAEE T0333 93 :NRPLVDGTMALVDDY 1j0aA 164 :TLGYVRAVGEIATQS T0333 108 :RPDLVVYEQGA 1j0aA 181 :KFDSIVVAAGS T0333 119 :TVGLLA 1j0aA 195 :LAGLSL T0333 125 :ADRAG 1j0aA 202 :LSILN T0333 130 :VPAVQRNQS 1j0aA 209 :IRPVGIAVG T0333 140 :WRTRGMHRSIASFLTDLMDKHQVSLPEPVATIESFPPSL 1j0aA 218 :RFGEVMTSKLDNLIKEAAELLGVKVEVRPELYDYSFGEY T0333 209 :ARP 1j0aA 257 :GKI T0333 226 :GIGAVEPIIAAAGEVDADF 1j0aA 260 :TGEVAQIIRKVGTREGIIL T0333 253 :I 1j0aA 296 :K T0333 257 :GTLPRNV 1j0aA 297 :GELGEKI T0333 280 :AVVHHGGGGTVM 1j0aA 304 :LFIHTGGISGTF Number of specific fragments extracted= 17 number of extra gaps= 0 total=148 Number of alignments=7 # 1j0aA read from 1j0aA/merged-good-all-a2m # found chain 1j0aA in template set T0333 10 :GHLFPLIQLAWGFRTAGHDVLIAVAEHA 1j0aA 79 :VHSNHAFVTGLAAKKLGLDAILVLRGKE T0333 38 :DRAAAAGLEVVDVA 1j0aA 113 :LLDKIMGIETRVYD T0333 52 :PDYSAVKVFEQVAKDNP 1j0aA 129 :DSFELMKYAEEIAEELK T0333 69 :RFAETVATRPAIDLEEWGVQIAA 1j0aA 147 :EGRKPYVIPPGGASPIGTLGYVR T0333 99 :GTMALVDD 1j0aA 170 :AVGEIATQ T0333 107 :YRPDLVVY 1j0aA 180 :VKFDSIVV T0333 115 :EQGA 1j0aA 190 :GSGG T0333 119 :TVGLL 1j0aA 195 :LAGLS T0333 124 :AADRAG 1j0aA 201 :GLSILN T0333 130 :VPAVQRNQSA 1j0aA 209 :IRPVGIAVGR T0333 140 :WRTRGMHRSIASFLTD 1j0aA 221 :EVMTSKLDNLIKEAAE T0333 170 :TIE 1j0aA 237 :LLG T0333 173 :SFPP 1j0aA 241 :KVEV T0333 191 :WVPYGGG 1j0aA 245 :RPELYDY T0333 200 :LGDR 1j0aA 252 :SFGE T0333 223 :QAFGIGAVEPIIAAAGEV 1j0aA 256 :YGKITGEVAQIIRKVGTR T0333 241 :DAD 1j0aA 275 :GII T0333 253 :I 1j0aA 278 :L T0333 254 :SPLG 1j0aA 297 :GELG T0333 261 :RNV 1j0aA 301 :EKI T0333 280 :AVVHHGGGGTVM 1j0aA 304 :LFIHTGGISGTF Number of specific fragments extracted= 21 number of extra gaps= 0 total=169 Number of alignments=8 # 1j0aA read from 1j0aA/merged-good-all-a2m # found chain 1j0aA in template set T0333 1 :MLFVSSPG 1j0aA 72 :VVITVGAV T0333 11 :HLFPLIQLAWGFRTAGHDVLIAV 1j0aA 80 :HSNHAFVTGLAAKKLGLDAILVL T0333 35 :EHADRAAAAGLEVVDVAPDYSAV 1j0aA 110 :GNYLLDKIMGIETRVYDAKDSFE T0333 59 :VF 1j0aA 133 :LM T0333 61 :EQVAKDNPRFAETVATRPAIDLEEWGVQIAAVNRPLVD 1j0aA 142 :EELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSE T0333 107 :YRPDLVVYEQGAT 1j0aA 180 :VKFDSIVVAAGSG T0333 120 :VGL 1j0aA 196 :AGL T0333 123 :LAADRAGV 1j0aA 200 :LGLSILNE T0333 131 :PAVQRNQSAWRT 1j0aA 210 :RPVGIAVGRFGE T0333 144 :GMHRSIASFLT 1j0aA 222 :VMTSKLDNLIK T0333 178 :L 1j0aA 238 :L T0333 182 :AEPEGWFMRWVPYGGGA 1j0aA 239 :GVKVEVRPELYDYSFGE T0333 225 :FGIGAVEPIIAAAGEVDA 1j0aA 259 :ITGEVAQIIRKVGTREGI T0333 257 :GTLPRNV 1j0aA 297 :GELGEKI T0333 280 :AVVHHGGGGTVM 1j0aA 304 :LFIHTGGISGTF Number of specific fragments extracted= 15 number of extra gaps= 0 total=184 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xv5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xv5A expands to /projects/compbio/data/pdb/1xv5.pdb.gz 1xv5A:# T0333 read from 1xv5A/merged-good-all-a2m # 1xv5A read from 1xv5A/merged-good-all-a2m # adding 1xv5A to template set # found chain 1xv5A in template set Warning: unaligning (T0333)G8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xv5A)G1015 Warning: unaligning (T0333)G10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xv5A)G1015 Warning: unaligning (T0333)G267 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xv5A)Y1275 Warning: unaligning (T0333)T269 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xv5A)Y1275 T0333 1 :M 1xv5A 1001 :M T0333 2 :LFV 1xv5A 1005 :IFM T0333 5 :SSP 1xv5A 1010 :GLE T0333 11 :HLFPLIQLAWGFRTAGHDVLIAVAEHADR 1xv5A 1016 :VTKFSLEQRDWFIKNGHEVTLVYAKDKSF T0333 41 :AAAGL 1xv5A 1045 :TRTSS T0333 46 :EVVDVAP 1xv5A 1057 :IPVILAK T0333 81 :DL 1xv5A 1064 :EY T0333 98 :DGTMALVDDY 1xv5A 1066 :DKALKLVNDC T0333 110 :DLVVYEQGAT 1xv5A 1076 :DILIINSVPA T0333 120 :VGLLAADRA 1xv5A 1091 :ATINNYKKL T0333 129 :GVPAVQRNQSAW 1xv5A 1106 :SIRVVVYQHDHS T0333 144 :GMHRSIAS 1xv5A 1141 :SDNGDFNK T0333 152 :FLTDLMDKHQVSLPEPV 1xv5A 1150 :LMKEWYPETVSLFDDIE T0333 187 :WFMR 1xv5A 1167 :EAPT T0333 192 :VPYGGGAV 1xv5A 1171 :VYNFQPPM T0333 200 :LGDRL 1xv5A 1190 :DVSEI T0333 210 :RPEVAITMGTIELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1xv5A 1195 :NMNINRWIGRTTTWKGFYQMFDFHEKFLKPAGKSTVMEGLERS T0333 253 :ISPLGT 1xv5A 1255 :NREIDK T0333 259 :LPRN 1xv5A 1263 :LAPN T0333 263 :VRAV 1xv5A 1269 :AQIL T0333 270 :PLHTLLRTCTAVVHHG 1xv5A 1279 :EMLERMSKSGFGYQLS T0333 288 :GTVMTAIDAGIPQLLA 1xv5A 1307 :YTHLELGACGTIPVFW T0333 304 :PDPRDQFQ 1xv5A 1330 :KFRVDNTP T0333 318 :VSRRGIG 1xv5A 1338 :LTSHDSG T0333 325 :LV 1xv5A 1346 :IW T0333 327 :STSDKV 1xv5A 1351 :NDMEST T0333 334 :ADLLRRLIGDES 1xv5A 1357 :FERIKELSSDRA T0333 346 :LRTAAREVREEMVALP 1xv5A 1370 :YDREREKAYEFLYQHQ T0333 363 :PAETVRRIVERI 1xv5A 1386 :DSSFCFKEQFDI Number of specific fragments extracted= 29 number of extra gaps= 0 total=213 Number of alignments=10 # 1xv5A read from 1xv5A/merged-good-all-a2m # found chain 1xv5A in template set Warning: unaligning (T0333)G8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xv5A)G1015 Warning: unaligning (T0333)G10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xv5A)G1015 Warning: unaligning (T0333)G267 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xv5A)Y1275 Warning: unaligning (T0333)T269 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xv5A)Y1275 T0333 1 :M 1xv5A 1001 :M T0333 2 :LFV 1xv5A 1005 :IFM T0333 5 :SSP 1xv5A 1010 :GLE T0333 11 :HLFPLIQLAWGFRTAGHDVLIAVAEHADRAAA 1xv5A 1016 :VTKFSLEQRDWFIKNGHEVTLVYAKDKSFTRT T0333 43 :AGLEVVDVAPDYS 1xv5A 1054 :SFSIPVILAKEYD T0333 99 :GTMALVDD 1xv5A 1067 :KALKLVND T0333 109 :PDLVVY 1xv5A 1075 :CDILII T0333 115 :EQGA 1xv5A 1082 :SVPA T0333 119 :TVGLLAADRA 1xv5A 1090 :EATINNYKKL T0333 129 :GVPAVQRNQSAWRTRGMHRSIASFLTDLMDKHQVSLPE 1xv5A 1106 :SIRVVVYQHDHSVLSLRRNLGLEETVRRADVIFSHSDN T0333 167 :PVATIE 1xv5A 1151 :MKEWYP T0333 173 :SFP 1xv5A 1158 :TVS T0333 182 :AEPEGWFMRWVPYGGGAV 1xv5A 1161 :LFDDIEEAPTVYNFQPPM T0333 209 :ARPE 1xv5A 1193 :EINM T0333 213 :VAITMGTIE 1xv5A 1198 :INRWIGRTT T0333 223 :QAFGIGAVEPIIAAAGEV 1xv5A 1207 :TWKGFYQMFDFHEKFLKP T0333 241 :DADFVLALGDLDI 1xv5A 1226 :GKSTVMEGLERSP T0333 254 :SPLGTLP 1xv5A 1256 :REIDKMN T0333 261 :RNVRAV 1xv5A 1267 :QPAQIL T0333 271 :LHTLLRTCTAVVHHG 1xv5A 1280 :MLERMSKSGFGYQLS T0333 286 :GGGTVMTAIDAGIPQLLA 1xv5A 1305 :LEYTHLELGACGTIPVFW T0333 313 :TAREAVSRRG 1xv5A 1324 :STGENLKFRV T0333 323 :IG 1xv5A 1343 :SG T0333 325 :LVSTS 1xv5A 1346 :IWFDE T0333 330 :DKVD 1xv5A 1352 :DMES T0333 334 :ADLLRRLIGDESLRTAAREVREEMVALP 1xv5A 1357 :FERIKELSSDRALYDREREKAYEFLYQH T0333 362 :TPAETVRRIVERISG 1xv5A 1386 :DSSFCFKEQFDIITK Number of specific fragments extracted= 27 number of extra gaps= 0 total=240 Number of alignments=11 # 1xv5A read from 1xv5A/merged-good-all-a2m # found chain 1xv5A in template set Warning: unaligning (T0333)G8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xv5A)G1015 Warning: unaligning (T0333)G10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xv5A)G1015 Warning: unaligning (T0333)G267 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xv5A)Y1275 Warning: unaligning (T0333)T269 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xv5A)Y1275 T0333 1 :MLFVS 1xv5A 1003 :ICIFM T0333 6 :SP 1xv5A 1011 :LE T0333 11 :HLFPLIQLAWGFRTAGHDVLIAV 1xv5A 1016 :VTKFSLEQRDWFIKNGHEVTLVY T0333 50 :VAPDYSAVKVF 1xv5A 1040 :KDKSFTRTSSH T0333 92 :VNRPLVDGTMALVDDY 1xv5A 1060 :ILAKEYDKALKLVNDC T0333 110 :DLVVYEQGAT 1xv5A 1076 :DILIINSVPA T0333 120 :VGLLAADRA 1xv5A 1091 :ATINNYKKL T0333 129 :GVPAVQRNQSAWRTRGMHRSIASFLT 1xv5A 1106 :SIRVVVYQHDHSVLSLRRNLGLEETV T0333 156 :LMDKHQVSLPEPVATIESFPPSLL 1xv5A 1156 :PETVSLFDDIEEAPTVYNFQPPMD T0333 197 :GA 1xv5A 1180 :IV T0333 199 :VLGDRL 1xv5A 1189 :KDVSEI T0333 210 :RPEVAITMGTIELQAFGIGAVEPIIAAAGEVDADFVLALGD 1xv5A 1195 :NMNINRWIGRTTTWKGFYQMFDFHEKFLKPAGKSTVMEGLE T0333 251 :LDISPL 1xv5A 1256 :REIDKM T0333 259 :LPRN 1xv5A 1263 :LAPN T0333 263 :VRAV 1xv5A 1269 :AQIL T0333 270 :PLHTLL 1xv5A 1276 :INSEML T0333 276 :RTCTAVVHHGGG 1xv5A 1285 :SKSGFGYQLSKL T0333 288 :GTVMTAIDAGIPQLLA 1xv5A 1307 :YTHLELGACGTIPVFW T0333 310 :FQHTARE 1xv5A 1323 :KSTGENL T0333 323 :IGLVSTSDKVDADLLRRLIGD 1xv5A 1346 :IWFDENDMESTFERIKELSSD T0333 344 :ESLRTAAREVREEMVALPTPAETVRRIVERISG 1xv5A 1368 :ALYDREREKAYEFLYQHQDSSFCFKEQFDIITK Number of specific fragments extracted= 21 number of extra gaps= 0 total=261 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v4vA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0333 read from 1v4vA/merged-good-all-a2m # 1v4vA read from 1v4vA/merged-good-all-a2m # found chain 1v4vA in training set T0333 1 :M 1v4vA 5 :M T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTA 1v4vA 8 :VVLAFGTRPEATKMAPVYLALRGI T0333 26 :GHDVLIAV 1v4vA 33 :GLKPLVLL T0333 34 :AEHADRAAAA 1v4vA 42 :GQHREQLRQA T0333 44 :GLEVVDVA 1v4vA 56 :GIQEDRNL T0333 61 :EQ 1v4vA 64 :DV T0333 76 :TRPAIDLEEWGV 1v4vA 66 :MQERQALPDLAA T0333 95 :PLVDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1v4vA 78 :RILPQAARALKEMGADYVLVHGDTLTTFAVAWAA T0333 129 :GVPAVQRNQSAW 1v4vA 115 :GIPVGHVEAGLR T0333 141 :RTRGMHRSIASFLTDLMDKH 1v4vA 128 :GNLKEPFPEEANRRLTDVLT T0333 168 :VATIESF 1v4vA 148 :DLDFAPT T0333 176 :PSLLLEAEPEGWFMRWVPYGGGAV 1v4vA 155 :PLAKANLLKEGKREEGILVTGQTG T0333 200 :LGDRLPPVPARPEVAITMGTIELQAFGIGAVEPIIAAAGEVD 1v4vA 188 :LGRLPEGLPEGPYVTVTMHRRENWPLLSDLAQALKRVAEAFP T0333 242 :ADFVLALGDLD 1v4vA 231 :LTFVYPVHLNP T0333 253 :ISPL 1v4vA 251 :LKGV T0333 261 :RNVRAVGWTP 1v4vA 255 :RNFVLLDPLE T0333 271 :LHTLLRTCTAVVHHGG 1v4vA 268 :MAALMRASLLLVTDSG T0333 288 :GTVMTAIDAGIPQLLAPDPRDQFQ 1v4vA 284 :GLQEEGAALGVPVVVLRNVTERPE T0333 318 :VSRRGIG 1v4vA 308 :GLKAGIL T0333 325 :LV 1v4vA 316 :LA T0333 327 :STSDKV 1v4vA 319 :TDPEGV T0333 334 :ADLLRRLIGDESLRTAARE 1v4vA 325 :YRVVKGLLENPEELSRMRK Number of specific fragments extracted= 22 number of extra gaps= 0 total=283 Number of alignments=13 # 1v4vA read from 1v4vA/merged-good-all-a2m # found chain 1v4vA in training set T0333 1 :M 1v4vA 5 :M T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTA 1v4vA 8 :VVLAFGTRPEATKMAPVYLALRGI T0333 26 :GHDVLIAV 1v4vA 33 :GLKPLVLL T0333 52 :PDYSAVKVFEQ 1v4vA 41 :TGQHREQLRQA T0333 63 :VAKDNPRFAETVATRPAIDLEEWGVQIAA 1v4vA 53 :SLFGIQEDRNLDVMQERQALPDLAARILP T0333 99 :GTMALVDDYRPDLVVYEQGA 1v4vA 82 :QAARALKEMGADYVLVHGDT T0333 119 :TVGLLAADRAGVPAVQRNQSA 1v4vA 105 :FAVAWAAFLEGIPVGHVEAGL T0333 140 :WRTRGMHRSIASF 1v4vA 129 :NLKEPFPEEANRR T0333 153 :LTDLMDKHQVSLPEPVATIE 1v4vA 143 :TDVLTDLDFAPTPLAKANLL T0333 173 :SFPPS 1v4vA 165 :GKREE T0333 191 :WVPYGG 1v4vA 170 :GILVTG T0333 204 :LPPVP 1v4vA 189 :GRLPE T0333 209 :ARPEVAITMGTIE 1v4vA 197 :EGPYVTVTMHRRE T0333 223 :QAFGIGAVEPIIAAAGEV 1v4vA 210 :NWPLLSDLAQALKRVAEA T0333 241 :DADFVLALGDLDI 1v4vA 230 :HLTFVYPVHLNPV T0333 254 :SPLGTL 1v4vA 249 :PVLKGV T0333 261 :RNVRAVGWTP 1v4vA 255 :RNFVLLDPLE T0333 271 :LHTLLRTCTAVVHHGGG 1v4vA 268 :MAALMRASLLLVTDSGG T0333 289 :TVMTAIDAGIPQLLAPDPRDQF 1v4vA 285 :LQEEGAALGVPVVVLRNVTERP T0333 313 :TAREA 1v4vA 307 :EGLKA T0333 322 :GIGLVSTSDKVD 1v4vA 312 :GILKLAGTDPEG T0333 334 :ADLLRRLIGDESLRTAARE 1v4vA 325 :YRVVKGLLENPEELSRMRK Number of specific fragments extracted= 22 number of extra gaps= 0 total=305 Number of alignments=14 # 1v4vA read from 1v4vA/merged-good-all-a2m # found chain 1v4vA in training set T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTA 1v4vA 8 :VVLAFGTRPEATKMAPVYLALRGI T0333 26 :GHDVLIAV 1v4vA 33 :GLKPLVLL T0333 34 :AEHADRAAA 1v4vA 42 :GQHREQLRQ T0333 43 :AGLEVVDVAPDYS 1v4vA 55 :FGIQEDRNLDVMQ T0333 66 :DNPRFA 1v4vA 68 :ERQALP T0333 91 :AVNRPLVDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1v4vA 74 :DLAARILPQAARALKEMGADYVLVHGDTLTTFAVAWAA T0333 129 :GVPAVQRNQSAWRTRGMHRSIASFLT 1v4vA 115 :GIPVGHVEAGLRSGNLKEPFPEEANR T0333 183 :EPEGWFMRWVPYGGGA 1v4vA 165 :GKREEGILVTGQTGVD T0333 199 :VLGDRLPPVPARPEVAITMGTIELQAFGIGAVEPIIAAAGEV 1v4vA 187 :KLGRLPEGLPEGPYVTVTMHRRENWPLLSDLAQALKRVAEAF T0333 241 :DADFVLALGD 1v4vA 230 :HLTFVYPVHL T0333 257 :GTLPRNVRAVGWTP 1v4vA 251 :LKGVRNFVLLDPLE T0333 271 :LHTLLRTCTAVVHHGG 1v4vA 268 :MAALMRASLLLVTDSG T0333 288 :GTVMTAIDAGIPQLLAPDPRDQFQHT 1v4vA 284 :GLQEEGAALGVPVVVLRNVTERPEGL T0333 318 :VSRRGIGLV 1v4vA 310 :KAGILKLAG T0333 328 :TSDKVDADLLRRLIGDESLRTAARE 1v4vA 319 :TDPEGVYRVVKGLLENPEELSRMRK Number of specific fragments extracted= 15 number of extra gaps= 0 total=320 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o5iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o5iA expands to /projects/compbio/data/pdb/1o5i.pdb.gz 1o5iA:# T0333 read from 1o5iA/merged-good-all-a2m # 1o5iA read from 1o5iA/merged-good-all-a2m # adding 1o5iA to template set # found chain 1o5iA in template set Warning: unaligning (T0333)Y54 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o5iA)D59 Warning: unaligning (T0333)S55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o5iA)D59 T0333 2 :LFVSSPGIG 1o5iA 10 :VLVLAASRG T0333 14 :PLIQLAWGFRTAGHDVLIAV 1o5iA 19 :IGRAVADVLSQEGAEVTICA T0333 35 :EHADRAAAAGLEVVDVAPD 1o5iA 39 :RNEELLKRSGHRYVVCDLR T0333 56 :AVKVFEQVAKDNPRFAETV 1o5iA 73 :LVLNAGGPKAGFFDELTNE T0333 81 :DLEEWGVQIAAVNRPLVDGTMALVDDY 1o5iA 92 :DFKEAIDSLFLNMIKIVRNYLPAMKEK T0333 108 :RPDLVVYEQGAT 1o5iA 120 :WGRIVAITSFSV T0333 120 :VGLLAADRA 1o5iA 144 :ARMALTGFL T0333 129 :GVPAVQRNQSAW 1o5iA 163 :GITVNCVAPGWT T0333 141 :RTRGMHRSIASFLTDLMDKHQVS 1o5iA 198 :RRMAKPEEIASVVAFLCSEKASY T0333 166 :EPVATIESF 1o5iA 221 :LTGQTIVVD Number of specific fragments extracted= 10 number of extra gaps= 1 total=330 Number of alignments=16 # 1o5iA read from 1o5iA/merged-good-all-a2m # found chain 1o5iA in template set Warning: unaligning (T0333)Y54 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o5iA)D59 Warning: unaligning (T0333)S55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o5iA)D59 T0333 14 :PLIQLAWGFRTAGHDVLIAV 1o5iA 19 :IGRAVADVLSQEGAEVTICA T0333 35 :EHADRAAAAGLEVVDVAPD 1o5iA 39 :RNEELLKRSGHRYVVCDLR T0333 56 :AVKVFEQV 1o5iA 60 :LDLLFEKV T0333 65 :KDNPRFAETVATRPAIDLEEWGVQ 1o5iA 68 :KEVDILVLNAGGPKAGFFDELTNE T0333 89 :IAAVNRPLVDGTMALVDD 1o5iA 93 :FKEAIDSLFLNMIKIVRN T0333 121 :GLLAADRAGVPAVQRNQSA 1o5iA 111 :YLPAMKEKGWGRIVAITSF T0333 140 :WRTRGMHRSIASFLTDLM 1o5iA 139 :YTSNSARMALTGFLKTLS T0333 158 :DKHQVSLPEPVATIE 1o5iA 166 :VNCVAPGWTETERVK T0333 173 :SFPPS 1o5iA 182 :LLSEE T0333 209 :ARP 1o5iA 196 :PMR T0333 223 :QAFGIGAVEPIIAAAGE 1o5iA 199 :RMAKPEEIASVVAFLCS T0333 254 :SPLGTLPRNVRAVG 1o5iA 216 :EKASYLTGQTIVVD Number of specific fragments extracted= 12 number of extra gaps= 1 total=342 Number of alignments=17 # 1o5iA read from 1o5iA/merged-good-all-a2m # found chain 1o5iA in template set Warning: unaligning (T0333)Y54 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o5iA)D59 Warning: unaligning (T0333)S55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o5iA)D59 Warning: unaligning (T0333)A182 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o5iA)E136 Warning: unaligning (T0333)E183 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o5iA)E136 T0333 2 :LFVSSPGI 1o5iA 10 :VLVLAASR T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1o5iA 18 :GIGRAVADVLSQEGAEVTICA T0333 36 :HADRAAAAGLEVVDVAPD 1o5iA 40 :NEELLKRSGHRYVVCDLR T0333 56 :AVKVFEQVAK 1o5iA 60 :LDLLFEKVKE T0333 66 :DNPRFAETVATRPAIDLEEWGVQIAAVNRPLVDGTMALVDDYRPDLVVYE 1o5iA 77 :AGGPKAGFFDELTNEDFKEAIDSLFLNMIKIVRNYLPAMKEKGWGRIVAI T0333 174 :FPPSLLLE 1o5iA 127 :TSFSVISP T0333 184 :P 1o5iA 137 :N T0333 223 :QAFGIGAVEPIIAAAGEV 1o5iA 138 :LYTSNSARMALTGFLKTL T0333 241 :DADF 1o5iA 163 :GITV T0333 245 :VLALGDLDISPL 1o5iA 168 :CVAPGWTETERV T0333 317 :A 1o5iA 180 :K T0333 327 :STSDKVDADL 1o5iA 182 :LLSEEKKKQV T0333 358 :VALPTPAETVRRIVERI 1o5iA 198 :RRMAKPEEIASVVAFLC Number of specific fragments extracted= 13 number of extra gaps= 2 total=355 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2acvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2acvA expands to /projects/compbio/data/pdb/2acv.pdb.gz 2acvA:# T0333 read from 2acvA/merged-good-all-a2m # 2acvA read from 2acvA/merged-good-all-a2m # adding 2acvA to template set # found chain 2acvA in template set T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTA 2acvA 13 :IFIPAPGIGHLASALEFAKLLTNH T0333 26 :GHDVLIAVAEH 2acvA 39 :NLYITVFCIKF T0333 37 :ADRAAAA 2acvA 56 :DSYIKSV T0333 44 :GLEVVDVAP 2acvA 68 :QIQLIDLPE T0333 65 :KDNPRFAETV 2acvA 78 :EPPPQELLKS T0333 85 :WGVQIAAVNRPLVDGTMALVDDY 2acvA 88 :PEFYILTFLESLIPHVKATIKTI T0333 108 :RPDLVVYEQGATVGLLAADRAGVPAVQRNQSAW 2acvA 114 :KVVGLVLDFFCVSMIDVGNEFGIPSYLFLTSNV T0333 141 :RTRGMHRSIASFLTDL 2acvA 194 :NKDGGYIAYYKLAERF T0333 165 :PEPVATIESFPPSLL 2acvA 210 :RDTKGIIVNTFSDLE T0333 180 :LEAEPEGWFM 2acvA 231 :LYDHDEKIPP T0333 192 :VPYGGGAV 2acvA 241 :IYAVGPLL T0333 200 :LGDRLPPVPARPEVAITMGTIELQ 2acvA 266 :ILKWLDEQPDKSVVFLCFGSMGVS T0333 225 :FGIGAVEPIIAAAGEVDADFVLALGDLD 2acvA 290 :FGPSQIREIALGLKHSGVRFLWSNSAEK T0333 253 :ISPLGT 2acvA 321 :PEGFLE T0333 261 :RNVRAVGWTPLHTLLRT 2acvA 332 :GKGMICGWAPQVEVLAH T0333 278 :CTAVVHHGGGGTVMTAIDAGIPQLLAPDPRDQFQHTAR 2acvA 351 :IGGFVSHCGWNSILESMWFGVPILTWPIYAEQQLNAFR T0333 318 :VSR 2acvA 389 :LVK T0333 321 :RGIG 2acvA 393 :WGVG T0333 325 :LV 2acvA 398 :GL T0333 327 :STSDKV 2acvA 410 :VAAEEI T0333 334 :ADLLRRLIG 2acvA 416 :EKGLKDLMD T0333 344 :ES 2acvA 425 :KD T0333 346 :LRTAAREVREE 2acvA 429 :VHKKVQEMKEM T0333 357 :MVALPT 2acvA 443 :AVVDGG T0333 363 :PAETVRRIVERI 2acvA 450 :SLISVGKLIDDI Number of specific fragments extracted= 25 number of extra gaps= 0 total=380 Number of alignments=19 # 2acvA read from 2acvA/merged-good-all-a2m # found chain 2acvA in template set T0333 1 :M 2acvA 3 :M T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTA 2acvA 13 :IFIPAPGIGHLASALEFAKLLTNH T0333 26 :GHDVLIAVAEHA 2acvA 39 :NLYITVFCIKFP T0333 52 :PDYSAVKVFEQVAKDNP 2acvA 51 :GMPFADSYIKSVLASQP T0333 69 :RFAETVATRPAIDLEEWGVQ 2acvA 69 :IQLIDLPEVEPPPQELLKSP T0333 89 :IAAVNRPLVDGTMALVDD 2acvA 92 :ILTFLESLIPHVKATIKT T0333 107 :YRPDLVVYEQGATVGLLAADRAGVPAVQRNQSA 2acvA 113 :NKVVGLVLDFFCVSMIDVGNEFGIPSYLFLTSN T0333 140 :WRTRGMHRSIASF 2acvA 193 :FNKDGGYIAYYKL T0333 153 :LTDLMDKHQVSLPE 2acvA 208 :RFRDTKGIIVNTFS T0333 167 :PVATIESFPPSLL 2acvA 227 :SIDALYDHDEKIP T0333 191 :WVPYGGGAVLGDRLPPVP 2acvA 240 :PIYAVGPLLDLKGQPNPK T0333 209 :ARPEVAITMGTIE 2acvA 275 :DKSVVFLCFGSMG T0333 223 :QAFGIGAVEPIIAAAGEVDADFVLALGDLD 2acvA 288 :VSFGPSQIREIALGLKHSGVRFLWSNSAEK T0333 254 :SPLGTLP 2acvA 318 :KVFPEGF T0333 261 :RNVRAVGWTPLHTLLR 2acvA 332 :GKGMICGWAPQVEVLA T0333 277 :TCTAVVHHGGGGTVMTAIDAGIPQLLAPDPRDQF 2acvA 350 :AIGGFVSHCGWNSILESMWFGVPILTWPIYAEQQ T0333 313 :TAREAVSR 2acvA 384 :LNAFRLVK T0333 321 :RGIGLVSTS 2acvA 393 :WGVGLGLRV T0333 330 :DKVD 2acvA 411 :AAEE T0333 334 :ADLLRRLIGDE 2acvA 416 :EKGLKDLMDKD T0333 345 :SLRTAAREVREEMVALP 2acvA 431 :KKVQEMKEMSRNAVVDG T0333 362 :TPAETVRRIVERIS 2acvA 449 :SSLISVGKLIDDIT Number of specific fragments extracted= 22 number of extra gaps= 0 total=402 Number of alignments=20 # 2acvA read from 2acvA/merged-good-all-a2m # found chain 2acvA in template set T0333 1 :MLFVSSPGIGHLFPLIQLAWGFRTA 2acvA 12 :LIFIPAPGIGHLASALEFAKLLTNH T0333 26 :GHDVLIAV 2acvA 39 :NLYITVFC T0333 34 :A 2acvA 50 :P T0333 35 :EHADRAAA 2acvA 57 :SYIKSVLA T0333 43 :AGLEVVDVAPDYSAVKVFEQV 2acvA 67 :PQIQLIDLPEVEPPPQELLKS T0333 85 :WGVQIAAVNRPLVDGTMALVDDY 2acvA 88 :PEFYILTFLESLIPHVKATIKTI T0333 108 :RPDLVVYEQGATVGLLAADRAGVPAVQRNQSAWRTRGMHRSIASFLT 2acvA 114 :KVVGLVLDFFCVSMIDVGNEFGIPSYLFLTSNVGFLSLMLSLKNRQI T0333 182 :AEPEGWFMRWVPYGGGA 2acvA 235 :DEKIPPIYAVGPLLDLK T0333 199 :VLGDRLPPVPARPEVAITMGTIE 2acvA 265 :LILKWLDEQPDKSVVFLCFGSMG T0333 222 :L 2acvA 289 :S T0333 225 :FGIGAVEPIIAAAGEVDADFVLALGDLD 2acvA 290 :FGPSQIREIALGLKHSGVRFLWSNSAEK T0333 255 :P 2acvA 318 :K T0333 258 :TLPRN 2acvA 319 :VFPEG T0333 264 :RAVGWTPLHTLL 2acvA 335 :MICGWAPQVEVL T0333 276 :RTCTAVVHHGGGGTVMTAIDAGIPQLLAPDPRDQFQHTAREAV 2acvA 349 :KAIGGFVSHCGWNSILESMWFGVPILTWPIYAEQQLNAFRLVK T0333 319 :SRRGIGLV 2acvA 393 :WGVGLGLR T0333 327 :STSDKVDADLLRRLIGDE 2acvA 409 :VVAAEEIEKGLKDLMDKD T0333 345 :SLRTAAREVREEMVAL 2acvA 428 :IVHKKVQEMKEMSRNA T0333 361 :PTPAETVRRIVERI 2acvA 448 :GSSLISVGKLIDDI Number of specific fragments extracted= 19 number of extra gaps= 0 total=421 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vljA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0333 read from 1vljA/merged-good-all-a2m # 1vljA read from 1vljA/merged-good-all-a2m # found chain 1vljA in training set T0333 18 :LAWGFRTAGH 1vljA 22 :IGEEIKNAGI T0333 28 :DVLIAVAEH 1vljA 33 :KVLFLYGGG T0333 37 :ADRAAAAGLEVVDVAP 1vljA 53 :VDSLKKHGIEWVEVSG T0333 55 :SA 1vljA 70 :KP T0333 67 :N 1vljA 72 :N T0333 81 :DLE 1vljA 73 :PVL T0333 95 :PLVDGTMALVDDYRPDLVV 1vljA 76 :SKVHEAVEVAKKEKVEAVL T0333 114 :YEQGA 1vljA 96 :VGGGS T0333 119 :TVGLLAADRA 1vljA 103 :DSAKAVAAGA T0333 130 :VPAVQRNQSAW 1vljA 132 :LPIFDVLTISA T0333 141 :RTRGMHRSIASFLTDLMDKHQVSLPEPVA 1vljA 205 :FDGSSPEISNEIAEGTIRTIMKMTERLIE T0333 175 :PPSLL 1vljA 234 :KPDDY T0333 180 :LEAEPEGWFMRWVPYGGGAV 1vljA 248 :ATIALNGTMAVGRRGGEWAC T0333 200 :LGDRLPP 1vljA 312 :IFGFEGE T0333 226 :GIGAVEPIIAA 1vljA 319 :GEELILKGIEA T0333 312 :HTAR 1vljA 330 :FKNW T0333 318 :VSRRGIG 1vljA 334 :LKKVGAP T0333 325 :LV 1vljA 342 :SL T0333 327 :STSDKV 1vljA 348 :IPEEDI T0333 344 :ESLRTAAREVREE 1vljA 354 :DKIVDNVMLLVEK T0333 362 :T 1vljA 380 :V T0333 363 :PAETVRRIVERI 1vljA 382 :EREDVREILKLA Number of specific fragments extracted= 22 number of extra gaps= 0 total=443 Number of alignments=22 # 1vljA read from 1vljA/merged-good-all-a2m # found chain 1vljA in training set T0333 18 :LAWGFRTAGH 1vljA 22 :IGEEIKNAGI T0333 28 :DVLIAVAEHA 1vljA 33 :KVLFLYGGGS T0333 38 :DRAAAAGLEVVDVA 1vljA 54 :DSLKKHGIEWVEVS T0333 75 :ATRPAIDLEEWG 1vljA 68 :GVKPNPVLSKVH T0333 99 :GTMALVDDYRPDLVVY 1vljA 80 :EAVEVAKKEKVEAVLG T0333 115 :EQGA 1vljA 97 :GGGS T0333 119 :TVGLLAADRAG 1vljA 103 :DSAKAVAAGAL T0333 130 :VPAVQRNQSA 1vljA 132 :LPIFDVLTIS T0333 140 :WRTRGMHRSIASFLTDL 1vljA 317 :GEGEELILKGIEAFKNW T0333 168 :VATIE 1vljA 334 :LKKVG T0333 173 :SFPPS 1vljA 340 :PVSLK T0333 203 :RLPPVP 1vljA 345 :DAGIPE T0333 209 :ARP 1vljA 372 :GAS T0333 217 :MGTIELQAF 1vljA 375 :LGRIMVLER T0333 228 :GAVEPIIAAAG 1vljA 384 :EDVREILKLAA Number of specific fragments extracted= 15 number of extra gaps= 0 total=458 Number of alignments=23 # 1vljA read from 1vljA/merged-good-all-a2m # found chain 1vljA in training set T0333 18 :LAWGFRTAGHD 1vljA 22 :IGEEIKNAGIR T0333 29 :VLIAV 1vljA 34 :VLFLY T0333 34 :A 1vljA 40 :G T0333 35 :EHADRAAAAGLEVVDVAPDYSAV 1vljA 51 :QVVDSLKKHGIEWVEVSGVKPNP T0333 93 :NRPLVDGTMALVDDYRPDLVVY 1vljA 74 :VLSKVHEAVEVAKKEKVEAVLG T0333 115 :EQGAT 1vljA 97 :GGGSV T0333 120 :VGLLAADRAGV 1vljA 104 :SAKAVAAGALY T0333 131 :PAVQRNQSAWRTRGMHR 1vljA 133 :PIFDVLTISATGTEMNG T0333 155 :DLMDKHQVS 1vljA 314 :GFEGEGEEL T0333 226 :GIGAVEPIIAAAGEVDADF 1vljA 323 :ILKGIEAFKNWLKKVGAPV T0333 252 :DI 1vljA 342 :SL T0333 255 :PLGTLPRN 1vljA 344 :KDAGIPEE T0333 307 :RDQFQHTAREAV 1vljA 354 :DKIVDNVMLLVE T0333 319 :SRRG 1vljA 371 :KGAS T0333 325 :LV 1vljA 375 :LG T0333 327 :STSDKVDADLLRRL 1vljA 380 :VLEREDVREILKLA Number of specific fragments extracted= 16 number of extra gaps= 0 total=474 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pswA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pswA expands to /projects/compbio/data/pdb/1psw.pdb.gz 1pswA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M 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 # T0333 read from 1pswA/merged-good-all-a2m # 1pswA read from 1pswA/merged-good-all-a2m # adding 1pswA to template set # found chain 1pswA in template set Warning: unaligning (T0333)V50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pswA)E65 Warning: unaligning (T0333)D81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pswA)E65 T0333 1 :M 1pswA 1 :M T0333 2 :LFVSSPGI 1pswA 3 :ILVIGPSW T0333 10 :GHLFPLIQLAWGFRTA 1pswA 12 :GDMMMSQSLYRTLQAR T0333 26 :GHDVLIAVAEHADRAAAA 1pswA 30 :QAIIDVMAPAWCRPLLSR T0333 45 :L 1pswA 48 :M T0333 46 :EVVD 1pswA 53 :EAIP T0333 82 :LEEWGVQI 1pswA 66 :IGERRKLG T0333 102 :ALVDDYRPDLVVYEQGAT 1pswA 74 :HSLREKRYDRAYVLPNSF T0333 121 :GLLAADRAGVPAVQRNQSAW 1pswA 93 :SALVPLFAGIPHRTGWRGEM T0333 141 :RTRGMHRSIASFL 1pswA 124 :DKEAWPLMVERYI T0333 156 :LMDKHQVSLPEP 1pswA 137 :ALAYDKGIMRTA T0333 181 :EAEPEGWFMRWVPYGGGAV 1pswA 149 :QDLPQPLLWPQLQVSEGEK T0333 200 :LGDRLPPVPARPEVAITMGT 1pswA 170 :TCNQFSLSSERPMIGFCPGA T0333 220 :IELQA 1pswA 191 :FGPAK T0333 225 :FGIGAVEPIIAAAGEVDADFVLALG 1pswA 197 :WPHYHYAELAKQLIDEGYQVVLFGS T0333 254 :SPLGT 1pswA 222 :AKDHE T0333 261 :RNVRAV 1pswA 241 :AWCRNL T0333 267 :GWTPLHTL 1pswA 248 :GETQLDQA T0333 275 :LRTCTAVVHHGG 1pswA 259 :IAACKAIVTNDS T0333 288 :GTVMTAIDAGIPQLLAPDP 1pswA 271 :GLMHVAAALNRPLVALYGP T0333 324 :G 1pswA 302 :A T0333 325 :LV 1pswA 304 :VI T0333 327 :STSDKV 1pswA 330 :ITPQRV T0333 347 :RTAAREVREE 1pswA 336 :LEELNALLLQ Number of specific fragments extracted= 24 number of extra gaps= 0 total=498 Number of alignments=25 # 1pswA read from 1pswA/merged-good-all-a2m # found chain 1pswA in template set Warning: unaligning (T0333)V50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pswA)E65 Warning: unaligning (T0333)K58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pswA)E65 Warning: unaligning (T0333)V332 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pswA)E321 T0333 1 :M 1pswA 1 :M T0333 2 :LFVSSPGI 1pswA 3 :ILVIGPSW T0333 10 :GHLFPLIQLAWGFRTA 1pswA 12 :GDMMMSQSLYRTLQAR T0333 26 :GHDVLIAVAEHADRAAA 1pswA 30 :QAIIDVMAPAWCRPLLS T0333 43 :AGL 1pswA 49 :PEV T0333 46 :EVVD 1pswA 53 :EAIP T0333 59 :V 1pswA 66 :I T0333 83 :EEW 1pswA 67 :GER T0333 98 :DGTMALVDDYRPDLVVY 1pswA 70 :RKLGHSLREKRYDRAYV T0333 116 :QGA 1pswA 92 :KSA T0333 123 :LAADRAGVPAVQRNQSA 1pswA 95 :LVPLFAGIPHRTGWRGE T0333 140 :WRTRGMHRSIASFLTDL 1pswA 123 :LDKEAWPLMVERYIALA T0333 166 :EPVATIE 1pswA 140 :YDKGIMR T0333 173 :SFPPS 1pswA 150 :DLPQP T0333 191 :WVP 1pswA 155 :LLW T0333 202 :D 1pswA 158 :P T0333 205 :PPV 1pswA 159 :QLQ T0333 209 :ARPEVAITMGTIELQAFG 1pswA 179 :ERPMIGFCPGAEFGPAKR T0333 227 :IGAVEPIIAAAGEVDADFVLALGDLDI 1pswA 199 :HYHYAELAKQLIDEGYQVVLFGSAKDH T0333 254 :SPLGTLP 1pswA 230 :EILAALN T0333 261 :RNVRAV 1pswA 241 :AWCRNL T0333 267 :GWTP 1pswA 248 :GETQ T0333 271 :LHTLLRTCTAVVHHGGG 1pswA 255 :AVILIAACKAIVTNDSG T0333 289 :TVMTAIDAGIPQLLAPDP 1pswA 272 :LMHVAAALNRPLVALYGP T0333 321 :RGIGLVSTS 1pswA 300 :HKARVIRLI T0333 333 :D 1pswA 322 :G T0333 334 :ADLLRRL 1pswA 324 :HQSLIDI T0333 362 :TPAETVRRIVERI 1pswA 331 :TPQRVLEELNALL Number of specific fragments extracted= 28 number of extra gaps= 0 total=526 Number of alignments=26 # 1pswA read from 1pswA/merged-good-all-a2m # found chain 1pswA in template set Warning: unaligning (T0333)V50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pswA)E65 Warning: unaligning (T0333)P78 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pswA)E65 T0333 1 :MLFVSSPGIGHLFPLIQLAWGFRTA 1pswA 3 :ILVIGPSWVGDMMMSQSLYRTLQAR T0333 26 :GHDVLIAV 1pswA 30 :QAIIDVMA T0333 34 :AEHADRAAAAG 1pswA 39 :AWCRPLLSRMP T0333 46 :EVVD 1pswA 53 :EAIP T0333 79 :A 1pswA 66 :I T0333 95 :PLVDGTMALVDDYRPDLVVYEQGATVGLLAADRAGVPAVQRNQSAWRTRGMHRSIASFLTDLMDKHQVS 1pswA 67 :GERRKLGHSLREKRYDRAYVLPNSFKSALVPLFAGIPHRTGWRGEMRYGLLNDVRVLDKEAWPLMVERY T0333 169 :A 1pswA 136 :I T0333 171 :IESFPPSLLLEAEPEGWFMRWVPYGGGA 1pswA 137 :ALAYDKGIMRTAQDLPQPLLWPQLQVSE T0333 199 :VLGDRLPPVPARPEVAITMGTIE 1pswA 169 :YTCNQFSLSSERPMIGFCPGAEF T0333 222 :LQAFGIGAVEPIIAAAGEVDADFVLALG 1pswA 194 :AKRWPHYHYAELAKQLIDEGYQVVLFGS T0333 254 :SPL 1pswA 222 :AKD T0333 261 :RNVRAV 1pswA 241 :AWCRNL T0333 267 :GWTPLHTLL 1pswA 248 :GETQLDQAV T0333 276 :RTCTAVVHHG 1pswA 260 :AACKAIVTND T0333 287 :GGTVMTAIDAGIPQLLAPDPRD 1pswA 270 :SGLMHVAAALNRPLVALYGPSS T0333 320 :RRGIGL 1pswA 300 :HKARVI T0333 327 :STSDKVDADLLRRLIG 1pswA 329 :DITPQRVLEELNALLL Number of specific fragments extracted= 17 number of extra gaps= 0 total=543 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q7zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0333 read from 1q7zA/merged-good-all-a2m # 1q7zA read from 1q7zA/merged-good-all-a2m # found chain 1q7zA in training set T0333 2 :LFVSSPGIGHLF 1q7zA 15 :VLLLDGAYGTEF T0333 14 :PLIQLAWGFRTAGHDVLIAV 1q7zA 45 :VVLKVHRSYIESGSDVILTN T0333 34 :AEHADR 1q7zA 66 :FGATRM T0333 40 :AAAAGL 1q7zA 73 :LRKHGL T0333 56 :AVKVFEQVAKDNPRFAETVA 1q7zA 101 :LVFGDIGPTGELPYPLGSTL T0333 86 :GVQIAAVNRPLV 1q7zA 121 :FEEFYENFRETV T0333 102 :ALVDDYRPDLVVYEQGATVGLLAADRA 1q7zA 133 :EIMVEEGVDGIIFETFSDILELKAAVL T0333 129 :GVPAVQRNQSAW 1q7zA 167 :DVFLIAHMTFDE T0333 141 :RTRGMHRSIASFLTDLMDKHQVSLPEPVATIESF 1q7zA 271 :GCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVS T0333 187 :WFMRWVPY 1q7zA 305 :SPSKLVTF T0333 209 :ARPEVAI 1q7zA 313 :DHFVVIG T0333 218 :GT 1q7zA 326 :GR T0333 220 :I 1q7zA 330 :L T0333 221 :ELQAFG 1q7zA 333 :EMQKGN T0333 227 :IGAVEPIIAAAGE 1q7zA 340 :EIVIKEAKTQVEK T0333 241 :DADFV 1q7zA 353 :GAEVL T0333 246 :LALGD 1q7zA 359 :VNFGI T0333 253 :ISPL 1q7zA 364 :ESQI T0333 270 :PLHTLLR 1q7zA 368 :DVRYVEK T0333 288 :GTVMTAIDAGIPQLLAPDPRD 1q7zA 375 :IVQTLPYVSNVPLSLDIQNVD T0333 312 :HTAR 1q7zA 396 :LTER T0333 318 :VSRRGIGLV 1q7zA 400 :ALRAYPGRS T0333 327 :STSDKV 1q7zA 415 :VDEEEL T0333 334 :ADLLRRLI 1q7zA 421 :EMKINLLK T0333 342 :GDES 1q7zA 446 :SFEE T0333 346 :LRTAAREVREE 1q7zA 453 :YFEKALKILER T0333 357 :MVALP 1q7zA 479 :LGAEG T0333 363 :PAETVRRIVERI 1q7zA 484 :KPVEVLKTIEFI Number of specific fragments extracted= 28 number of extra gaps= 0 total=571 Number of alignments=28 # 1q7zA read from 1q7zA/merged-good-all-a2m # found chain 1q7zA in training set T0333 13 :FPLIQLAWGFRTAGHDVLIAVAE 1q7zA 44 :DVVLKVHRSYIESGSDVILTNTF T0333 36 :HADRAAAAGLE 1q7zA 69 :TRMKLRKHGLE T0333 52 :PDY 1q7zA 80 :DKL T0333 55 :SAVKVFEQVAKDNPRFAE 1q7zA 88 :NAVRIARRAAGEKLVFGD T0333 73 :TVATRPAIDLEEWGVQIA 1q7zA 112 :LPYPLGSTLFEEFYENFR T0333 99 :GTMALVDDYRPDLVVY 1q7zA 130 :ETVEIMVEEGVDGIIF T0333 117 :GA 1q7zA 148 :FS T0333 119 :TVGLLAADRAG 1q7zA 156 :AAVLAAREVSR T0333 130 :VPAVQRNQSA 1q7zA 168 :VFLIAHMTFD T0333 140 :WRTRGMHRSIASFLTDLMDKHQVSLPEPVATIE 1q7zA 208 :SLGPEEILPIFQELSQYTDKFLVVEPNAGKPIV T0333 173 :SFPPSLLLEA 1q7zA 248 :PLKPHDFAVH T0333 191 :WVPYGGGAV 1q7zA 265 :GVNIFGGCC T0333 205 :PPVP 1q7zA 291 :KPLQ T0333 209 :ARPEVAI 1q7zA 313 :DHFVVIG T0333 217 :MGTIE 1q7zA 322 :INPAG T0333 222 :LQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1q7zA 334 :MQKGNEEIVIKEAKTQVEKGAEVLDVNFGIE T0333 254 :SP 1q7zA 365 :SQ T0333 269 :TPLHTLLR 1q7zA 367 :IDVRYVEK T0333 289 :TVMTAIDAGIPQLLAPDP 1q7zA 376 :VQTLPYVSNVPLSLDIQN T0333 307 :RDQF 1q7zA 417 :EEEL T0333 312 :HTAREAVSRRGIGLVSTS 1q7zA 421 :EMKINLLKKYGGTLIVLL T0333 330 :DKVD 1q7zA 442 :DVPK T0333 334 :ADLLRRL 1q7zA 447 :FEERKEY T0333 347 :RTAAREVREEMV 1q7zA 454 :FEKALKILERHD T0333 359 :ALPTPA 1q7zA 481 :AEGKPV T0333 365 :ETVRRIVE 1q7zA 490 :KTIEFISS Number of specific fragments extracted= 26 number of extra gaps= 0 total=597 Number of alignments=29 # 1q7zA read from 1q7zA/merged-good-all-a2m # found chain 1q7zA in training set T0333 14 :PLIQLAWGFRTAGHDVLIAV 1q7zA 45 :VVLKVHRSYIESGSDVILTN T0333 34 :AEHADRAAAAGL 1q7zA 67 :GATRMKLRKHGL T0333 54 :YSAVKVF 1q7zA 79 :EDKLDPI T0333 61 :EQVAKDNPRF 1q7zA 111 :ELPYPLGSTL T0333 86 :G 1q7zA 121 :F T0333 91 :AVNRPLVDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1q7zA 122 :EEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAVL T0333 129 :GVPAVQRNQSAWRTRGMHRSIASFLT 1q7zA 167 :DVFLIAHMTFDEKGRSLTGTDPANFA T0333 160 :HQVSLPEPVATIESFP 1q7zA 293 :LQRKKKRIFAVSSPSK T0333 178 :LL 1q7zA 309 :LV T0333 181 :E 1q7zA 311 :T T0333 185 :EGWFMRWVPYGGGA 1q7zA 312 :FDHFVVIGERINPA T0333 199 :VLGDRLP 1q7zA 329 :KLWAEMQ T0333 224 :AFGIGAVEPIIAAAGEVDADFVLALGD 1q7zA 336 :KGNEEIVIKEAKTQVEKGAEVLDVNFG T0333 252 :DISPL 1q7zA 363 :IESQI T0333 287 :GGTVMTAIDAG 1q7zA 373 :EKIVQTLPYVS T0333 298 :IPQLLAPDPRDQFQHTARE 1q7zA 385 :VPLSLDIQNVDLTERALRA T0333 322 :GIGL 1q7zA 406 :GRSL T0333 326 :V 1q7zA 412 :S T0333 327 :STSDKVDADLLRRLI 1q7zA 414 :KVDEEELEMKINLLK T0333 342 :GDESLRTAAREVREEMVALP 1q7zA 446 :SFEERKEYFEKALKILERHD T0333 362 :TPAETVRRIVE 1q7zA 487 :EVLKTIEFISS Number of specific fragments extracted= 21 number of extra gaps= 0 total=618 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w5fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w5fA expands to /projects/compbio/data/pdb/1w5f.pdb.gz 1w5fA:# T0333 read from 1w5fA/merged-good-all-a2m # 1w5fA read from 1w5fA/merged-good-all-a2m # adding 1w5fA to template set # found chain 1w5fA in template set T0333 2 :LFVS 1w5fA 26 :VIGV T0333 12 :LFPLIQLAWGFRTA 1w5fA 30 :GGAGNNAINRMIEI T0333 26 :GHDVLIAVA 1w5fA 47 :GVEFVAVNT T0333 36 :HADRAAAAGL 1w5fA 56 :DLQVLEASNA T0333 46 :EVVDVAPD 1w5fA 67 :VKIQIGEN T0333 63 :VAKDN 1w5fA 75 :ITRGL T0333 81 :DLEEWGVQIAAVNRPLVDGTMALVDDYRPDLVVYEQGATVGLLA 1w5fA 80 :GAGGRPEIGEQAALESEEKIREVLQDTHMVFITAGFGGGTGTGA T0333 125 :ADRAGVPAVQRNQSAW 1w5fA 131 :AKEMGILTVAIVTTPF T0333 141 :RTRGMHRSIASFLTDLMDKHQVSL 1w5fA 188 :KIKDAFLKADETLHQGVKGISELI T0333 165 :PEPV 1w5fA 214 :RGYI T0333 175 :PPSLL 1w5fA 218 :RLTSR T0333 182 :AEPEGWFMRWVPYGGGAV 1w5fA 227 :ESVMKDAGAAILGIGVGK T0333 200 :LGDRLPPV 1w5fA 258 :ESKLIEHP T0333 208 :PARPEVAITM 1w5fA 267 :ENASSIVFNI T0333 221 :ELQAFGIGAVEPIIAAAGEV 1w5fA 278 :APSNIRMEEVHEAAMIIRQN T0333 241 :D 1w5fA 301 :D T0333 242 :ADFVLALGDL 1w5fA 304 :VKFGLIFDDE T0333 259 :LPRN 1w5fA 314 :VPDD T0333 263 :VRAVGWTPLHT 1w5fA 323 :FIATRFPDEDK Number of specific fragments extracted= 19 number of extra gaps= 0 total=637 Number of alignments=31 # 1w5fA read from 1w5fA/merged-good-all-a2m # found chain 1w5fA in template set T0333 11 :HLFPLIQLAWGFRTA 1w5fA 29 :VGGAGNNAINRMIEI T0333 26 :GHDVLIAVAE 1w5fA 47 :GVEFVAVNTD T0333 37 :ADRAAAAGLEVVDVAPDY 1w5fA 57 :LQVLEASNADVKIQIGEN T0333 72 :ETVATRPAIDLEEWGVQIAAVNR 1w5fA 75 :ITRGLGAGGRPEIGEQAALESEE T0333 99 :GTMALVDDYR 1w5fA 98 :KIREVLQDTH T0333 111 :LVVY 1w5fA 109 :VFIT T0333 115 :EQGATVGLLA 1w5fA 114 :GFGGGTGTGA T0333 125 :ADRAGVPAVQRNQSA 1w5fA 131 :AKEMGILTVAIVTTP T0333 140 :WRTRGMHRSIASFLTDLMDKHQVSLPE 1w5fA 151 :PERLKKAIEGLKKLRKHVDTLIKISNN T0333 167 :PVATIE 1w5fA 179 :LMEELP T0333 173 :SFPPS 1w5fA 186 :DVKIK T0333 314 :AREAVSR 1w5fA 222 :RFARIES T0333 321 :RGIGLVSTS 1w5fA 231 :KDAGAAILG T0333 330 :DKVD 1w5fA 245 :GEHR T0333 334 :ADLLRRLI 1w5fA 250 :REAAKKAM T0333 342 :G 1w5fA 281 :N T0333 343 :DESLRTAAREVREEMVAL 1w5fA 283 :RMEEVHEAAMIIRQNSSE T0333 361 :PTPAET 1w5fA 329 :PDEDKI Number of specific fragments extracted= 18 number of extra gaps= 0 total=655 Number of alignments=32 # 1w5fA read from 1w5fA/merged-good-all-a2m # found chain 1w5fA in template set T0333 1 :MLFVSS 1w5fA 24 :IKVIGV T0333 12 :LFPLIQLAWGFRTAGHD 1w5fA 30 :GGAGNNAINRMIEIGIH T0333 29 :VLIAV 1w5fA 48 :VEFVA T0333 34 :AEHADRAAAAGLEVVDVAPDYS 1w5fA 54 :NTDLQVLEASNADVKIQIGENI T0333 66 :DNPRFAETV 1w5fA 76 :TRGLGAGGR T0333 86 :GVQIAAVNRPLVDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1w5fA 85 :PEIGEQAALESEEKIREVLQDTHMVFITAGFGGGTGTGASPVI T0333 129 :GVPAVQRNQSAWRTRGM 1w5fA 135 :GILTVAIVTTPFYFEGP T0333 146 :HRSIASFLT 1w5fA 153 :RLKKAIEGL T0333 183 :EPEGWFMRWVPYGGGA 1w5fA 231 :KDAGAAILGIGVGKGE T0333 199 :VLGDRLPPVPARPEVAITMGTIE 1w5fA 258 :ESKLIEHPVENASSIVFNITAPS T0333 224 :AFGIGAVEPIIAAAGEV 1w5fA 281 :NIRMEEVHEAAMIIRQN T0333 241 :DADFVLALGD 1w5fA 303 :DVKFGLIFDD T0333 258 :TLPRN 1w5fA 313 :EVPDD Number of specific fragments extracted= 13 number of extra gaps= 0 total=668 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 4uagA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0333 read from 4uagA/merged-good-all-a2m # 4uagA read from 4uagA/merged-good-all-a2m # found chain 4uagA in training set Warning: unaligning (T0333)L156 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (4uagA)L199 Warning: unaligning (T0333)D158 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (4uagA)L199 Warning: unaligning (T0333)E181 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (4uagA)I220 Warning: unaligning (T0333)P184 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (4uagA)I220 Warning: unaligning (T0333)E185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (4uagA)R226 Warning: unaligning (T0333)A303 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (4uagA)P411 Warning: unaligning (T0333)P304 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (4uagA)P411 T0333 2 :LFVSSPG 4uagA 8 :VVIIGLG T0333 13 :FPLIQLAWGFRTAGHDVLIAV 4uagA 15 :LTGLSCVDFFLARGVTPRVMD T0333 34 :AEHADRAAAA 4uagA 40 :PPGLDKLPEA T0333 45 :LEVVDV 4uagA 50 :VERHTG T0333 53 :DYS 4uagA 56 :SLN T0333 56 :AVKVFEQVAKDN 4uagA 67 :LIVASPGIALAH T0333 91 :AVNRPLVDG 4uagA 79 :PSLSAAADA T0333 100 :TMALVDDYRPDLVVYEQGA 4uagA 95 :IELFCREAQAPIVAITGSN T0333 119 :TVGLLAADRAGVPAVQRNQSAW 4uagA 120 :TLVGEMAKAAGVNVGVGGNIGL T0333 141 :RTRGMHRSIASFLTD 4uagA 182 :DHMDRYPFGLQQYRA T0333 159 :KHQ 4uagA 200 :RIY T0333 165 :PEPVATIESFPPSLLL 4uagA 203 :ENAKVCVVNADDALTM T0333 191 :WVPYGGGAV 4uagA 227 :CVSFGVNMG T0333 200 :LGDRLPP 4uagA 329 :ALNGLHV T0333 209 :ARPEVAITMGT 4uagA 336 :DGTLHLLLGGD T0333 248 :LGDLDISPLGT 4uagA 347 :GKSADFSPLAR T0333 259 :LPRNVRAVGWT 4uagA 360 :NGDNVRLYCFG T0333 270 :PLHTLLRT 4uagA 372 :DGAQLAAL T0333 278 :CTA 4uagA 384 :AEQ T0333 288 :GTVMTAIDA 4uagA 388 :ETMEQAMRL T0333 297 :GIPQLL 4uagA 404 :GDMVLL T0333 305 :DPR 4uagA 412 :ACA T0333 308 :DQFQHTAR 4uagA 417 :DQFKNFEQ T0333 346 :LRTAAREVREE 4uagA 425 :RGNEFARLAKE Number of specific fragments extracted= 24 number of extra gaps= 2 total=692 Number of alignments=34 # 4uagA read from 4uagA/merged-good-all-a2m # found chain 4uagA in training set Warning: unaligning (T0333)I149 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (4uagA)L199 Warning: unaligning (T0333)S151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (4uagA)L199 Warning: unaligning (T0333)I171 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (4uagA)I220 Warning: unaligning (T0333)E172 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (4uagA)I220 Warning: unaligning (T0333)P205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (4uagA)E245 Warning: unaligning (T0333)H283 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (4uagA)P411 Warning: unaligning (T0333)H284 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (4uagA)P411 Warning: unaligning (T0333)G288 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (4uagA)L416 Warning: unaligning (T0333)R307 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (4uagA)L416 T0333 10 :GHLFPLIQLAWGFRTAGHDVLIAVAEHADRAAA 4uagA 12 :GLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLD T0333 43 :AGLEVVDVA 4uagA 48 :EAVERHTGS T0333 54 :YSAVKV 4uagA 57 :LNDEWL T0333 86 :GVQ 4uagA 63 :MAA T0333 89 :IAAVNRPLVD 4uagA 81 :LSAAADAGIE T0333 99 :GTMALVDDYRPDLVVY 4uagA 94 :DIELFCREAQAPIVAI T0333 115 :EQGA 4uagA 111 :GSNG T0333 119 :TVGLLAADRAGVPAVQRNQSA 4uagA 120 :TLVGEMAKAAGVNVGVGGNIG T0333 140 :WRTRGMHRS 4uagA 188 :PFGLQQYRA T0333 152 :FLTDLMDKHQVSLPEPVAT 4uagA 200 :RIYENAKVCVVNADDALTM T0333 191 :WVPYGGGAVLGDRL 4uagA 227 :CVSFGVNMGDYHLN T0333 209 :ARPEVAITMGTIE 4uagA 335 :VDGTLHLLLGGDG T0333 223 :QAFGIGAVEP 4uagA 348 :KSADFSPLAR T0333 237 :AGEV 4uagA 358 :YLNG T0333 241 :DADFVLALGDL 4uagA 363 :NVRLYCFGRDG T0333 254 :SPLGTLP 4uagA 374 :AQLAALR T0333 261 :RNVRAVGWTP 4uagA 382 :EVAEQTETME T0333 274 :LLR 4uagA 393 :AMR T0333 277 :TCT 4uagA 400 :RVQ T0333 280 :AVV 4uagA 407 :VLL T0333 285 :GGG 4uagA 412 :ACA T0333 308 :DQF 4uagA 417 :DQF T0333 313 :TAREA 4uagA 420 :KNFEQ T0333 346 :LRTAAREVREE 4uagA 425 :RGNEFARLAKE Number of specific fragments extracted= 24 number of extra gaps= 3 total=716 Number of alignments=35 # 4uagA read from 4uagA/merged-good-all-a2m # found chain 4uagA in training set Warning: unaligning (T0333)A247 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (4uagA)P411 Warning: unaligning (T0333)L248 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (4uagA)P411 Warning: unaligning (T0333)D252 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (4uagA)L416 Warning: unaligning (T0333)I253 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (4uagA)L416 Warning: unaligning (T0333)P361 because last residue in template chain is (4uagA)G437 T0333 1 :MLFVSSP 4uagA 8 :VVIIGLG T0333 13 :FPLIQLAWGFRTAGHDVLIAV 4uagA 15 :LTGLSCVDFFLARGVTPRVMD T0333 34 :AEHADRAAA 4uagA 40 :PPGLDKLPE T0333 44 :GLEVVDVAPDYSAVKVF 4uagA 49 :AVERHTGSLNDEWLMAA T0333 61 :EQVAKDNP 4uagA 72 :PGIALAHP T0333 85 :WGVQIAAVNRPLVDGTMALVDDYRPDLVVYEQGAT 4uagA 80 :SLSAAADAGIEIVGDIELFCREAQAPIVAITGSNG T0333 120 :VGLLAADRAGVPAVQRNQSAWRTRGMHR 4uagA 121 :LVGEMAKAAGVNVGVGGNIGLPALMLLD T0333 182 :AEPEGWFMRWVPYGGGA 4uagA 333 :LHVDGTLHLLLGGDGKS T0333 199 :VLGDRLPPVPARPEVAITMGTIE 4uagA 352 :FSPLARYLNGDNVRLYCFGRDGA T0333 222 :LQAFGIGA 4uagA 376 :LAALRPEV T0333 230 :VEPIIAAAGEV 4uagA 390 :MEQAMRLLAPR T0333 241 :DADFVL 4uagA 404 :GDMVLL T0333 249 :GDL 4uagA 412 :ACA T0333 254 :SPLGT 4uagA 417 :DQFKN T0333 346 :LRTAAREVREEMVAL 4uagA 422 :FEQRGNEFARLAKEL Number of specific fragments extracted= 15 number of extra gaps= 2 total=731 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o58A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0333 read from 1o58A/merged-good-all-a2m # 1o58A read from 1o58A/merged-good-all-a2m # found chain 1o58A in training set T0333 2 :LFVSSPG 1o58A 56 :IVEPTSG T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEH 1o58A 63 :NMGIAIAMIGAKRGHRVILTMPET T0333 37 :ADRAAAAGLEVVDV 1o58A 92 :RKVLKMLGAELVLT T0333 81 :DLEEWGVQIAAVNRPLVDG 1o58A 106 :PGELGMKGAVEKALEISRE T0333 100 :TMALVDDY 1o58A 138 :NVYSHQFT T0333 108 :RPDLVVYE 1o58A 157 :QIDAFVAG T0333 116 :QGATVGLLAADRA 1o58A 166 :GTGGTISGVGRVL T0333 129 :GVPAVQRNQSAW 1o58A 185 :GVKIVAVEPAKS T0333 174 :FPPSLLLEAEPEGWFMRWVPYGGGAV 1o58A 212 :IGAGFVPKILDRSVIDEVITVEDEEA T0333 236 :AAGEVD 1o58A 266 :VAQKLG T0333 242 :ADFVLAL 1o58A 274 :ARVVTVA T0333 304 :P 1o58A 281 :P Number of specific fragments extracted= 12 number of extra gaps= 0 total=743 Number of alignments=37 # 1o58A read from 1o58A/merged-good-all-a2m # found chain 1o58A in training set T0333 10 :GHLFPLIQLAWGFRTAGHDVLIAVAE 1o58A 60 :TSGNMGIAIAMIGAKRGHRVILTMPE T0333 37 :A 1o58A 87 :M T0333 38 :DRAAA 1o58A 89 :VERRK T0333 43 :AGLEVVDVAPDY 1o58A 98 :LGAELVLTPGEL T0333 55 :SAVKVFEQVAKDNPRFAETVATR 1o58A 113 :GAVEKALEISRETGAHMLNQFEN T0333 86 :GVQIAAVNRPLVDGTMALVD 1o58A 136 :PYNVYSHQFTTGPEILKQMD T0333 107 :YRPDLVVYE 1o58A 156 :YQIDAFVAG T0333 116 :QGA 1o58A 167 :TGG T0333 119 :TVGLLAADRAG 1o58A 173 :GVGRVLKGFFG T0333 130 :VPAVQRNQSA 1o58A 186 :VKIVAVEPAK T0333 140 :WRTRGMHRSIASFLTDLM 1o58A 231 :TVEDEEAYEMARYLAKKE T0333 167 :PVATIESFPPS 1o58A 263 :ALKVAQKLGPD T0333 191 :WVPYGGGAVLGDRL 1o58A 274 :ARVVTVAPDHAERY Number of specific fragments extracted= 13 number of extra gaps= 0 total=756 Number of alignments=38 # 1o58A read from 1o58A/merged-good-all-a2m # found chain 1o58A in training set T0333 4 :VSSPGIG 1o58A 56 :IVEPTSG T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1o58A 63 :NMGIAIAMIGAKRGHRVILTM T0333 34 :A 1o58A 85 :E T0333 35 :EHADRAAAAGLEVVDVAPDYSAVKVF 1o58A 90 :ERRKVLKMLGAELVLTPGELGMKGAV T0333 61 :EQVAKDNPRFAET 1o58A 119 :LEISRETGAHMLN T0333 75 :ATRPAIDLEEWGVQIAAVNRPLV 1o58A 132 :QFENPYNVYSHQFTTGPEILKQM T0333 106 :DYRPDLVVYEQGATVGL 1o58A 155 :DYQIDAFVAGVGTGGTI T0333 123 :LAADRA 1o58A 173 :GVGRVL T0333 129 :GVPAVQRNQSAWRTR 1o58A 185 :GVKIVAVEPAKSPVL T0333 162 :VSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1o58A 200 :SGGQPGKHAIQGIGAGFVPKILDRSVIDEVITVEDEE T0333 222 :LQAFGIGAVEPIIAAAGEV 1o58A 252 :VGISSGANVAAALKVAQKL T0333 241 :DADFVLALGDLD 1o58A 273 :DARVVTVAPDHA T0333 254 :S 1o58A 285 :E Number of specific fragments extracted= 13 number of extra gaps= 0 total=769 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6cA/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/T0333/1o6cA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0333/1o6cA/merged-good-all-a2m.gz for input Trying 1o6cA/merged-good-all-a2m Error: Couldn't open file 1o6cA/merged-good-all-a2m or 1o6cA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aebA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aebA expands to /projects/compbio/data/pdb/2aeb.pdb.gz 2aebA:Skipped atom 2231, because occupancy 0.290 <= existing 0.710 in 2aebA Skipped atom 2233, because occupancy 0.290 <= existing 0.710 in 2aebA Skipped atom 2235, because occupancy 0.290 <= existing 0.710 in 2aebA Skipped atom 2237, because occupancy 0.290 <= existing 0.710 in 2aebA Skipped atom 2239, because occupancy 0.290 <= existing 0.710 in 2aebA # T0333 read from 2aebA/merged-good-all-a2m # 2aebA read from 2aebA/merged-good-all-a2m # adding 2aebA to template set # found chain 2aebA in template set Warning: unaligning (T0333)A42 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)Q43 Warning: unaligning (T0333)A43 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)Q43 Warning: unaligning (T0333)G44 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)E44 Warning: unaligning (T0333)L45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aebA)C45 Warning: unaligning (T0333)Y54 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)A56 Warning: unaligning (T0333)K65 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)A56 Warning: unaligning (T0333)Y114 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)G99 Warning: unaligning (T0333)E115 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)G99 Warning: unaligning (T0333)Q137 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)H126 Warning: unaligning (T0333)S138 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)H126 Warning: unaligning (T0333)T142 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)G138 Warning: unaligning (T0333)R143 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)G138 Warning: unaligning (T0333)H272 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)E256 Warning: unaligning (T0333)T273 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)E256 Warning: unaligning (T0333)H312 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)G283 Warning: unaligning (T0333)T313 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)G283 T0333 2 :LFVSSPGIGH 2aebA 10 :IIGAPFSKGQ T0333 17 :QLAWGFRTAG 2aebA 26 :EGPTVLRKAG T0333 37 :ADRAA 2aebA 37 :LEKLK T0333 46 :EVVDVAP 2aebA 46 :DVKDYGD T0333 53 :D 2aebA 54 :P T0333 66 :DNPRFAETVAT 2aebA 57 :DIPNDSPFQIV T0333 81 :DL 2aebA 68 :KN T0333 86 :GVQIAAVNRPLVDGTMALVDDYRPDLVV 2aebA 70 :PRSVGKASEQLAGKVAEVKKNGRISLVL T0333 116 :QGATVGLLAADRA 2aebA 100 :DHSLAIGSISGHA T0333 129 :GVPAVQRN 2aebA 117 :DLGVIWVD T0333 139 :AW 2aebA 127 :TD T0333 141 :R 2aebA 136 :T T0333 144 :GMHRSIASFLTDLMDKHQVSLPEPVAT 2aebA 139 :NLHGQPVSFLLKELKGKIPDVPGFSWV T0333 184 :PEGWFMRWVPYGGGAV 2aebA 166 :TPCISAKDIVYIGLRD T0333 200 :LGDRLPPV 2aebA 189 :ILKTLGIK T0333 216 :TMGTIELQAFG 2aebA 197 :YFSMTEVDRLG T0333 227 :IGAVEPIIAAAGEVD 2aebA 209 :GKVMEETLSYLLGRK T0333 242 :ADFVLALG 2aebA 225 :RPIHLSFD T0333 250 :DLDISPLGT 2aebA 235 :GLDPSFTPA T0333 259 :LPR 2aebA 247 :PVV T0333 267 :GWTPL 2aebA 250 :GGLTY T0333 274 :LL 2aebA 257 :GL T0333 288 :GTVMTAIDAGIPQLL 2aebA 259 :YITEEIYKTGLLSGL T0333 303 :A 2aebA 276 :M T0333 304 :PDPR 2aebA 278 :VNPS T0333 314 :A 2aebA 284 :K T0333 343 :DESLRTAAREV 2aebA 285 :TPEEVTRTVNT T0333 367 :VRRIVE 2aebA 296 :AVAITL Number of specific fragments extracted= 28 number of extra gaps= 7 total=797 Number of alignments=40 # 2aebA read from 2aebA/merged-good-all-a2m # found chain 2aebA in template set Warning: unaligning (T0333)H27 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)R6 Warning: unaligning (T0333)D28 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)T7 Warning: unaligning (T0333)A42 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)Q43 Warning: unaligning (T0333)A43 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)Q43 Warning: unaligning (T0333)G44 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)E44 Warning: unaligning (T0333)L45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aebA)C45 Warning: unaligning (T0333)N67 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)A56 Warning: unaligning (T0333)P68 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)A56 Warning: unaligning (T0333)Y114 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)G99 Warning: unaligning (T0333)Q137 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)H126 Warning: unaligning (T0333)S138 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)H126 Warning: unaligning (T0333)H272 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)E256 Warning: unaligning (T0333)T273 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)E256 Warning: unaligning (T0333)L340 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)G283 Warning: unaligning (T0333)I341 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)G283 T0333 29 :VLIAVAEHA 2aebA 8 :IGIIGAPFS T0333 38 :DRAA 2aebA 38 :EKLK T0333 46 :EVVDVA 2aebA 46 :DVKDYG T0333 65 :KD 2aebA 53 :LP T0333 69 :RFAETVATRPAIDLEEWGVQIAAVNR 2aebA 57 :DIPNDSPFQIVKNPRSVGKASEQLAG T0333 99 :GTMALVDDYRPDLVV 2aebA 83 :KVAEVKKNGRISLVL T0333 115 :EQGA 2aebA 100 :DHSL T0333 119 :TVGLLAADRAG 2aebA 106 :GSISGHARVHP T0333 130 :VPAVQRN 2aebA 118 :LGVIWVD T0333 139 :A 2aebA 127 :T T0333 140 :WRTRGMHRSIASFLTDLM 2aebA 139 :NLHGQPVSFLLKELKGKI T0333 176 :PSLL 2aebA 157 :PDVP T0333 191 :WVPYGGGAVLGDR 2aebA 161 :GFSWVTPCISAKD T0333 212 :EVAITMGTIE 2aebA 174 :IVYIGLRDVD T0333 223 :QAFG 2aebA 184 :PGEH T0333 227 :IGAVE 2aebA 208 :IGKVM T0333 232 :PIIAAAGEV 2aebA 214 :ETLSYLLGR T0333 241 :DADFVLALG 2aebA 224 :KRPIHLSFD T0333 250 :DLDISPLGTLP 2aebA 235 :GLDPSFTPATG T0333 261 :R 2aebA 249 :V T0333 267 :GWTPL 2aebA 250 :GGLTY T0333 274 :LLR 2aebA 257 :GLY T0333 289 :TVMTAIDAGIP 2aebA 260 :ITEEIYKTGLL T0333 300 :QLLAPDPR 2aebA 273 :LDIMEVNP T0333 339 :R 2aebA 281 :S T0333 342 :GDESLRTAAREVREEM 2aebA 284 :KTPEEVTRTVNTAVAI Number of specific fragments extracted= 26 number of extra gaps= 7 total=823 Number of alignments=41 # 2aebA read from 2aebA/merged-good-all-a2m # found chain 2aebA in template set Warning: unaligning (T0333)A42 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)Q43 Warning: unaligning (T0333)A43 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)Q43 Warning: unaligning (T0333)G44 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)E44 Warning: unaligning (T0333)L45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aebA)C45 Warning: unaligning (T0333)Y54 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)A56 Warning: unaligning (T0333)S55 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)A56 Warning: unaligning (T0333)Y114 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)G99 Warning: unaligning (T0333)E115 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)G99 Warning: unaligning (T0333)Q137 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)H126 Warning: unaligning (T0333)S138 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)H126 Warning: unaligning (T0333)G144 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)L133 Warning: unaligning (T0333)M145 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)L133 Warning: unaligning (T0333)I149 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)G138 Warning: unaligning (T0333)A150 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)G138 Warning: unaligning (T0333)G228 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)E256 Warning: unaligning (T0333)A229 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)E256 Warning: unaligning (T0333)P255 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)G283 Warning: unaligning (T0333)L256 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)G283 T0333 1 :MLFVSSPG 2aebA 8 :IGIIGAPF T0333 9 :IGHLFPL 2aebA 21 :RGGVEEG T0333 19 :AWGFRTAG 2aebA 28 :PTVLRKAG T0333 36 :HADRAA 2aebA 36 :LLEKLK T0333 46 :EVVDVA 2aebA 46 :DVKDYG T0333 52 :PD 2aebA 53 :LP T0333 56 :A 2aebA 57 :D T0333 64 :AKDNPRFAETV 2aebA 58 :IPNDSPFQIVK T0333 85 :WGVQIAAVNRPLVDGTMALVDDYRPDLVV 2aebA 69 :NPRSVGKASEQLAGKVAEVKKNGRISLVL T0333 116 :QGATVGLLAADRA 2aebA 100 :DHSLAIGSISGHA T0333 129 :GVPAVQRN 2aebA 117 :DLGVIWVD T0333 139 :AWRTR 2aebA 127 :TDINT T0333 146 :HRS 2aebA 134 :TTT T0333 151 :SFLT 2aebA 139 :NLHG T0333 158 :DKH 2aebA 157 :PDV T0333 165 :PEPVA 2aebA 160 :PGFSW T0333 180 :LEAEPEGWFMRWVPYGGGA 2aebA 165 :VTPCISAKDIVYIGLRDVD T0333 199 :VLGDRLPPVPARPEVAITM 2aebA 213 :EETLSYLLGRKKRPIHLSF T0333 218 :GTIELQAFGI 2aebA 245 :GTPVVGGLTY T0333 230 :VEPIIAAAGEVD 2aebA 257 :GLYITEEIYKTG T0333 242 :ADFVLALG 2aebA 270 :LSGLDIME T0333 251 :LDIS 2aebA 278 :VNPS T0333 328 :TSDKVDADLLRRLI 2aebA 284 :KTPEEVTRTVNTAV Number of specific fragments extracted= 23 number of extra gaps= 8 total=846 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bxrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bxrA expands to /projects/compbio/data/pdb/1bxr.pdb.gz 1bxrA:Skipped atom 5851, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 5853, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 5855, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 5857, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 5962, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 5964, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 5966, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 5968, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 6787, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 6789, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 6791, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 6793, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 6795, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 7039, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 7041, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 7043, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 7045, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 7047, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 7049, because occupancy 0.500 <= existing 0.500 in 1bxrA Skipped atom 7051, because occupancy 0.500 <= existing 0.500 in 1bxrA # T0333 read from 1bxrA/merged-good-all-a2m # 1bxrA read from 1bxrA/merged-good-all-a2m # adding 1bxrA to template set # found chain 1bxrA in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1bxrA)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1bxrA)D558 T0333 2 :LFVSSPGI 1bxrA 10 :ILILGAGP T0333 10 :GHL 1bxrA 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1bxrA 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEH 1bxrA 51 :PAT T0333 39 :RAAAAGL 1bxrA 54 :IMTDPEM T0333 46 :EVVDVAP 1bxrA 62 :DATYIEP T0333 94 :RPL 1bxrA 71 :WEV T0333 100 :TMALVDDYRPDLVVYEQGATVGLLAADRA 1bxrA 74 :VRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1bxrA 112 :GVT T0333 135 :RNQSA 1bxrA 115 :MIGAT T0333 141 :RTRGMHRSIASFLTDL 1bxrA 505 :LAGVREAEIRKLRDQY T0333 165 :PEPVATIESFPPSLL 1bxrA 521 :DLHPVYKRVDTCAAE T0333 184 :PEGWFMRWVPYGGGAV 1bxrA 536 :FATDTAYMYSTYEEEC T0333 204 :LPPV 1bxrA 553 :ANPS T0333 210 :RPEVAITMGT 1bxrA 559 :REKIMVLGGG T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1bxrA 572 :IGQGIEFDYCCVHASLALREDGYETIMVNCNPE T0333 275 :LRTCTAVVHHG 1bxrA 610 :YDTSDRLYFEP T0333 286 :GGGTVMTAIDAGIP 1bxrA 622 :TLEDVLEIVRIEKP T0333 300 :QLLAPDPRD 1bxrA 637 :GVIVQYGGQ T0333 309 :QFQHTAR 1bxrA 647 :PLKLARA T0333 318 :VSRRGIGLV 1bxrA 654 :LEAAGVPVI T0333 327 :ST 1bxrA 664 :TS T0333 334 :ADLLRRLIG 1bxrA 666 :PDAIDRAED T0333 347 :RTAAREVREE 1bxrA 675 :RERFQHAVER T0333 363 :PAETVRRIVERIS 1bxrA 697 :AIEMAVEKAKEIG Number of specific fragments extracted= 25 number of extra gaps= 1 total=871 Number of alignments=43 # 1bxrA read from 1bxrA/merged-good-all-a2m # found chain 1bxrA in template set Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1bxrA)D558 T0333 2 :LFVSSPGI 1bxrA 12 :ILGAGPIV T0333 10 :GHL 1bxrA 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHADRAAAAG 1bxrA 28 :YSGAQACKALREEGYRVILVNSNPATIMTDPE T0333 45 :LEVVDVAPDYSA 1bxrA 61 :ADATYIEPIHWE T0333 99 :GTMALVDDYRPDLVVYEQGATVGLLAADRA 1bxrA 73 :VVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1bxrA 112 :GVT T0333 135 :RNQSA 1bxrA 115 :MIGAT T0333 173 :SFPP 1bxrA 521 :DLHP T0333 188 :FMRWVP 1bxrA 525 :VYKRVD T0333 198 :A 1bxrA 531 :T T0333 200 :LGDRLPPVP 1bxrA 532 :CAAEFATDT T0333 210 :RPEVAITMGTIELQAFGIGA 1bxrA 559 :REKIMVLGGGPNRIGQGIEF T0333 230 :VEPIIAAAGEVDADFVLALGDLD 1bxrA 582 :CVHASLALREDGYETIMVNCNPE T0333 259 :LP 1bxrA 605 :TV T0333 261 :RNVRAVGWT 1bxrA 614 :DRLYFEPVT T0333 271 :LHTLLR 1bxrA 626 :VLEIVR T0333 277 :TCTAVVHHGGGGTVMTAI 1bxrA 634 :KPKGVIVQYGGQTPLKLA T0333 295 :DAGIPQLLAPDPR 1bxrA 656 :AAGVPVIGTSPDA T0333 308 :DQF 1bxrA 674 :DRE T0333 313 :TAREAVSRRG 1bxrA 677 :RFQHAVERLK T0333 361 :P 1bxrA 799 :Y T0333 362 :TPAETVRRIVERIS 1bxrA 801 :LSQEIQDVMRQQVQ Number of specific fragments extracted= 22 number of extra gaps= 1 total=893 Number of alignments=44 # 1bxrA read from 1bxrA/merged-good-all-a2m # found chain 1bxrA in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1bxrA)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1bxrA)D558 T0333 1 :MLFVSSPGI 1bxrA 10 :ILILGAGPI T0333 10 :GH 1bxrA 21 :GQ T0333 12 :LFPLIQLAWGFRTAGHDVLIAV 1bxrA 27 :DYSGAQACKALREEGYRVILVN T0333 34 :A 1bxrA 51 :P T0333 43 :AG 1bxrA 58 :PE T0333 45 :LEVVDVAPDY 1bxrA 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1bxrA 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GV 1bxrA 112 :GV T0333 137 :QSAWRTRGMHRSIASFLT 1bxrA 114 :TMIGATADAIDKAEDRRR T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1bxrA 508 :VREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEEC T0333 203 :RLPPV 1bxrA 552 :EANPS T0333 210 :RPEVAITMGTIELQAFGIGAVEPII 1bxrA 559 :REKIMVLGGGPNRIGQGIEFDYCCV T0333 235 :AAAGEVDADFVLALGD 1bxrA 587 :LALREDGYETIMVNCN T0333 251 :LDI 1bxrA 608 :TDY T0333 276 :RTC 1bxrA 611 :DTS T0333 279 :TAVVHHGGGGTVMTAIDAGIP 1bxrA 615 :RLYFEPVTLEDVLEIVRIEKP T0333 300 :QLLAPDPRDQF 1bxrA 637 :GVIVQYGGQTP T0333 311 :QHTAREAVSRRGIGL 1bxrA 649 :KLARALEAAGVPVIG T0333 329 :SDKV 1bxrA 665 :SPDA T0333 337 :LRRLIG 1bxrA 669 :IDRAED T0333 350 :AREVREEMVALP 1bxrA 675 :RERFQHAVERLK T0333 362 :TPAETVRRIVER 1bxrA 697 :AIEMAVEKAKEI Number of specific fragments extracted= 22 number of extra gaps= 1 total=915 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c1xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c1xA expands to /projects/compbio/data/pdb/2c1x.pdb.gz 2c1xA:Skipped atom 3135, because occupancy 0.500 <= existing 0.500 in 2c1xA Skipped atom 3139, because occupancy 0.500 <= existing 0.500 in 2c1xA Skipped atom 3141, because occupancy 0.500 <= existing 0.500 in 2c1xA Skipped atom 3143, because occupancy 0.500 <= existing 0.500 in 2c1xA Skipped atom 3145, because occupancy 0.500 <= existing 0.500 in 2c1xA Skipped atom 3147, because occupancy 0.500 <= existing 0.500 in 2c1xA Skipped atom 3149, because occupancy 0.500 <= existing 0.500 in 2c1xA Skipped atom 3151, because occupancy 0.500 <= existing 0.500 in 2c1xA # T0333 read from 2c1xA/merged-good-all-a2m # 2c1xA read from 2c1xA/merged-good-all-a2m # adding 2c1xA to template set # found chain 2c1xA in template set Warning: unaligning (T0333)A41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c1xA)Q61 Warning: unaligning (T0333)A51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c1xA)Q61 Warning: unaligning (T0333)S327 because of BadResidue code BAD_PEPTIDE in next template residue (2c1xA)T398 Warning: unaligning (T0333)T328 because of BadResidue code BAD_PEPTIDE at template residue (2c1xA)T398 T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTA 2c1xA 11 :AVLAFPFSTHAAPLLAVVRRLAAA T0333 26 :GHDVLIAV 2c1xA 37 :HAVFSFFS T0333 34 :AEHADRA 2c1xA 46 :SQSNASI T0333 52 :PDYSAVKVFEQVAKDNPRFA 2c1xA 62 :CNIKSYDISDGVPEGYVFAG T0333 81 :DLEEWGVQIAAVNRPLVDGTMALVDDY 2c1xA 82 :RPQEDIELFTRAAPESFRQGMVMAVAE T0333 108 :RPDLVVYEQGATVGLLAADRAGVPAVQRNQSAW 2c1xA 112 :PVSCLVADAFIWFAADMAAEMGVAWLPFWTAGP T0333 141 :RTRGMHRSIASFLTDLMDKHQVSLPEPVATIESFPPSLL 2c1xA 188 :QEGIVFGNLNSLFSRMLHRMGQVLPKATAVFINSFEELD T0333 188 :FMRWVPYGGGAV 2c1xA 236 :KLKTYLNIGPFN T0333 200 :LGDRLPPVPARPEVAITMGTIELQ 2c1xA 261 :CLQWLKERKPTSVVYISFGTVTTP T0333 226 :GIGAVEPIIAAAGEVDADFVLALGDLDISPLGT 2c1xA 285 :PPAEVVALSEALEASRVPFIWSLRDKARVHLPE T0333 259 :LPRNVRAVGWTPLHTLLRT 2c1xA 323 :TRGYGMVVPWAPQAEVLAH T0333 278 :CTAVVHHGGGGTVMTAIDAGIPQLLAPDPRDQFQHTAR 2c1xA 344 :VGAFVTHCGWNSLWESVAGGVPLICRPFFGDQRLNGRM T0333 318 :VSR 2c1xA 382 :VED T0333 321 :RGIG 2c1xA 386 :LEIG T0333 325 :LV 2c1xA 391 :RI T0333 329 :SDKV 2c1xA 399 :KSGL T0333 334 :ADLLRRLIGDES 2c1xA 403 :MSCFDQILSQEK T0333 346 :LRTAAREVREEMVA 2c1xA 418 :LRENLRALRETADR T0333 360 :LPT 2c1xA 435 :PKG T0333 363 :PAETVRRIVERI 2c1xA 439 :STENFITLVDLV T0333 375 :S 2c1xA 455 :D Number of specific fragments extracted= 21 number of extra gaps= 1 total=936 Number of alignments=46 # 2c1xA read from 2c1xA/merged-good-all-a2m # found chain 2c1xA in template set Warning: unaligning (T0333)V199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c1xA)G260 Warning: unaligning (T0333)D330 because of BadResidue code BAD_PEPTIDE at template residue (2c1xA)T398 T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTA 2c1xA 11 :AVLAFPFSTHAAPLLAVVRRLAAA T0333 26 :GHDVLIAVAE 2c1xA 37 :HAVFSFFSTS T0333 38 :DRAAA 2c1xA 47 :QSNAS T0333 43 :AGLEVVDVAPDY 2c1xA 62 :CNIKSYDISDGV T0333 72 :ETVATRPAIDLEEWGVQIAAVNRPLV 2c1xA 74 :PEGYVFAGRPQEDIELFTRAAPESFR T0333 99 :GTMALVDD 2c1xA 100 :QGMVMAVA T0333 107 :YRPDLVVYEQGATVGLLAADRAGVPAVQRNQSA 2c1xA 111 :RPVSCLVADAFIWFAADMAAEMGVAWLPFWTAG T0333 140 :WRTRGMHRSIASFLTDLMDKHQVSLPEPVATIE 2c1xA 198 :SLFSRMLHRMGQVLPKATAVFINSFEELDDSLT T0333 173 :SFPP 2c1xA 235 :SKLK T0333 191 :WVPYGGG 2c1xA 239 :TYLNIGP T0333 209 :ARPEVAITMGTIE 2c1xA 270 :PTSVVYISFGTVT T0333 222 :LQAFGIGAVEPIIAAA 2c1xA 284 :PPPAEVVALSEALEAS T0333 241 :DADFVLALGDLDISPLGTLP 2c1xA 300 :RVPFIWSLRDKARVHLPEGF T0333 261 :RNVRAVGWTPLHTLLR 2c1xA 325 :GYGMVVPWAPQAEVLA T0333 277 :TCTAVVHHGGGGTVMTAIDAGIPQLLAPDPRDQF 2c1xA 343 :AVGAFVTHCGWNSLWESVAGGVPLICRPFFGDQR T0333 313 :TAREAVSR 2c1xA 377 :LNGRMVED T0333 321 :RGIGLVSTS 2c1xA 386 :LEIGVRIEG T0333 331 :KVD 2c1xA 399 :KSG T0333 334 :ADLLRRLIGD 2c1xA 403 :MSCFDQILSQ T0333 345 :SLRTAAREVREEMVAL 2c1xA 413 :EKGKKLRENLRALRET T0333 361 :PTPAETVRRIVERISG 2c1xA 437 :GSSTENFITLVDLVSK Number of specific fragments extracted= 21 number of extra gaps= 1 total=957 Number of alignments=47 # 2c1xA read from 2c1xA/merged-good-all-a2m # found chain 2c1xA in template set Warning: unaligning (T0333)A41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c1xA)Q61 Warning: unaligning (T0333)V199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c1xA)G260 Warning: unaligning (T0333)T328 because of BadResidue code BAD_PEPTIDE in next template residue (2c1xA)T398 Warning: unaligning (T0333)S329 because of BadResidue code BAD_PEPTIDE at template residue (2c1xA)T398 T0333 1 :MLFVSSPGIGHLFPLIQLAWGFRTA 2c1xA 10 :VAVLAFPFSTHAAPLLAVVRRLAAA T0333 26 :GHDVLIAV 2c1xA 37 :HAVFSFFS T0333 34 :AEHADRA 2c1xA 46 :SQSNASI T0333 43 :AGLEVVDVAPDYSAV 2c1xA 62 :CNIKSYDISDGVPEG T0333 63 :VAKD 2c1xA 77 :YVFA T0333 76 :TRPAIDLEEWGVQIAAVNRPLVDGTMALV 2c1xA 81 :GRPQEDIELFTRAAPESFRQGMVMAVAET T0333 106 :DYRPDLVVYEQGATVGLLAADRAGVPAVQRNQSAWRTRGMHRSIASFLT 2c1xA 110 :GRPVSCLVADAFIWFAADMAAEMGVAWLPFWTAGPNSLSTHVYIDEIRE T0333 155 :DLMDKHQVSLPEPVATIESFPPSLL 2c1xA 202 :RMLHRMGQVLPKATAVFINSFEELD T0333 186 :GWFMRWVPY 2c1xA 237 :LKTYLNIGP T0333 200 :LGDRLPPVPARPEVAITMGTIELQ 2c1xA 261 :CLQWLKERKPTSVVYISFGTVTTP T0333 226 :GIGAVEPIIAAAGEVDADFVLALGD 2c1xA 285 :PPAEVVALSEALEASRVPFIWSLRD T0333 254 :SPLGTLPRN 2c1xA 310 :KARVHLPEG T0333 263 :VRAVGWTPLHTLL 2c1xA 327 :GMVVPWAPQAEVL T0333 276 :RTCTAVVHHGGGGTVMTAIDAGIPQLLAPDPRDQFQHTAREAV 2c1xA 342 :EAVGAFVTHCGWNSLWESVAGGVPLICRPFFGDQRLNGRMVED T0333 319 :SRRGIGLV 2c1xA 386 :LEIGVRIE T0333 327 :S 2c1xA 396 :V T0333 330 :DKVDADLLRRLIGDES 2c1xA 399 :KSGLMSCFDQILSQEK T0333 346 :LRTAAREVREEMVAL 2c1xA 418 :LRENLRALRETADRA T0333 361 :PTPAETVRRIVERISG 2c1xA 437 :GSSTENFITLVDLVSK Number of specific fragments extracted= 19 number of extra gaps= 1 total=976 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3pfk/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3pfk expands to /projects/compbio/data/pdb/3pfk.pdb.gz 3pfk:Warning: there is no chain 3pfk will retry with 3pfkA # T0333 read from 3pfk/merged-good-all-a2m # 3pfk read from 3pfk/merged-good-all-a2m # adding 3pfk to template set # found chain 3pfk in template set Warning: unaligning (T0333)P165 because of BadResidue code BAD_PEPTIDE at template residue (3pfk)H160 T0333 1 :M 3pfk 1 :M T0333 2 :LFVSSPGIGHLFPLI 3pfk 6 :VLTSGGDSPGMNAAI T0333 17 :QLAWGFRTAGHDVLIAV 3pfk 22 :SVVRKAIYHGVEVYGVY T0333 35 :EHADRAAAA 3pfk 39 :HGYAGLIAG T0333 55 :SAVKVFEQVAKDNPRFAETVATRP 3pfk 48 :NIKKLEVGDVGDIIHRGGTILYTA T0333 81 :DLEEW 3pfk 72 :RCPEF T0333 94 :RPLVDGTMALVDDYRP 3pfk 79 :EEGQKKGIEQLKKHGI T0333 110 :DLVVYE 3pfk 96 :GLVVIG T0333 118 :ATVGLLAADRA 3pfk 102 :GDGSYQGAKKL T0333 129 :GVPAVQRNQSAW 3pfk 116 :GFPCVGVPGTID T0333 141 :RTRGMHRSIASFLTDLMDKHQVSL 3pfk 134 :DFTIGFDTALNTVIDAIDKIRDTA T0333 166 :EP 3pfk 161 :ER T0333 170 :TI 3pfk 163 :TY T0333 191 :WVPYGGGAV 3pfk 165 :VIEVMGRHA T0333 200 :LGDRLPPV 3pfk 190 :LIPEADYD T0333 226 :GIGAVEPIIAAAGEVD 3pfk 198 :MNDVIARLKRGHERGK T0333 242 :ADFVLALGDLD 3pfk 215 :HSIIIVAEGVG T0333 253 :ISPLGTLP 3pfk 248 :GHVQRGGS T0333 270 :P 3pfk 256 :P T0333 343 :DESLRTAAREVREE 3pfk 257 :TAFDRVLASRLGAR T0333 357 :MVALPT 3pfk 299 :ALANKH T0333 363 :PAETVRRIVE 3pfk 308 :DQRMYALSKE Number of specific fragments extracted= 22 number of extra gaps= 1 total=998 Number of alignments=49 # 3pfk read from 3pfk/merged-good-all-a2m # found chain 3pfk in template set T0333 1 :M 3pfk 1 :M T0333 2 :LFVSSPGI 3pfk 6 :VLTSGGDS T0333 10 :GHLFPLIQLAWGFRTAGHDVLIA 3pfk 15 :GMNAAIRSVVRKAIYHGVEVYGV T0333 34 :AEHADRAAAAGLEVVDVA 3pfk 38 :YHGYAGLIAGNIKKLEVG T0333 53 :DY 3pfk 56 :DV T0333 65 :KDNPRFAE 3pfk 58 :GDIIHRGG T0333 73 :TVATRPAIDLEEWGV 3pfk 67 :ILYTARCPEFKTEEG T0333 97 :VDGTMALVDDYRP 3pfk 82 :QKKGIEQLKKHGI T0333 110 :DLVVYE 3pfk 96 :GLVVIG T0333 117 :GATVGLLA 3pfk 102 :GDGSYQGA T0333 126 :DRA 3pfk 110 :KKL T0333 129 :GVPAVQRNQSA 3pfk 116 :GFPCVGVPGTI T0333 140 :WRTRGMHRSIA 3pfk 144 :NTVIDAIDKIR T0333 158 :DKHQVSLPEPVATIE 3pfk 164 :YVIEVMGRHAGDIAL T0333 173 :SF 3pfk 185 :GA T0333 191 :WVPYGG 3pfk 187 :ETILIP T0333 222 :LQAFGIGAVEPIIAAAGEV 3pfk 193 :EADYDMNDVIARLKRGHER T0333 241 :DADFVLALGDLDI 3pfk 214 :KHSIIIVAEGVGS T0333 254 :SPLGTLP 3pfk 249 :HVQRGGS T0333 271 :LHTL 3pfk 264 :ASRL T0333 294 :ID 3pfk 268 :GA T0333 313 :TAREAVSRRGIGLVSTS 3pfk 270 :RAVELLLEGKGGRCVGI T0333 330 :DK 3pfk 288 :NN T0333 337 :LRRLIG 3pfk 296 :IAEALA T0333 343 :DESLRTAARE 3pfk 308 :DQRMYALSKE Number of specific fragments extracted= 25 number of extra gaps= 0 total=1023 Number of alignments=50 # 3pfk read from 3pfk/merged-good-all-a2m # found chain 3pfk in template set T0333 1 :MLFVSSPGIGHLF 3pfk 4 :IGVLTSGGDSPGM T0333 14 :PLIQLAWGFRTAGHDVLIAV 3pfk 19 :AIRSVVRKAIYHGVEVYGVY T0333 35 :EHADRAAAAGLEVVD 3pfk 39 :HGYAGLIAGNIKKLE T0333 54 :YSAVKVF 3pfk 54 :VGDVGDI T0333 61 :EQVAKDNPRFAE 3pfk 67 :ILYTARCPEFKT T0333 94 :RPLVDGTMALVDDYRPDLVVYEQGATVGLLAADRA 3pfk 79 :EEGQKKGIEQLKKHGIQGLVVIGGDGSYQGAKKLT T0333 129 :GVPAVQRNQSAWRT 3pfk 116 :GFPCVGVPGTIDND T0333 175 :PPSLLLEA 3pfk 130 :IPGTDFTI T0333 221 :E 3pfk 138 :G T0333 226 :GIGAVEPIIAAAGEV 3pfk 139 :FDTALNTVIDAIDKI T0333 241 :DADFVLALGD 3pfk 162 :RTYVIEVMGR T0333 284 :HGGGGTVMTAIDAGIPQLLAP 3pfk 172 :HAGDIALWSGLAGGAETILIP T0333 305 :DPRDQFQHTAREAVSRRGIGL 3pfk 197 :DMNDVIARLKRGHERGKKHSI T0333 327 :STSDKVDADLLRRLIG 3pfk 224 :VGSGVDFGRQIQEATG T0333 343 :DESLRTAAREVREE 3pfk 257 :TAFDRVLASRLGAR T0333 366 :TVRRIVE 3pfk 271 :AVELLLE Number of specific fragments extracted= 16 number of extra gaps= 0 total=1039 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pfkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pfkA expands to /projects/compbio/data/pdb/1pfk.pdb.gz 1pfkA:# T0333 read from 1pfkA/merged-good-all-a2m # 1pfkA read from 1pfkA/merged-good-all-a2m # adding 1pfkA to template set # found chain 1pfkA in template set T0333 1 :M 1pfkA 0 :M T0333 2 :LFVSSPGIGHLFPLI 1pfkA 6 :VLTSGGDAPGMNAAI T0333 17 :QLAWGFRTAGHDVLIA 1pfkA 22 :GVVRSALTEGLEVMGI T0333 34 :AEHADRAAAA 1pfkA 38 :YDGYLGLYED T0333 55 :SAVKVFEQVAKDNPRFAETVATRP 1pfkA 48 :RMVQLDRYSVSDMINRGGTFLGSA T0333 81 :DLEEWGV 1pfkA 72 :RFPEFRD T0333 94 :RPLVDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1pfkA 79 :ENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLT T0333 129 :GVPAVQRNQSAW 1pfkA 116 :GFPCIGLPGTID T0333 141 :RTRGMHRSIASFLTDLMDKHQVSLPEPVATI 1pfkA 134 :DYTIGFFTALSTVVEAIDRLRDTSSSHQRIS T0333 191 :WVPYGGGAV 1pfkA 165 :VVEVMGRYC T0333 209 :ARPEVA 1pfkA 185 :GCEFVV T0333 217 :MGTIELQ 1pfkA 191 :VPEVEFS T0333 226 :GIGAVEPIIAAAGEV 1pfkA 198 :REDLVNEIKAGIAKG T0333 241 :DADFVLALGDLD 1pfkA 214 :KHAIVAITEHMC T0333 253 :ISPLGT 1pfkA 248 :GHIQRG T0333 286 :G 1pfkA 254 :G T0333 304 :PDPRD 1pfkA 256 :PVPYD T0333 309 :QFQHTAR 1pfkA 264 :ASRMGAY T0333 318 :VSR 1pfkA 271 :AID T0333 321 :RGIG 1pfkA 277 :AGYG T0333 325 :LV 1pfkA 282 :RC T0333 327 :STSDKV 1pfkA 286 :IQNEQL T0333 337 :LRRLI 1pfkA 296 :IIDAI T0333 342 :GDESLRTAARE 1pfkA 307 :FKGDWLDCAKK Number of specific fragments extracted= 24 number of extra gaps= 0 total=1063 Number of alignments=52 # 1pfkA read from 1pfkA/merged-good-all-a2m # found chain 1pfkA in template set T0333 1 :M 1pfkA 0 :M T0333 2 :LFVSSPGI 1pfkA 6 :VLTSGGDA T0333 10 :GHLFPLIQLAWGFRTAGHDVLIA 1pfkA 15 :GMNAAIRGVVRSALTEGLEVMGI T0333 36 :HADRAAAAGLEVVDVAPDYS 1pfkA 38 :YDGYLGLYEDRMVQLDRYSV T0333 65 :KDNPRFAETVATRPAIDLEEWGVQIA 1pfkA 58 :SDMINRGGTFLGSARFPEFRDENIRA T0333 99 :GTMALVDDYRPDLVVY 1pfkA 84 :VAIENLKKRGIDALVV T0333 115 :E 1pfkA 101 :G T0333 117 :GATVGLLAADRA 1pfkA 102 :GDGSYMGAMRLT T0333 129 :GVPAVQRNQSA 1pfkA 116 :GFPCIGLPGTI T0333 140 :WRTRGMHRSIASF 1pfkA 144 :STVVEAIDRLRDT T0333 158 :DKHQVSLPEPVATIE 1pfkA 164 :SVVEVMGRYCGDLTL T0333 173 :SFPPS 1pfkA 181 :AIAGG T0333 191 :WVPYGGGAVLGDR 1pfkA 186 :CEFVVVPEVEFSR T0333 228 :GAVEPIIAAAGEV 1pfkA 199 :EDLVNEIKAGIAK T0333 241 :DADFVLALGDLDI 1pfkA 214 :KHAIVAITEHMCD T0333 254 :SPLGTLP 1pfkA 249 :HIQRGGS T0333 268 :WTP 1pfkA 256 :PVP T0333 308 :DQFQHTAREAVSRRGIGLVSTS 1pfkA 265 :SRMGAYAIDLLLAGYGGRCVGI T0333 330 :DK 1pfkA 288 :NE T0333 337 :LRRLIG 1pfkA 296 :IIDAIE T0333 343 :DESLRTAARE 1pfkA 308 :KGDWLDCAKK Number of specific fragments extracted= 21 number of extra gaps= 0 total=1084 Number of alignments=53 # 1pfkA read from 1pfkA/merged-good-all-a2m # found chain 1pfkA in template set T0333 1 :MLFVSSPG 1pfkA 4 :IGVLTSGG T0333 9 :IGHLFPLIQLAWGFRTAGHDVLIAV 1pfkA 14 :PGMNAAIRGVVRSALTEGLEVMGIY T0333 35 :EHADRAAAA 1pfkA 39 :DGYLGLYED T0333 46 :EVVDVA 1pfkA 48 :RMVQLD T0333 54 :YSAVKVFEQVAKDNPRFAETVATRPAID 1pfkA 54 :RYSVSDMINRGGTFLGSARFPEFRDENI T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1pfkA 82 :RAVAIENLKKRGIDALVVIGGDGSYMGAMRLT T0333 129 :GVPAVQRNQSAWRTRGMHRSIA 1pfkA 116 :GFPCIGLPGTIDNDIKGTDYTI T0333 225 :FGIGAVEPIIAAAGEV 1pfkA 138 :GFFTALSTVVEAIDRL T0333 241 :DADFVLALGD 1pfkA 162 :RISVVEVMGR T0333 252 :D 1pfkA 172 :Y T0333 285 :GGGGTVMTAIDAGIPQLLAPD 1pfkA 173 :CGDLTLAAAIAGGCEFVVVPE T0333 327 :STSDKVDADLLRRLIGDE 1pfkA 195 :EFSREDLVNEIKAGIAKG T0333 359 :ALPTPAETVRRIVERI 1pfkA 223 :HMCDVDELAHFIEKET Number of specific fragments extracted= 13 number of extra gaps= 0 total=1097 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wqaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wqaA expands to /projects/compbio/data/pdb/1wqa.pdb.gz 1wqaA:# T0333 read from 1wqaA/merged-good-all-a2m # 1wqaA read from 1wqaA/merged-good-all-a2m # adding 1wqaA to template set # found chain 1wqaA in template set T0333 13 :FPLIQLAWGFRTAG 1wqaA 25 :KIGMAFGTLLKREG T0333 27 :HDVLIAV 1wqaA 42 :PLVVVGR T0333 34 :A 1wqaA 51 :R T0333 91 :AVNRPLVDGTMALVDDYRPDLVVYE 1wqaA 52 :VSGEMLKEALISGLLSVGCDVIDVG T0333 116 :QGATVGLLAADRAGVPAVQRNQSAW 1wqaA 78 :APTPAVQWATKHFNADGGAVITASH T0333 141 :RTRGMHRSIASFLTDLMDK 1wqaA 116 :NGMGLKKEREAIVEELFFK T0333 160 :HQVSLPEPVAT 1wqaA 136 :DFDRAKWYEIG T0333 185 :E 1wqaA 147 :E T0333 189 :MRWVPYGGGAV 1wqaA 148 :VRREDIIKPYI T0333 200 :LGDRLP 1wqaA 161 :IKSKVD T0333 210 :RPEVAITMGT 1wqaA 174 :KPFVVVDTSN T0333 220 :IELQ 1wqaA 185 :AGSL T0333 225 :F 1wqaA 189 :T T0333 233 :IIAAAGEVDADFVLALGDLD 1wqaA 190 :LPYLLRELGCKVITVNAQPD T0333 278 :CTAVVHHG 1wqaA 236 :ADFGVAQD T0333 286 :GGGTVMTAIDA 1wqaA 261 :GDKTFALVADA T0333 297 :GIPQLLAPDP 1wqaA 277 :GGGLLVTTVA T0333 318 :VSRRGIG 1wqaA 295 :AKKHGAK T0333 325 :LV 1wqaA 303 :MR T0333 327 :STS 1wqaA 381 :GDR T0333 334 :ADLLRRLI 1wqaA 384 :HAIVNKVA T0333 342 :GDES 1wqaA 434 :KSKE T0333 346 :LRTAAREVREE 1wqaA 442 :YLNLGIELLEK Number of specific fragments extracted= 23 number of extra gaps= 0 total=1120 Number of alignments=55 # 1wqaA read from 1wqaA/merged-good-all-a2m # found chain 1wqaA in template set T0333 12 :LFPLIQLAWGFRTAG 1wqaA 24 :MKIGMAFGTLLKREG T0333 27 :HDVLIAVA 1wqaA 42 :PLVVVGRD T0333 52 :PDYSAVKVFE 1wqaA 50 :TRVSGEMLKE T0333 99 :GTMALVDDYRPDLVVYE 1wqaA 60 :ALISGLLSVGCDVIDVG T0333 116 :QGATVGLLAADRAGVPAVQRNQSA 1wqaA 78 :APTPAVQWATKHFNADGGAVITAS T0333 140 :WRTRGMHRSIASFLTDLM 1wqaA 148 :VRREDIIKPYIEAIKSKV T0333 158 :DKHQVSLPEPVATIE 1wqaA 175 :PFVVVDTSNGAGSLT T0333 173 :SF 1wqaA 198 :GC T0333 191 :WVPYG 1wqaA 200 :KVITV T0333 197 :GAVLGDRLPPVPARP 1wqaA 205 :NAQPDGYFPARNPEP T0333 223 :QAFGIGAVEPIIAAA 1wqaA 220 :NEENLKEFMEIVKAL T0333 241 :DADFVLALGDLDI 1wqaA 235 :GADFGVAQDGDAD T0333 255 :PLGTLP 1wqaA 254 :ENGRFI T0333 261 :RNVRAVGWT 1wqaA 277 :GGGLLVTTV T0333 270 :P 1wqaA 288 :S T0333 271 :LHTLLR 1wqaA 291 :LDDIAK T0333 277 :TCTAVVHHGGGGTVMTAIDAGIPQLLAPDP 1wqaA 299 :GAKVMRTKVGDLIVARALYENNGTIGGEEN T0333 307 :R 1wqaA 381 :G T0333 308 :DQFQHTAREAVSRRG 1wqaA 384 :HAIVNKVAEMARERG T0333 323 :IGLVSTS 1wqaA 414 :GWVLVRA T0333 342 :GDESLRTAAREVREEMVA 1wqaA 434 :KSKEKAQEYLNLGIELLE Number of specific fragments extracted= 21 number of extra gaps= 0 total=1141 Number of alignments=56 # 1wqaA read from 1wqaA/merged-good-all-a2m # found chain 1wqaA in template set T0333 1 :MLFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAV 1wqaA 44 :VVVGRDTRVSGEMLKEALISGLLSVGCDVIDVG T0333 34 :AEHADRAAAAGLEVVDV 1wqaA 81 :PAVQWATKHFNADGGAV T0333 51 :APDYSA 1wqaA 100 :ASHNPP T0333 66 :DNPRFAETVATRP 1wqaA 135 :EDFDRAKWYEIGE T0333 83 :EEWGVQIAAVNRPLVD 1wqaA 151 :EDIIKPYIEAIKSKVD T0333 101 :MALVDDYRPDLVVY 1wqaA 167 :VEAIKKRKPFVVVD T0333 115 :EQGATVGLLAADRAGVPAVQRNQSAWRTRGMHRSIASF 1wqaA 184 :GAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNE T0333 155 :DLMDKHQVSLPEPVATIESFPPSL 1wqaA 222 :ENLKEFMEIVKALGADFGVAQDGD T0333 186 :GWFMRWVPYGGGA 1wqaA 246 :ADRAVFIDENGRF T0333 202 :DRLPPVPARPEVAITMGTIE 1wqaA 270 :DAVLKEKGGGLLVTTVATSN T0333 232 :PIIAAAGEVDADFVLALGDL 1wqaA 290 :LLDDIAKKHGAKVMRTKVGD T0333 310 :FQHTAREAVSRRGIGL 1wqaA 310 :LIVARALYENNGTIGG T0333 333 :DADLLRR 1wqaA 360 :FSELIDE T0333 343 :DESLRTAAREVREEMVALP 1wqaA 380 :EGDRHAIVNKVAEMARERG Number of specific fragments extracted= 14 number of extra gaps= 0 total=1155 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c3jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c3jA expands to /projects/compbio/data/pdb/1c3j.pdb.gz 1c3jA:# T0333 read from 1c3jA/merged-good-all-a2m # 1c3jA read from 1c3jA/merged-good-all-a2m # adding 1c3jA to template set # found chain 1c3jA in template set Warning: unaligning (T0333)D81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1c3jA)N77 Warning: unaligning (T0333)A91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1c3jA)N77 Warning: unaligning (T0333)T119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1c3jA)A118 T0333 1 :M 1c3jA 1 :M T0333 2 :LFVSSPGI 1c3jA 3 :IAIINMGN T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHAD 1c3jA 21 :SETIYLFKVISEMGLNVDIISLKNGV T0333 47 :VVDVAPDYS 1c3jA 47 :YTKSFDEVD T0333 60 :FE 1c3jA 65 :VN T0333 95 :PLVDGTMALVDDY 1c3jA 78 :LAILSAQKFMAKY T0333 108 :RPDLVVYE 1c3jA 93 :KIYYLFTD T0333 116 :QGA 1c3jA 104 :PFS T0333 129 :GVPAVQRNQS 1c3jA 129 :KSPIKVISQG T0333 144 :GMHR 1c3jA 139 :INLD T0333 152 :FLTDLMDKH 1c3jA 143 :IAKAAHKKV T0333 165 :PEPVATIESFPPSLLLEAEPEGWFMR 1c3jA 152 :DNVIEFEYFPIEQYKIHMNDFQLSKP T0333 209 :ARPEV 1c3jA 178 :TKKTL T0333 214 :AITMGTIELQAF 1c3jA 184 :VIYGGSFRSGQR T0333 230 :VEPIIAAAGEVDADFVLA 1c3jA 196 :ESKMVEFLFDTGLNIEFF T0333 249 :GDLDISPLGT 1c3jA 214 :GNAREKQFKN T0333 259 :LPRNVRAVGWTPLHTLLRT 1c3jA 228 :WTKAPVFTGKIPMNMVSEK T0333 278 :CTAVVHHG 1c3jA 250 :AIAALIIG T0333 288 :GTVMTAIDAGIPQLLA 1c3jA 268 :LRVWETMASDAVMLID T0333 315 :R 1c3jA 291 :R T0333 325 :LV 1c3jA 292 :II T0333 327 :STSDKV 1c3jA 301 :NNRAEL T0333 334 :ADLLRRLIGDESLRTAA 1c3jA 307 :IDRVNELKHSDVLRKEM T0333 351 :REVREEMVA 1c3jA 328 :HDILNKTRA T0333 363 :PAETVRRIVERI 1c3jA 337 :KKAEWQDAFKKA Number of specific fragments extracted= 25 number of extra gaps= 0 total=1180 Number of alignments=58 # 1c3jA read from 1c3jA/merged-good-all-a2m # found chain 1c3jA in template set Warning: unaligning (T0333)T142 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1c3jA)A118 T0333 11 :HLFPLIQLAWGFRTAGHDVLIAVAE 1c3jA 19 :PSSETIYLFKVISEMGLNVDIISLK T0333 65 :KDNP 1c3jA 44 :NGVY T0333 75 :ATRPAIDLEE 1c3jA 49 :KSFDEVDVND T0333 109 :P 1c3jA 59 :Y T0333 110 :DLVVYE 1c3jA 61 :RLIVVN T0333 119 :TVGLLAADRAGVPAVQRNQSA 1c3jA 81 :LSAQKFMAKYKSKIYYLFTDI T0333 143 :RGMHRSIA 1c3jA 119 :YLYTEEEL T0333 158 :DKHQVSLPEPVATIE 1c3jA 131 :PIKVISQGINLDIAK T0333 173 :SFPP 1c3jA 150 :KVDN T0333 191 :WVPYGGGAVLG 1c3jA 154 :VIEFEYFPIEQ T0333 202 :DRLPPVP 1c3jA 170 :NDFQLSK T0333 209 :ARPEVAITMGTIE 1c3jA 179 :KKTLDVIYGGSFR T0333 223 :QAFGIGAVEPIIAAA 1c3jA 192 :SGQRESKMVEFLFDT T0333 241 :DADFVLALG 1c3jA 207 :GLNIEFFGN T0333 250 :DLDISPLGTLP 1c3jA 217 :REKQFKNPKYP T0333 261 :RNVRAVGWTPLHTLLR 1c3jA 230 :KAPVFTGKIPMNMVSE T0333 277 :TCTAVVHHG 1c3jA 249 :QAIAALIIG T0333 286 :GGGTVMTAIDAGIPQLLA 1c3jA 266 :ITLRVWETMASDAVMLID T0333 308 :DQ 1c3jA 296 :AR T0333 325 :LVST 1c3jA 298 :FYVN T0333 330 :DKVD 1c3jA 302 :NRAE T0333 334 :ADLLRRLIGDESLRTAAREVREEMVALP 1c3jA 307 :IDRVNELKHSDVLRKEMLSIQHDILNKT T0333 362 :TPAETVRRIVERIS 1c3jA 337 :KKAEWQDAFKKAID Number of specific fragments extracted= 23 number of extra gaps= 0 total=1203 Number of alignments=59 # 1c3jA read from 1c3jA/merged-good-all-a2m # found chain 1c3jA in template set Warning: unaligning (T0333)Q116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1c3jA)N77 Warning: unaligning (T0333)H146 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1c3jA)A118 T0333 1 :MLFVSSPG 1c3jA 3 :IAIINMGN T0333 11 :HLFPLIQLAWGFRTAGHDVLIAV 1c3jA 19 :PSSETIYLFKVISEMGLNVDIIS T0333 34 :A 1c3jA 44 :N T0333 45 :LEVVDVAPDYSAVKVF 1c3jA 45 :GVYTKSFDEVDVNDYD T0333 110 :DLVVYE 1c3jA 61 :RLIVVN T0333 117 :GATVGLLAADRAGVPAVQRNQSAWRTRGM 1c3jA 79 :AILSAQKFMAKYKSKIYYLFTDIRLPFSQ T0333 155 :DLMDKHQVSLPEPVATIESFPP 1c3jA 119 :YLYTEEELLIKSPIKVISQGIN T0333 182 :AEPEGWFMRWVPYGGGA 1c3jA 148 :HKKVDNVIEFEYFPIEQ T0333 199 :VLGDRLPPVPARPEVAITMGTIELQAFG 1c3jA 168 :HMNDFQLSKPTKKTLDVIYGGSFRSGQR T0333 230 :VEPIIAAAGEVDADFVLA 1c3jA 196 :ESKMVEFLFDTGLNIEFF T0333 249 :GDLDISPL 1c3jA 214 :GNAREKQF T0333 257 :GTLPRNVRAVGWTPLHTLL 1c3jA 226 :YPWTKAPVFTGKIPMNMVS T0333 276 :RTCTAVVHHG 1c3jA 248 :SQAIAALIIG T0333 287 :GGTVMTAIDAGIPQLLA 1c3jA 267 :TLRVWETMASDAVMLID T0333 327 :STSDKVDADLLRRLIGDESLRTAA 1c3jA 300 :VNNRAELIDRVNELKHSDVLRKEM T0333 351 :REVREEMVA 1c3jA 325 :SIQHDILNK T0333 360 :LPTPAETVRRIVERIS 1c3jA 335 :RAKKAEWQDAFKKAID Number of specific fragments extracted= 17 number of extra gaps= 0 total=1220 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ofuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ofuA expands to /projects/compbio/data/pdb/1ofu.pdb.gz 1ofuA:# T0333 read from 1ofuA/merged-good-all-a2m # 1ofuA read from 1ofuA/merged-good-all-a2m # adding 1ofuA to template set # found chain 1ofuA in template set T0333 2 :LFVS 1ofuA 16 :VIGV T0333 12 :LFPLIQLAWGFRTAG 1ofuA 20 :GGGGGNAVNHMAKNN T0333 27 :HDVLIAV 1ofuA 38 :VEFICAN T0333 34 :AEHAD 1ofuA 47 :AQALK T0333 44 :GLEVVDV 1ofuA 52 :NIAARTV T0333 57 :VKVFEQVAKDNPRFA 1ofuA 59 :LQLGPGVTKGLGAGA T0333 81 :DLE 1ofuA 74 :NPE T0333 88 :QIAAVNRPLVDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1ofuA 77 :VGRQAALEDRERISEVLEGADMVFITTGMGGGTGTGAAPII T0333 129 :GVPAVQRNQSAW 1ofuA 125 :GILTVAVVTRPF T0333 141 :RTRGMHRSIASFLTDLMDKHQVSL 1ofuA 178 :SLLAAFAKADDVLAGAVRGISDII T0333 165 :PEPVA 1ofuA 204 :PGMIN T0333 175 :PPS 1ofuA 209 :VDF T0333 181 :EA 1ofuA 217 :VM T0333 184 :PEG 1ofuA 219 :SEM T0333 187 :WFMRWVPYGGGAV 1ofuA 224 :AMMGTGCASGPNR T0333 200 :LGDRLPPVPARPE 1ofuA 249 :LLEDVNLQGARGI T0333 213 :VAITMG 1ofuA 263 :VNITAG T0333 223 :QAFGIGAVEPIIAAAGEV 1ofuA 269 :PDLSLGEYSDVGNIIEQF T0333 241 :D 1ofuA 290 :H T0333 242 :ADFVLALGDLDISP 1ofuA 293 :VKVGTVIDADMRDE Number of specific fragments extracted= 20 number of extra gaps= 0 total=1240 Number of alignments=61 # 1ofuA read from 1ofuA/merged-good-all-a2m # found chain 1ofuA in template set T0333 13 :FPLIQLAWGFRTAGHD 1ofuA 21 :GGGGNAVNHMAKNNVE T0333 29 :VLIAV 1ofuA 38 :VEFIC T0333 34 :AEHADRAAAAGLEVVDVAPDY 1ofuA 44 :NTDAQALKNIAARTVLQLGPG T0333 72 :ETVATRPAIDLEEWGVQIAAVNR 1ofuA 65 :VTKGLGAGANPEVGRQAALEDRE T0333 99 :GTMALVDD 1ofuA 88 :RISEVLEG T0333 109 :PDLVVY 1ofuA 96 :ADMVFI T0333 115 :EQGA 1ofuA 104 :GMGG T0333 119 :TVGLLA 1ofuA 112 :GAAPII T0333 125 :ADRAGVPAVQRNQSA 1ofuA 121 :AKEMGILTVAVVTRP T0333 140 :WRTRGMHRSIASFLTDLMDKHQVSLPEPVATIE 1ofuA 141 :RKRMQIADEGIRALAESVDSLITIPNEKLLTIL T0333 173 :SFP 1ofuA 176 :DAS T0333 223 :QAFGIGAVEPIIAAAGE 1ofuA 179 :LLAAFAKADDVLAGAVR T0333 289 :TVMTAID 1ofuA 196 :GISDIIK T0333 304 :PDPR 1ofuA 204 :PGMI T0333 308 :DQF 1ofuA 210 :DFA T0333 313 :TAREAV 1ofuA 213 :DVKTVM T0333 321 :RGIGLVSTS 1ofuA 219 :SEMGMAMMG T0333 330 :DKVD 1ofuA 233 :GPNR T0333 334 :ADLLRRLI 1ofuA 238 :REATEAAI T0333 342 :G 1ofuA 270 :D T0333 343 :DESLRTAAREVREEMVAL 1ofuA 272 :SLGEYSDVGNIIEQFASE Number of specific fragments extracted= 21 number of extra gaps= 0 total=1261 Number of alignments=62 # 1ofuA read from 1ofuA/merged-good-all-a2m # found chain 1ofuA in template set T0333 1 :MLFVSS 1ofuA 14 :IKVIGV T0333 12 :LFPLIQLAWGFRTAGHD 1ofuA 20 :GGGGGNAVNHMAKNNVE T0333 44 :GLEVVDVAPDYSAVKVF 1ofuA 37 :GVEFICANTDAQALKNI T0333 61 :EQVAKDNPRFA 1ofuA 64 :GVTKGLGAGAN T0333 86 :GVQIAAVNRPLVDGTMALVDDYRPDLVVYEQGAT 1ofuA 75 :PEVGRQAALEDRERISEVLEGADMVFITTGMGGG T0333 120 :VGLLAADRA 1ofuA 113 :AAPIIAEVA T0333 129 :GVPAVQRNQSAWRTRGMH 1ofuA 125 :GILTVAVVTRPFPFEGRK T0333 158 :DKHQVSLPEPVATIE 1ofuA 211 :FADVKTVMSEMGMAM T0333 189 :MRWVPYGGGA 1ofuA 226 :MGTGCASGPN T0333 199 :VLGDRLPPVPARP 1ofuA 248 :PLLEDVNLQGARG T0333 212 :EVAITMGTI 1ofuA 262 :LVNITAGPD T0333 225 :FGIGAVEPIIAAAGEV 1ofuA 271 :LSLGEYSDVGNIIEQF T0333 241 :DADFVLALGD 1ofuA 292 :TVKVGTVIDA T0333 258 :TLPRNVR 1ofuA 302 :DMRDELH Number of specific fragments extracted= 14 number of extra gaps= 0 total=1275 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a9xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0333 read from 1a9xA/merged-good-all-a2m # 1a9xA read from 1a9xA/merged-good-all-a2m # found chain 1a9xA in training set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1a9xA)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1a9xA)D558 T0333 2 :LFVSSPGI 1a9xA 10 :ILILGAGP T0333 10 :GHL 1a9xA 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1a9xA 28 :YSGAQACKALREEGYRVINVN T0333 34 :AEHADRAAAA 1a9xA 51 :PATIMTDPEM T0333 45 :LEVVDVAP 1a9xA 61 :ADATYIEP T0333 94 :RPL 1a9xA 71 :WEV T0333 100 :TMALVDDYRPDLVVYEQGATVGLLAADRA 1a9xA 74 :VRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1a9xA 112 :GVT T0333 136 :NQSAW 1a9xA 115 :MIGAT T0333 141 :RTRGMHRSIASFLTDL 1a9xA 505 :LAGVREAEIRKLRDQY T0333 165 :PEPVATIESFPPSLL 1a9xA 521 :DLHPVYKRVDTCAAE T0333 199 :V 1a9xA 536 :F T0333 200 :LGDR 1a9xA 547 :YEEE T0333 204 :LPPV 1a9xA 553 :ANPS T0333 210 :RPEVAITMGT 1a9xA 559 :REKIMVLGGG T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLAL 1a9xA 572 :IGQGIEFDYCCVHASLALREDGYETIMVN T0333 277 :T 1a9xA 611 :D T0333 278 :CTAVVHHG 1a9xA 613 :SDRLYFEP T0333 286 :GGGTVMTAIDAGIP 1a9xA 622 :TLEDVLEIVRIEKP T0333 300 :QLLAPDPRD 1a9xA 637 :GVIVQYGGQ T0333 309 :QFQHTAR 1a9xA 647 :PLKLARA T0333 318 :VSRRGIG 1a9xA 654 :LEAAGVP T0333 325 :LVST 1a9xA 662 :IGTS T0333 334 :ADLLRRLIG 1a9xA 666 :PDAIDRAED T0333 347 :RTAAREVREEMV 1a9xA 675 :RERFQHAVERLK T0333 362 :TPAETVRRIVERI 1a9xA 696 :TAIEMAVEKAKEI Number of specific fragments extracted= 26 number of extra gaps= 1 total=1301 Number of alignments=64 # 1a9xA read from 1a9xA/merged-good-all-a2m # found chain 1a9xA in training set T0333 2 :LF 1a9xA 12 :IL T0333 5 :SSPGI 1a9xA 15 :AGPIV T0333 10 :GHL 1a9xA 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHADRAAAAG 1a9xA 28 :YSGAQACKALREEGYRVINVNSNPATIMTDPE T0333 45 :LEVVDVAPDYSA 1a9xA 61 :ADATYIEPIHWE T0333 99 :GTMALVDDYRPDLVVYEQGATVGLLAADRA 1a9xA 73 :VVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1a9xA 112 :GVT T0333 135 :RNQSA 1a9xA 115 :MIGAT T0333 140 :WRTRGMHRSIASFLTDLM 1a9xA 800 :TLSQEIQDVMRQQVQKLA T0333 168 :VA 1a9xA 874 :LA T0333 173 :SFPPSLLL 1a9xA 878 :GVTKEVIP T0333 186 :GWFMRWVPYGGGAVLGDRLPPVP 1a9xA 886 :PYYSVKEVVLPFNKFPGVDPLLG T0333 209 :ARPEVAITM 1a9xA 941 :KHGRALLSV T0333 223 :QAFGIGAVEPIIAAAGEVDADFVL 1a9xA 950 :REGDKERVVDLAAKLLKQGFELDA Number of specific fragments extracted= 14 number of extra gaps= 0 total=1315 Number of alignments=65 # 1a9xA read from 1a9xA/merged-good-all-a2m # found chain 1a9xA in training set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1a9xA)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1a9xA)D558 T0333 1 :MLFVSSPGI 1a9xA 10 :ILILGAGPI T0333 10 :GH 1a9xA 21 :GQ T0333 12 :LFPLIQLAWGFRTAGHDVLIAV 1a9xA 27 :DYSGAQACKALREEGYRVINVN T0333 34 :AEHA 1a9xA 51 :PATI T0333 40 :AAAAG 1a9xA 55 :MTDPE T0333 45 :LEVVDVAPDY 1a9xA 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1a9xA 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GV 1a9xA 112 :GV T0333 137 :QSAWRTRGMHRSIASFLT 1a9xA 114 :TMIGATADAIDKAEDRRR T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1a9xA 508 :VREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEEC T0333 204 :LPPV 1a9xA 553 :ANPS T0333 210 :RPEVAITMGTIELQAFGIGAVEPII 1a9xA 559 :REKIMVLGGGPNRIGQGIEFDYCCV T0333 235 :AAAGEVDADFVLALGD 1a9xA 587 :LALREDGYETIMVNCN T0333 275 :LRTC 1a9xA 610 :YDTS T0333 279 :TAVVHHGGGGTVMTAIDAGIP 1a9xA 615 :RLYFEPVTLEDVLEIVRIEKP T0333 300 :QLLAP 1a9xA 637 :GVIVQ T0333 305 :DPRDQFQHTAREAVSRRGIGL 1a9xA 643 :GGQTPLKLARALEAAGVPVIG T0333 329 :SD 1a9xA 665 :SP T0333 335 :DLLRRLIGDESLRTAAREV 1a9xA 667 :DAIDRAEDRERFQHAVERL T0333 360 :LPTPAETVRRIVER 1a9xA 695 :VTAIEMAVEKAKEI Number of specific fragments extracted= 20 number of extra gaps= 1 total=1335 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 6pfkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 6pfkA expands to /projects/compbio/data/pdb/6pfk.pdb.gz 6pfkA:Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 6pfkA Skipped atom 1877, because occupancy 0.500 <= existing 0.500 in 6pfkA Skipped atom 1879, because occupancy 0.500 <= existing 0.500 in 6pfkA Skipped atom 1881, because occupancy 0.500 <= existing 0.500 in 6pfkA Skipped atom 1883, because occupancy 0.500 <= existing 0.500 in 6pfkA Skipped atom 1885, because occupancy 0.500 <= existing 0.500 in 6pfkA # T0333 read from 6pfkA/merged-good-all-a2m # 6pfkA read from 6pfkA/merged-good-all-a2m # adding 6pfkA to template set # found chain 6pfkA in template set Warning: unaligning (T0333)T24 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)H30 Warning: unaligning (T0333)A25 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)H30 Warning: unaligning (T0333)S55 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)I49 Warning: unaligning (T0333)A56 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)I49 Warning: unaligning (T0333)P68 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)H62 Warning: unaligning (T0333)R69 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)H62 Warning: unaligning (T0333)E83 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)T78 Warning: unaligning (T0333)E84 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)T78 Warning: unaligning (T0333)R141 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)F135 Warning: unaligning (T0333)T142 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)F135 Warning: unaligning (T0333)T170 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)Y164 Warning: unaligning (T0333)I171 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)Y164 Warning: unaligning (T0333)E221 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)E193 Warning: unaligning (T0333)L222 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)E193 Warning: unaligning (T0333)I227 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)N199 Warning: unaligning (T0333)S254 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)V250 Warning: unaligning (T0333)P255 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)V250 T0333 1 :M 6pfkA 1 :M T0333 2 :LFVSSPGIGHLFPLI 6pfkA 6 :VLTSGGDSPGMNAAI T0333 17 :QLAWGFR 6pfkA 22 :SVVRKAI T0333 26 :GHDVLIAV 6pfkA 31 :GVEVYGVY T0333 35 :EHADRAAAA 6pfkA 39 :HGYAGLIAG T0333 57 :VKVFEQVAKDN 6pfkA 50 :KKLEVGDVGDI T0333 70 :FAETVATRPAI 6pfkA 63 :RGGTILYTARC T0333 81 :DL 6pfkA 75 :EF T0333 94 :RPLVDGTMALVDDYRP 6pfkA 79 :EEGQKKGIEQLKKHGI T0333 110 :DLVVYE 6pfkA 96 :GLVVIG T0333 118 :ATVGLLAADRA 6pfkA 102 :GDGSYQGAKKL T0333 129 :GVPAVQRNQSAW 6pfkA 116 :GFPCVGVPGTID T0333 143 :RGMHRSIASFLTDLMDKHQVSLPEPVA 6pfkA 136 :TIGFDTALNTVIDAIDKIRDTATSHER T0333 172 :E 6pfkA 165 :V T0333 192 :VPYGGGAV 6pfkA 166 :IEVMGRHA T0333 209 :ARPEVA 6pfkA 185 :GAETIL T0333 220 :I 6pfkA 191 :I T0333 223 :QAFG 6pfkA 194 :ADYD T0333 228 :GAVEPIIAAAGEV 6pfkA 200 :DVIARLKRGHERG T0333 241 :DADFVLALGDLD 6pfkA 214 :KHSIIIVAEGVG T0333 253 :I 6pfkA 248 :G T0333 256 :LGTLP 6pfkA 251 :QRGGS T0333 304 :PDPRD 6pfkA 256 :PTAFD T0333 309 :QFQHTAR 6pfkA 264 :ASRLGAR T0333 318 :VSR 6pfkA 271 :AVE T0333 321 :RGIG 6pfkA 277 :EGKG T0333 325 :LV 6pfkA 282 :RC T0333 327 :ST 6pfkA 294 :HD T0333 337 :LRRLIG 6pfkA 296 :IAEALA T0333 343 :DESLRTAARE 6pfkA 308 :DQRMYALSKE Number of specific fragments extracted= 30 number of extra gaps= 9 total=1365 Number of alignments=67 # 6pfkA read from 6pfkA/merged-good-all-a2m # found chain 6pfkA in template set Warning: unaligning (T0333)T24 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)H30 Warning: unaligning (T0333)A25 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)H30 Warning: unaligning (T0333)G44 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)I49 Warning: unaligning (T0333)L45 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)I49 Warning: unaligning (T0333)P68 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)H62 Warning: unaligning (T0333)E83 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)T78 Warning: unaligning (T0333)E84 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)T78 Warning: unaligning (T0333)R141 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)F135 Warning: unaligning (T0333)T142 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)F135 Warning: unaligning (T0333)V192 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)Y164 Warning: unaligning (T0333)P193 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)Y164 Warning: unaligning (T0333)E221 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)E193 Warning: unaligning (T0333)L222 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)E193 Warning: unaligning (T0333)I227 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)N199 Warning: unaligning (T0333)G228 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)N199 Warning: unaligning (T0333)S254 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)V250 Warning: unaligning (T0333)P255 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)V250 Warning: unaligning (T0333)D330 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)N289 Warning: unaligning (T0333)K331 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)N289 T0333 1 :M 6pfkA 1 :M T0333 2 :LFVSSPGI 6pfkA 6 :VLTSGGDS T0333 10 :GHLFPLIQLAWGFR 6pfkA 15 :GMNAAIRSVVRKAI T0333 26 :GHDVLIA 6pfkA 31 :GVEVYGV T0333 34 :AEHADRAAAA 6pfkA 38 :YHGYAGLIAG T0333 46 :EVVDVA 6pfkA 50 :KKLEVG T0333 53 :DY 6pfkA 56 :DV T0333 65 :KDN 6pfkA 58 :GDI T0333 69 :RFAETVATRPAIDL 6pfkA 63 :RGGTILYTARCPEF T0333 85 :WGVQ 6pfkA 79 :EEGQ T0333 98 :DGTMALVDDYRP 6pfkA 83 :KKGIEQLKKHGI T0333 110 :DLVVYE 6pfkA 96 :GLVVIG T0333 118 :ATVGLLAADRA 6pfkA 102 :GDGSYQGAKKL T0333 129 :GVPAVQRNQSA 6pfkA 116 :GFPCVGVPGTI T0333 140 :W 6pfkA 133 :T T0333 143 :RGMHRSIASFLTDL 6pfkA 136 :TIGFDTALNTVIDA T0333 168 :VATIESFPPSLL 6pfkA 150 :IDKIRDTATSHE T0333 191 :W 6pfkA 162 :R T0333 194 :YGGGA 6pfkA 165 :VIEVM T0333 204 :LPPVP 6pfkA 170 :GRHAG T0333 209 :ARPEVA 6pfkA 185 :GAETIL T0333 223 :QAFG 6pfkA 194 :ADYD T0333 229 :AVEPIIAAAGEV 6pfkA 200 :DVIARLKRGHER T0333 241 :DADFVLALGDLDI 6pfkA 214 :KHSIIIVAEGVGS T0333 256 :LGTLP 6pfkA 251 :QRGGS T0333 271 :LHTLLR 6pfkA 264 :ASRLGA T0333 313 :TAREAVSRRGIGLVSTS 6pfkA 270 :RAVELLLEGKGGRCVGI T0333 337 :LRRLIG 6pfkA 296 :IAEALA T0333 343 :DESLRTAAREV 6pfkA 308 :DQRMYALSKEL Number of specific fragments extracted= 29 number of extra gaps= 10 total=1394 Number of alignments=68 # 6pfkA read from 6pfkA/merged-good-all-a2m # found chain 6pfkA in template set Warning: unaligning (T0333)T24 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)H30 Warning: unaligning (T0333)A25 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)H30 Warning: unaligning (T0333)G44 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)I49 Warning: unaligning (T0333)L45 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)I49 Warning: unaligning (T0333)A71 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)T78 Warning: unaligning (T0333)E72 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)T78 Warning: unaligning (T0333)L179 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)F135 Warning: unaligning (T0333)L180 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)F135 Warning: unaligning (T0333)A242 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)Y164 Warning: unaligning (T0333)D243 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)Y164 Warning: unaligning (T0333)P304 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)E193 Warning: unaligning (T0333)P306 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)N199 Warning: unaligning (T0333)R307 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)N199 T0333 1 :MLFVSSPGIGHL 6pfkA 4 :IGVLTSGGDSPG T0333 13 :F 6pfkA 17 :N T0333 14 :PLIQLAWGFR 6pfkA 19 :AIRSVVRKAI T0333 26 :GHDVLIAVA 6pfkA 31 :GVEVYGVYH T0333 36 :HADRAAAA 6pfkA 40 :GYAGLIAG T0333 46 :E 6pfkA 50 :K T0333 49 :DV 6pfkA 51 :KL T0333 53 :DYSAVKVF 6pfkA 53 :EVGDVGDI T0333 61 :EQVAKDNPRF 6pfkA 67 :ILYTARCPEF T0333 94 :RPLVDGTMALVDDYRPDLVVYEQGATVGLLAADRA 6pfkA 79 :EEGQKKGIEQLKKHGIEGLVVIGGDGSYQGAKKLT T0333 129 :GVPAVQRNQSAWRT 6pfkA 116 :GFPCVGVPGTIDND T0333 175 :PPSL 6pfkA 130 :IPGT T0333 181 :E 6pfkA 136 :T T0333 220 :IE 6pfkA 137 :IG T0333 226 :GIGAVEPIIAAAGEV 6pfkA 139 :FDTALNTVIDAIDKI T0333 241 :D 6pfkA 161 :E T0333 244 :FVLALGD 6pfkA 165 :VIEVMGR T0333 284 :HGGGGTVMTAIDAGIPQLLA 6pfkA 172 :HAGDIALWSGLAGGAETILI T0333 305 :D 6pfkA 197 :D T0333 308 :DQFQHTAREAVSRRGIGL 6pfkA 200 :DVIARLKRGHERGKKHSI T0333 327 :STSDKVDADLLRRLIG 6pfkA 224 :VGSGVDFGRQIQEATG T0333 343 :DESLRTAAREVREE 6pfkA 257 :TAFDRVLASRLGAR T0333 366 :TVRRIVE 6pfkA 271 :AVELLLE Number of specific fragments extracted= 23 number of extra gaps= 7 total=1417 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rq2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rq2A expands to /projects/compbio/data/pdb/1rq2.pdb.gz 1rq2A:Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 293, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 295, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 297, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 299, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 301, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 303, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 733, because occupancy 0.330 <= existing 0.330 in 1rq2A Skipped atom 734, because occupancy 0.330 <= existing 0.330 in 1rq2A Skipped atom 906, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 910, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 912, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 914, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 916, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1237, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1503, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1505, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1527, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1538, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1540, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1542, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1603, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1770, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1772, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1774, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1776, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1778, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1780, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1782, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1784, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1844, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1846, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1848, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 2041, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 2043, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 2045, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 2135, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 2137, because occupancy 0.500 <= existing 0.500 in 1rq2A # T0333 read from 1rq2A/merged-good-all-a2m # 1rq2A read from 1rq2A/merged-good-all-a2m # adding 1rq2A to template set # found chain 1rq2A in template set Warning: unaligning (T0333)A64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rq2A)G69 Warning: unaligning (T0333)F70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rq2A)G69 T0333 2 :LFVS 1rq2A 13 :VVGI T0333 12 :LFPLIQLAWGFRTAG 1rq2A 17 :GGGGVNAVNRMIEQG T0333 27 :HDVLIAVAE 1rq2A 35 :VEFIAINTD T0333 37 :ADRAAAAGLEVVD 1rq2A 44 :AQALLMSDADVKL T0333 50 :VAPD 1rq2A 58 :VGRD T0333 63 :V 1rq2A 62 :S T0333 71 :A 1rq2A 70 :A T0333 81 :DLE 1rq2A 71 :DPE T0333 88 :QIAAVNRPLVDGTMALVDDYRPDLVVYEQGA 1rq2A 74 :VGRKAAEDAKDEIEELLRGADMVFVTAGEGG T0333 119 :TVGLLAADRA 1rq2A 109 :GGAPVVASIA T0333 129 :GVPAVQRNQSAW 1rq2A 122 :GALTVGVVTRPF T0333 141 :RTRGMHRSIASFLTDLMDK 1rq2A 171 :DAAVSLMDAFRSADEVLLN T0333 160 :HQVSL 1rq2A 198 :ITTPG T0333 171 :IES 1rq2A 203 :LIN T0333 175 :PPS 1rq2A 206 :VDF T0333 180 :LEAEPEG 1rq2A 213 :GIMSGAG T0333 187 :WFMRWVPYGGGAV 1rq2A 221 :ALMGIGSARGEGR T0333 200 :LGDRLPP 1rq2A 247 :LEASMEG T0333 209 :ARPEVAITMGT 1rq2A 254 :AQGVLMSIAGG T0333 223 :QAFGIGAVEPIIAAAGEV 1rq2A 265 :SDLGLFEINEAASLVQDA T0333 241 :DADFVLAL 1rq2A 286 :DANIIFGT T0333 249 :G 1rq2A 296 :D T0333 254 :SPLG 1rq2A 297 :DSLG T0333 261 :RNVRA 1rq2A 301 :DEVRV Number of specific fragments extracted= 24 number of extra gaps= 0 total=1441 Number of alignments=70 # 1rq2A read from 1rq2A/merged-good-all-a2m # found chain 1rq2A in template set Warning: unaligning (T0333)T73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rq2A)G69 Warning: unaligning (T0333)A79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rq2A)G69 T0333 12 :LFPLIQLAWGFRTAG 1rq2A 17 :GGGGVNAVNRMIEQG T0333 27 :HDVLIAVAE 1rq2A 35 :VEFIAINTD T0333 37 :ADRAAAAGLEVVDVAPDY 1rq2A 44 :AQALLMSDADVKLDVGRD T0333 72 :E 1rq2A 62 :S T0333 80 :IDLEEWGVQIAAVNR 1rq2A 70 :ADPEVGRKAAEDAKD T0333 99 :GTMALVDD 1rq2A 85 :EIEELLRG T0333 109 :PDLVVY 1rq2A 93 :ADMVFV T0333 115 :E 1rq2A 101 :G T0333 118 :A 1rq2A 104 :G T0333 119 :TVGLL 1rq2A 109 :GGAPV T0333 124 :AADRAGVPAVQRNQSA 1rq2A 117 :IARKLGALTVGVVTRP T0333 140 :WRTRGMHRSIASFLTDLMDKHQVS 1rq2A 138 :KRRSNQAENGIAALRESCDTLIVI T0333 168 :VATIESFPP 1rq2A 163 :NDRLLQMGD T0333 205 :PPVP 1rq2A 172 :AAVS T0333 209 :ARPEVAITMGTIE 1rq2A 253 :GAQGVLMSIAGGS T0333 224 :AFGIGAVEPIIAAAGEV 1rq2A 266 :DLGLFEINEAASLVQDA T0333 241 :DADFVLAL 1rq2A 286 :DANIIFGT T0333 254 :SPLG 1rq2A 297 :DSLG T0333 261 :RNVRA 1rq2A 301 :DEVRV Number of specific fragments extracted= 19 number of extra gaps= 0 total=1460 Number of alignments=71 # 1rq2A read from 1rq2A/merged-good-all-a2m # found chain 1rq2A in template set Warning: unaligning (T0333)P68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rq2A)G69 Warning: unaligning (T0333)V74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rq2A)G69 T0333 1 :MLFVSS 1rq2A 11 :IKVVGI T0333 12 :LFPLIQLAWGFRTAGHD 1rq2A 17 :GGGGVNAVNRMIEQGLK T0333 44 :GLEVVDVAPDYSAVKVF 1rq2A 34 :GVEFIAINTDAQALLMS T0333 66 :DN 1rq2A 61 :DS T0333 75 :AT 1rq2A 70 :AD T0333 86 :GVQIAAVNRPLVDGTMALVDDYRPDLVVYEQGAT 1rq2A 72 :PEVGRKAAEDAKDEIEELLRGADMVFVTAGEGGG T0333 120 :VGLLAADRA 1rq2A 110 :GAPVVASIA T0333 129 :GVPAVQRNQSAWRTRGMHRSIA 1rq2A 122 :GALTVGVVTRPFSFEGKRRSNQ T0333 155 :DLMDKHQVSLPEPVATIESF 1rq2A 205 :NVDFADVKGIMSGAGTALMG T0333 191 :WVPYGGGA 1rq2A 225 :IGSARGEG T0333 199 :VLGDRLPPVPARPEVAITMGTIEL 1rq2A 243 :NSPLLEASMEGAQGVLMSIAGGSD T0333 225 :FGIGAVEPIIAAAGEV 1rq2A 267 :LGLFEINEAASLVQDA T0333 241 :DADFVLALGDL 1rq2A 286 :DANIIFGTVID T0333 254 :SPLGT 1rq2A 297 :DSLGD Number of specific fragments extracted= 14 number of extra gaps= 0 total=1474 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f0kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f0kA expands to /projects/compbio/data/pdb/1f0k.pdb.gz 1f0kA:# T0333 read from 1f0kA/merged-good-all-a2m # 1f0kA read from 1f0kA/merged-good-all-a2m # adding 1f0kA to template set # found chain 1f0kA in template set T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAV 1f0kA 10 :MVMAGGTGGHVFPGLAVAHHLMAQGWQVRWLG T0333 34 :AEHADRAAAAGLEVVDVA 1f0kA 45 :RMEADLVPKHGIEIDFIR T0333 61 :EQVAKDN 1f0kA 63 :ISGLRGK T0333 81 :DLEEWGVQI 1f0kA 70 :GIKALIAAP T0333 91 :AVNRPLVDGTMALVDDYRPDLVVYE 1f0kA 79 :LRIFNAWRQARAIMKAYKPDVVLGM T0333 116 :QGATVGLLAADRAGVPAVQRNQS 1f0kA 106 :YVSGPGGLAAWSLGIPVVLHEQN T0333 144 :GMHRSIASFLT 1f0kA 129 :GIAGLTNKWLA T0333 165 :PEPVATIESF 1f0kA 140 :KIATKVMQAF T0333 185 :EGWFMR 1f0kA 150 :PGAFPN T0333 192 :VPYGGGAV 1f0kA 156 :AEVVGNPV T0333 200 :LGDRLPPVPARPEVAITMGT 1f0kA 173 :PQQRLAGREGPVRVLVVGGS T0333 224 :AFGIGAVEPIIAAAGEVD 1f0kA 193 :QGARILNQTMPQVAAKLG T0333 242 :ADFVLALGDLDISPLGT 1f0kA 213 :VTIWHQSGKGSQQSVEQ T0333 259 :LPRNVRAVGWT 1f0kA 235 :GQPQHKVTEFI T0333 270 :PLHTLLRTCTAVVHHGGGGTVMTAIDAGIPQLLAPDPR 1f0kA 247 :DMAAAYAWADVVVCRSGALTVSEIAAAGLPALFVPFQH T0333 308 :DQFQHTAR 1f0kA 288 :QQYWNALP T0333 318 :VSRRGIGLVSTSDKVDADLLRRLI 1f0kA 296 :LEKAGAAKIIEQPQLSVDAVANTL T0333 347 :RTAAREVREEMVALPT 1f0kA 324 :RETLLTMAERARAASI T0333 363 :PAETVRRIVERI 1f0kA 342 :ATERVANEVSRV Number of specific fragments extracted= 19 number of extra gaps= 0 total=1493 Number of alignments=73 # 1f0kA read from 1f0kA/merged-good-all-a2m # found chain 1f0kA in template set T0333 3 :FVSSPGIGHLFPLIQLAWGFRTAGHDVLIAVAEHA 1f0kA 11 :VMAGGTGGHVFPGLAVAHHLMAQGWQVRWLGTADR T0333 38 :DRAAAAGLEVVDVA 1f0kA 49 :DLVPKHGIEIDFIR T0333 74 :VATRPAIDLEEWGVQIAAVNRPLV 1f0kA 63 :ISGLRGKGIKALIAAPLRIFNAWR T0333 99 :GTMALVDDYRPDLVVY 1f0kA 87 :QARAIMKAYKPDVVLG T0333 115 :EQGATVGLLAADRAGVPAVQR 1f0kA 105 :GYVSGPGGLAAWSLGIPVVLH T0333 141 :RTRGMHRSIASFLTDLMDKHQVSLPEP 1f0kA 126 :EQNGIAGLTNKWLAKIATKVMQAFPGA T0333 175 :PP 1f0kA 153 :FP T0333 191 :WVPYGGGAVLGDRLPPVP 1f0kA 155 :NAEVVGNPVRTDVLALPL T0333 209 :ARPEVAITMGTIELQAFGIGAVEPIIAAAGE 1f0kA 181 :EGPVRVLVVGGSQGARILNQTMPQVAAKLGD T0333 241 :DADFVLALGDLDISPLGTLP 1f0kA 212 :SVTIWHQSGKGSQQSVEQAY T0333 261 :RNVRAVGWT 1f0kA 237 :PQHKVTEFI T0333 270 :PLHTLLRTCTAVVHHGGGGTVMTAIDAGIPQLLAPDPR 1f0kA 247 :DMAAAYAWADVVVCRSGALTVSEIAAAGLPALFVPFQH T0333 308 :DQF 1f0kA 288 :QQY T0333 313 :TAREAVSRRGIGLVST 1f0kA 291 :WNALPLEKAGAAKIIE T0333 330 :DKVD 1f0kA 307 :QPQL T0333 334 :ADLLRRLIG 1f0kA 312 :VDAVANTLA T0333 343 :D 1f0kA 323 :S T0333 347 :RTAAREVREEMVAL 1f0kA 324 :RETLLTMAERARAA T0333 361 :P 1f0kA 340 :P T0333 362 :TPAETVRRIVERIS 1f0kA 342 :ATERVANEVSRVAR Number of specific fragments extracted= 20 number of extra gaps= 0 total=1513 Number of alignments=74 # 1f0kA read from 1f0kA/merged-good-all-a2m # found chain 1f0kA in template set T0333 1 :MLFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAV 1f0kA 9 :LMVMAGGTGGHVFPGLAVAHHLMAQGWQVRWLG T0333 34 :AEHADRAAAAGLEVVDVAPDYSAVKVFEQVAKDNP 1f0kA 45 :RMEADLVPKHGIEIDFIRISGLRGKGIKALIAAPL T0333 92 :VNRPLVDGTMALVDDYRPDLVVYEQGATVGL 1f0kA 80 :RIFNAWRQARAIMKAYKPDVVLGMGGYVSGP T0333 123 :LAADRAGVPAVQRNQSAWRTRGM 1f0kA 113 :LAAWSLGIPVVLHEQNGIAGLTN T0333 162 :VSLPEPVATIESFPPSLL 1f0kA 136 :KWLAKIATKVMQAFPGAF T0333 186 :GWFMRWVPYGGGA 1f0kA 154 :PNAEVVGNPVRTD T0333 199 :VLGDRLPPVPARPEVAITMGTIE 1f0kA 172 :LPQQRLAGREGPVRVLVVGGSQG T0333 226 :GIGAVEPIIAAAGEVD 1f0kA 195 :ARILNQTMPQVAAKLG T0333 242 :ADFVLALGDLDISPL 1f0kA 213 :VTIWHQSGKGSQQSV T0333 257 :GT 1f0kA 234 :AG T0333 260 :PRNVRAVGWT 1f0kA 236 :QPQHKVTEFI T0333 270 :PLHTLLRTCTAVVHHGGGGTVMTAIDAGIPQLLAP 1f0kA 247 :DMAAAYAWADVVVCRSGALTVSEIAAAGLPALFVP T0333 305 :DPRD 1f0kA 283 :QHKD T0333 309 :QFQHTAREAVSRRGIGLV 1f0kA 289 :QYWNALPLEKAGAAKIIE T0333 327 :STSDKVDADLLRR 1f0kA 309 :QLSVDAVANTLAG T0333 341 :IGDESLRTAAREVREEMV 1f0kA 322 :WSRETLLTMAERARAASI T0333 360 :LPTPAETVRRIVERIS 1f0kA 340 :PDATERVANEVSRVAR Number of specific fragments extracted= 17 number of extra gaps= 0 total=1530 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xuuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xuuA expands to /projects/compbio/data/pdb/1xuu.pdb.gz 1xuuA:# T0333 read from 1xuuA/merged-good-all-a2m # 1xuuA read from 1xuuA/merged-good-all-a2m # adding 1xuuA to template set # found chain 1xuuA in template set T0333 2 :LFVSSPGI 1xuuA 22 :IICEIGIN T0333 10 :GHLFPLIQLAWGFRTAGHDVLIAVAEHADRA 1xuuA 32 :GSLKTAFEMVDAAYNAGAEVVKHQTHIVEDE T0333 67 :NPRFAETVATRPAIDLEEWGVQI 1xuuA 64 :SDEAKQVIPGNADVSIYEIMERC T0333 94 :RPLVDGTMALVDDYRPDLVVYE 1xuuA 90 :EEDEIKLKEYVESKGMIFISTP T0333 117 :GATVGLLAADRAGVPAVQRNQSAWRTRGMHRSIAS 1xuuA 112 :FSRAAALRLQRMDIPAYKIGSGECNNYPLIKLVAS T0333 209 :ARPEVAITMGT 1xuuA 147 :FGKPIILSTGM T0333 226 :GIGAVEPIIAAAGEVDADFV 1xuuA 159 :SIESIKKSVEIIREAGVPYA T0333 246 :LALG 1xuuA 180 :LHCT T0333 250 :DLDISPLG 1xuuA 187 :PTPYEDVR T0333 271 :LHTLLRT 1xuuA 198 :MNDLSEA T0333 278 :CTAVVHHG 1xuuA 208 :AIIGLSDH T0333 287 :GGTVMTAIDAGIPQLLAPDP 1xuuA 219 :NYACLGAVALGGSILERHFT T0333 308 :DQFQHTAR 1xuuA 246 :PDIVCSMN T0333 334 :ADLLRRL 1xuuA 254 :PDTFKEL T0333 347 :RTAAREVREEMV 1xuuA 261 :KQGAHALKLARG Number of specific fragments extracted= 15 number of extra gaps= 0 total=1545 Number of alignments=76 # 1xuuA read from 1xuuA/merged-good-all-a2m # found chain 1xuuA in template set T0333 2 :LFV 1xuuA 22 :IIC T0333 5 :SSPGI 1xuuA 26 :IGINH T0333 10 :GHLFPLIQLAWGFRTAGHDVLIAVAEHADRA 1xuuA 32 :GSLKTAFEMVDAAYNAGAEVVKHQTHIVEDE T0333 67 :NP 1xuuA 63 :MS T0333 69 :RFAETVATRPAIDLEEWGVQ 1xuuA 67 :AKQVIPGNADVSIYEIMERC T0333 89 :IA 1xuuA 93 :EI T0333 99 :GTMALVDDYRPDLVVYE 1xuuA 95 :KLKEYVESKGMIFISTP T0333 117 :GATVGLLAADRAGVPAVQRN 1xuuA 112 :FSRAAALRLQRMDIPAYKIG T0333 141 :RTRGMHRSIASFLTDL 1xuuA 132 :SGECNNYPLIKLVASF T0333 210 :RPEVAITMGTIE 1xuuA 148 :GKPIILSTGMNS T0333 223 :Q 1xuuA 160 :I T0333 228 :GAVEPIIAAAGEVDADFVLALG 1xuuA 161 :ESIKKSVEIIREAGVPYALLHC T0333 250 :DLDISPLG 1xuuA 187 :PTPYEDVR T0333 269 :TP 1xuuA 195 :LG T0333 271 :LHTLLR 1xuuA 198 :MNDLSE T0333 277 :TCTAVVHHG 1xuuA 207 :DAIIGLSDH T0333 286 :GGGTVMTAIDAGIPQLLAPDPR 1xuuA 218 :DNYACLGAVALGGSILERHFTD T0333 308 :DQF 1xuuA 250 :CSM T0333 314 :AREAVSR 1xuuA 253 :NPDTFKE T0333 346 :LRTAAREVREEMV 1xuuA 260 :LKQGAHALKLARG Number of specific fragments extracted= 20 number of extra gaps= 0 total=1565 Number of alignments=77 # 1xuuA read from 1xuuA/merged-good-all-a2m # found chain 1xuuA in template set T0333 1 :MLFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAVAEHADRA 1xuuA 23 :ICEIGINHEGSLKTAFEMVDAAYNAGAEVVKHQTHIVEDE T0333 55 :SAVKVFEQ 1xuuA 63 :MSDEAKQV T0333 70 :FAETVATRPAIDLEEW 1xuuA 71 :IPGNADVSIYEIMERC T0333 91 :AVNRPLVDGTMALVDDYRPDLVVYE 1xuuA 87 :ALNEEDEIKLKEYVESKGMIFISTP T0333 117 :GATVGLLAADRAGVPAVQRNQSAWRTRGMHRSIASFL 1xuuA 112 :FSRAAALRLQRMDIPAYKIGSGECNNYPLIKLVASFG T0333 211 :PEVAITMGTI 1xuuA 149 :KPIILSTGMN T0333 226 :GIGAVEPIIAAAGEVDADFVLALGD 1xuuA 159 :SIESIKKSVEIIREAGVPYALLHCT T0333 251 :LDISPL 1xuuA 188 :TPYEDV T0333 271 :LHTLLRTCTAVVHH 1xuuA 201 :LSEAFPDAIIGLSD T0333 287 :GGTVMTAIDAGIPQLLAP 1xuuA 219 :NYACLGAVALGGSILERH T0333 306 :PRD 1xuuA 240 :RMD T0333 323 :IGLV 1xuuA 243 :RPGP T0333 327 :STSDKVDAD 1xuuA 251 :SMNPDTFKE T0333 346 :LRTAAREVREE 1xuuA 260 :LKQGAHALKLA Number of specific fragments extracted= 14 number of extra gaps= 0 total=1579 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1udc/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1udc expands to /projects/compbio/data/pdb/1udc.pdb.gz 1udc:Warning: there is no chain 1udc will retry with 1udcA # T0333 read from 1udc/merged-good-all-a2m # 1udc read from 1udc/merged-good-all-a2m # adding 1udc to template set # found chain 1udc in template set T0333 1 :M 1udc 1 :M T0333 2 :LFVSSPGI 1udc 3 :VLVTGGSG T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1udc 11 :YIGSHTCVQLLQNGHDVIILD T0333 34 :AEH 1udc 33 :LCN T0333 37 :ADRAAAA 1udc 41 :LPVIERL T0333 44 :GLEVVDVAPD 1udc 51 :HPTFVEGDIR T0333 81 :DL 1udc 61 :NE T0333 98 :DGTMALVDDYRPDLVVYEQGAT 1udc 63 :ALMTEILHDHAIDTVIHFAGLK T0333 120 :VGLLAADRAGVPAVQRNQSAW 1udc 106 :RLISAMRAANVKNFIFSSSAT T0333 141 :RTRGMHRSIASFLTDLMDK 1udc 193 :PQGIPNNLMPYIAQVAVGR T0333 167 :PVATIESF 1udc 212 :RDSLAIFG T0333 181 :EAEPEGWFMRWVPYGGGAV 1udc 220 :NDYPTEDGTGVRDYIHVMD T0333 201 :GDRLPPV 1udc 247 :MEKLANK T0333 209 :ARPEVAITMGTIELQ 1udc 254 :PGVHIYNLGAGVGNS T0333 226 :GIGAVEPIIAAAGEV 1udc 269 :VLDVVNAFSKACGKP T0333 241 :DADFV 1udc 285 :NYHFA T0333 250 :DL 1udc 290 :PR T0333 253 :ISPL 1udc 292 :REGD Number of specific fragments extracted= 18 number of extra gaps= 0 total=1597 Number of alignments=79 # 1udc read from 1udc/merged-good-all-a2m # found chain 1udc in template set T0333 9 :IGHLFPLIQLAWGFRTAGHDVLIAV 1udc 7 :GGSGYIGSHTCVQLLQNGHDVIILD T0333 34 :AE 1udc 33 :LC T0333 37 :A 1udc 35 :N T0333 38 :DRAAA 1udc 42 :PVIER T0333 43 :AGLEVVD 1udc 50 :KHPTFVE T0333 52 :PDYSAVK 1udc 57 :GDIRNEA T0333 99 :GTMALVDDYRPDLVVY 1udc 64 :LMTEILHDHAIDTVIH T0333 115 :E 1udc 82 :G T0333 116 :QGATVGLLAADRAGVPAVQRNQSA 1udc 102 :NGTLRLISAMRAANVKNFIFSSSA T0333 140 :WRTRGMHRSIASFLTDLM 1udc 147 :SPYGKSKLMVEQILTDLQ T0333 191 :WVPYGGGAVLGDRLPPVP 1udc 177 :YFNPVGAHPSGDMGEDPQ T0333 209 :ARPEVAITMGTIE 1udc 253 :KPGVHIYNLGAGV T0333 223 :Q 1udc 266 :G T0333 225 :FGIGAVEPIIAAAGEV 1udc 267 :NSVLDVVNAFSKACGK T0333 241 :DADFV 1udc 285 :NYHFA T0333 250 :DLDISPLGTL 1udc 290 :PRREGDLPAY T0333 268 :WTPLHTLLR 1udc 300 :WADASKADR Number of specific fragments extracted= 17 number of extra gaps= 0 total=1614 Number of alignments=80 # 1udc read from 1udc/merged-good-all-a2m # found chain 1udc in template set T0333 1 :MLFV 1udc 3 :VLVT T0333 9 :IGHLFPLIQLAWGFRTAGHDVLIAV 1udc 7 :GGSGYIGSHTCVQLLQNGHDVIILD T0333 35 :EHADRAAAA 1udc 39 :SVLPVIERL T0333 44 :GLEVVDVAPDYSAV 1udc 49 :GKHPTFVEGDIRNE T0333 98 :DGTMALVDDYRPDLVVYEQG 1udc 63 :ALMTEILHDHAIDTVIHFAG T0333 118 :ATVGLLAADRAGVPAVQRNQSAWRTRGMHRSIASFLT 1udc 104 :TLRLISAMRAANVKNFIFSSSATVYGDQPKIPYVESF T0333 183 :EPEGWFMRWVPYGGGA 1udc 209 :VGRRDSLAIFGNDYPT T0333 200 :LGDRLPPVPARPEVAIT 1udc 243 :HVVAMEKLANKPGVHIY T0333 217 :MGTIE 1udc 261 :LGAGV T0333 222 :LQ 1udc 267 :NS T0333 226 :GIGAVEPIIAAAGE 1udc 269 :VLDVVNAFSKACGK Number of specific fragments extracted= 11 number of extra gaps= 0 total=1625 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 4pfk/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 4pfk expands to /projects/compbio/data/pdb/4pfk.pdb.gz 4pfk:Warning: there is no chain 4pfk will retry with 4pfkA # T0333 read from 4pfk/merged-good-all-a2m # 4pfk read from 4pfk/merged-good-all-a2m # adding 4pfk to template set # found chain 4pfk in template set Warning: unaligning (T0333)D81 because of BadResidue code BAD_PEPTIDE in next template residue (4pfk)T78 Warning: unaligning (T0333)L82 because of BadResidue code BAD_PEPTIDE at template residue (4pfk)T78 Warning: unaligning (T0333)Q134 because of BadResidue code BAD_PEPTIDE in next template residue (4pfk)V122 Warning: unaligning (T0333)R135 because of BadResidue code BAD_PEPTIDE at template residue (4pfk)V122 Warning: unaligning (T0333)V192 because of BadResidue code BAD_PEPTIDE in next template residue (4pfk)F135 Warning: unaligning (T0333)P193 because of BadResidue code BAD_PEPTIDE at template residue (4pfk)F135 T0333 1 :M 4pfk 1 :M T0333 2 :LFVSSPGIGHLFPLI 4pfk 6 :VLTSGGDSPGMNAAI T0333 17 :QLAWGFRTAGHDVLIAV 4pfk 22 :SVVRKAIYHGVEVYGVY T0333 35 :EHADRAAAA 4pfk 39 :HGYAGLIAG T0333 55 :SAVKVFEQVAKDNPRFAE 4pfk 48 :NIKKLEVGDVGDIIHRGG T0333 73 :TVATRPAI 4pfk 69 :YTARCPEF T0333 83 :EEWG 4pfk 79 :EEGQ T0333 98 :DGTMALVDDYRP 4pfk 83 :KKGIEQLKKHGI T0333 110 :DLVVYE 4pfk 96 :GLVVIG T0333 118 :ATVGLLAADRA 4pfk 102 :GDGSYQGAKKL T0333 129 :GVPAV 4pfk 116 :GFPCV T0333 136 :NQS 4pfk 123 :PGT T0333 184 :PEGWFMRW 4pfk 126 :IDNDIPGT T0333 194 :YGGG 4pfk 136 :TIGF T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLALGDL 4pfk 140 :DTALNTVIDAIDKIRDTATSHERTYVIEVMGR T0333 284 :HGGGGTVMTAIDAGIPQLLA 4pfk 172 :HAGDIALWSGLAGGAETILI T0333 304 :PDPRDQFQHTAR 4pfk 196 :YDMNDVIARLKR T0333 318 :VSRRGIG 4pfk 208 :GHERGKK T0333 325 :LV 4pfk 216 :SI T0333 327 :STSDKV 4pfk 225 :GSGVDF T0333 334 :ADLLRRLI 4pfk 231 :GRQIQEAT T0333 343 :DESLRTAAREVREE 4pfk 257 :TAFDRVLASRLGAR T0333 357 :MVALPT 4pfk 299 :ALANKH T0333 363 :PAETVRRIVER 4pfk 308 :DQRMYALSKEL Number of specific fragments extracted= 24 number of extra gaps= 3 total=1649 Number of alignments=82 # 4pfk read from 4pfk/merged-good-all-a2m # found chain 4pfk in template set Warning: unaligning (T0333)D81 because of BadResidue code BAD_PEPTIDE in next template residue (4pfk)T78 Warning: unaligning (T0333)L82 because of BadResidue code BAD_PEPTIDE at template residue (4pfk)T78 Warning: unaligning (T0333)Q134 because of BadResidue code BAD_PEPTIDE in next template residue (4pfk)V122 Warning: unaligning (T0333)R135 because of BadResidue code BAD_PEPTIDE at template residue (4pfk)V122 T0333 1 :M 4pfk 1 :M T0333 2 :LFVSSPGI 4pfk 6 :VLTSGGDS T0333 10 :GHLFPLIQLAWGFRTAGHDVLIA 4pfk 15 :GMNAAIRSVVRKAIYHGVEVYGV T0333 34 :AEHADRAAAAGLEVVDVA 4pfk 38 :YHGYAGLIAGNIKKLEVG T0333 53 :DY 4pfk 56 :DV T0333 65 :KDNPRFAE 4pfk 58 :GDIIHRGG T0333 73 :TVATRPAI 4pfk 69 :YTARCPEF T0333 83 :EEWGV 4pfk 79 :EEGQK T0333 99 :GTMALVDDYRP 4pfk 84 :KGIEQLKKHGI T0333 110 :DLVVYE 4pfk 96 :GLVVIG T0333 117 :GATVGLLA 4pfk 102 :GDGSYQGA T0333 126 :DRA 4pfk 110 :KKL T0333 129 :GVPAV 4pfk 116 :GFPCV T0333 136 :NQSA 4pfk 123 :PGTI T0333 140 :WRTRGMHRSIASFL 4pfk 144 :NTVIDAIDKIRDTA T0333 158 :DKHQVSLPEPVATIE 4pfk 164 :YVIEVMGRHAGDIAL T0333 173 :SF 4pfk 185 :GA T0333 191 :WVPYGG 4pfk 187 :ETILIP T0333 221 :E 4pfk 193 :E T0333 223 :QAFGIGAVEPIIAAAGEV 4pfk 194 :ADYDMNDVIARLKRGHER T0333 241 :DADFVLALGDLDI 4pfk 214 :KHSIIIVAEGVGS T0333 254 :SPLG 4pfk 238 :TGFE T0333 261 :RNVRAVGWT 4pfk 242 :TRVTVLGHV T0333 270 :P 4pfk 253 :G T0333 271 :LHTLLR 4pfk 264 :ASRLGA T0333 313 :TAREAVSRRGIGLVSTS 4pfk 270 :RAVELLLEGKGGRCVGI T0333 330 :DK 4pfk 288 :NN T0333 337 :LRRLIG 4pfk 296 :IAEALA T0333 343 :DESLRTAAREV 4pfk 308 :DQRMYALSKEL Number of specific fragments extracted= 29 number of extra gaps= 2 total=1678 Number of alignments=83 # 4pfk read from 4pfk/merged-good-all-a2m # found chain 4pfk in template set Warning: unaligning (T0333)R77 because of BadResidue code BAD_PEPTIDE in next template residue (4pfk)T78 Warning: unaligning (T0333)P78 because of BadResidue code BAD_PEPTIDE at template residue (4pfk)T78 Warning: unaligning (T0333)Q134 because of BadResidue code BAD_PEPTIDE in next template residue (4pfk)V122 Warning: unaligning (T0333)R135 because of BadResidue code BAD_PEPTIDE at template residue (4pfk)V122 Warning: unaligning (T0333)R147 because of BadResidue code BAD_PEPTIDE in next template residue (4pfk)F135 Warning: unaligning (T0333)S148 because of BadResidue code BAD_PEPTIDE at template residue (4pfk)F135 T0333 1 :MLFVSSPGIGHLF 4pfk 4 :IGVLTSGGDSPGM T0333 14 :PLIQLAWGFRTAGHDVLIAVAEHADRAAA 4pfk 19 :AIRSVVRKAIYHGVEVYGVYHGYAGLIAG T0333 44 :GLE 4pfk 48 :NIK T0333 53 :DYSAVKVFEQVAKDNPRFAETVAT 4pfk 53 :EVGDVGDIIHRGGTILYTARCPEF T0333 94 :RPLVDGTMALVDDYRPDLVVYEQGATVGLLAADRA 4pfk 79 :EEGQKKGIEQLKKHGIQGLVVIGGDGSYQGAKKLT T0333 129 :GVPAV 4pfk 116 :GFPCV T0333 136 :NQSAWRTRGMH 4pfk 123 :PGTIDNDIPGT T0333 149 :IASF 4pfk 136 :TIGF T0333 222 :LQAFGIGAVEPIIAAAGEVDADFVLALGDL 4pfk 142 :ALNTVIDAIDKIRDTATSHERTYVIEVMGR T0333 284 :HGGGGTVMTAIDAGIPQLLAP 4pfk 172 :HAGDIALWSGLAGGAETILIP T0333 305 :DPRDQFQHTAREAVSRRGIGL 4pfk 197 :DMNDVIARLKRGHERGKKHSI T0333 327 :STSDKVDADLLRRLIG 4pfk 224 :VGSGVDFGRQIQEATG T0333 343 :DESLRTAAREVREE 4pfk 257 :TAFDRVLASRLGAR T0333 366 :TVRRIVE 4pfk 271 :AVELLLE Number of specific fragments extracted= 14 number of extra gaps= 3 total=1692 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zxxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zxxA expands to /projects/compbio/data/pdb/1zxx.pdb.gz 1zxxA:# T0333 read from 1zxxA/merged-good-all-a2m # 1zxxA read from 1zxxA/merged-good-all-a2m # adding 1zxxA to template set # found chain 1zxxA in template set T0333 1 :M 1zxxA 1 :M T0333 2 :LFVSSPGIGHLFPLI 1zxxA 6 :ILTSGGDAPGMNAAV T0333 17 :QLAWGFRTAGHDVLIAV 1zxxA 22 :AVTRVAIANGLEVFGIR T0333 35 :EHADRAAAA 1zxxA 39 :YGFAGLVAG T0333 55 :SAVKVFEQVAKDNPRFAETVATRP 1zxxA 48 :DIFPLESEDVAHLINVSGTFLYSA T0333 81 :DLEEWGV 1zxxA 72 :RYPEFAE T0333 94 :RPLVDGTMALVDDYRPDLVV 1zxxA 79 :EEGQLAGIEQLKKHGIDAVV T0333 114 :YE 1zxxA 100 :IG T0333 117 :GATVGLLAADR 1zxxA 102 :GDGSYHGALQL T0333 129 :GVPAVQRNQS 1zxxA 116 :GFNSIGLPGT T0333 157 :MDKH 1zxxA 126 :IDND T0333 192 :VP 1zxxA 130 :IP T0333 203 :RLPP 1zxxA 132 :YTDA T0333 216 :TMGTIELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1zxxA 136 :TIGYDTACMTAMDAIDKIRDTASSHHRVFIVNVMGRN T0333 285 :GGGGTVMTAIDAGIPQLLA 1zxxA 173 :CGDIAMRVGVACGADAIVI T0333 304 :PDPRDQFQHTAR 1zxxA 196 :YDVEEIANRLKQ T0333 318 :VSRRGIG 1zxxA 208 :AQESGKD T0333 325 :LV 1zxxA 216 :GL T0333 327 :STSDKV 1zxxA 225 :MTADQF T0333 334 :ADLLRR 1zxxA 231 :MAELKK T0333 343 :DESLRTAAREVREE 1zxxA 257 :TVSDRVLASKLGSE T0333 357 :MVALP 1zxxA 275 :LLEGK Number of specific fragments extracted= 22 number of extra gaps= 0 total=1714 Number of alignments=85 # 1zxxA read from 1zxxA/merged-good-all-a2m # found chain 1zxxA in template set T0333 1 :M 1zxxA 1 :M T0333 2 :LFVSSPGI 1zxxA 6 :ILTSGGDA T0333 10 :GHLFPLIQLAWGFRTAGHDVLIA 1zxxA 15 :GMNAAVRAVTRVAIANGLEVFGI T0333 34 :AEHADRAAAAGLEVV 1zxxA 38 :RYGFAGLVAGDIFPL T0333 52 :PDYSA 1zxxA 53 :ESEDV T0333 65 :KDNPRFAE 1zxxA 58 :AHLINVSG T0333 73 :TVATRPAIDLEEWGVQI 1zxxA 67 :FLYSARYPEFAEEEGQL T0333 99 :GTMALVDDYRPDLVVY 1zxxA 84 :AGIEQLKKHGIDAVVV T0333 115 :E 1zxxA 101 :G T0333 117 :GA 1zxxA 102 :GD T0333 119 :TVGLLAADRAGVPAVQRNQSA 1zxxA 106 :YHGALQLTRHGFNSIGLPGTI T0333 162 :VSLPEPVATIE 1zxxA 168 :VMGRNCGDIAM T0333 173 :SF 1zxxA 185 :GA T0333 191 :WVPYGG 1zxxA 187 :DAIVIP T0333 202 :D 1zxxA 193 :E T0333 223 :QAFGIGAVEPIIAAAGEV 1zxxA 194 :RPYDVEEIANRLKQAQES T0333 241 :DADFVLALGDLDI 1zxxA 214 :DHGLVVVAEGVMT T0333 254 :SPLGTLP 1zxxA 249 :HMQRGGT T0333 308 :DQFQHTAREAVSRRGIGLVSTS 1zxxA 265 :SKLGSEAVHLLLEGKGGLAVGI T0333 330 :DK 1zxxA 288 :NG T0333 337 :LRRLIG 1zxxA 296 :ILDLFD T0333 343 :DESLRTAAR 1zxxA 307 :DYDLLKLNA Number of specific fragments extracted= 22 number of extra gaps= 0 total=1736 Number of alignments=86 # 1zxxA read from 1zxxA/merged-good-all-a2m # found chain 1zxxA in template set T0333 1 :MLFVSSPG 1zxxA 4 :IGILTSGG T0333 9 :IGHLFPLIQLAWGFRTAGHDVLIAVAEHADRAAA 1zxxA 14 :PGMNAAVRAVTRVAIANGLEVFGIRYGFAGLVAG T0333 46 :EVVDVAP 1zxxA 48 :DIFPLES T0333 55 :SAVKVFEQVAKDNPRFAETVATRPAID 1zxxA 55 :EDVAHLINVSGTFLYSARYPEFAEEEG T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1zxxA 82 :QLAGIEQLKKHGIDAVVVIGGDGSYHGALQLT T0333 129 :GVPAVQRNQSAWRTRGMHRS 1zxxA 116 :GFNSIGLPGTIDNDIPYTDA T0333 216 :TMGTIELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1zxxA 136 :TIGYDTACMTAMDAIDKIRDTASSHHRVFIVNVMGRN T0333 285 :GGGGTVMTAIDAGIPQLLAPDPR 1zxxA 173 :CGDIAMRVGVACGADAIVIPERP T0333 308 :DQFQHTAREAVSRRGIGL 1zxxA 200 :EIANRLKQAQESGKDHGL T0333 326 :V 1zxxA 222 :E T0333 327 :STSDKVDADLLRR 1zxxA 224 :VMTADQFMAELKK T0333 343 :DESLRTAAREVREE 1zxxA 257 :TVSDRVLASKLGSE T0333 366 :TVRRIVE 1zxxA 271 :AVHLLLE Number of specific fragments extracted= 13 number of extra gaps= 0 total=1749 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pfkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2pfkA expands to /projects/compbio/data/pdb/2pfk.pdb.gz 2pfkA:# T0333 read from 2pfkA/merged-good-all-a2m # 2pfkA read from 2pfkA/merged-good-all-a2m # adding 2pfkA to template set # found chain 2pfkA in template set Warning: unaligning (T0333)E61 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2pfkA)Y55 Warning: unaligning (T0333)Q62 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2pfkA)Y55 Warning: unaligning (T0333)G129 because of BadResidue code BAD_PEPTIDE at template residue (2pfkA)G116 Warning: unaligning (T0333)D243 because of BadResidue code BAD_PEPTIDE in next template residue (2pfkA)F188 Warning: unaligning (T0333)F244 because of BadResidue code BAD_PEPTIDE at template residue (2pfkA)F188 Warning: unaligning (T0333)A296 because of BadResidue code BAD_PEPTIDE in next template residue (2pfkA)G212 Warning: unaligning (T0333)G297 because of BadResidue code BAD_PEPTIDE at template residue (2pfkA)G212 T0333 1 :M 2pfkA 0 :M T0333 2 :LFVSSPGIGHLFPLI 2pfkA 6 :VLTSGGDAPGMNAAI T0333 17 :QLAWGFRTAGHDVLIA 2pfkA 22 :GVVRSALTEGLEVMGI T0333 34 :AEHADRAAAA 2pfkA 38 :YDGYLGLYED T0333 55 :SAVKVF 2pfkA 48 :RMVQLD T0333 63 :VAKDNPRFAETVATRP 2pfkA 56 :SVSDMINRGGTFLGSA T0333 81 :DLEEWGV 2pfkA 72 :RFPEFRD T0333 94 :RPLVDGTMALVDDYRPDLVV 2pfkA 79 :ENIRAVAIENLKKRGIDALV T0333 114 :YE 2pfkA 100 :IG T0333 117 :GAT 2pfkA 102 :GDG T0333 121 :GLLAADRA 2pfkA 105 :SYMGAMRL T0333 130 :VPAVQRNQSAW 2pfkA 117 :FPCIGLPGTID T0333 141 :RTRGMHRSIASFLTDLMDKHQVSLP 2pfkA 134 :DYTIGFFTALSTVVEAIDRLRDTSS T0333 180 :LE 2pfkA 159 :SH T0333 209 :ARPEVAITMGT 2pfkA 161 :QRISVVEVMGR T0333 226 :GIGAVEPIIAAA 2pfkA 173 :CGDLTLAAAIAG T0333 241 :DA 2pfkA 185 :GC T0333 245 :VLA 2pfkA 189 :VVV T0333 249 :GDLD 2pfkA 192 :PEVE T0333 269 :TPLHTLL 2pfkA 196 :FSREDLV T0333 288 :GTVMTAID 2pfkA 203 :NEIKAGIA T0333 298 :I 2pfkA 213 :K T0333 299 :PQLLAPDPR 2pfkA 216 :AIVAITEHM T0333 308 :DQFQHTAR 2pfkA 226 :DVDELAHF T0333 318 :VSR 2pfkA 234 :IEK T0333 321 :RGIG 2pfkA 238 :TGRE T0333 325 :L 2pfkA 243 :R T0333 327 :STSDKV 2pfkA 246 :VLGHIQ T0333 334 :A 2pfkA 252 :R T0333 344 :ESLRTAAREVREE 2pfkA 258 :PYDRILASRMGAY T0333 357 :MVALP 2pfkA 275 :LLAGY Number of specific fragments extracted= 31 number of extra gaps= 4 total=1780 Number of alignments=88 # 2pfkA read from 2pfkA/merged-good-all-a2m # found chain 2pfkA in template set Warning: unaligning (T0333)P52 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2pfkA)Y55 Warning: unaligning (T0333)D53 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2pfkA)Y55 Warning: unaligning (T0333)A128 because of BadResidue code BAD_PEPTIDE in next template residue (2pfkA)G116 Warning: unaligning (T0333)G129 because of BadResidue code BAD_PEPTIDE at template residue (2pfkA)G116 Warning: unaligning (T0333)W191 because of BadResidue code BAD_PEPTIDE in next template residue (2pfkA)F188 Warning: unaligning (T0333)V192 because of BadResidue code BAD_PEPTIDE at template residue (2pfkA)F188 Warning: unaligning (T0333)V240 because of BadResidue code BAD_PEPTIDE in next template residue (2pfkA)G212 T0333 1 :M 2pfkA 0 :M T0333 2 :LFVSSPGI 2pfkA 6 :VLTSGGDA T0333 10 :GHLFPLIQLAWGFRTAGHDVLIA 2pfkA 15 :GMNAAIRGVVRSALTEGLEVMGI T0333 36 :HADRAAAAGLEVVDVA 2pfkA 38 :YDGYLGLYEDRMVQLD T0333 54 :Y 2pfkA 56 :S T0333 65 :KDNPRFAE 2pfkA 58 :SDMINRGG T0333 73 :TVATRPAIDLEEWG 2pfkA 67 :FLGSARFPEFRDEN T0333 96 :LVDGTMALVDDYRPDLVVY 2pfkA 81 :IRAVAIENLKKRGIDALVV T0333 115 :EQGATVGLLAADR 2pfkA 102 :GDGSYMGAMRLTE T0333 130 :VPAVQRNQSA 2pfkA 117 :FPCIGLPGTI T0333 140 :WRTRGMHRSIA 2pfkA 144 :STVVEAIDRLR T0333 158 :DKHQVSLPEPVATIE 2pfkA 164 :SVVEVMGRYCGDLTL T0333 173 :SF 2pfkA 185 :GC T0333 193 :PYGG 2pfkA 189 :VVVP T0333 202 :D 2pfkA 193 :E T0333 223 :QAFGIGAVEPIIAAAGE 2pfkA 194 :VEFSREDLVNEIKAGIA T0333 241 :DADFVLALGDL 2pfkA 214 :KHAIVAITEHM T0333 269 :TPLH 2pfkA 225 :CDVD T0333 313 :TAREAVSR 2pfkA 229 :ELAHFIEK T0333 321 :RGIG 2pfkA 240 :RETR T0333 325 :LVSTS 2pfkA 245 :TVLGH T0333 330 :DKVD 2pfkA 252 :RGGS T0333 334 :A 2pfkA 257 :V T0333 344 :ESLRTAARE 2pfkA 258 :PYDRILASR T0333 366 :TVRRIVERI 2pfkA 267 :MGAYAIDLL Number of specific fragments extracted= 25 number of extra gaps= 4 total=1805 Number of alignments=89 # 2pfkA read from 2pfkA/merged-good-all-a2m # found chain 2pfkA in template set Warning: unaligning (T0333)P52 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2pfkA)Y55 Warning: unaligning (T0333)S55 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2pfkA)Y55 Warning: unaligning (T0333)G129 because of BadResidue code BAD_PEPTIDE at template residue (2pfkA)G116 Warning: unaligning (T0333)P299 because of BadResidue code BAD_PEPTIDE in next template residue (2pfkA)F188 Warning: unaligning (T0333)Q300 because of BadResidue code BAD_PEPTIDE at template residue (2pfkA)F188 Warning: unaligning (T0333)D343 because of BadResidue code BAD_PEPTIDE in next template residue (2pfkA)G212 Warning: unaligning (T0333)E344 because of BadResidue code BAD_PEPTIDE at template residue (2pfkA)G212 T0333 1 :MLFVSSPG 2pfkA 4 :IGVLTSGG T0333 9 :IGHLFPLIQLAWGFRTAGHDVLIAV 2pfkA 14 :PGMNAAIRGVVRSALTEGLEVMGIY T0333 35 :EHADRAAAA 2pfkA 39 :DGYLGLYED T0333 46 :EVVDVA 2pfkA 48 :RMVQLD T0333 56 :AVKVFEQVAKDNPRFAETVATRPAID 2pfkA 56 :SVSDMINRGGTFLGSARFPEFRDENI T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 2pfkA 82 :RAVAIENLKKRGIDALVVIGGDGSYMGAMRLT T0333 130 :VPAVQRNQSAWRTRGMHRSIAS 2pfkA 117 :FPCIGLPGTIDNDIKGTDYTIG T0333 226 :GIGAVEPIIAAAGEV 2pfkA 139 :FFTALSTVVEAIDRL T0333 241 :DADFVLALGDL 2pfkA 162 :RISVVEVMGRY T0333 285 :GGGGTVMTAIDAGI 2pfkA 173 :CGDLTLAAAIAGGC T0333 301 :LLAP 2pfkA 189 :VVVP T0333 327 :STSDKVDADLLRRLIG 2pfkA 195 :EFSREDLVNEIKAGIA T0333 359 :ALPTPAETVRRIVERIS 2pfkA 223 :HMCDVDELAHFIEKETG Number of specific fragments extracted= 13 number of extra gaps= 4 total=1818 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pn3A/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/T0333/1pn3A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0333/1pn3A/merged-good-all-a2m.gz for input Trying 1pn3A/merged-good-all-a2m Error: Couldn't open file 1pn3A/merged-good-all-a2m or 1pn3A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b69A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b69A expands to /projects/compbio/data/pdb/2b69.pdb.gz 2b69A: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 604, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2b69A 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 743, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2b69A 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 920, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2b69A 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 1267, because occupancy 0.400 <= existing 0.600 in 2b69A Skipped atom 1271, because occupancy 0.400 <= existing 0.600 in 2b69A Skipped atom 1273, because occupancy 0.400 <= existing 0.600 in 2b69A Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1280, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1282, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1284, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1286, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1288, because occupancy 0.500 <= existing 0.500 in 2b69A 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 1428, because occupancy 0.500 <= existing 0.500 in 2b69A 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 1432, because occupancy 0.500 <= existing 0.500 in 2b69A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 2b69A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1436, because occupancy 0.500 <= existing 0.500 in 2b69A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 2b69A 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 1580, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1584, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1586, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1588, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1590, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1592, because occupancy 0.500 <= existing 0.500 in 2b69A 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 1954, because occupancy 0.200 <= existing 0.800 in 2b69A Skipped atom 1958, because occupancy 0.200 <= existing 0.800 in 2b69A Skipped atom 1960, because occupancy 0.200 <= existing 0.800 in 2b69A Skipped atom 1962, because occupancy 0.200 <= existing 0.800 in 2b69A Skipped atom 1964, because occupancy 0.200 <= existing 0.800 in 2b69A Skipped atom 1966, because occupancy 0.200 <= existing 0.800 in 2b69A Skipped atom 1968, because occupancy 0.200 <= existing 0.800 in 2b69A Skipped atom 1970, because occupancy 0.200 <= existing 0.800 in 2b69A Skipped atom 1995, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 1999, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 2001, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 2003, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 2005, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 2105, because occupancy 0.200 <= existing 0.800 in 2b69A Skipped atom 2109, because occupancy 0.200 <= existing 0.800 in 2b69A Skipped atom 2111, because occupancy 0.200 <= existing 0.800 in 2b69A 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 2261, because occupancy 0.500 <= existing 0.500 in 2b69A 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 2265, because occupancy 0.500 <= existing 0.500 in 2b69A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2267, because occupancy 0.500 <= existing 0.500 in 2b69A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2269, because occupancy 0.500 <= existing 0.500 in 2b69A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2271, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 2438, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 2442, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 2444, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 2446, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 2448, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 2450, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 2452, because occupancy 0.500 <= existing 0.500 in 2b69A Skipped atom 2454, because occupancy 0.500 <= existing 0.500 in 2b69A # T0333 read from 2b69A/merged-good-all-a2m # 2b69A read from 2b69A/merged-good-all-a2m # adding 2b69A to template set # found chain 2b69A in template set T0333 2 :LFVSSPGI 2b69A 7 :ILITGGAG T0333 13 :FPLIQLAWGFRTAGHDVLIAV 2b69A 15 :FVGSHLTDKLMMDGHEVTVVD T0333 35 :EH 2b69A 37 :FF T0333 37 :ADRAAAAGLEVVDVAP 2b69A 46 :EHWIGHENFELINHDV T0333 53 :DYSAVKVFEQVAKDNPRFAET 2b69A 66 :YIEVDQIYHLASPASPPNYMY T0333 81 :DLEEWGVQ 2b69A 87 :NPIKTLKT T0333 93 :NRPLVDGTMALVDDYRPDLVVYEQGATV 2b69A 95 :NTIGTLNMLGLAKRVGARLLLASTSEVY T0333 141 :RTRGMH 2b69A 142 :GPRACY T0333 147 :RSIASFLTDLMDKHQ 2b69A 152 :RVAETMCYAYMKQEG T0333 192 :V 2b69A 167 :V T0333 209 :ARPEVAI 2b69A 168 :EVRVARI T0333 216 :TMGTIELQAFGIGAVEPIIAAAGEVDADF 2b69A 177 :TFGPRMHMNDGRVVSNFILQALQGEPLTV T0333 248 :LGDLDIS 2b69A 206 :YGSGSQT T0333 266 :VGWTPLHTLL 2b69A 213 :RAFQYVSDLV T0333 288 :GTVMTAIDAGIP 2b69A 223 :NGLVALMNSNVS T0333 300 :QLLAPDPRD 2b69A 236 :PVNLGNPEE T0333 309 :QFQHTAR 2b69A 247 :ILEFAQL T0333 318 :VSR 2b69A 254 :IKN T0333 321 :RGIG 2b69A 258 :VGSG T0333 325 :LV 2b69A 263 :EI T0333 327 :STS 2b69A 294 :VPL T0333 334 :ADLLRRL 2b69A 297 :EEGLNKA T0333 347 :RTAAREVREE 2b69A 304 :IHYFRKELEY Number of specific fragments extracted= 23 number of extra gaps= 0 total=1841 Number of alignments=91 # 2b69A read from 2b69A/merged-good-all-a2m # found chain 2b69A in template set Warning: unaligning (T0333)D333 because of BadResidue code BAD_PEPTIDE in next template residue (2b69A)D280 T0333 9 :IGHLFPLIQLAWGFRTAGHDVLIAV 2b69A 11 :GGAGFVGSHLTDKLMMDGHEVTVVD T0333 34 :AEHADRAAA 2b69A 38 :FTGRKRNVE T0333 43 :AGLEVVDVAPDY 2b69A 52 :ENFELINHDVVE T0333 66 :DNPR 2b69A 64 :PLYI T0333 129 :GVPAVQRNQSA 2b69A 68 :EVDQIYHLASP T0333 140 :WRTRGMHRSIASFLTD 2b69A 93 :KTNTIGTLNMLGLAKR T0333 156 :LMDKHQVSLPEPVATIE 2b69A 110 :GARLLLASTSEVYGDPE T0333 173 :SFPPSLLL 2b69A 129 :PQSEDYWG T0333 199 :V 2b69A 137 :H T0333 204 :LPPVP 2b69A 138 :VNPIG T0333 209 :ARPE 2b69A 166 :GVEV T0333 213 :VAITMGTIE 2b69A 171 :VARIFNTFG T0333 222 :LQAFGIGAVEPIIAAAGEV 2b69A 182 :MHMNDGRVVSNFILQALQG T0333 261 :RNVRAVGWTP 2b69A 201 :EPLTVYGSGS T0333 271 :LHTLLR 2b69A 218 :VSDLVN T0333 289 :TVMTAIDAGIP 2b69A 224 :GLVALMNSNVS T0333 300 :QLLAPDPR 2b69A 236 :PVNLGNPE T0333 312 :HTAREAVSR 2b69A 248 :LEFAQLIKN T0333 321 :RGIG 2b69A 258 :VGSG T0333 325 :LVST 2b69A 265 :QFLS T0333 330 :DKV 2b69A 276 :KRK T0333 334 :ADLLRRLIG 2b69A 281 :IKKAKLMLG T0333 358 :VALP 2b69A 290 :WEPV T0333 362 :TPAETVRRIVERIS 2b69A 295 :PLEEGLNKAIHYFR Number of specific fragments extracted= 24 number of extra gaps= 1 total=1865 Number of alignments=92 # 2b69A read from 2b69A/merged-good-all-a2m # found chain 2b69A in template set T0333 1 :MLFV 2b69A 7 :ILIT T0333 9 :IGHLFPLIQLAWGFRTAGHDVLIAV 2b69A 11 :GGAGFVGSHLTDKLMMDGHEVTVVD T0333 50 :VAPDYSAVKVF 2b69A 38 :FTGRKRNVEHW T0333 61 :EQVAKDNPRFAE 2b69A 59 :HDVVEPLYIEVD T0333 73 :TVATRPAIDLEEWGVQIAAVNRPLVDGTMALVDDYRPDLVVYEQGATV 2b69A 75 :LASPASPPNYMYNPIKTLKTNTIGTLNMLGLAKRVGARLLLASTSEVY T0333 137 :QSAWRTRGMHRSI 2b69A 126 :EVHPQSEDYWGHV T0333 193 :PYGGGA 2b69A 139 :NPIGPR T0333 199 :VLGDRLPPVPARPEVAITMGTIE 2b69A 157 :MCYAYMKQEGVEVRVARIFNTFG T0333 222 :LQAFGIGAVEPIIAAAGEVDADF 2b69A 183 :HMNDGRVVSNFILQALQGEPLTV T0333 248 :LGDLDI 2b69A 206 :YGSGSQ T0333 263 :VRAVGWT 2b69A 212 :TRAFQYV T0333 287 :GGTVMTAIDAGIP 2b69A 222 :VNGLVALMNSNVS T0333 300 :QLLAPDPRD 2b69A 236 :PVNLGNPEE T0333 309 :QFQHTAREAV 2b69A 247 :ILEFAQLIKN T0333 319 :SRRGIGL 2b69A 258 :VGSGSEI T0333 326 :V 2b69A 291 :E T0333 327 :STSDKV 2b69A 293 :VVPLEE T0333 349 :AAREVREEMVAL 2b69A 299 :GLNKAIHYFRKE Number of specific fragments extracted= 18 number of extra gaps= 0 total=1883 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iirA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0333 read from 1iirA/merged-good-all-a2m # 1iirA read from 1iirA/merged-good-all-a2m # found chain 1iirA in training set Warning: unaligning (T0333)P52 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iirA)R63 Warning: unaligning (T0333)V63 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iirA)R63 Warning: unaligning (T0333)M217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iirA)G249 Warning: unaligning (T0333)G218 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iirA)G249 T0333 1 :M 1iirA 1 :M T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAV 1iirA 4 :LLATCGSRGDTEPLVALAVRVRDLGADVRMCA T0333 34 :AEHADRAAAAGLEVVDVA 1iirA 37 :PDCAERLAEVGVPHVPVG T0333 64 :AKDN 1iirA 64 :AKPL T0333 81 :DLEEWGVQIAAVNRPLVDGTMALVDDY 1iirA 68 :TAEDVRRFTTEAIATQFDEIPAAAEGC T0333 110 :DLVVYEQGATVGLLA 1iirA 95 :AAVVTTGLLAAAIGV T0333 125 :ADRAGVPAVQRNQSAW 1iirA 113 :AEKLGIPYFYAFHCPS T0333 141 :RTRGMHRSIASFLTDLMDKH 1iirA 158 :NNQSAYQRYGGLLNSHRDAI T0333 161 :QVSLPE 1iirA 179 :LPPVED T0333 169 :ATIESFPPSLLLEAEPEGWFMR 1iirA 190 :YTDHPWVAADPVLAPLQPTDLD T0333 192 :VPYGGGAV 1iirA 212 :AVQTGAWI T0333 200 :LGDRLPP 1iirA 230 :LAAFLDA T0333 209 :ARPEVAIT 1iirA 237 :GPPPVYLG T0333 222 :L 1iirA 250 :A T0333 226 :GIGAVEPIIAAAGEVDADFVLALGDLDI 1iirA 251 :PADAVRVAIDAIRAHGRRVILSRGWADL T0333 255 :PLGTLPRNVRAVGWTPLHTLLRTCTAVVHHGGGGTVMTAIDAGIPQLLAPDPRDQFQHTAR 1iirA 279 :VLPDDGADCFAIGEVNHQVLFGRVAAVIHHGGAGTTHVAARAGAPQILLPQMADQPYYAGR T0333 318 :VSRRGIG 1iirA 340 :VAELGVG T0333 325 :LV 1iirA 348 :AH T0333 327 :STSDKV 1iirA 354 :PTFDSL T0333 334 :ADLLRRLIG 1iirA 360 :SAALATALT T0333 344 :ESLRTAAREVREE 1iirA 369 :PETHARATAVAGT T0333 363 :PAETVRRIVERI 1iirA 386 :GAAVAARLLLDA Number of specific fragments extracted= 22 number of extra gaps= 1 total=1905 Number of alignments=94 # 1iirA read from 1iirA/merged-good-all-a2m # found chain 1iirA in training set Warning: unaligning (T0333)P52 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iirA)R63 Warning: unaligning (T0333)T76 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iirA)R63 Warning: unaligning (T0333)W140 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iirA)I149 Warning: unaligning (T0333)M217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iirA)G249 Warning: unaligning (T0333)G218 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iirA)G249 T0333 1 :M 1iirA 1 :M T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAVAE 1iirA 4 :LLATCGSRGDTEPLVALAVRVRDLGADVRMCAPP T0333 36 :HADRAAAAGLEVVDVA 1iirA 39 :CAERLAEVGVPHVPVG T0333 77 :RPAIDLEEWGVQIAAVNRPLVDGTMALVDD 1iirA 64 :AKPLTAEDVRRFTTEAIATQFDEIPAAAEG T0333 109 :PDLVVYEQGATVGLL 1iirA 94 :CAAVVTTGLLAAAIG T0333 124 :AADRAGVPAVQRNQSA 1iirA 112 :VAEKLGIPYFYAFHCP T0333 141 :RTRGMHRSIASFLTDLM 1iirA 150 :DIPAQWERNNQSAYQRY T0333 158 :DKHQVSLPEPVATIESFPP 1iirA 192 :DHPWVAADPVLAPLQPTDL T0333 191 :WVPYGGGAVLGDR 1iirA 211 :DAVQTGAWILPDE T0333 205 :PPVP 1iirA 224 :RPLS T0333 209 :ARPEVAIT 1iirA 237 :GPPPVYLG T0333 222 :LQAFGIGAVEPIIAAA 1iirA 250 :APADAVRVAIDAIRAH T0333 241 :DADFVLA 1iirA 266 :GRRVILS T0333 254 :SPLGTLP 1iirA 273 :RGWADLV T0333 261 :RNVRAVGWTPLHTLLRTCTAVVHHGGGGTVMTAIDAGIPQLLAPDPRDQF 1iirA 285 :ADCFAIGEVNHQVLFGRVAAVIHHGGAGTTHVAARAGAPQILLPQMADQP T0333 313 :TAREAVSRRGIGLVSTS 1iirA 335 :YYAGRVAELGVGVAHDG T0333 330 :DKVD 1iirA 355 :TFDS T0333 334 :ADLLRRLIG 1iirA 360 :SAALATALT T0333 344 :ESLRTAAREVREEM 1iirA 369 :PETHARATAVAGTI T0333 359 :ALPTPAETVRRIVERISG 1iirA 383 :RTDGAAVAARLLLDAVSR Number of specific fragments extracted= 20 number of extra gaps= 1 total=1925 Number of alignments=95 # 1iirA read from 1iirA/merged-good-all-a2m # found chain 1iirA in training set Warning: unaligning (T0333)P52 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iirA)R63 Warning: unaligning (T0333)K65 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iirA)R63 Warning: unaligning (T0333)S151 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iirA)I149 Warning: unaligning (T0333)M217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iirA)G249 Warning: unaligning (T0333)G218 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iirA)G249 T0333 1 :MLFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAV 1iirA 3 :VLLATCGSRGDTEPLVALAVRVRDLGADVRMCA T0333 34 :AEHADRAAAAGLEVVDVA 1iirA 37 :PDCAERLAEVGVPHVPVG T0333 66 :DNPRF 1iirA 64 :AKPLT T0333 75 :A 1iirA 69 :A T0333 83 :EEWGVQIAAVNRPLVDGTMALVD 1iirA 70 :EDVRRFTTEAIATQFDEIPAAAE T0333 108 :RPDLVVYEQGATVGL 1iirA 93 :GCAAVVTTGLLAAAI T0333 123 :LAADRAGVPAVQRNQSAWRTRGMHRSIA 1iirA 111 :SVAEKLGIPYFYAFHCPSYVPSPYYPPP T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGG 1iirA 180 :PPVEDIFTFGYTDHPWVAADPVLAPLQPTDLDAVQTGAWILPD T0333 199 :VLGDRL 1iirA 225 :PLSPEL T0333 205 :PPVPARPEVAIT 1iirA 233 :FLDAGPPPVYLG T0333 222 :L 1iirA 250 :A T0333 226 :GIGAVEPIIAAAGEVDADFVLALGDLDI 1iirA 251 :PADAVRVAIDAIRAHGRRVILSRGWADL T0333 255 :PLGTLPRNVRAVGWTPLHTLLRTCTAVVHHGGGGTVMTAIDAGIPQLLAPDPRDQFQHTAREAVSRRGIGLV 1iirA 279 :VLPDDGADCFAIGEVNHQVLFGRVAAVIHHGGAGTTHVAARAGAPQILLPQMADQPYYAGRVAELGVGVAHD T0333 327 :STSDKVDADLLRRLIG 1iirA 353 :IPTFDSLSAALATALT T0333 344 :ESLRTAAREVREEMV 1iirA 369 :PETHARATAVAGTIR T0333 360 :LPTPAETVRRIVERIS 1iirA 384 :TDGAAVAARLLLDAVS Number of specific fragments extracted= 16 number of extra gaps= 1 total=1941 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bif/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bif expands to /projects/compbio/data/pdb/1bif.pdb.gz 1bif:Warning: there is no chain 1bif will retry with 1bifA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 686, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1640, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1839, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1845, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 1847, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 2488, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 2490, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 2492, because occupancy 0.500 <= existing 0.500 in 1bif Skipped atom 2494, because occupancy 0.500 <= existing 0.500 in 1bif # T0333 read from 1bif/merged-good-all-a2m # 1bif read from 1bif/merged-good-all-a2m # adding 1bif to template set # found chain 1bif in template set T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAV 1bif 42 :VMVGLPARGKTYISKKLTRYLNFIGVPTREFN T0333 36 :HADRAAAA 1bif 74 :VGQYRRDM T0333 64 :AKDNPRFAETVA 1bif 82 :VKTYKSFEFFLP T0333 81 :DLEEWGVQIAAVNRPLVDGTMALVDDYRPDLVVYEQGAT 1bif 94 :DNEEGLKIRKQCALAALNDVRKFLSEEGGHVAVFDATNT T0333 120 :VGLLAADRAGVPAVQRNQSAW 1bif 139 :MIFNFGEQNGYKTFFVESICV T0333 141 :RTRGMHRSIASFLTDLMDKHQVSLPEPVAT 1bif 178 :YVNRDSDEATEDFMRRIECYENSYESLDEE T0333 174 :FPPSLL 1bif 208 :QDRDLS T0333 180 :LEAEPEGWFMRWVP 1bif 217 :IMDVGQSYVVNRVA T0333 196 :GGA 1bif 231 :DHI T0333 201 :GDRLPP 1bif 241 :LMNIHV T0333 209 :ARPEVAITMGT 1bif 247 :TPRSIYLCRHG T0333 220 :IELQAF 1bif 260 :ELNLKG T0333 227 :IGAVEPIIAAAGEVD 1bif 278 :REFSKHLAQFISDQN T0333 242 :ADFVL 1bif 296 :LKVFT T0333 251 :LD 1bif 301 :SQ T0333 253 :ISPLGT 1bif 328 :AGVCEE T0333 259 :LPRNV 1bif 358 :RYPKG T0333 269 :TPLHTLLRT 1bif 363 :ESYEDLVQR T0333 278 :CTAVVHHGGGGTVMTAI 1bif 384 :NVLVICHQAVMRCLLAY Number of specific fragments extracted= 19 number of extra gaps= 0 total=1960 Number of alignments=97 # 1bif read from 1bif/merged-good-all-a2m # found chain 1bif in template set T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAV 1bif 42 :VMVGLPARGKTYISKKLTRYLNFIGVPTREFN T0333 56 :AVKVFEQVAKDNPRFAETVATR 1bif 74 :VGQYRRDMVKTYKSFEFFLPDN T0333 83 :EEWGVQIAAVNRPLVDGTMALVDDYRPDLVVYEQGA 1bif 96 :EEGLKIRKQCALAALNDVRKFLSEEGGHVAVFDATN T0333 119 :TVGLLAADRAGVPAVQRNQSA 1bif 138 :AMIFNFGEQNGYKTFFVESIC T0333 209 :ARP 1bif 248 :PRS T0333 213 :VAITMG 1bif 251 :IYLCRH T0333 227 :IGAVEPIIAAAGEV 1bif 274 :SPRGREFSKHLAQF T0333 241 :DADFVLA 1bif 295 :DLKVFTS T0333 250 :DLDI 1bif 302 :QMKR T0333 254 :SPLGTLP 1bif 329 :GVCEEMT T0333 261 :RN 1bif 360 :PK T0333 268 :WTPLHTLLR 1bif 362 :GESYEDLVQ T0333 277 :TCT 1bif 381 :RQE T0333 280 :AVVHHGGGGTVMTAIDAGI 1bif 386 :LVICHQAVMRCLLAYFLDK Number of specific fragments extracted= 14 number of extra gaps= 0 total=1974 Number of alignments=98 # 1bif read from 1bif/merged-good-all-a2m # found chain 1bif in template set T0333 1 :MLFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAV 1bif 41 :IVMVGLPARGKTYISKKLTRYLNFIGVPTREFN T0333 57 :VKVFEQVAKDNPRFAETVATRP 1bif 75 :GQYRRDMVKTYKSFEFFLPDNE T0333 84 :EWGVQIAAVNRPLVDGTMALVDDYRPDLVVYEQGAT 1bif 97 :EGLKIRKQCALAALNDVRKFLSEEGGHVAVFDATNT T0333 120 :VGLLAADRAGVPAVQRNQSAWRTRGMHRSIASFLT 1bif 139 :MIFNFGEQNGYKTFFVESICVDPEVIAANIVQVKL T0333 155 :DLMDKHQVSLPEPVATIESFPPS 1bif 199 :NSYESLDEEQDRDLSYIKIMDVG T0333 188 :FMRWVPYGGGA 1bif 222 :QSYVVNRVADH T0333 204 :LPPVPARPEVAITM 1bif 242 :MNIHVTPRSIYLCR T0333 218 :GTIE 1bif 257 :GESE T0333 222 :LQAFGIGAVEPIIAAAGEV 1bif 273 :LSPRGREFSKHLAQFISDQ T0333 241 :DADFVLALG 1bif 295 :DLKVFTSQM T0333 311 :QHTAREAVS 1bif 304 :KRTIQTAEA T0333 321 :RGIGL 1bif 313 :LSVPY T0333 327 :STSDKVDADL 1bif 333 :EMTYEEIQDH T0333 343 :DESLRTAAR 1bif 344 :PLEFALRDQ T0333 359 :AL 1bif 353 :DK T0333 361 :PTPAETVRRIV 1bif 363 :ESYEDLVQRLE Number of specific fragments extracted= 16 number of extra gaps= 0 total=1990 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gqyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gqyA expands to /projects/compbio/data/pdb/1gqy.pdb.gz 1gqyA:# T0333 read from 1gqyA/merged-good-all-a2m # 1gqyA read from 1gqyA/merged-good-all-a2m # adding 1gqyA to template set # found chain 1gqyA in template set Warning: unaligning (T0333)G10 because of BadResidue code BAD_PEPTIDE at template residue (1gqyA)G30 Warning: unaligning (T0333)D252 because of BadResidue code BAD_PEPTIDE in next template residue (1gqyA)E408 Warning: unaligning (T0333)I253 because of BadResidue code BAD_PEPTIDE at template residue (1gqyA)E408 T0333 2 :LFVSSPGI 1gqyA 21 :IHFIGIGG T0333 15 :LIQLAWGFRTAGHDVLIAV 1gqyA 31 :MSGIAEILLNEGYQISGSD T0333 34 :AEHADRAAAAGLEVVD 1gqyA 53 :GVVTQRLAQAGAKIYI T0333 50 :VAPDYSAVKVFEQVAKDN 1gqyA 74 :HIEGASVVVVSSAIKDDN T0333 84 :EWGVQIAAV 1gqyA 92 :PELVTSKQK T0333 93 :NRPLVDGT 1gqyA 107 :RAQMLAEI T0333 104 :VDDY 1gqyA 115 :MRFR T0333 109 :PDLVVYEQGA 1gqyA 119 :HGIAVAGTHG T0333 119 :TVGLLAADRAGVPAVQRNQSAW 1gqyA 134 :AMISMIYTQAKLDPTFVNGGLV T0333 141 :RTRGMHRSIASFLTD 1gqyA 305 :EEGIANEAILEALAD T0333 164 :LPEPVATIESF 1gqyA 320 :FQGAGRRFDQL T0333 179 :LLEAEPEG 1gqyA 331 :GEFIRPNG T0333 189 :MRWVPYGGGAV 1gqyA 340 :VRLVDDYGHHP T0333 200 :LGDRLP 1gqyA 360 :AREGWG T0333 209 :ARPEVAITMGTIELQ 1gqyA 366 :DKRIVMIFQPHRYSR T0333 226 :GIGAVEPIIAAAGEVDADFVLALGDL 1gqyA 381 :TRDLFDDFVQVLSQVDALIMLDVYAA T0333 254 :SPLG 1gqyA 409 :APIV T0333 307 :R 1gqyA 413 :G T0333 308 :DQFQHTAR 1gqyA 415 :DSKSLCRS T0333 318 :VSRRGIG 1gqyA 423 :IRNLGKV T0333 325 :LV 1gqyA 432 :IL T0333 327 :STSDKV 1gqyA 435 :SDTSQL T0333 334 :ADLLRRLI 1gqyA 441 :GDVLDQII T0333 346 :LRTAAREVREEMV 1gqyA 462 :VSKISRGLAESWK Number of specific fragments extracted= 24 number of extra gaps= 2 total=2014 Number of alignments=100 # 1gqyA read from 1gqyA/merged-good-all-a2m # found chain 1gqyA in template set Warning: unaligning (T0333)P14 because of BadResidue code BAD_PEPTIDE at template residue (1gqyA)G30 Warning: unaligning (T0333)G201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gqyA)D205 T0333 15 :LIQLAWGFRTAGHDVLIAVAE 1gqyA 31 :MSGIAEILLNEGYQISGSDIA T0333 36 :HADRAAAAGLEVVDVAPDY 1gqyA 55 :VTQRLAQAGAKIYIGHAEE T0333 56 :AV 1gqyA 74 :HI T0333 65 :KDNPRFAETVATRPAIDLEEWGVQ 1gqyA 76 :EGASVVVVSSAIKDDNPELVTSKQ T0333 89 :IAA 1gqyA 107 :RAQ T0333 99 :GTMALVDD 1gqyA 110 :MLAEIMRF T0333 108 :RPDLVVYEQGA 1gqyA 118 :RHGIAVAGTHG T0333 119 :TVGLLAADRAGVPAVQRNQSA 1gqyA 134 :AMISMIYTQAKLDPTFVNGGL T0333 158 :DKHQVSLPEPVATIESFPP 1gqyA 168 :RYLIAEADESDASFLHLQP T0333 191 :WVPYGGGAVL 1gqyA 187 :MVSVVTNMEP T0333 209 :ARP 1gqyA 222 :FYG T0333 213 :VAITM 1gqyA 225 :LAVMC T0333 223 :QAF 1gqyA 230 :ADD T0333 228 :GAVEPIIAAA 1gqyA 233 :PVLMELVPKV T0333 241 :DADFVLALGDLDI 1gqyA 243 :GRQVITYGFSEQA T0333 254 :SPLGTLP 1gqyA 321 :QGAGRRF T0333 261 :RN 1gqyA 336 :PN T0333 263 :VRAVGWTP 1gqyA 340 :VRLVDDYG T0333 271 :LHTLLR 1gqyA 353 :VGVTIK T0333 280 :AVVHHG 1gqyA 370 :VMIFQP T0333 286 :GGGTVMTAIDAGIPQLLAPDPR 1gqyA 384 :LFDDFVQVLSQVDALIMLDVYA T0333 308 :DQF 1gqyA 415 :DSK T0333 313 :TAREAVSRRG 1gqyA 418 :SLCRSIRNLG T0333 323 :I 1gqyA 430 :D T0333 325 :LVST 1gqyA 432 :ILVS T0333 330 :DKVD 1gqyA 436 :DTSQ T0333 334 :ADLLRRLIG 1gqyA 441 :GDVLDQIIQ T0333 359 :AL 1gqyA 450 :DG T0333 361 :PTPAETVRRIVERISG 1gqyA 460 :GSVSKISRGLAESWKN Number of specific fragments extracted= 29 number of extra gaps= 1 total=2043 Number of alignments=101 # 1gqyA read from 1gqyA/merged-good-all-a2m # found chain 1gqyA in template set Warning: unaligning (T0333)I9 because of BadResidue code BAD_PEPTIDE in next template residue (1gqyA)G30 Warning: unaligning (T0333)G10 because of BadResidue code BAD_PEPTIDE at template residue (1gqyA)G30 Warning: unaligning (T0333)D252 because of BadResidue code BAD_PEPTIDE in next template residue (1gqyA)E408 Warning: unaligning (T0333)I253 because of BadResidue code BAD_PEPTIDE at template residue (1gqyA)E408 T0333 1 :MLFVSSPG 1gqyA 21 :IHFIGIGG T0333 15 :LIQLAWGFRTAGHDVLIAV 1gqyA 31 :MSGIAEILLNEGYQISGSD T0333 34 :AEHADRAAAAGLEVVDVAPDYSAVKVF 1gqyA 53 :GVVTQRLAQAGAKIYIGHAEEHIEGAS T0333 61 :EQVAKDNPR 1gqyA 95 :VTSKQKRIP T0333 96 :LVDGTMALVDDYRPDLVVYEQGATVGL 1gqyA 107 :RAQMLAEIMRFRHGIAVAGTHGKTTTT T0333 123 :LAADRAGVPAVQRNQSAWRTRGMHRSIASFLT 1gqyA 138 :MIYTQAKLDPTFVNGGLVKSAGKNAHLGASRY T0333 155 :DLMDKHQVSLPEPVATIESFPPS 1gqyA 311 :EAILEALADFQGAGRRFDQLGEF T0333 183 :EPEGWFMRWVPYGGGA 1gqyA 334 :IRPNGKVRLVDDYGHH T0333 204 :LPPVPARPEVAITMGTIELQ 1gqyA 361 :REGWGDKRIVMIFQPHRYSR T0333 226 :GIGAVEPIIAAAGEVDADFVLALGDL 1gqyA 381 :TRDLFDDFVQVLSQVDALIMLDVYAA T0333 254 :SPLG 1gqyA 409 :APIV T0333 306 :PRDQFQHTAREAVSRRGIGLVSTSDKVDADLLRRLIGD 1gqyA 413 :GADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQD T0333 345 :SLRTAAREVREEMV 1gqyA 461 :SVSKISRGLAESWK Number of specific fragments extracted= 13 number of extra gaps= 2 total=2056 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1thtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1thtA expands to /projects/compbio/data/pdb/1tht.pdb.gz 1thtA:# T0333 read from 1thtA/merged-good-all-a2m # 1thtA read from 1thtA/merged-good-all-a2m # adding 1thtA to template set # found chain 1thtA in template set Warning: unaligning (T0333)D38 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1thtA)E83 Warning: unaligning (T0333)V47 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1thtA)E83 Warning: unaligning (T0333)G195 because of BadResidue code BAD_PEPTIDE in next template residue (1thtA)G169 Warning: unaligning (T0333)G196 because of BadResidue code BAD_PEPTIDE at template residue (1thtA)G169 T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAVAEHA 1thtA 38 :ILIASGFARRMDHFAGLAEYLSTNGFHVFRYDSLHH T0333 48 :V 1thtA 84 :F T0333 81 :DLE 1thtA 85 :TMT T0333 88 :QIAA 1thtA 88 :TGKN T0333 96 :LVDGTMALVDDYRP 1thtA 92 :SLCTVYHWLQTKGT T0333 110 :DLVVYEQGATVGLLAADRAG 1thtA 107 :NIGLIAASLSARVAYEVISD T0333 130 :VPAVQRNQS 1thtA 129 :LSFLITAVG T0333 146 :HRSIASFLTDLMDKHQVSL 1thtA 138 :VVNLRDTLEKALGFDYLSL T0333 184 :PEGWFMRWVPY 1thtA 157 :PIDELPNDLDF T0333 197 :GAV 1thtA 170 :HKL T0333 200 :LGDRLPP 1thtA 182 :FEHHWDT T0333 230 :VEPIIAAAGEVDADFVLALGDLD 1thtA 189 :LDSTLDKVANTSVPLIAFTANND T0333 253 :ISPLGT 1thtA 223 :LAHIRT T0333 261 :RNVRAVGWT 1thtA 229 :GHCKLYSLL T0333 270 :P 1thtA 242 :D T0333 271 :LHTLL 1thtA 250 :LRNFY T0333 288 :GTVMTAID 1thtA 255 :QSVTKAAI T0333 318 :VSRRGIGLV 1thtA 263 :AMDGGSLEI T0333 327 :ST 1thtA 278 :PD T0333 334 :ADLLRRL 1thtA 280 :FEQLTIA T0333 347 :RTAAREVREEMVALP 1thtA 287 :TVNERRLKAEIENRT Number of specific fragments extracted= 21 number of extra gaps= 1 total=2077 Number of alignments=103 # 1thtA read from 1thtA/merged-good-all-a2m # found chain 1thtA in template set Warning: unaligning (T0333)F70 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1thtA)E83 Warning: unaligning (T0333)A79 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1thtA)E83 T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAGHDVLIA 1thtA 38 :ILIASGFARRMDHFAGLAEYLSTNGFHVFRY T0333 65 :KDNPR 1thtA 69 :DSLHH T0333 80 :IDLEEWGVQIA 1thtA 84 :FTMTTGKNSLC T0333 99 :GTMALVDDYRP 1thtA 95 :TVYHWLQTKGT T0333 110 :DLVVYEQGATVGLLAADRAG 1thtA 107 :NIGLIAASLSARVAYEVISD T0333 130 :VPAVQRNQSAWRTRGMHRSIA 1thtA 129 :LSFLITAVGVVNLRDTLEKAL T0333 164 :LPEPVATIE 1thtA 150 :GFDYLSLPI T0333 173 :SFPP 1thtA 160 :ELPN T0333 191 :WVPY 1thtA 164 :DLDF T0333 209 :ARPE 1thtA 198 :NTSV T0333 213 :VAITMGTIE 1thtA 203 :LIAFTANND T0333 223 :QAFGIGAVEPIIAAAGE 1thtA 212 :DWVKQEEVYDMLAHIRT T0333 261 :RNVRAVGWT 1thtA 229 :GHCKLYSLL T0333 271 :LHTLLR 1thtA 250 :LRNFYQ T0333 314 :AREAVSR 1thtA 257 :VTKAAIA T0333 321 :RG 1thtA 266 :GG T0333 343 :DESLRTAAREVREEMVA 1thtA 279 :DFEQLTIATVNERRLKA Number of specific fragments extracted= 17 number of extra gaps= 0 total=2094 Number of alignments=104 # 1thtA read from 1thtA/merged-good-all-a2m # found chain 1thtA in template set Warning: unaligning (T0333)Q62 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1thtA)E83 Warning: unaligning (T0333)A71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1thtA)E83 Warning: unaligning (T0333)V192 because of BadResidue code BAD_PEPTIDE in next template residue (1thtA)G169 Warning: unaligning (T0333)P193 because of BadResidue code BAD_PEPTIDE at template residue (1thtA)G169 T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAV 1thtA 38 :ILIASGFARRMDHFAGLAEYLSTNGFHVFRYD T0333 34 :AE 1thtA 71 :LH T0333 61 :E 1thtA 73 :H T0333 72 :E 1thtA 84 :F T0333 78 :P 1thtA 85 :T T0333 86 :G 1thtA 86 :M T0333 91 :AVNRPLVDGTMALVDDYRP 1thtA 87 :TTGKNSLCTVYHWLQTKGT T0333 110 :DLVVYE 1thtA 107 :NIGLIA T0333 117 :GATVGLLAADRA 1thtA 113 :ASLSARVAYEVI T0333 129 :GVPAVQRNQSAWRTRGMHRSIASF 1thtA 128 :ELSFLITAVGVVNLRDTLEKALGF T0333 176 :PSLLLEAEPEGWFMRW 1thtA 152 :DYLSLPIDELPNDLDF T0333 194 :YGGGA 1thtA 170 :HKLGS T0333 225 :FG 1thtA 187 :DT T0333 230 :VEPIIAAAGEVDADFVLALGD 1thtA 189 :LDSTLDKVANTSVPLIAFTAN T0333 251 :LDISPL 1thtA 214 :VKQEEV T0333 259 :LPRNVRAVGWT 1thtA 227 :RTGHCKLYSLL T0333 270 :PL 1thtA 242 :DL T0333 287 :GGTVMTAID 1thtA 254 :YQSVTKAAI T0333 317 :AVSRRGIGLV 1thtA 263 :AMDGGSLEID T0333 327 :STSDKVDAD 1thtA 277 :EPDFEQLTI T0333 346 :LRTAAREVREEMVALP 1thtA 286 :ATVNERRLKAEIENRT Number of specific fragments extracted= 21 number of extra gaps= 1 total=2115 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jdbB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jdbB expands to /projects/compbio/data/pdb/1jdb.pdb.gz 1jdbB:Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 993, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 995, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 999, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 3191, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 3193, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 3195, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 3197, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 3199, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 3290, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 3292, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 3294, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 3296, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 4027, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 4029, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 4031, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 4033, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 5771, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 5773, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 5775, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 5777, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 6942, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 6944, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 6946, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 6948, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 6950, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 6952, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 6954, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 7362, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 7364, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 7366, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 7368, because occupancy 0.500 <= existing 0.500 in 1jdbB Skipped atom 7370, because occupancy 0.500 <= existing 0.500 in 1jdbB # T0333 read from 1jdbB/merged-good-all-a2m # 1jdbB read from 1jdbB/merged-good-all-a2m # adding 1jdbB to template set # found chain 1jdbB in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1jdbB)D557 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1jdbB)D557 Warning: unaligning (T0333)R210 because of BadResidue code BAD_PEPTIDE in next template residue (1jdbB)E559 Warning: unaligning (T0333)P211 because of BadResidue code BAD_PEPTIDE at template residue (1jdbB)E559 T0333 2 :LFVSSPGI 1jdbB 9 :ILILGAGP T0333 10 :GHL 1jdbB 20 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1jdbB 27 :YSGAQACKALREEGYRVILVN T0333 34 :AEHADRAAAA 1jdbB 50 :PATIMTDPEM T0333 45 :LEVVDVAP 1jdbB 60 :ADATYIEP T0333 94 :RPL 1jdbB 70 :WEV T0333 100 :TMALVDDYRPDLVVYEQGATVGLLAADRA 1jdbB 73 :VRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1jdbB 111 :GVT T0333 135 :RNQSA 1jdbB 114 :MIGAT T0333 141 :RTRGMHRSIASFLTDL 1jdbB 504 :LAGVREAEIRKLRDQY T0333 165 :PEPVATIESFPPSLL 1jdbB 520 :DLHPVYKRVDTCAAE T0333 199 :V 1jdbB 535 :F T0333 200 :LGDR 1jdbB 546 :YEEE T0333 204 :LPPV 1jdbB 552 :ANPS T0333 212 :EVAITMG 1jdbB 560 :KIMVLGG T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1jdbB 571 :IGQGIEFDYCCVHASLALREDGYETIMVNCNPE T0333 275 :LRTCTAVVHHG 1jdbB 609 :YDTSDRLYFEP T0333 286 :GGGTVMTAIDAGIP 1jdbB 621 :TLEDVLEIVRIEKP T0333 300 :QLLAPDPRD 1jdbB 636 :GVIVQYGGQ T0333 309 :QFQHTAR 1jdbB 646 :PLKLARA T0333 318 :VSRRGIG 1jdbB 653 :LEAAGVP T0333 325 :LVST 1jdbB 661 :IGTS T0333 334 :ADLLRRLIG 1jdbB 665 :PDAIDRAED T0333 347 :RTAAREVREE 1jdbB 674 :RERFQHAVER T0333 362 :TPAETVRRIVERI 1jdbB 695 :TAIEMAVEKAKEI Number of specific fragments extracted= 25 number of extra gaps= 1 total=2140 Number of alignments=106 # 1jdbB read from 1jdbB/merged-good-all-a2m # found chain 1jdbB in template set T0333 2 :LF 1jdbB 11 :IL T0333 5 :SSPGI 1jdbB 14 :AGPIV T0333 10 :GHL 1jdbB 20 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHADRAAAAG 1jdbB 27 :YSGAQACKALREEGYRVILVNSNPATIMTDPE T0333 45 :LEVVDVAPDYS 1jdbB 60 :ADATYIEPIHW T0333 98 :DGTMALVDDYRPDLVVYEQGATVGLLAADRA 1jdbB 71 :EVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1jdbB 111 :GVT T0333 135 :RNQSA 1jdbB 114 :MIGAT T0333 140 :WRTRGMHRSIASFLTDLM 1jdbB 799 :TLSQEIQDVMRQQVQKLA T0333 173 :SFPPSLLLE 1jdbB 877 :GVTKEVIPP T0333 187 :WFMRWVPYGGGAVLGDRLPPV 1jdbB 886 :YYSVKEVVLPFNKFPGVDPLL T0333 209 :ARPEVAITM 1jdbB 940 :KHGRALLSV T0333 223 :QAFGIGAVEPIIAAAGEVDADFVLA 1jdbB 949 :REGDKERVVDLAAKLLKQGFELDAT T0333 254 :SPLG 1jdbB 981 :GEAG T0333 261 :RNVRAVGWT 1jdbB 985 :INPRLVNKV T0333 271 :LHTLLR 1jdbB 1000 :IQDRIK T0333 277 :TCTAVVHHG 1jdbB 1008 :EYTYIINTT T0333 286 :GGGTV 1jdbB 1018 :GRRAI T0333 308 :DQF 1jdbB 1024 :DSR T0333 313 :TAREAVSRRGIGLV 1jdbB 1027 :VIRRSALQYKVHYD Number of specific fragments extracted= 20 number of extra gaps= 0 total=2160 Number of alignments=107 # 1jdbB read from 1jdbB/merged-good-all-a2m # found chain 1jdbB in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1jdbB)D557 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1jdbB)D557 Warning: unaligning (T0333)R210 because of BadResidue code BAD_PEPTIDE in next template residue (1jdbB)E559 Warning: unaligning (T0333)P211 because of BadResidue code BAD_PEPTIDE at template residue (1jdbB)E559 T0333 1 :MLFVSSPGI 1jdbB 9 :ILILGAGPI T0333 10 :GH 1jdbB 20 :GQ T0333 12 :LFPLIQLAWGFRTAGHDVLIAV 1jdbB 26 :DYSGAQACKALREEGYRVILVN T0333 34 :AEHA 1jdbB 50 :PATI T0333 45 :LEVVDVAPDY 1jdbB 60 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1jdbB 70 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GV 1jdbB 111 :GV T0333 137 :QSAWRTRGMHRSIASFLT 1jdbB 113 :TMIGATADAIDKAEDRRR T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1jdbB 507 :VREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEEC T0333 203 :RLPPV 1jdbB 551 :EANPS T0333 212 :EVAITMGTIELQAFGIGAVEPIIA 1jdbB 560 :KIMVLGGGPNRIGQGIEFDYCCVH T0333 236 :AAGEVDADFVLALGD 1jdbB 587 :ALREDGYETIMVNCN T0333 251 :LD 1jdbB 603 :ET T0333 271 :LHTLLRTCTAVVH 1jdbB 605 :VSTDYDTSDRLYF T0333 284 :HGGGGTVMTAIDAGIP 1jdbB 619 :PVTLEDVLEIVRIEKP T0333 300 :QLLAP 1jdbB 636 :GVIVQ T0333 305 :DPRDQFQHTAREAVSRRGIGL 1jdbB 642 :GGQTPLKLARALEAAGVPVIG T0333 329 :SD 1jdbB 664 :SP T0333 335 :DLLRRLIGDESLRTAAREV 1jdbB 666 :DAIDRAEDRERFQHAVERL T0333 360 :LPTPAETVRRIVER 1jdbB 694 :VTAIEMAVEKAKEI Number of specific fragments extracted= 20 number of extra gaps= 1 total=2180 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w78A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w78A expands to /projects/compbio/data/pdb/1w78.pdb.gz 1w78A:Bad short name: CX for alphabet: pdb_atoms Bad short name: OX1 for alphabet: pdb_atoms Bad short name: OX2 for alphabet: pdb_atoms # T0333 read from 1w78A/merged-good-all-a2m # 1w78A read from 1w78A/merged-good-all-a2m # adding 1w78A to template set # found chain 1w78A in template set Warning: unaligning (T0333)I253 because of BadResidue code BAD_PEPTIDE at template residue (1w78A)G359 T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAVAEHADRAAAA 1w78A 51 :VFTVAGTNGKGTTCRTLESILMAAGYKVGVYSSPHLVRYTER T0333 57 :VKVFEQVAKD 1w78A 93 :VRVQGQELPE T0333 91 :AVNRPLVDGTMALVDDYRPD 1w78A 103 :SAHTASFAEIESARGDISLT T0333 117 :GATVGLLAADRAGVPAVQRNQSAW 1w78A 127 :GTLSALWLFKQAQLDVVILEVGLG T0333 141 :RTRGMHRSIASFLTDLMDK 1w78A 201 :GEPEMPSTIADVAQEKGAL T0333 161 :QVS 1w78A 220 :LQR T0333 165 :PEPVATIESFPPSLLLEA 1w78A 223 :RGVEWNYSVTDHDWAFSD T0333 184 :PEGWFMRWVPYGGGAV 1w78A 241 :AHGTLENLPLPLVPQP T0333 209 :ARPEVAITMGT 1w78A 295 :ESPRVIFDVAH T0333 226 :GIGAVEPIIAAAGEVD 1w78A 306 :NPHAAEYLTGRMKALP T0333 242 :ADFVLALG 1w78A 324 :GRVLAVIG T0333 250 :DLD 1w78A 335 :DKD T0333 254 :SPLGT 1w78A 360 :PRGAT T0333 261 :RNVRAVGWT 1w78A 373 :GNGKSFDSV T0333 271 :LHTLLRTC 1w78A 385 :WDAAMADA T0333 279 :TAVVHHGGGGTVMTAID 1w78A 396 :DTVLVCGSFHTVAHVME Number of specific fragments extracted= 16 number of extra gaps= 1 total=2196 Number of alignments=109 # 1w78A read from 1w78A/merged-good-all-a2m # found chain 1w78A in template set Warning: unaligning (T0333)F152 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w78A)A189 Warning: unaligning (T0333)T154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w78A)A189 T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAVAE 1w78A 51 :VFTVAGTNGKGTTCRTLESILMAAGYKVGVYSSP T0333 65 :KDNPRFAETVATRPAIDLEEWGVQIA 1w78A 85 :HLVRYTERVRVQGQELPESAHTASFA T0333 99 :GTMALVDDYRP 1w78A 111 :EIESARGDISL T0333 116 :QGATVGLLAADRAGVPAVQRNQSA 1w78A 126 :YGTLSALWLFKQAQLDVVILEVGL T0333 140 :WRTRGMHRSIAS 1w78A 175 :DWLGPDRESIGR T0333 155 :DLM 1w78A 190 :GIF T0333 158 :DKHQVSLPEPVATIE 1w78A 196 :KPAIVGEPEMPSTIA T0333 173 :SF 1w78A 217 :GA T0333 191 :WVPYGGGAVLGDR 1w78A 219 :LLQRRGVEWNYSV T0333 205 :PPVP 1w78A 232 :TDHD T0333 209 :ARPEVAITMGTIE 1w78A 295 :ESPRVIFDVAHNP T0333 223 :QAF 1w78A 308 :HAA T0333 228 :GAVEPIIAAAGE 1w78A 311 :EYLTGRMKALPK T0333 241 :DADFVLALG 1w78A 323 :NGRVLAVIG T0333 250 :DL 1w78A 334 :HD T0333 254 :SPLG 1w78A 336 :KDIA T0333 313 :TAREAVSRRGIGLVSTS 1w78A 340 :GTLAWLKSVVDDWYCAP T0333 330 :DKVD 1w78A 360 :PRGA T0333 334 :ADLLRRLIGD 1w78A 365 :AEQLLEHLGN T0333 360 :LP 1w78A 377 :SF T0333 362 :TPAETVRRIVER 1w78A 380 :SVAQAWDAAMAD Number of specific fragments extracted= 21 number of extra gaps= 0 total=2217 Number of alignments=110 # 1w78A read from 1w78A/merged-good-all-a2m # found chain 1w78A in template set Warning: unaligning (T0333)D250 because of BadResidue code BAD_PEPTIDE in next template residue (1w78A)G359 Warning: unaligning (T0333)L251 because of BadResidue code BAD_PEPTIDE at template residue (1w78A)G359 T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAV 1w78A 51 :VFTVAGTNGKGTTCRTLESILMAAGYKVGVYS T0333 34 :AEHAD 1w78A 84 :PHLVR T0333 56 :AV 1w78A 89 :YT T0333 59 :VF 1w78A 91 :ER T0333 90 :AAVNRPLVDGTMALVDDYRPD 1w78A 102 :ESAHTASFAEIESARGDISLT T0333 116 :QGATVGLLAADRAGVPAVQRNQSAWRTRGMHRSIASFLT 1w78A 126 :YGTLSALWLFKQAQLDVVILEVGLGGRLDATNIVDADVA T0333 174 :FPPSLLLEAEPE 1w78A 285 :ILPGRFQIVSES T0333 188 :FMRWVPYGGGA 1w78A 297 :PRVIFDVAHNP T0333 199 :VLGDRLPPVPARPEVAITMGTIE 1w78A 312 :YLTGRMKALPKNGRVLAVIGMLH T0333 222 :LQ 1w78A 336 :KD T0333 230 :VEPIIAAAGEVDADFVLALG 1w78A 338 :IAGTLAWLKSVVDDWYCAPL T0333 252 :DI 1w78A 360 :PR T0333 327 :STSDKVDADLL 1w78A 362 :GATAEQLLEHL T0333 342 :GD 1w78A 373 :GN T0333 360 :LPTPAETVRRIVERIS 1w78A 378 :FDSVAQAWDAAMADAK Number of specific fragments extracted= 15 number of extra gaps= 1 total=2232 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yrbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yrbA expands to /projects/compbio/data/pdb/1yrb.pdb.gz 1yrbA:WARNING: atom 113 has residue number 1 < previous residue 500 in 1yrbA Skipped atom 589, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 591, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1274, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1286, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1288, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1290, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1292, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1294, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1296, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1298, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1698, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1700, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1702, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1704, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1706, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1708, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1802, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1804, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1806, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1808, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1810, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1812, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1814, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1829, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1839, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1845, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1847, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1849, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 1928, because occupancy 0.300 <= existing 0.700 in 1yrbA Skipped atom 1930, because occupancy 0.300 <= existing 0.700 in 1yrbA Skipped atom 1932, because occupancy 0.300 <= existing 0.700 in 1yrbA Skipped atom 1934, because occupancy 0.300 <= existing 0.700 in 1yrbA Skipped atom 1936, because occupancy 0.300 <= existing 0.700 in 1yrbA Skipped atom 1938, because occupancy 0.300 <= existing 0.700 in 1yrbA Skipped atom 1940, because occupancy 0.300 <= existing 0.700 in 1yrbA Skipped atom 2052, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 2054, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 2056, because occupancy 0.500 <= existing 0.500 in 1yrbA Skipped atom 2058, because occupancy 0.500 <= existing 0.500 in 1yrbA # T0333 read from 1yrbA/merged-good-all-a2m # 1yrbA read from 1yrbA/merged-good-all-a2m # adding 1yrbA to template set # found chain 1yrbA in template set T0333 1 :M 1yrbA 1 :M T0333 2 :LFVSS 1yrbA 3 :VVFVG T0333 7 :PGIGHLFPLIQLAWGFRT 1yrbA 9 :AGSGKTTLTGEFGRYLED T0333 26 :GHDVLIAV 1yrbA 27 :NYKVAYVN T0333 34 :A 1yrbA 37 :T T0333 46 :EVVDVAPDYS 1yrbA 38 :GVKELPYEPS T0333 56 :AVKVFEQVAKDNPRFA 1yrbA 53 :FVTVEEIMREGYGPNG T0333 81 :DLEEWGVQIAAVNRPLVDGTMALVDDY 1yrbA 69 :AIVESYDRLMEKFNEYLNKILRLEKEN T0333 110 :DLVVYEQGAT 1yrbA 96 :DYVLIDTPGQ T0333 120 :VGLLAADRAGVPAVQRNQS 1yrbA 114 :FGVRLMENLPYPLVVYISD T0333 201 :GDRLPP 1yrbA 133 :PEILKK T0333 226 :GIGAVEPIIAAAG 1yrbA 139 :PNDYCFVRFFALL T0333 239 :EVDADFVLALGD 1yrbA 155 :RLGATTIPALNK T0333 253 :ISPLGT 1yrbA 167 :VDLLSE T0333 307 :RDQFQHTAR 1yrbA 173 :EEKERHRKY T0333 318 :VSR 1yrbA 182 :FED T0333 334 :ADLLRRLIG 1yrbA 185 :IDYLTARLK T0333 343 :DES 1yrbA 197 :SMQ T0333 346 :LRTAAREVREE 1yrbA 203 :AYKMCSMMTEV T0333 357 :MVALP 1yrbA 224 :AKTRE T0333 363 :PAETVRRIVERI 1yrbA 229 :GFEDLETLAYEH Number of specific fragments extracted= 21 number of extra gaps= 0 total=2253 Number of alignments=112 # 1yrbA read from 1yrbA/merged-good-all-a2m # found chain 1yrbA in template set T0333 1 :M 1yrbA 1 :M T0333 2 :LFVSSPGI 1yrbA 3 :VVFVGTAG T0333 10 :GHLFPLIQLAWGFRT 1yrbA 12 :GKTTLTGEFGRYLED T0333 26 :GHDVLIAV 1yrbA 27 :NYKVAYVN T0333 34 :AEHA 1yrbA 37 :TGVK T0333 48 :VDVAPDYSAVKVFEQ 1yrbA 48 :IDVREFVTVEEIMRE T0333 66 :DN 1yrbA 63 :GY T0333 80 :IDLEEWGVQIAAVNRPLVD 1yrbA 65 :GPNGAIVESYDRLMEKFNE T0333 99 :GTMALVDD 1yrbA 87 :KILRLEKE T0333 109 :PDLVVYEQGA 1yrbA 95 :NDYVLIDTPG T0333 120 :V 1yrbA 106 :M T0333 141 :RTRGMHRSIASFLTDL 1yrbA 107 :ETFLFHEFGVRLMENL T0333 175 :PPS 1yrbA 123 :PYP T0333 213 :VAITMGTIELQAFGIGA 1yrbA 126 :LVVYISDPEILKKPNDY T0333 230 :VEPIIAAA 1yrbA 149 :ALLIDLRL T0333 241 :DADFVLALGDLD 1yrbA 157 :GATTIPALNKVD T0333 255 :PLG 1yrbA 169 :LLS T0333 308 :DQFQHTAREAVSR 1yrbA 172 :EEEKERHRKYFED T0333 334 :ADLLRRLIG 1yrbA 185 :IDYLTARLK T0333 343 :DESLRTA 1yrbA 197 :SMQGLMA T0333 351 :REVREEMV 1yrbA 204 :YKMCSMMT T0333 359 :ALPTPAETVRRIVERIS 1yrbA 226 :TREGFEDLETLAYEHYC Number of specific fragments extracted= 22 number of extra gaps= 0 total=2275 Number of alignments=113 # 1yrbA read from 1yrbA/merged-good-all-a2m # found chain 1yrbA in template set T0333 1 :MLFVSSPGIGHLFPLIQLAWGFRT 1yrbA 3 :VVFVGTAGSGKTTLTGEFGRYLED T0333 26 :GHDVLIAV 1yrbA 27 :NYKVAYVN T0333 43 :AGLEVVDVAPDYSAVKVF 1yrbA 37 :TGVKELPYEPSIDVREFV T0333 61 :EQVAKDNPR 1yrbA 57 :EEIMREGYG T0333 78 :PAIDLEEWGVQIAAVNRPLVDGTMALVDDY 1yrbA 66 :PNGAIVESYDRLMEKFNEYLNKILRLEKEN T0333 110 :DLVVYEQGAT 1yrbA 96 :DYVLIDTPGQ T0333 120 :VGLLAADRAGVPAVQRNQSAWRTRGMHR 1yrbA 114 :FGVRLMENLPYPLVVYISDPEILKKPND T0333 226 :GIGAVEPIIAAAGEVDADFVLALGDL 1yrbA 142 :YCFVRFFALLIDLRLGATTIPALNKV T0333 254 :S 1yrbA 168 :D T0333 327 :STSDKVDAD 1yrbA 169 :LLSEEEKER T0333 346 :LRTAAR 1yrbA 178 :HRKYFE T0333 352 :EVREEMVALPTPA 1yrbA 187 :YLTARLKLDPSMQ T0333 365 :ETVRRIVER 1yrbA 202 :MAYKMCSMM Number of specific fragments extracted= 13 number of extra gaps= 0 total=2288 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2acwA/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/T0333/2acwA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0333/2acwA/merged-good-all-a2m.gz for input Trying 2acwA/merged-good-all-a2m Error: Couldn't open file 2acwA/merged-good-all-a2m or 2acwA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ve1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ve1A expands to /projects/compbio/data/pdb/1ve1.pdb.gz 1ve1A:# T0333 read from 1ve1A/merged-good-all-a2m # 1ve1A read from 1ve1A/merged-good-all-a2m # adding 1ve1A to template set # found chain 1ve1A in template set T0333 2 :LFVSSPGI 1ve1A 64 :VIVEPTSG T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEH 1ve1A 72 :NTGIGLAMIAASRGYRLILTMPAQ T0333 37 :ADRAAAAGLEVVDVAPDYSAVKVFEQVAK 1ve1A 101 :KRVLKAFGAELVLTDPERRMLAAREEALR T0333 66 :DNPRFAET 1ve1A 135 :GAFMPDQF T0333 81 :DLEEWGVQIAAVNR 1ve1A 143 :KNPANVRAHYETTG T0333 98 :DGTMALVDD 1ve1A 157 :PELYEALEG T0333 108 :RPDLVVYE 1ve1A 166 :RIDAFVYG T0333 116 :QGATVGLLAADRA 1ve1A 175 :GTGGTITGVGRYL T0333 129 :GVPAVQRNQS 1ve1A 193 :HVKVIAVEPA T0333 178 :LLLEAEPEGWFMRWVPYGGGAVLGDRLPPVPARPEVAI 1ve1A 203 :RSNVLSGGKMGQHGFQGMGPGFIPENLDLSLLDGVIQV T0333 226 :GIGAVEPIIAAAGEVDADF 1ve1A 242 :EEDAFPLARRLAREEGLFL T0333 285 :GGGGTVMTAIDA 1ve1A 263 :SSGGIVWAALQV T0333 297 :GIPQLLA 1ve1A 281 :GKRVACI T0333 304 :PDP 1ve1A 289 :PDG Number of specific fragments extracted= 14 number of extra gaps= 0 total=2302 Number of alignments=115 # 1ve1A read from 1ve1A/merged-good-all-a2m # found chain 1ve1A in template set T0333 3 :FVSSPG 1ve1A 65 :IVEPTS T0333 12 :LFPLIQLAWGFRTAGHDVLIAVAE 1ve1A 71 :GNTGIGLAMIAASRGYRLILTMPA T0333 36 :HA 1ve1A 96 :MS T0333 38 :DRAAAAGLEVVDVAPDYSAVKVFEQVAKDNPRFAETVATRPAI 1ve1A 102 :RVLKAFGAELVLTDPERRMLAAREEALRLKEELGAFMPDQFKN T0333 86 :GVQIAAVNRPLVDGTMALVDD 1ve1A 145 :PANVRAHYETTGPELYEALEG T0333 108 :RPDLVVYEQGA 1ve1A 166 :RIDAFVYGSGT T0333 119 :TVGLLAADRA 1ve1A 178 :GTITGVGRYL T0333 129 :GVPAVQRNQSA 1ve1A 193 :HVKVIAVEPAR T0333 147 :R 1ve1A 230 :D T0333 154 :TDLMDKHQVSLPE 1ve1A 231 :LSLLDGVIQVWEE T0333 167 :PVATIE 1ve1A 245 :AFPLAR T0333 173 :SFPPS 1ve1A 257 :GLFLG T0333 220 :IE 1ve1A 262 :MS T0333 223 :QAFGIGAVEPIIAAAGE 1ve1A 264 :SGGIVWAALQVARELGP T0333 241 :DADFVLALG 1ve1A 281 :GKRVACISP T0333 250 :DLDI 1ve1A 291 :GGWK Number of specific fragments extracted= 16 number of extra gaps= 0 total=2318 Number of alignments=116 # 1ve1A read from 1ve1A/merged-good-all-a2m # found chain 1ve1A in template set T0333 4 :VSSPGIG 1ve1A 65 :IVEPTSG T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1ve1A 72 :NTGIGLAMIAASRGYRLILTM T0333 34 :A 1ve1A 94 :A T0333 35 :EHADRAAAAGLEVVDVAPDYSAVKVF 1ve1A 99 :ERKRVLKAFGAELVLTDPERRMLAAR T0333 61 :EQVAKDNPRFAETVATRPA 1ve1A 128 :LRLKEELGAFMPDQFKNPA T0333 88 :QIAAVNRPLVDGTMALVDD 1ve1A 147 :NVRAHYETTGPELYEALEG T0333 108 :RPDLVVYEQGATVGL 1ve1A 166 :RIDAFVYGSGTGGTI T0333 123 :LAADRA 1ve1A 182 :GVGRYL T0333 129 :GVPAVQRNQSAWRT 1ve1A 193 :HVKVIAVEPARSNV T0333 161 :QVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1ve1A 207 :LSGGKMGQHGFQGMGPGFIPENLDLSLLDGVIQVWEED T0333 199 :VLGDRLPPVPARPEVAITMGTIE 1ve1A 271 :ALQVARELGPGKRVACISPDGGW T0333 222 :L 1ve1A 295 :Y Number of specific fragments extracted= 12 number of extra gaps= 0 total=2330 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vcoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vcoA expands to /projects/compbio/data/pdb/1vco.pdb.gz 1vcoA:# T0333 read from 1vcoA/merged-good-all-a2m # 1vcoA read from 1vcoA/merged-good-all-a2m # adding 1vcoA to template set # found chain 1vcoA in template set Warning: unaligning (T0333)L251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)D314 Warning: unaligning (T0333)L256 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)A347 Warning: unaligning (T0333)T269 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)A347 T0333 2 :LFVSSPGI 1vcoA 15 :VFITGGVV T0333 10 :GHLFPLIQLAWGFRTAGHDVLIAV 1vcoA 26 :GKGILTSSLGALLRARGYRVTAIK T0333 34 :AEHADRAAAAGL 1vcoA 52 :PYVNVDAGTMRP T0333 46 :EVVDVAPDYS 1vcoA 67 :GEVFVTADGA T0333 58 :KVFEQVAKDNPR 1vcoA 107 :SVIQKERRGEYL T0333 71 :AETVATRP 1vcoA 119 :SQTVQVIP T0333 91 :AVNRPLVDGTMALVDDYRPDLVVYEQGAT 1vcoA 127 :HITDEIKERIRKVAEEQKAEIVVVEVGGT T0333 120 :VGLLAADRA 1vcoA 163 :PFLEAIRQF T0333 129 :GVPAVQRNQSAW 1vcoA 178 :GNTLYLHLTLVP T0333 141 :RTRGMHRSIASFLTDLMDKHQVSL 1vcoA 194 :SEEFKTKPTQHSVATLRGVGIQPD T0333 169 :ATIESFPPSLL 1vcoA 222 :RSARPVPEEVR T0333 181 :EAEPE 1vcoA 236 :ALFTN T0333 187 :WFMRWVPYGGGAV 1vcoA 241 :VRPGHVFSSPTVE T0333 200 :LGDRLPP 1vcoA 271 :VERALGL T0333 209 :ARP 1vcoA 278 :EAV T0333 224 :AFGIGAVEPIIAAAGEVD 1vcoA 281 :IPNLSFWQEAVRVLKHPE T0333 242 :ADFVLALGD 1vcoA 301 :VKIAIAGKY T0333 253 :ISP 1vcoA 341 :AES T0333 270 :PLHTLLRTCTAVVHHG 1vcoA 348 :DLEEAFRDVSGILVPG T0333 287 :GGTVMTAIDAGIPQLLA 1vcoA 374 :VRAAQYARERKIPYLGI Number of specific fragments extracted= 20 number of extra gaps= 0 total=2350 Number of alignments=118 # 1vcoA read from 1vcoA/merged-good-all-a2m # found chain 1vcoA in template set Warning: unaligning (T0333)E83 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1vcoA)Y85 Warning: unaligning (T0333)E84 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1vcoA)Y85 Warning: unaligning (T0333)E221 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)D314 Warning: unaligning (T0333)F225 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)D314 Warning: unaligning (T0333)L256 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)A347 Warning: unaligning (T0333)T269 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)A347 T0333 3 :FVSSPGI 1vcoA 16 :FITGGVV T0333 10 :GHLFPLIQLAWGFRTAGHDVLIAV 1vcoA 26 :GKGILTSSLGALLRARGYRVTAIK T0333 34 :AEHADRA 1vcoA 52 :PYVNVDA T0333 52 :PDYSAVK 1vcoA 59 :GTMRPYE T0333 65 :KDNPRFAETVATRPAIDL 1vcoA 66 :HGEVFVTADGAETDLDIG T0333 85 :WGVQ 1vcoA 86 :ERFL T0333 89 :IAAVNR 1vcoA 129 :TDEIKE T0333 99 :GTMALVDDYRPDLVVY 1vcoA 135 :RIRKVAEEQKAEIVVV T0333 115 :EQGA 1vcoA 154 :GTVG T0333 119 :TVGLLAADRA 1vcoA 162 :LPFLEAIRQF T0333 130 :VPAVQRNQSA 1vcoA 180 :TLYLHLTLVP T0333 140 :WRTRGMHRSIASFLTD 1vcoA 196 :EFKTKPTQHSVATLRG T0333 156 :LMDKHQVSLPE 1vcoA 215 :QPDILVLRSAR T0333 167 :PVATIE 1vcoA 231 :VRRKVA T0333 173 :SFPPS 1vcoA 240 :NVRPG T0333 191 :WVPYGG 1vcoA 245 :HVFSSP T0333 205 :PPVP 1vcoA 251 :TVEH T0333 209 :ARPE 1vcoA 297 :PERT T0333 213 :VAITMGTI 1vcoA 302 :KIAIAGKY T0333 226 :GIGAVEPIIAAAGEV 1vcoA 315 :AYLSLLEALRHAGIK T0333 241 :DADFVLA 1vcoA 331 :RARVEVK T0333 250 :DLDISP 1vcoA 338 :WVDAES T0333 270 :PLHTLLRTCTAVVHHG 1vcoA 348 :DLEEAFRDVSGILVPG T0333 286 :GGGTVMTAIDAGIPQLLAPDPR 1vcoA 373 :KVRAAQYARERKIPYLGICLGL T0333 309 :QF 1vcoA 395 :QI T0333 313 :TAREAVSRRG 1vcoA 397 :AVIEFARNVA Number of specific fragments extracted= 26 number of extra gaps= 1 total=2376 Number of alignments=119 # 1vcoA read from 1vcoA/merged-good-all-a2m # found chain 1vcoA in template set Warning: unaligning (T0333)L251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)D314 Warning: unaligning (T0333)P255 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)D314 Warning: unaligning (T0333)L274 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)A347 T0333 1 :MLFVSSPG 1vcoA 14 :YVFITGGV T0333 9 :IGHLFPLIQLAWGFRTAGHDVLIA 1vcoA 25 :LGKGILTSSLGALLRARGYRVTAI T0333 47 :VVDVAPDYSAVKVF 1vcoA 49 :KIDPYVNVDAGTMR T0333 61 :EQVAKDNPRFAETVATRP 1vcoA 109 :IQKERRGEYLSQTVQVIP T0333 91 :AVNRPLVDGTMALVDDYRPDLVVYEQGAT 1vcoA 127 :HITDEIKERIRKVAEEQKAEIVVVEVGGT T0333 120 :VGLLAADRA 1vcoA 163 :PFLEAIRQF T0333 129 :GVPAVQRNQSAWRTRGMHRSIASFLT 1vcoA 178 :GNTLYLHLTLVPYLETSEEFKTKPTQ T0333 155 :DLMDKHQVSLPEP 1vcoA 226 :PVPEEVRRKVALF T0333 182 :AEPEGWFMRWVPYGGGA 1vcoA 239 :TNVRPGHVFSSPTVEHL T0333 223 :QAFGIGAVEPIIAAAGEVD 1vcoA 280 :VIPNLSFWQEAVRVLKHPE T0333 242 :ADFVLALGD 1vcoA 301 :VKIAIAGKY T0333 256 :L 1vcoA 315 :A T0333 264 :RA 1vcoA 333 :RV T0333 266 :VGWTPLHT 1vcoA 336 :VKWVDAES T0333 275 :LRTCTAVVHHGG 1vcoA 353 :FRDVSGILVPGG T0333 287 :GGTVMTAIDAGIPQLLA 1vcoA 374 :VRAAQYARERKIPYLGI Number of specific fragments extracted= 16 number of extra gaps= 0 total=2392 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rrvA/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/T0333/1rrvA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0333/1rrvA/merged-good-all-a2m.gz for input Trying 1rrvA/merged-good-all-a2m Error: Couldn't open file 1rrvA/merged-good-all-a2m or 1rrvA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v71A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v71A expands to /projects/compbio/data/pdb/1v71.pdb.gz 1v71A:# T0333 read from 1v71A/merged-good-all-a2m # 1v71A read from 1v71A/merged-good-all-a2m # adding 1v71A to template set # found chain 1v71A in template set T0333 3 :FVSSPGIGHLFPLIQLAWG 1v71A 77 :VLTFSSGNHAQAIALSAKI T0333 25 :AGHDVLIAV 1v71A 96 :LGIPAKIIM T0333 34 :AEH 1v71A 106 :LDA T0333 37 :ADRAAAAGLEVVDVAPD 1v71A 113 :VAATKGYGGQVIMYDRY T0333 81 :DLEEWGVQIAAV 1v71A 132 :DREKMAKEISER T0333 94 :RPLVDG 1v71A 155 :PHVLAG T0333 100 :TMALVDDY 1v71A 165 :AKELFEEV T0333 108 :RPDLVVYEQGA 1v71A 174 :PLDALFVCLGG T0333 119 :TVGLLAADRA 1v71A 189 :SGSALAARHF T0333 129 :GVPAVQRNQSAW 1v71A 201 :NCEVYGVEPEAG T0333 141 :RTRGMHRSIASFLTDLMDKHQVSL 1v71A 238 :QTQHLGNYTFSIIKEKVDDILTVS T0333 175 :PPSLL 1v71A 262 :DEELI T0333 181 :EAEPE 1v71A 273 :AARMK T0333 190 :RWVPYGGGAV 1v71A 278 :IVVEPTGCLS T0333 200 :LGDRLPP 1v71A 294 :MKEKLKN T0333 211 :PEVAITMGT 1v71A 301 :KRIGIIISG T0333 226 :GIGAVEPII 1v71A 313 :DIERYAHFL Number of specific fragments extracted= 17 number of extra gaps= 0 total=2409 Number of alignments=121 # 1v71A read from 1v71A/merged-good-all-a2m # found chain 1v71A in template set T0333 4 :VSSPGI 1v71A 78 :LTFSSG T0333 13 :FPLIQLAWGFRTAGHDVLIAVAE 1v71A 84 :NHAQAIALSAKILGIPAKIIMPL T0333 36 :HA 1v71A 108 :AP T0333 38 :DRAAAAGLEVVDVA 1v71A 114 :AATKGYGGQVIMYD T0333 52 :PDYSAVKVFEQVAKDNPRFAETVATRP 1v71A 129 :YKDDREKMAKEISEREGLTIIPPYDHP T0333 90 :AAVNRPLV 1v71A 156 :HVLAGQGT T0333 99 :GTMALVDDYR 1v71A 164 :AAKELFEEVG T0333 109 :PDLVVY 1v71A 175 :LDALFV T0333 115 :EQGA 1v71A 183 :GGGG T0333 119 :TVGLLAADRA 1v71A 189 :SGSALAARHF T0333 129 :GVPAVQRNQSA 1v71A 201 :NCEVYGVEPEA T0333 140 :WRTRGMHRSIASFLTDLMDKHQVSLP 1v71A 237 :AQTQHLGNYTFSIIKEKVDDILTVSD T0333 228 :GAVEPIIAAAGEV 1v71A 263 :EELIDCLKFYAAR T0333 241 :DADF 1v71A 277 :KIVV T0333 250 :DLDI 1v71A 281 :EPTG T0333 254 :SPLGTL 1v71A 296 :EKLKNK T0333 279 :TAVVHHGGGGT 1v71A 302 :RIGIIISGGNV T0333 343 :DESLRTAA 1v71A 313 :DIERYAHF Number of specific fragments extracted= 18 number of extra gaps= 0 total=2427 Number of alignments=122 # 1v71A read from 1v71A/merged-good-all-a2m # found chain 1v71A in template set T0333 3 :FVSSPGI 1v71A 77 :VLTFSSG T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1v71A 84 :NHAQAIALSAKILGIPAKIIM T0333 34 :A 1v71A 106 :L T0333 35 :EHADRAAAAGLEVVDVAPDYSAVKVF 1v71A 111 :AKVAATKGYGGQVIMYDRYKDDREKM T0333 61 :EQVAKDNPRFAETVATR 1v71A 138 :KEISEREGLTIIPPYDH T0333 83 :EEWGVQIAAVNRPLVDGT 1v71A 155 :PHVLAGQGTAAKELFEEV T0333 108 :RPDLVVYEQGAT 1v71A 174 :PLDALFVCLGGG T0333 120 :VGLLAADRA 1v71A 190 :GSALAARHF T0333 129 :GVPAVQRNQSAWRTRGMHRSIASFLT 1v71A 201 :NCEVYGVEPEAGNDGQQSFRKGSIVH T0333 202 :DRLPPVPARPEVAITMGTIEL 1v71A 292 :RAMKEKLKNKRIGIIISGGNV T0333 226 :GIGAVEPII 1v71A 313 :DIERYAHFL Number of specific fragments extracted= 11 number of extra gaps= 0 total=2438 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oi7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0333 read from 1oi7A/merged-good-all-a2m # 1oi7A read from 1oi7A/merged-good-all-a2m # found chain 1oi7A in training set Warning: unaligning (T0333)G195 because of BadResidue code BAD_PEPTIDE in next template residue (1oi7A)G121 Warning: unaligning (T0333)G196 because of BadResidue code BAD_PEPTIDE at template residue (1oi7A)G121 Warning: unaligning (T0333)R307 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1oi7A)V255 T0333 2 :LFVSSPGI 1oi7A 10 :VLVQGITG T0333 14 :PLIQLAWGFRTAGHDVLIAV 1oi7A 19 :EGQFHTKQMLTYGTKIVAGV T0333 34 :AEHADR 1oi7A 40 :PGKGGM T0333 41 :AAAGLEVVD 1oi7A 46 :EVLGVPVYD T0333 81 :DLE 1oi7A 55 :TVK T0333 99 :GT 1oi7A 58 :EA T0333 104 :VDDYRPDLVVYEQGAT 1oi7A 60 :VAHHEVDASIIFVPAP T0333 120 :VGLLAAD 1oi7A 80 :AALEAAH T0333 128 :AGVPAVQRNQS 1oi7A 87 :AGIPLIVLITE T0333 144 :GMHR 1oi7A 98 :GIPT T0333 148 :SIASFLTDLMDKHQ 1oi7A 103 :DMVRAVEEIKALGS T0333 192 :VPY 1oi7A 117 :RLI T0333 197 :GAV 1oi7A 122 :NCP T0333 200 :LGDRL 1oi7A 138 :PGHVF T0333 209 :ARPEVAITMG 1oi7A 143 :KRGRVGIISR T0333 226 :GIGAVEPIIAAAGEVDADF 1oi7A 153 :SGTLTYEAAAALSQAGLGT T0333 245 :VLALGDLDI 1oi7A 174 :TVGIGGDPV T0333 256 :L 1oi7A 183 :I T0333 268 :WTPLHTLLRT 1oi7A 184 :GTTFKDLLPL T0333 278 :CTAVVHHG 1oi7A 200 :TEAVVLIG T0333 286 :GGGTVMTAIDA 1oi7A 210 :GGSDEEEAAAW T0333 297 :GIPQLLAPDP 1oi7A 226 :KKPVVGFIGG T0333 327 :STS 1oi7A 256 :GTP T0333 344 :ESLRTAAREV 1oi7A 259 :ESKLRAFAEA T0333 360 :LP 1oi7A 273 :AD T0333 363 :PAETVRRIVERI 1oi7A 275 :TIDEIVELVKKA Number of specific fragments extracted= 26 number of extra gaps= 1 total=2464 Number of alignments=124 # 1oi7A read from 1oi7A/merged-good-all-a2m # found chain 1oi7A in training set Warning: unaligning (T0333)V162 because of BadResidue code BAD_PEPTIDE in next template residue (1oi7A)G121 Warning: unaligning (T0333)S163 because of BadResidue code BAD_PEPTIDE at template residue (1oi7A)G121 Warning: unaligning (T0333)R307 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1oi7A)V255 Warning: unaligning (T0333)S329 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1oi7A)V255 T0333 11 :HLFPLIQLAWGFRTAGHDVLIAVAEHADRAAAAGLEVVD 1oi7A 16 :TGREGQFHTKQMLTYGTKIVAGVTPGKGGMEVLGVPVYD T0333 99 :GTMALVDDYRPDLVVYEQGA 1oi7A 55 :TVKEAVAHHEVDASIIFVPA T0333 119 :TVGLLAADRAGVPAVQRNQSA 1oi7A 78 :ADAALEAAHAGIPLIVLITEG T0333 141 :RTRGMHRSIASFLTDLMDKHQ 1oi7A 99 :IPTLDMVRAVEEIKALGSRLI T0333 164 :LPE 1oi7A 122 :NCP T0333 191 :WVP 1oi7A 133 :KIG T0333 198 :AVLGDRLP 1oi7A 136 :IMPGHVFK T0333 211 :PEVAITMGTIE 1oi7A 144 :RGRVGIISRSG T0333 228 :GAVEPIIAAAGEV 1oi7A 155 :TLTYEAAAALSQA T0333 241 :DADFVLALGDLDI 1oi7A 170 :GTTTTVGIGGDPV T0333 271 :LHTLLR 1oi7A 187 :FKDLLP T0333 277 :TCTAVVHHG 1oi7A 199 :ETEAVVLIG T0333 286 :GGGTVMTAIDA 1oi7A 210 :GGSDEEEAAAW T0333 297 :GIPQLLAPDP 1oi7A 226 :KKPVVGFIGG T0333 330 :DKVD 1oi7A 257 :TPES T0333 334 :ADLLRRL 1oi7A 262 :LRAFAEA T0333 361 :PTPAETVRRIVERI 1oi7A 274 :DTIDEIVELVKKAL Number of specific fragments extracted= 17 number of extra gaps= 1 total=2481 Number of alignments=125 # 1oi7A read from 1oi7A/merged-good-all-a2m # found chain 1oi7A in training set Warning: unaligning (T0333)P193 because of BadResidue code BAD_PEPTIDE in next template residue (1oi7A)G121 Warning: unaligning (T0333)Y194 because of BadResidue code BAD_PEPTIDE at template residue (1oi7A)G121 Warning: unaligning (T0333)S327 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1oi7A)V255 T0333 2 :LFVSSPGI 1oi7A 10 :VLVQGITG T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1oi7A 18 :REGQFHTKQMLTYGTKIVAGV T0333 34 :AEHAD 1oi7A 40 :PGKGG T0333 43 :AGLEVV 1oi7A 48 :LGVPVY T0333 52 :PDY 1oi7A 54 :DTV T0333 101 :MALVDDYRPDLVVYEQGAT 1oi7A 57 :KEAVAHHEVDASIIFVPAP T0333 120 :VGLLAA 1oi7A 80 :AALEAA T0333 127 :RAGVPAVQRNQSAWRTRGMHRSIASFLT 1oi7A 86 :HAGIPLIVLITEGIPTLDMVRAVEEIKA T0333 187 :WFMRWV 1oi7A 114 :LGSRLI T0333 195 :GGGA 1oi7A 122 :NCPG T0333 199 :VLGDR 1oi7A 137 :MPGHV T0333 208 :PARPEVAITM 1oi7A 142 :FKRGRVGIIS T0333 225 :FGIGAVEPIIAAAGEVDADF 1oi7A 152 :RSGTLTYEAAAALSQAGLGT T0333 245 :VLALGDLDI 1oi7A 174 :TVGIGGDPV T0333 256 :L 1oi7A 183 :I T0333 268 :WTPLHTLL 1oi7A 184 :GTTFKDLL T0333 276 :RTCTAVVH 1oi7A 198 :PETEAVVL T0333 303 :AP 1oi7A 206 :IG T0333 305 :DPRDQFQHTAREAV 1oi7A 210 :GGSDEEEAAAWVKD T0333 323 :I 1oi7A 229 :V T0333 328 :TSDKVDADLLRRL 1oi7A 256 :GTPESKLRAFAEA T0333 360 :LPTPAETVRRIVERI 1oi7A 273 :ADTIDEIVELVKKAL Number of specific fragments extracted= 22 number of extra gaps= 1 total=2503 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vgvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vgvA expands to /projects/compbio/data/pdb/1vgv.pdb.gz 1vgvA: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 92, because occupancy 0.500 <= existing 0.500 in 1vgvA Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 1vgvA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1vgvA Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 1vgvA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 1vgvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M 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 # T0333 read from 1vgvA/merged-good-all-a2m # 1vgvA read from 1vgvA/merged-good-all-a2m # adding 1vgvA to template set # found chain 1vgvA in template set T0333 1 :M 1vgvA 1 :M T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAG 1vgvA 3 :VLTVFGTRPEAIKMAPLVHALAKDP T0333 27 :HDVLIAV 1vgvA 29 :FEAKVCV T0333 34 :AEHADRAAAA 1vgvA 37 :AQHREMLDQV T0333 44 :GL 1vgvA 51 :SI T0333 55 :SAVKVFEQ 1vgvA 53 :VPDYDLNI T0333 76 :TRPAIDLEEWGVQIAAVNRP 1vgvA 61 :MQPGQGLTEITCRILEGLKP T0333 103 :LVDDYRPDLVVYEQGA 1vgvA 81 :ILAEFKPDVVLVHGDT T0333 119 :TVGLLAADRAGVPAVQRNQSAW 1vgvA 100 :LATSLAAFYQRIPVGHVEAGLR T0333 141 :RTRGMHRSIASFLTDLMD 1vgvA 123 :GDLYSPWPEEANRTLTGH T0333 166 :EPVATIESFPPSLLLEAEPE 1vgvA 141 :LAMYHFSPTETSRQNLLREN T0333 187 :WFMRWVPYGGGAV 1vgvA 161 :VADSRIFITGNTV T0333 200 :LGDRLPP 1vgvA 197 :NYPFIDP T0333 209 :ARPEVAITMGTIELQA 1vgvA 204 :DKKMILVTGHRRESFG T0333 225 :FGIGAVEPIIAAAGEVD 1vgvA 221 :GFEEICHALADIATTHQ T0333 242 :ADFVLALG 1vgvA 239 :IQIVYPVH T0333 251 :L 1vgvA 248 :N T0333 254 :SPLGT 1vgvA 249 :PNVRE T0333 259 :LPRNVRAVGWT 1vgvA 261 :HVKNVILIDPQ T0333 270 :PLHTLLRTCTAVVHHGG 1vgvA 275 :PFVWLMNHAWLILTDSG T0333 288 :GTVMTAIDAGIPQLLAPDPRDQFQ 1vgvA 292 :GIQEEAPSLGKPVLVMRDTTERPE T0333 318 :VSRRGIG 1vgvA 316 :AVTAGTV T0333 325 :LV 1vgvA 324 :LV T0333 327 :STSDKV 1vgvA 327 :TDKQRI T0333 334 :ADLLRRLIGDESLRTAAR 1vgvA 333 :VEEVTRLLKDENEYQAMS T0333 358 :VALP 1vgvA 357 :GDGQ T0333 363 :PAETVRRIVERI 1vgvA 361 :ACSRILEALKNN Number of specific fragments extracted= 27 number of extra gaps= 0 total=2530 Number of alignments=127 # 1vgvA read from 1vgvA/merged-good-all-a2m # found chain 1vgvA in template set T0333 1 :M 1vgvA 1 :M T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAG 1vgvA 3 :VLTVFGTRPEAIKMAPLVHALAKDP T0333 27 :HDVLIAVAE 1vgvA 29 :FEAKVCVTA T0333 52 :PDYSAVKVFEQV 1vgvA 38 :QHREMLDQVLKL T0333 65 :KDNPRFAETVATRPAIDLEEWGVQIAA 1vgvA 50 :FSIVPDYDLNIMQPGQGLTEITCRILE T0333 99 :GTMALVDDYRPDLVVYE 1vgvA 77 :GLKPILAEFKPDVVLVH T0333 117 :GA 1vgvA 95 :DT T0333 119 :TVGLLAADRAGVPAVQRNQSA 1vgvA 100 :LATSLAAFYQRIPVGHVEAGL T0333 140 :WRTRGMHRSIASF 1vgvA 124 :DLYSPWPEEANRT T0333 153 :LTDLMDKHQVSLPEPVATIE 1vgvA 138 :TGHLAMYHFSPTETSRQNLL T0333 173 :SFPPS 1vgvA 160 :NVADS T0333 191 :WVPYGGGAV 1vgvA 165 :RIFITGNTV T0333 200 :LGDRLPPVPARPEVAITMG 1vgvA 194 :LAANYPFIDPDKKMILVTG T0333 219 :TIELQAFGIGAVEPIIAAAGEV 1vgvA 214 :RRESFGRGFEEICHALADIATT T0333 241 :DADFVLALG 1vgvA 238 :DIQIVYPVH T0333 250 :DLDI 1vgvA 248 :NPNV T0333 254 :SPLGTL 1vgvA 257 :RILGHV T0333 261 :RNVRAVGWTP 1vgvA 263 :KNVILIDPQE T0333 271 :LHTLLRTCTAVVHHGGGG 1vgvA 276 :FVWLMNHAWLILTDSGGI T0333 290 :VMTAIDAGIPQLLAPDPRDQF 1vgvA 294 :QEEAPSLGKPVLVMRDTTERP T0333 313 :T 1vgvA 315 :E T0333 318 :VSRRGIGLVSTSDKVD 1vgvA 316 :AVTAGTVRLVGTDKQR T0333 334 :ADLLRRLIGDESLRTAAR 1vgvA 333 :VEEVTRLLKDENEYQAMS T0333 365 :ETVRRIVERIS 1vgvA 360 :QACSRILEALK Number of specific fragments extracted= 24 number of extra gaps= 0 total=2554 Number of alignments=128 # 1vgvA read from 1vgvA/merged-good-all-a2m # found chain 1vgvA in template set T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAG 1vgvA 3 :VLTVFGTRPEAIKMAPLVHALAKDP T0333 27 :HDVLIAV 1vgvA 31 :AKVCVTA T0333 34 :AEHADRAAA 1vgvA 40 :REMLDQVLK T0333 43 :AGLEVVDVAPDYSAVK 1vgvA 50 :FSIVPDYDLNIMQPGQ T0333 78 :PA 1vgvA 66 :GL T0333 83 :EEWGV 1vgvA 68 :TEITC T0333 95 :PLVDGTMALVDDYRPDLVVYEQGATVGL 1vgvA 73 :RILEGLKPILAEFKPDVVLVHGDTTTTL T0333 123 :LAADRAGVPAVQRNQSAWRTRGMHRSIASFLT 1vgvA 104 :LAAFYQRIPVGHVEAGLRTGDLYSPWPEEANR T0333 184 :PEGWFMRWVPYGGGA 1vgvA 161 :VADSRIFITGNTVID T0333 199 :VLGDRL 1vgvA 193 :ELAANY T0333 205 :PPVPARPEVAITMGTIELQ 1vgvA 200 :FIDPDKKMILVTGHRRESF T0333 226 :G 1vgvA 219 :G T0333 228 :GAVEPIIAAAGEV 1vgvA 220 :RGFEEICHALADI T0333 241 :DADFVLALGD 1vgvA 238 :DIQIVYPVHL T0333 251 :LDISPLGTLPRNVRAVGWTPLHTLL 1vgvA 253 :EPVNRILGHVKNVILIDPQEYLPFV T0333 276 :RTCTAVVHHGG 1vgvA 281 :NHAWLILTDSG T0333 293 :AIDAGIPQLLAPDPRDQF 1vgvA 297 :APSLGKPVLVMRDTTERP T0333 315 :REAVSRRGIGLV 1vgvA 315 :EAVTAGTVRLVG T0333 329 :SDKVDADLLRRLIGDESL 1vgvA 328 :DKQRIVEEVTRLLKDENE T0333 354 :REEMVALPTPA 1vgvA 346 :YQAMSRAHNPY T0333 365 :ETVRRIVERIS 1vgvA 360 :QACSRILEALK Number of specific fragments extracted= 21 number of extra gaps= 0 total=2575 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1keeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1keeA expands to /projects/compbio/data/pdb/1kee.pdb.gz 1keeA:Skipped atom 218, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 220, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 4284, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 4286, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 4288, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 4290, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 7611, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 7613, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 7615, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 7617, because occupancy 0.500 <= existing 0.500 in 1keeA Skipped atom 7619, because occupancy 0.500 <= existing 0.500 in 1keeA # T0333 read from 1keeA/merged-good-all-a2m # 1keeA read from 1keeA/merged-good-all-a2m # adding 1keeA to template set # found chain 1keeA in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1keeA)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1keeA)D558 T0333 2 :LFVSSPGI 1keeA 10 :ILILGAGP T0333 10 :GHL 1keeA 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1keeA 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEHA 1keeA 51 :PATI T0333 39 :RAAAAGLEVVDVAP 1keeA 55 :MTDPEMADATYIEP T0333 94 :RPL 1keeA 71 :WEV T0333 100 :TMALVDDYRPDLVVYEQGATVGLLAADRA 1keeA 74 :VRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1keeA 112 :GVT T0333 136 :NQSAW 1keeA 115 :MIGAT T0333 141 :RTRGMHRSIASFLTDL 1keeA 505 :LAGVREAEIRKLRDQY T0333 165 :PEPVATIESFPPSLL 1keeA 521 :DLHPVYKRVDTCAAE T0333 184 :PEGWFMRWVPYGGGAV 1keeA 536 :FATDTAYMYSTYEEEC T0333 204 :LPPV 1keeA 553 :ANPS T0333 210 :RPEVAITMGT 1keeA 559 :REKIMVLGGG T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLAL 1keeA 572 :IGQGIEFDYCCVHASLALREDGYETIMVN T0333 277 :T 1keeA 611 :D T0333 278 :CTAVVHHG 1keeA 613 :SDRLYFEP T0333 286 :GGGTVMTAIDAGIP 1keeA 622 :TLEDVLEIVRIEKP T0333 300 :QLLAPDPRD 1keeA 637 :GVIVQYGGQ T0333 309 :QFQHTAR 1keeA 647 :PLKLARA T0333 318 :VSRRGIG 1keeA 654 :LEAAGVP T0333 325 :LVST 1keeA 662 :IGTS T0333 334 :ADLLRRLIG 1keeA 666 :PDAIDRAED T0333 347 :RTAAREVREE 1keeA 675 :RERFQHAVER T0333 363 :PAETVRRIVERI 1keeA 697 :AIEMAVEKAKEI Number of specific fragments extracted= 25 number of extra gaps= 1 total=2600 Number of alignments=130 # 1keeA read from 1keeA/merged-good-all-a2m # found chain 1keeA in template set T0333 1 :M 1keeA 1 :M T0333 2 :LFVSSPGI 1keeA 12 :ILGAGPIV T0333 10 :GHL 1keeA 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHADRAAAAG 1keeA 28 :YSGAQACKALREEGYRVILVNSNPATIMTDPE T0333 45 :LEVVDVAPDYSA 1keeA 61 :ADATYIEPIHWE T0333 99 :GTMALVDDYRPDLVVYEQGATVGLLAADRA 1keeA 73 :VVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1keeA 112 :GVT T0333 135 :RNQSA 1keeA 115 :MIGAT T0333 140 :WRTRGMHRSIASFLT 1keeA 800 :TLSQEIQDVMRQQVQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=2609 Number of alignments=131 # 1keeA read from 1keeA/merged-good-all-a2m # found chain 1keeA in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1keeA)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1keeA)D558 T0333 1 :MLFVSSPGI 1keeA 10 :ILILGAGPI T0333 10 :GH 1keeA 21 :GQ T0333 12 :LFPLIQLAWGFRTAGHDVLIAV 1keeA 27 :DYSGAQACKALREEGYRVILVN T0333 34 :AEH 1keeA 51 :PAT T0333 39 :RAAAAG 1keeA 54 :IMTDPE T0333 45 :LEVVDVAPDY 1keeA 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1keeA 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GV 1keeA 112 :GV T0333 137 :QSAWRTRGMHRSIASFLT 1keeA 114 :TMIGATADAIDKAEDRRR T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1keeA 508 :VREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEEC T0333 203 :RLPPV 1keeA 552 :EANPS T0333 210 :RPEVAITMGTIELQAFGIGAVEPII 1keeA 559 :REKIMVLGGGPNRIGQGIEFDYCCV T0333 235 :AAAGEVDADFVLALGD 1keeA 587 :LALREDGYETIMVNCN T0333 279 :TAVVHHGGGGTVMTAIDAGIP 1keeA 615 :RLYFEPVTLEDVLEIVRIEKP T0333 300 :QLLAP 1keeA 637 :GVIVQ T0333 305 :DPRDQFQHTAREAVSRRGIGL 1keeA 643 :GGQTPLKLARALEAAGVPVIG T0333 329 :SD 1keeA 665 :SP T0333 335 :DLLRRLIGDESLRTAAREV 1keeA 667 :DAIDRAEDRERFQHAVERL T0333 360 :LPTPAETVRRIVER 1keeA 695 :VTAIEMAVEKAKEI Number of specific fragments extracted= 19 number of extra gaps= 1 total=2628 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1keeC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1keeC expands to /projects/compbio/data/pdb/1kee.pdb.gz 1keeC:Skipped atom 11370, because occupancy 0.500 <= existing 0.500 in 1keeC Skipped atom 11372, because occupancy 0.500 <= existing 0.500 in 1keeC Skipped atom 11374, because occupancy 0.500 <= existing 0.500 in 1keeC Skipped atom 11376, because occupancy 0.500 <= existing 0.500 in 1keeC Skipped atom 11378, because occupancy 0.500 <= existing 0.500 in 1keeC Skipped atom 11380, because occupancy 0.500 <= existing 0.500 in 1keeC Skipped atom 11382, because occupancy 0.500 <= existing 0.500 in 1keeC Skipped atom 18754, because occupancy 0.500 <= existing 0.500 in 1keeC Skipped atom 18756, because occupancy 0.500 <= existing 0.500 in 1keeC Skipped atom 18758, because occupancy 0.500 <= existing 0.500 in 1keeC Skipped atom 18760, because occupancy 0.500 <= existing 0.500 in 1keeC Skipped atom 18762, because occupancy 0.500 <= existing 0.500 in 1keeC # T0333 read from 1keeC/merged-good-all-a2m # 1keeC read from 1keeC/merged-good-all-a2m # adding 1keeC to template set # found chain 1keeC in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1keeC)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1keeC)D558 T0333 2 :LFVSSPGI 1keeC 10 :ILILGAGP T0333 10 :GHL 1keeC 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1keeC 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEHADRAAAA 1keeC 51 :PATIMTDPEM T0333 45 :LEVVDVAP 1keeC 61 :ADATYIEP T0333 93 :NRPL 1keeC 70 :HWEV T0333 100 :TMALVDDYRPDLVVYEQGATVGLLAADRA 1keeC 74 :VRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1keeC 112 :GVT T0333 135 :RNQSA 1keeC 115 :MIGAT T0333 141 :RTRGMHRSIASFLTDL 1keeC 505 :LAGVREAEIRKLRDQY T0333 165 :PEPVATIESFPPSLL 1keeC 521 :DLHPVYKRVDTCAAE T0333 199 :V 1keeC 536 :F T0333 200 :LGDR 1keeC 547 :YEEE T0333 204 :LPPV 1keeC 553 :ANPS T0333 210 :RPEVAITMGT 1keeC 559 :REKIMVLGGG T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1keeC 572 :IGQGIEFDYCCVHASLALREDGYETIMVNCNPE T0333 275 :LRTCTAVVHHG 1keeC 610 :YDTSDRLYFEP T0333 286 :GGGTVMTAIDAGIP 1keeC 622 :TLEDVLEIVRIEKP T0333 300 :QLLAPDPRD 1keeC 637 :GVIVQYGGQ T0333 309 :QFQHTAR 1keeC 647 :PLKLARA T0333 318 :VSRRGIG 1keeC 654 :LEAAGVP T0333 325 :LVST 1keeC 662 :IGTS T0333 334 :ADLLRRLIG 1keeC 666 :PDAIDRAED T0333 347 :RTAAREVREE 1keeC 675 :RERFQHAVER T0333 363 :PAETVRRIVERI 1keeC 697 :AIEMAVEKAKEI Number of specific fragments extracted= 25 number of extra gaps= 1 total=2653 Number of alignments=133 # 1keeC read from 1keeC/merged-good-all-a2m # found chain 1keeC in template set T0333 2 :LF 1keeC 12 :IL T0333 6 :SPGI 1keeC 16 :GPIV T0333 10 :GHL 1keeC 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHADRAAAAG 1keeC 28 :YSGAQACKALREEGYRVILVNSNPATIMTDPE T0333 45 :LEVVDVAPDYS 1keeC 61 :ADATYIEPIHW T0333 98 :DGTMALVDDYRPDLVVYEQGATVGLLAADRA 1keeC 72 :EVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1keeC 112 :GVT T0333 135 :RNQSA 1keeC 115 :MIGAT T0333 140 :WRTRGMHRSIASFLTDLM 1keeC 800 :TLSQEIQDVMRQQVQKLA T0333 168 :VATI 1keeC 874 :LAEQ T0333 173 :SFPPSLLL 1keeC 878 :GVTKEVIP T0333 186 :GWFMRWVPYGGGAVLGDRLPPVP 1keeC 886 :PYYSVKEVVLPFNKFPGVDPLLG T0333 209 :ARPEVAITM 1keeC 941 :KHGRALLSV T0333 223 :QAFGIGAVEPIIAAAGEVDADFVL 1keeC 950 :REGDKERVVDLAAKLLKQGFELDA T0333 250 :D 1keeC 985 :G T0333 261 :RNVRAVGWT 1keeC 986 :INPRLVNKV T0333 271 :LHTLLR 1keeC 1001 :IQDRIK T0333 277 :TCTAVVHHG 1keeC 1009 :EYTYIINTT T0333 286 :GGGT 1keeC 1019 :GRRA T0333 308 :DQF 1keeC 1025 :DSR T0333 313 :TAREAVSRRGIGLV 1keeC 1028 :VIRRSALQYKVHYD Number of specific fragments extracted= 21 number of extra gaps= 0 total=2674 Number of alignments=134 # 1keeC read from 1keeC/merged-good-all-a2m # found chain 1keeC in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1keeC)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1keeC)D558 T0333 1 :MLFVSSPGI 1keeC 10 :ILILGAGPI T0333 10 :GH 1keeC 21 :GQ T0333 12 :LFPLIQLAWGFRTAGHDVLIAV 1keeC 27 :DYSGAQACKALREEGYRVILVN T0333 34 :AEHA 1keeC 51 :PATI T0333 40 :A 1keeC 55 :M T0333 45 :LEVVDVAPDY 1keeC 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1keeC 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GV 1keeC 112 :GV T0333 137 :QSAWRTRGMHRSIAS 1keeC 114 :TMIGATADAIDKAED T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1keeC 508 :VREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEEC T0333 203 :RLPPV 1keeC 552 :EANPS T0333 210 :RPEVAITMGTIELQAFGIGAVEPIIA 1keeC 559 :REKIMVLGGGPNRIGQGIEFDYCCVH T0333 236 :AAGEVDADFVLALGD 1keeC 588 :ALREDGYETIMVNCN T0333 251 :LDISPL 1keeC 608 :TDYDTS T0333 264 :RAVGWTPLHTLL 1keeC 616 :LYFEPVTLEDVL T0333 276 :RTCTAVVHHGGGGTV 1keeC 633 :EKPKGVIVQYGGQTP T0333 310 :FQHTAREAVSRRGIGL 1keeC 648 :LKLARALEAAGVPVIG T0333 329 :SDK 1keeC 665 :SPD T0333 336 :LLRRLIGDESLRTAAREV 1keeC 668 :AIDRAEDRERFQHAVERL T0333 360 :LPTPAETVRRIVER 1keeC 695 :VTAIEMAVEKAKEI Number of specific fragments extracted= 20 number of extra gaps= 1 total=2694 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1keeE/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1keeE expands to /projects/compbio/data/pdb/1kee.pdb.gz 1keeE:Skipped atom 23343, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 23345, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 23347, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 23349, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 23351, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 23705, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 23707, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 23709, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 23711, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 23713, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 27244, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 27246, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 27248, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 27250, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 27252, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29428, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29430, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29432, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29434, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29436, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29527, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29529, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29531, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29533, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29535, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29760, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29762, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29764, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29766, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29768, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29770, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29772, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29820, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29822, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29824, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29826, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29828, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29830, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29832, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29867, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29869, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29871, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29873, because occupancy 0.500 <= existing 0.500 in 1keeE Skipped atom 29875, because occupancy 0.500 <= existing 0.500 in 1keeE # T0333 read from 1keeE/merged-good-all-a2m # 1keeE read from 1keeE/merged-good-all-a2m # adding 1keeE to template set # found chain 1keeE in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1keeE)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1keeE)D558 T0333 2 :LFVSSPGI 1keeE 10 :ILILGAGP T0333 10 :GHL 1keeE 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1keeE 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEHADRAAAA 1keeE 51 :PATIMTDPEM T0333 45 :LEVVDVAP 1keeE 61 :ADATYIEP T0333 94 :RPL 1keeE 71 :WEV T0333 100 :TMALVDDYRPDLVVYEQGATVGLLAADRA 1keeE 74 :VRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1keeE 112 :GVT T0333 135 :RNQSAW 1keeE 115 :MIGATA T0333 141 :RTRGMHRSIASFLTDL 1keeE 505 :LAGVREAEIRKLRDQY T0333 165 :PEPVATIESFPPSLL 1keeE 521 :DLHPVYKRVDTCAAE T0333 183 :EPE 1keeE 536 :FAT T0333 187 :WFMRWVPYGGGAV 1keeE 539 :DTAYMYSTYEEEC T0333 203 :RLPPV 1keeE 552 :EANPS T0333 210 :RPEVAITMG 1keeE 559 :REKIMVLGG T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1keeE 572 :IGQGIEFDYCCVHASLALREDGYETIMVNCNPE T0333 275 :LRTCTAVVHHG 1keeE 610 :YDTSDRLYFEP T0333 286 :GGGTVMTAIDAGIP 1keeE 622 :TLEDVLEIVRIEKP T0333 300 :QLLAPDPRD 1keeE 637 :GVIVQYGGQ T0333 309 :QFQHTAR 1keeE 647 :PLKLARA T0333 318 :VSRRGIG 1keeE 654 :LEAAGVP T0333 325 :LVST 1keeE 662 :IGTS T0333 334 :ADLLRRLIG 1keeE 666 :PDAIDRAED T0333 347 :RTAAREVREE 1keeE 675 :RERFQHAVER T0333 362 :TPAETVRRIVERI 1keeE 696 :TAIEMAVEKAKEI Number of specific fragments extracted= 25 number of extra gaps= 1 total=2719 Number of alignments=136 # 1keeE read from 1keeE/merged-good-all-a2m # found chain 1keeE in template set T0333 1 :M 1keeE 1 :M T0333 2 :LFVSSPGI 1keeE 12 :ILGAGPIV T0333 10 :GHL 1keeE 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHADRAAAAG 1keeE 28 :YSGAQACKALREEGYRVILVNSNPATIMTDPE T0333 45 :LEVVDVAPDYSA 1keeE 61 :ADATYIEPIHWE T0333 99 :GTMALVDDYRPDLVVYEQGATVGLLAADRA 1keeE 73 :VVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1keeE 112 :GVT T0333 135 :RNQSA 1keeE 115 :MIGAT T0333 362 :TPAETVRRIVER 1keeE 697 :AIEMAVEKAKEI Number of specific fragments extracted= 9 number of extra gaps= 0 total=2728 Number of alignments=137 # 1keeE read from 1keeE/merged-good-all-a2m # found chain 1keeE in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1keeE)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1keeE)D558 T0333 1 :MLFVSSPGI 1keeE 10 :ILILGAGPI T0333 10 :GHL 1keeE 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1keeE 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEHA 1keeE 51 :PATI T0333 45 :LEVVDVAPDY 1keeE 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1keeE 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GV 1keeE 112 :GV T0333 137 :QSAWRTRGMHRSIASFLT 1keeE 114 :TMIGATADAIDKAEDRRR T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1keeE 508 :VREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEEC T0333 203 :RLPPV 1keeE 552 :EANPS T0333 210 :RPEVAITMGTIELQAFGIGAVEPIIA 1keeE 559 :REKIMVLGGGPNRIGQGIEFDYCCVH T0333 236 :AAGEVDADFVLALGD 1keeE 588 :ALREDGYETIMVNCN T0333 251 :LDISPLGTLPR 1keeE 604 :ETVSTDYDTSD T0333 279 :TAVVHHGGGGTVMTAIDAGIP 1keeE 615 :RLYFEPVTLEDVLEIVRIEKP T0333 300 :QLLAP 1keeE 637 :GVIVQ T0333 305 :DPRDQFQHTAREAVSRRGIGL 1keeE 643 :GGQTPLKLARALEAAGVPVIG T0333 329 :SDK 1keeE 665 :SPD T0333 336 :LLRRLIGDESLRTAAREV 1keeE 668 :AIDRAEDRERFQHAVERL T0333 360 :LPTPAETVRRIVER 1keeE 695 :VTAIEMAVEKAKEI Number of specific fragments extracted= 19 number of extra gaps= 1 total=2747 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1keeG/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1keeG expands to /projects/compbio/data/pdb/1kee.pdb.gz 1keeG:# T0333 read from 1keeG/merged-good-all-a2m # 1keeG read from 1keeG/merged-good-all-a2m # adding 1keeG to template set # found chain 1keeG in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1keeG)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1keeG)D558 T0333 2 :LFVSSPGI 1keeG 10 :ILILGAGP T0333 10 :GHL 1keeG 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1keeG 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEHADRAAAA 1keeG 51 :PATIMTDPEM T0333 45 :LEVVDVAP 1keeG 61 :ADATYIEP T0333 94 :RPL 1keeG 71 :WEV T0333 100 :TMALVDDYRPDLVVYEQGATVGLLAADRA 1keeG 74 :VRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1keeG 112 :GVT T0333 136 :NQSAW 1keeG 115 :MIGAT T0333 141 :RTRGMHRSIASFLTDL 1keeG 505 :LAGVREAEIRKLRDQY T0333 165 :PEPVATIESFPPSLL 1keeG 521 :DLHPVYKRVDTCAAE T0333 184 :PEGWFMRWVPYGGGAV 1keeG 536 :FATDTAYMYSTYEEEC T0333 203 :RLPPV 1keeG 552 :EANPS T0333 210 :RPEVAITMGT 1keeG 559 :REKIMVLGGG T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1keeG 572 :IGQGIEFDYCCVHASLALREDGYETIMVNCNPE T0333 275 :LRTCTAVVHHG 1keeG 610 :YDTSDRLYFEP T0333 286 :GGGTVMTAIDAGIP 1keeG 622 :TLEDVLEIVRIEKP T0333 300 :QLLAPDPRD 1keeG 637 :GVIVQYGGQ T0333 309 :QFQHTAR 1keeG 647 :PLKLARA T0333 318 :VSRRGIG 1keeG 654 :LEAAGVP T0333 325 :LVST 1keeG 662 :IGTS T0333 334 :ADLLRRLIG 1keeG 666 :PDAIDRAED T0333 347 :RTAAREVREE 1keeG 675 :RERFQHAVER T0333 363 :PAETVRRIVERI 1keeG 697 :AIEMAVEKAKEI Number of specific fragments extracted= 24 number of extra gaps= 1 total=2771 Number of alignments=139 # 1keeG read from 1keeG/merged-good-all-a2m # found chain 1keeG in template set Warning: unaligning (T0333)L271 because of BadResidue code BAD_PEPTIDE in next template residue (1keeG)Q1002 Warning: unaligning (T0333)H272 because of BadResidue code BAD_PEPTIDE at template residue (1keeG)Q1002 T0333 2 :LFVSSPGI 1keeG 12 :ILGAGPIV T0333 10 :GHL 1keeG 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHADRAAAAG 1keeG 28 :YSGAQACKALREEGYRVILVNSNPATIMTDPE T0333 45 :LEVVDVAPDYSA 1keeG 61 :ADATYIEPIHWE T0333 99 :GTMALVDDYRPDLVVYEQGATVGLLAADRA 1keeG 73 :VVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1keeG 112 :GVT T0333 135 :RNQSA 1keeG 115 :MIGAT T0333 140 :WRTRGMHRSIASFLTDLM 1keeG 800 :TLSQEIQDVMRQQVQKLA T0333 172 :E 1keeG 875 :A T0333 173 :SFPPSLLL 1keeG 878 :GVTKEVIP T0333 186 :GWFMRWVPYGGGAVLGDRLPPVP 1keeG 886 :PYYSVKEVVLPFNKFPGVDPLLG T0333 209 :ARPEVAITM 1keeG 941 :KHGRALLSV T0333 223 :QAFGIGAVEPIIAAAGEVDADFVL 1keeG 950 :REGDKERVVDLAAKLLKQGFELDA T0333 261 :RNVRAVGWT 1keeG 986 :INPRLVNKV T0333 270 :P 1keeG 997 :G T0333 273 :TLLR 1keeG 1003 :DRIK T0333 277 :TCTAVVHHG 1keeG 1009 :EYTYIINTT T0333 286 :GGGT 1keeG 1019 :GRRA T0333 308 :DQF 1keeG 1025 :DSR T0333 313 :TAREAVSRRGIGLV 1keeG 1028 :VIRRSALQYKVHYD Number of specific fragments extracted= 20 number of extra gaps= 1 total=2791 Number of alignments=140 # 1keeG read from 1keeG/merged-good-all-a2m # found chain 1keeG in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1keeG)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1keeG)D558 T0333 1 :MLFVSSPGI 1keeG 10 :ILILGAGPI T0333 10 :GHL 1keeG 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1keeG 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEHADRAAA 1keeG 51 :PATIMTDPE T0333 45 :LEVVDVAPDY 1keeG 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1keeG 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GV 1keeG 112 :GV T0333 136 :NQ 1keeG 114 :TM T0333 139 :AWRTRGMHRSIASFLT 1keeG 116 :IGATADAIDKAEDRRR T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1keeG 508 :VREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEEC T0333 203 :RLPPV 1keeG 552 :EANPS T0333 210 :RPEVAITMGTIELQAFGIGAVEPII 1keeG 559 :REKIMVLGGGPNRIGQGIEFDYCCV T0333 235 :AAAGEVDADFVLALGD 1keeG 587 :LALREDGYETIMVNCN T0333 251 :LDIS 1keeG 608 :TDYD T0333 277 :TC 1keeG 612 :TS T0333 279 :TAVVHHGGGGTVMTAIDAGIP 1keeG 615 :RLYFEPVTLEDVLEIVRIEKP T0333 300 :QLLAP 1keeG 637 :GVIVQ T0333 305 :DPRDQFQHTAREAVSRRGIGL 1keeG 643 :GGQTPLKLARALEAAGVPVIG T0333 329 :SD 1keeG 665 :SP T0333 335 :DLLRRLIGDESLRTAAREV 1keeG 667 :DAIDRAEDRERFQHAVERL T0333 360 :LPTPAETVRRIVER 1keeG 695 :VTAIEMAVEKAKEI Number of specific fragments extracted= 21 number of extra gaps= 1 total=2812 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ihuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ihuA expands to /projects/compbio/data/pdb/1ihu.pdb.gz 1ihuA:# T0333 read from 1ihuA/merged-good-all-a2m # 1ihuA read from 1ihuA/merged-good-all-a2m # adding 1ihuA to template set # found chain 1ihuA in template set Warning: unaligning (T0333)E185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihuA)Q308 Warning: unaligning (T0333)G197 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihuA)Q308 Warning: unaligning (T0333)D252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihuA)N378 Warning: unaligning (T0333)C278 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihuA)T480 T0333 2 :LFVSS 1ihuA 11 :LFFTG T0333 7 :PGIGHLFPLIQLAWGFRTAGHDVLIAVAEHADRAAAA 1ihuA 17 :GGVGKTSISCATAIRLAEQGKRVLLVSTDPASNVGQV T0333 44 :GLEVVDVAP 1ihuA 59 :GNTIQAIAS T0333 53 :DYS 1ihuA 70 :GLS T0333 56 :AVKVFEQVAKDNP 1ihuA 150 :IRLLQLPGAWSSF T0333 141 :RTRGMHRSIASFLTDLMDKHQVSLPEPV 1ihuA 244 :ANDTLAAAIWEREQEALANLPADLAGLP T0333 169 :ATIESFPPSLL 1ihuA 273 :DTLFLQPVNMV T0333 180 :LEAEP 1ihuA 291 :LLSTQ T0333 198 :AV 1ihuA 309 :RP T0333 200 :LGD 1ihuA 322 :IAR T0333 209 :ARPEVAITMGTIELQ 1ihuA 325 :NEHGLIMLMGKGGVG T0333 226 :GIGAVEPIIAAAGEVDADFVLALGDL 1ihuA 340 :KTTMAAAIAVRLADMGFDVHLTTSDP T0333 253 :ISPLG 1ihuA 436 :IREAG T0333 261 :RNVRAVGWTP 1ihuA 441 :KRFVVMDTAP T0333 271 :LHTLLRT 1ihuA 454 :TLLLLDA T0333 297 :GIPQLLAPDP 1ihuA 490 :RTKVLLVTLP T0333 308 :DQFQHTAR 1ihuA 506 :EAANLQAD T0333 318 :VSRRGIG 1ihuA 514 :LERAGIH T0333 325 :LV 1ihuA 522 :WG T0333 327 :STSDKV 1ihuA 535 :TRSPLL T0333 338 :RRL 1ihuA 541 :RMR T0333 347 :RTAAREVREEMVA 1ihuA 544 :AQQELPQIESVKR T0333 360 :LPTPAETVRRIV 1ihuA 571 :EPTGIDKLKQLA Number of specific fragments extracted= 23 number of extra gaps= 0 total=2835 Number of alignments=142 # 1ihuA read from 1ihuA/merged-good-all-a2m # found chain 1ihuA in template set Warning: unaligning (T0333)D252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihuA)N378 T0333 2 :LFVSSPGI 1ihuA 11 :LFFTGKGG T0333 10 :GHLFPLIQLAWGFRTAGHDVLIAVAEHADRAAA 1ihuA 20 :GKTSISCATAIRLAEQGKRVLLVSTDPASNVGQ T0333 43 :AGLEVVDVAPDYSAVKVFEQVAKDNP 1ihuA 69 :PGLSALEIDPQAAAQQYRARIVDPIK T0333 78 :PAIDLEEWGVQ 1ihuA 95 :GVLPDDVVSSI T0333 89 :IAAVNRPLVD 1ihuA 120 :FDEFTGLLTD T0333 99 :GTMA 1ihuA 131 :SLLT T0333 106 :D 1ihuA 135 :R T0333 109 :PDLVVYEQGA 1ihuA 136 :FDHIIFDTAP T0333 119 :TVGLLAAD 1ihuA 147 :GHTIRLLQ T0333 136 :NQ 1ihuA 155 :LP T0333 140 :WRTRGMHRSIASFLTD 1ihuA 180 :EKQREQYAYAVEALSD T0333 156 :LMDKHQVSLPE 1ihuA 198 :RTRLVLVARLQ T0333 167 :PVATIE 1ihuA 211 :TLQEVA T0333 173 :SFP 1ihuA 226 :GLK T0333 191 :WVPYGGGAVLGDRLPPVP 1ihuA 229 :NQYLVINGVLPKTEAAND T0333 209 :ARPEVAITMGTIE 1ihuA 325 :NEHGLIMLMGKGG T0333 223 :QAF 1ihuA 338 :VGK T0333 228 :GAVEPIIAAAGEV 1ihuA 341 :TTMAAAIAVRLAD T0333 241 :DADFVLALGDL 1ihuA 355 :GFDVHLTTSDP T0333 254 :SPLGTLP 1ihuA 437 :REAGKRF T0333 271 :LHTLLR 1ihuA 481 :PMMLLQ T0333 277 :TCTAVVHHG 1ihuA 490 :RTKVLLVTL T0333 286 :GGGTVMTAIDAGI 1ihuA 507 :AANLQADLERAGI T0333 299 :PQLLAPDPR 1ihuA 523 :GWIINNSLS T0333 308 :DQFQHTAREAVSRRGI 1ihuA 544 :AQQELPQIESVKRQHA T0333 324 :GLVSTS 1ihuA 562 :VALVPV T0333 330 :DKVD 1ihuA 570 :SEPT T0333 334 :ADLLRRLI 1ihuA 575 :IDKLKQLA Number of specific fragments extracted= 28 number of extra gaps= 0 total=2863 Number of alignments=143 # 1ihuA read from 1ihuA/merged-good-all-a2m # found chain 1ihuA in template set Warning: unaligning (T0333)A150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihuA)A170 Warning: unaligning (T0333)A169 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihuA)Q308 Warning: unaligning (T0333)E181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihuA)Q308 Warning: unaligning (T0333)D252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihuA)N378 Warning: unaligning (T0333)R261 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihuA)N378 T0333 1 :MLFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAV 1ihuA 11 :LFFTGKGGVGKTSISCATAIRLAEQGKRVLLVS T0333 34 :A 1ihuA 46 :P T0333 37 :ADRAAA 1ihuA 47 :ASNVGQ T0333 43 :AGLEVVDVAPDYSAVKVFEQVAKDNPRFAETVATRPAIDLEEWGVQIAAVNRPLVDGTMA 1ihuA 69 :PGLSALEIDPQAAAQQYRARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLT T0333 103 :LVD 1ihuA 132 :LLT T0333 108 :RPDLVVYEQGAT 1ihuA 135 :RFDHIIFDTAPT T0333 120 :VGLLAA 1ihuA 149 :TIRLLQ T0333 130 :V 1ihuA 155 :L T0333 143 :RGMHRSI 1ihuA 156 :PGAWSSF T0333 155 :DLMDKHQVSLPEPV 1ihuA 282 :MVGVSALSRLLSTQ T0333 182 :AEPEGW 1ihuA 309 :RPDIPS T0333 203 :RLPPVPARPEVAITMGTIELQ 1ihuA 319 :VDDIARNEHGLIMLMGKGGVG T0333 226 :GIGAVEPIIAAAGEVDADFVLALGDL 1ihuA 340 :KTTMAAAIAVRLADMGFDVHLTTSDP T0333 262 :NV 1ihuA 379 :NL Number of specific fragments extracted= 14 number of extra gaps= 0 total=2877 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i24A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i24A expands to /projects/compbio/data/pdb/1i24.pdb.gz 1i24A:Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 269, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 271, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 273, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 275, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 277, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 310, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 376, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 378, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 380, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 382, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 384, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 386, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 388, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 390, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 392, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 394, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 396, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 398, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 400, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 402, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 404, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 406, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 408, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 410, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 412, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 414, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 416, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 487, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 519, because occupancy 0.200 <= existing 0.800 in 1i24A Skipped atom 521, because occupancy 0.200 <= existing 0.800 in 1i24A Skipped atom 563, because occupancy 0.300 <= existing 0.700 in 1i24A Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 727, because occupancy 0.400 <= existing 0.600 in 1i24A Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 916, because occupancy 0.200 <= existing 0.600 in 1i24A Skipped atom 917, because occupancy 0.200 <= existing 0.600 in 1i24A Skipped atom 1313, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 1317, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 1319, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 1321, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 1323, because occupancy 0.350 <= existing 0.650 in 1i24A Skipped atom 1392, because occupancy 0.450 <= existing 0.550 in 1i24A Skipped atom 1394, because occupancy 0.450 <= existing 0.550 in 1i24A Skipped atom 1396, because occupancy 0.450 <= existing 0.550 in 1i24A Skipped atom 1642, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 1644, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 1646, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 1648, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 1907, because occupancy 0.400 <= existing 0.600 in 1i24A Skipped atom 1909, because occupancy 0.400 <= existing 0.600 in 1i24A Skipped atom 1911, because occupancy 0.400 <= existing 0.600 in 1i24A Skipped atom 1913, because occupancy 0.400 <= existing 0.600 in 1i24A Skipped atom 1915, because occupancy 0.400 <= existing 0.600 in 1i24A Skipped atom 1917, because occupancy 0.400 <= existing 0.600 in 1i24A Skipped atom 2153, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2215, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2217, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2219, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2221, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2299, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2301, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2303, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2305, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2307, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2309, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2452, because occupancy 0.400 <= existing 0.600 in 1i24A Skipped atom 2721, because occupancy 0.400 <= existing 0.600 in 1i24A Skipped atom 2802, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2883, because occupancy 0.400 <= existing 0.600 in 1i24A Skipped atom 2968, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2970, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2972, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2974, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 2976, because occupancy 0.500 <= existing 0.500 in 1i24A Skipped atom 3143, because occupancy 0.400 <= existing 0.600 in 1i24A # T0333 read from 1i24A/merged-good-all-a2m # 1i24A read from 1i24A/merged-good-all-a2m # adding 1i24A to template set # found chain 1i24A in template set T0333 2 :LFVSS 1i24A 4 :VMVIG T0333 10 :GHLFPLIQLAWGFRTAGHDVLIAV 1i24A 9 :GDGYCGWATALHLSKKNYEVCIVD T0333 34 :AEHADRAAAAGLEV 1i24A 34 :LVRRLFDHQLGLES T0333 77 :RPAIDLEEWGVQIAAV 1i24A 49 :TPIASIHDRISRWKAL T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLA 1i24A 79 :FEFLAESFKSFEPDSVVHFGEQRSAPYS T0333 143 :RGMHRSIASF 1i24A 110 :RSRAVYTQHN T0333 153 :LTDLMDKHQVSLPEPVATIESFPPSLL 1i24A 124 :TLNVLFAIKEFGEECHLVKLGTMGEYG T0333 184 :PEGWFMRWVPYGGGAV 1i24A 153 :NIDIEEGYITITHNGR T0333 204 :LPPV 1i24A 174 :YPKQ T0333 218 :GTIELQAFGIGAVEPIIAAAGEVDADFV 1i24A 178 :ASSFYHLSKVHDSHNIAFTCKAWGIRAT T0333 246 :LAL 1i24A 212 :VYG T0333 250 :DLD 1i24A 216 :KTD T0333 253 :ISPLG 1i24A 223 :HEELR T0333 286 :GGGTVMTAIDAGIPQLLA 1i24A 239 :ALNRFCVQAAVGHPLTVY T0333 304 :PDPRDQFQHTAR 1i24A 266 :LDIRDTVQCVEI T0333 318 :VSR 1i24A 278 :AIA T0333 321 :RGIGLV 1i24A 285 :AGEFRV T0333 327 :STSDKV 1i24A 298 :FSVNEL T0333 347 :RTAAREVREE 1i24A 304 :ASLVTKAGSK T0333 357 :MVA 1i24A 342 :LME T0333 360 :LPT 1i24A 349 :PHY T0333 363 :PAETVRRIVERI 1i24A 353 :SDSLLDSLLNFA Number of specific fragments extracted= 22 number of extra gaps= 0 total=2899 Number of alignments=145 # 1i24A read from 1i24A/merged-good-all-a2m # found chain 1i24A in template set T0333 9 :IGHLFPLIQLAWGFRTAGHDVLIAVAEHADRA 1i24A 8 :GGDGYCGWATALHLSKKNYEVCIVDNLVRRLF T0333 41 :AAAGLEVVD 1i24A 41 :HQLGLESLT T0333 52 :PDYSAVKVFEQVAKDNPRFAETVATRPAIDL 1i24A 50 :PIASIHDRISRWKALTGKSIELYVGDICDFE T0333 99 :GTMALVDDYRPDLVVY 1i24A 81 :FLAESFKSFEPDSVVH T0333 115 :EQGA 1i24A 99 :EQRS T0333 119 :TVG 1i24A 104 :PYS T0333 123 :L 1i24A 107 :M T0333 141 :RTRGMHRSIASFLTDLM 1i24A 108 :IDRSRAVYTQHNNVIGT T0333 158 :DKHQVSLPEPVATIE 1i24A 139 :HLVKLGTMGEYGTPN T0333 173 :SFPPSLLLEAEPEGWFMRW 1i24A 155 :DIEEGYITITHNGRTDTLP T0333 205 :PPVP 1i24A 174 :YPKQ T0333 217 :MGTIE 1i24A 178 :ASSFY T0333 223 :QAFGIGAVEPIIAAAGEVDADFVLAL 1i24A 183 :HLSKVHDSHNIAFTCKAWGIRATDLN T0333 249 :G 1i24A 214 :G T0333 250 :DLDI 1i24A 216 :KTDE T0333 254 :SPLGTLP 1i24A 224 :EELRNRL T0333 286 :GGGTVMTAIDAGIPQLLAPDPR 1i24A 239 :ALNRFCVQAAVGHPLTVYGKGG T0333 308 :DQFQ 1i24A 270 :DTVQ T0333 313 :TAREAVSR 1i24A 274 :CVEIAIAN T0333 321 :RGIGLVSTS 1i24A 285 :AGEFRVFNQ T0333 347 :RTAAREVREEMVAL 1i24A 300 :VNELASLVTKAGSK T0333 361 :PTPAETVRRIVERI 1i24A 351 :YLSDSLLDSLLNFA Number of specific fragments extracted= 22 number of extra gaps= 0 total=2921 Number of alignments=146 # 1i24A read from 1i24A/merged-good-all-a2m # found chain 1i24A in template set T0333 1 :MLFV 1i24A 4 :VMVI T0333 9 :IGHLFPLIQLAWGFRTAGHDVLIAV 1i24A 8 :GGDGYCGWATALHLSKKNYEVCIVD T0333 34 :AEHADRAAAAGLEVV 1i24A 34 :LVRRLFDHQLGLESL T0333 51 :APDYSAVKVFEQVAKDNPRF 1i24A 49 :TPIASIHDRISRWKALTGKS T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLA 1i24A 79 :FEFLAESFKSFEPDSVVHFGEQRSAPYS T0333 140 :WRTRGMHRSIASFLT 1i24A 107 :MIDRSRAVYTQHNNV T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1i24A 126 :NVLFAIKEFGEECHLVKLGTMGEYGTPNIDIEEGYITITHNGRT T0333 218 :GTIELQAFGIGAVEPIIAAAGEVDADFVLALGD 1i24A 178 :ASSFYHLSKVHDSHNIAFTCKAWGIRATDLNQG T0333 251 :LDISPLGT 1i24A 217 :TDETEMHE T0333 259 :LP 1i24A 226 :LR T0333 267 :GWTPLHTLL 1i24A 228 :NRLDYDAVF T0333 286 :GGGTVMTAIDAGIPQLLAP 1i24A 239 :ALNRFCVQAAVGHPLTVYG T0333 305 :DPRDQFQHTAREAV 1i24A 267 :DIRDTVQCVEIAIA T0333 319 :SRRGIGLV 1i24A 285 :AGEFRVFN T0333 327 :STSDKVDADLLRRLIG 1i24A 297 :QFSVNELASLVTKAGS Number of specific fragments extracted= 15 number of extra gaps= 0 total=2936 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ff9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ff9A expands to /projects/compbio/data/pdb/1ff9.pdb.gz 1ff9A:# T0333 read from 1ff9A/merged-good-all-a2m # 1ff9A read from 1ff9A/merged-good-all-a2m # adding 1ff9A to template set # found chain 1ff9A in template set Warning: unaligning (T0333)G117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ff9A)F80 T0333 2 :LFVSSPGI 1ff9A 6 :VLMLGSGF T0333 15 :LIQLAWGFRTAGHDVLIAV 1ff9A 15 :TRPTLDVLTDSGIKVTVAC T0333 35 :EHADRAAAA 1ff9A 34 :RTLESAKKL T0333 44 :GLEVVDVAPDYS 1ff9A 48 :HSTPISLDVNDD T0333 98 :DGTMALVDDY 1ff9A 60 :AALDAEVAKH T0333 110 :DLVVYE 1ff9A 70 :DLVISL T0333 118 :ATVGLLAADRAGVPAVQRNQSAW 1ff9A 81 :HATVIKSAIRQKKHVVTTSYVSP T0333 141 :RTRGMHRSIASFLTDLMDKHQVSL 1ff9A 168 :LGYKFSWSSRGVLLALRNAASFYK T0333 168 :VATIESFPPSLL 1ff9A 192 :DGKVTNVAGPEL T0333 180 :LEAEPEGWFMR 1ff9A 210 :YFIYPGFAFVA T0333 192 :VPYGGGAVLGDRLPPVPARPEVAITMGTIELQ 1ff9A 221 :YPNRDSTPYKERYQIPEADNIVRGTLRYQGFP T0333 232 :PIIAAAGEVD 1ff9A 253 :QFIKVLVDIG T0333 248 :LGDLDISPLGT 1ff9A 264 :LSDEEQPFLKE T0333 269 :TPLHTLLRT 1ff9A 276 :IPWKEATQK T0333 318 :V 1ff9A 285 :I T0333 321 :RGIG 1ff9A 286 :VKAS T0333 327 :ST 1ff9A 291 :AS T0333 334 :ADLLRRLI 1ff9A 293 :EQDIVSTI T0333 342 :GDESLRTAAREVREEMV 1ff9A 307 :ESTEEQKRIVAGLKWLG T0333 360 :LPTPAETVRRIVERI 1ff9A 333 :RGNALDTLCATLEEK Number of specific fragments extracted= 20 number of extra gaps= 0 total=2956 Number of alignments=148 # 1ff9A read from 1ff9A/merged-good-all-a2m # found chain 1ff9A in template set Warning: unaligning (T0333)G117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ff9A)F80 T0333 10 :GHLFPLIQLAWGFRTAGHDVLIAV 1ff9A 10 :GSGFVTRPTLDVLTDSGIKVTVAC T0333 35 :EHADRAAA 1ff9A 34 :RTLESAKK T0333 43 :AGLEVVDVAPDYSA 1ff9A 47 :QHSTPISLDVNDDA T0333 99 :GTMALVDD 1ff9A 61 :ALDAEVAK T0333 109 :PDLVVY 1ff9A 69 :HDLVIS T0333 118 :ATVGLLAADRAGV 1ff9A 81 :HATVIKSAIRQKK T0333 132 :AVQRNQSA 1ff9A 94 :HVVTTSYV T0333 140 :WRTRGMHRSIASFLTDL 1ff9A 128 :GIDHLYAIKTIEEVHAA T0333 185 :EGWFMRWVPYGGGAVLGDRLPPVP 1ff9A 145 :GGKIKTFLSYCGGLPAPESSDNPL T0333 209 :ARPEVAITM 1ff9A 238 :ADNIVRGTL T0333 223 :QAFGIGAVEPIIAAAGE 1ff9A 247 :RYQGFPQFIKVLVDIGF T0333 248 :LGDLDISPLGTLP 1ff9A 264 :LSDEEQPFLKEAI T0333 270 :PLHTL 1ff9A 277 :PWKEA T0333 314 :AREAV 1ff9A 282 :TQKIV T0333 322 :GI 1ff9A 287 :KA T0333 328 :TS 1ff9A 289 :SS T0333 330 :DKVD 1ff9A 292 :SEQD T0333 334 :ADLLRRLIG 1ff9A 297 :VSTIVSNAT T0333 343 :DESLRTAAREVREEMV 1ff9A 308 :STEEQKRIVAGLKWLG T0333 361 :PTPAETVRRIVERIS 1ff9A 423 :PMNSKINDPLMKELK T0333 376 :G 1ff9A 441 :G Number of specific fragments extracted= 21 number of extra gaps= 0 total=2977 Number of alignments=149 # 1ff9A read from 1ff9A/merged-good-all-a2m # found chain 1ff9A in template set Warning: unaligning (T0333)G117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ff9A)F80 T0333 1 :MLFVSSPG 1ff9A 6 :VLMLGSGF T0333 14 :PLIQLAWGFRTAGHDVLIAV 1ff9A 14 :VTRPTLDVLTDSGIKVTVAC T0333 36 :HADRAAAAG 1ff9A 35 :TLESAKKLS T0333 45 :LEVVDVAPDYS 1ff9A 49 :STPISLDVNDD T0333 98 :DGTMALVD 1ff9A 60 :AALDAEVA T0333 108 :RPDLVVYEQ 1ff9A 68 :KHDLVISLI T0333 120 :VGLLAADRAGVPAVQRNQSAWRTRGMHRSIASFLT 1ff9A 83 :TVIKSAIRQKKHVVTTSYVSPAMMELDQAAKDAGI T0333 181 :EAEPEGWFMRWVPYGGGA 1ff9A 209 :PYFIYPGFAFVAYPNRDS T0333 199 :VLGDRLPPVPARPEVAITMGTIEL 1ff9A 228 :PYKERYQIPEADNIVRGTLRYQGF T0333 227 :IGAVEPIIA 1ff9A 252 :PQFIKVLVD T0333 240 :VD 1ff9A 261 :IG T0333 248 :LGDLDISPLGTLPR 1ff9A 264 :LSDEEQPFLKEAIP T0333 309 :QFQHTAREA 1ff9A 278 :WKEATQKIV T0333 327 :STSDKVDADLLRR 1ff9A 290 :SASEQDIVSTIVS T0333 342 :GDESLRTAAREVREEM 1ff9A 307 :ESTEEQKRIVAGLKWL Number of specific fragments extracted= 15 number of extra gaps= 0 total=2992 Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bisA/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/T0333/2bisA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0333/2bisA/merged-good-all-a2m.gz for input Trying 2bisA/merged-good-all-a2m Error: Couldn't open file 2bisA/merged-good-all-a2m or 2bisA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f6dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f6dA expands to /projects/compbio/data/pdb/1f6d.pdb.gz 1f6dA: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 92, because occupancy 0.500 <= existing 0.500 in 1f6dA Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 1f6dA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1f6dA Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 1f6dA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 1f6dA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M 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 # T0333 read from 1f6dA/merged-good-all-a2m # 1f6dA read from 1f6dA/merged-good-all-a2m # adding 1f6dA to template set # found chain 1f6dA in template set T0333 1 :M 1f6dA 1 :M T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAG 1f6dA 3 :VLTVFGTRPEAIKMAPLVHALAKDP T0333 27 :HDVLIAV 1f6dA 29 :FEAKVCV T0333 34 :AEHADRAAAA 1f6dA 37 :AQHREMLDQV T0333 66 :DNPRFAETVATRPAIDLEEWGVQIAAVNRPL 1f6dA 51 :SIVPDYDLNIMQPGQGLTEITCRILEGLKPI T0333 104 :VDDYRPDLVVYEQGA 1f6dA 82 :LAEFKPDVVLVHGDT T0333 119 :TVGLLAADRAGVPAVQRNQSAW 1f6dA 100 :LATSLAAFYQRIPVGHVEAGLR T0333 141 :RTRGMHRSIASFLTDLMD 1f6dA 123 :GDLYSPWPEEANRTLTGH T0333 166 :EPVATIESFPPSLLLEAEPE 1f6dA 141 :LAMYHFSPTETSRQNLLREN T0333 187 :WFMRWVPYGGGAV 1f6dA 161 :VADSRIFITGNTV T0333 200 :LGDRLPP 1f6dA 197 :NYPFIDP T0333 209 :ARPEVAITMGTIELQ 1f6dA 204 :DKKMILVTGHRRESF T0333 224 :AFGIGAVEPIIAAAGEVD 1f6dA 220 :RGFEEICHALADIATTHQ T0333 242 :ADFVLALG 1f6dA 239 :IQIVYPVH T0333 251 :L 1f6dA 248 :N T0333 254 :SPLGT 1f6dA 249 :PNVRE T0333 259 :LPRNVRAVGWT 1f6dA 261 :HVKNVILIDPQ T0333 270 :PLHTLLRTCTAVVHHGG 1f6dA 275 :PFVWLMNHAWLILTDSG T0333 288 :GTVMTAIDAGIPQLLAPDPRDQFQ 1f6dA 292 :GIQEEAPSLGKPVLVMRDTTERPE T0333 318 :VSRRGIG 1f6dA 316 :AVTAGTV T0333 325 :LV 1f6dA 324 :LV T0333 327 :STSDKV 1f6dA 327 :TDKQRI T0333 334 :ADLLRRLIGDESLRTAARE 1f6dA 333 :VEEVTRLLKDENEYQAMSR T0333 357 :MVALP 1f6dA 356 :YGDGQ T0333 363 :PAETVRRIVER 1f6dA 361 :ACSRILEALKN Number of specific fragments extracted= 25 number of extra gaps= 0 total=3017 Number of alignments=151 # 1f6dA read from 1f6dA/merged-good-all-a2m # found chain 1f6dA in template set T0333 1 :M 1f6dA 1 :M T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAG 1f6dA 3 :VLTVFGTRPEAIKMAPLVHALAKDP T0333 27 :HDVLIAVAE 1f6dA 29 :FEAKVCVTA T0333 52 :PDYSAVKVFEQV 1f6dA 38 :QHREMLDQVLKL T0333 65 :KDNPRFAETVATRPAIDLEEWGVQIAA 1f6dA 50 :FSIVPDYDLNIMQPGQGLTEITCRILE T0333 99 :GTMALVDDYRPDLVVYEQGA 1f6dA 77 :GLKPILAEFKPDVVLVHGDT T0333 119 :TVGLLAADRAGVPAVQRNQSA 1f6dA 100 :LATSLAAFYQRIPVGHVEAGL T0333 140 :WRTRGMHRSIASF 1f6dA 124 :DLYSPWPEEANRT T0333 153 :LTDLMDKHQVSLPEPVATIE 1f6dA 138 :TGHLAMYHFSPTETSRQNLL T0333 173 :SFPPS 1f6dA 160 :NVADS T0333 191 :WVPYGGGAV 1f6dA 165 :RIFITGNTV T0333 200 :LGDRLPPVPARPEVAITMG 1f6dA 194 :LAANYPFIDPDKKMILVTG T0333 219 :TIELQAFGIGAVEPIIAAAGEV 1f6dA 214 :RRESFGRGFEEICHALADIATT T0333 241 :DADFVLALG 1f6dA 238 :DIQIVYPVH T0333 250 :DLDI 1f6dA 248 :NPNV T0333 254 :SPLGTL 1f6dA 257 :RILGHV T0333 261 :RNVRAVGWTP 1f6dA 263 :KNVILIDPQE T0333 271 :LHTLLRTCTAVVHHGGGG 1f6dA 276 :FVWLMNHAWLILTDSGGI T0333 290 :VMTAIDAGIPQLLAPDPRDQF 1f6dA 294 :QEEAPSLGKPVLVMRDTTERP T0333 313 :TAR 1f6dA 315 :EAV T0333 320 :RRGIGLVSTSDKVD 1f6dA 318 :TAGTVRLVGTDKQR T0333 334 :ADLLRRLIGDESLRTAARE 1f6dA 333 :VEEVTRLLKDENEYQAMSR T0333 360 :LPTP 1f6dA 352 :AHNP T0333 366 :TVRRIVERISG 1f6dA 361 :ACSRILEALKN Number of specific fragments extracted= 24 number of extra gaps= 0 total=3041 Number of alignments=152 # 1f6dA read from 1f6dA/merged-good-all-a2m # found chain 1f6dA in template set T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAG 1f6dA 3 :VLTVFGTRPEAIKMAPLVHALAKDP T0333 27 :HDVLIAV 1f6dA 31 :AKVCVTA T0333 34 :AEHADRAAA 1f6dA 40 :REMLDQVLK T0333 43 :AGLEVVDVAPDYS 1f6dA 50 :FSIVPDYDLNIMQ T0333 66 :DNPRF 1f6dA 63 :PGQGL T0333 83 :E 1f6dA 68 :T T0333 91 :AVNRPLVDGTMALVDDYRPDLVVYEQGATVGL 1f6dA 69 :EITCRILEGLKPILAEFKPDVVLVHGDTTTTL T0333 123 :LAADRAGVPAVQRNQSAWRTRGMHRSIASFLT 1f6dA 104 :LAAFYQRIPVGHVEAGLRTGDLYSPWPEEANR T0333 185 :EGWFMRWVPYGGGA 1f6dA 162 :ADSRIFITGNTVID T0333 200 :LGDRL 1f6dA 194 :LAANY T0333 205 :PPVPARPEVAITMGTIELQ 1f6dA 200 :FIDPDKKMILVTGHRRESF T0333 226 :G 1f6dA 219 :G T0333 228 :GAVEPIIAAAGEV 1f6dA 220 :RGFEEICHALADI T0333 241 :DADFVLALGD 1f6dA 238 :DIQIVYPVHL T0333 251 :LDISPLGTLPRNVRAVGWTPLHTLL 1f6dA 253 :EPVNRILGHVKNVILIDPQEYLPFV T0333 276 :RTCTAVVHHGG 1f6dA 281 :NHAWLILTDSG T0333 293 :AIDAGIPQLLAPDPRDQF 1f6dA 297 :APSLGKPVLVMRDTTERP T0333 315 :REAVSRRGIGLV 1f6dA 315 :EAVTAGTVRLVG T0333 329 :SDKVDADLLRRLIGDESLR 1f6dA 328 :DKQRIVEEVTRLLKDENEY T0333 355 :EEMVALPTPA 1f6dA 347 :QAMSRAHNPY T0333 365 :ETVRRIVERIS 1f6dA 360 :QACSRILEALK Number of specific fragments extracted= 21 number of extra gaps= 0 total=3062 Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bfwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bfwA expands to /projects/compbio/data/pdb/2bfw.pdb.gz 2bfwA:Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 24, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 26, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 89, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 257, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 263, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 311, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 313, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 315, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 399, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 401, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 434, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 436, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 438, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 946, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 948, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 950, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 952, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1030, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1032, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1189, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1191, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1193, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1485, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1487, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1489, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1640, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1642, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1644, because occupancy 0.500 <= existing 0.500 in 2bfwA Skipped atom 1646, because occupancy 0.500 <= existing 0.500 in 2bfwA # T0333 read from 2bfwA/merged-good-all-a2m # 2bfwA read from 2bfwA/merged-good-all-a2m # adding 2bfwA to template set # found chain 2bfwA in template set Warning: unaligning (T0333)G196 because first residue in template chain is (2bfwA)G218 T0333 197 :GAV 2bfwA 219 :IDC T0333 200 :LGDRLPPV 2bfwA 225 :NESYLTGS T0333 209 :ARPEVAITMGTIELQAFGIGAVEPIIAAAGEVD 2bfwA 247 :DEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKK T0333 242 :ADFVLALGDLD 2bfwA 284 :MRFIIIGKGDP T0333 259 :LPRNVRAV 2bfwA 306 :KHGNVKVI T0333 267 :GWTP 2bfwA 315 :EMLS T0333 271 :LHTLLRTCTAVVHHG 2bfwA 322 :VRELYGSVDFVIIPS T0333 286 :G 2bfwA 342 :G T0333 288 :GTVMTAIDAGIPQLLAPDPR 2bfwA 343 :LVALEAMCLGAIPIASAVGG T0333 318 :VSR 2bfwA 363 :LRD T0333 321 :RGIG 2bfwA 369 :NETG T0333 325 :LV 2bfwA 374 :LV T0333 327 :STSDKV 2bfwA 378 :GDPGEL T0333 334 :ADLLRRLIG 2bfwA 384 :ANAILKALE T0333 343 :DES 2bfwA 394 :SRS T0333 346 :LRTAAREVREE 2bfwA 401 :FRENCKKRAMS Number of specific fragments extracted= 16 number of extra gaps= 0 total=3078 Number of alignments=154 # 2bfwA read from 2bfwA/merged-good-all-a2m # found chain 2bfwA in template set Warning: unaligning (T0333)A198 because first residue in template chain is (2bfwA)G218 T0333 199 :VLGDRLPPVP 2bfwA 219 :IDCSFWNESY T0333 209 :ARPEVAITMGTIELQAFGIGAVEPIIAAAGEV 2bfwA 247 :DEGVTFMFIGRFDRGQKGVDVLLKAIEILSSK T0333 241 :DADFVLALGDLDI 2bfwA 283 :EMRFIIIGKGDPE T0333 255 :PLGTLPRNVRAVGWT 2bfwA 302 :SLEEKHGNVKVITEM T0333 270 :P 2bfwA 318 :S T0333 271 :LHTLLRTCTAVVHHG 2bfwA 322 :VRELYGSVDFVIIPS T0333 286 :GGGTVMTAIDAGIPQLLAPDPR 2bfwA 341 :FGLVALEAMCLGAIPIASAVGG T0333 314 :AREAVSR 2bfwA 363 :LRDIITN T0333 322 :GIGLVSTS 2bfwA 370 :ETGILVKA T0333 330 :DKVD 2bfwA 379 :DPGE T0333 334 :ADLLRRLIG 2bfwA 384 :ANAILKALE T0333 343 :DESLRTAAREVREEMVA 2bfwA 394 :SRSDLSKFRENCKKRAM Number of specific fragments extracted= 12 number of extra gaps= 0 total=3090 Number of alignments=155 # 2bfwA read from 2bfwA/merged-good-all-a2m # found chain 2bfwA in template set Warning: unaligning (T0333)P361 because last residue in template chain is (2bfwA)S413 T0333 207 :VPARPEVAITMGTIELQAFGIGAVEPIIAAAGEVD 2bfwA 245 :GMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKK T0333 242 :ADFVLALGD 2bfwA 284 :MRFIIIGKG T0333 255 :PL 2bfwA 295 :EL T0333 257 :GTLPRNVRAVGWTP 2bfwA 304 :EEKHGNVKVITEML T0333 271 :LHTLLRTCTAVVHHG 2bfwA 322 :VRELYGSVDFVIIPS T0333 287 :GGTVMTAIDAGIPQLLAPD 2bfwA 342 :GLVALEAMCLGAIPIASAV T0333 311 :QHTARE 2bfwA 361 :GGLRDI T0333 319 :SRRGIGLVSTSDKVDADLLRRLIG 2bfwA 369 :NETGILVKAGDPGELANAILKALE T0333 343 :DESLRTAAREVREEMVAL 2bfwA 395 :RSDLSKFRENCKKRAMSF Number of specific fragments extracted= 9 number of extra gaps= 0 total=3099 Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cs0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cs0A expands to /projects/compbio/data/pdb/1cs0.pdb.gz 1cs0A:Skipped atom 218, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 220, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 4294, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 4296, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 7661, because occupancy 0.500 <= existing 1.000 in 1cs0A Skipped atom 7663, because occupancy 0.500 <= existing 1.000 in 1cs0A Skipped atom 7665, because occupancy 0.500 <= existing 1.000 in 1cs0A Skipped atom 7667, because occupancy 0.500 <= existing 1.000 in 1cs0A Skipped atom 7669, because occupancy 0.500 <= existing 1.000 in 1cs0A # T0333 read from 1cs0A/merged-good-all-a2m # 1cs0A read from 1cs0A/merged-good-all-a2m # adding 1cs0A to template set # found chain 1cs0A in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1cs0A)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1cs0A)D558 T0333 2 :LFVSSPGI 1cs0A 10 :ILILGAGP T0333 10 :GHL 1cs0A 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1cs0A 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEHADRAAAA 1cs0A 51 :PATIMTDPEM T0333 45 :LEVVDVAP 1cs0A 61 :ADATYIEP T0333 93 :NRPL 1cs0A 70 :HWEV T0333 100 :TMALVDDYRPDLVVYEQGATVGLLAADRA 1cs0A 74 :VRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1cs0A 112 :GVT T0333 136 :NQSAW 1cs0A 115 :MIGAT T0333 141 :RTRGMHRSIASFLTDL 1cs0A 505 :LAGVREAEIRKLRDQY T0333 165 :PEPVATI 1cs0A 521 :DLHPVYK T0333 172 :ESFPPSLL 1cs0A 529 :VDTCAAEF T0333 185 :EGWFMRWVPYGG 1cs0A 537 :ATDTAYMYSTYE T0333 202 :DR 1cs0A 549 :EE T0333 204 :LPPV 1cs0A 553 :ANPS T0333 210 :RPEVAITMGT 1cs0A 559 :REKIMVLGGG T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1cs0A 572 :IGQGIEFDYCCVHASLALREDGYETIMVNCNPE T0333 277 :T 1cs0A 611 :D T0333 278 :CTAVVHHG 1cs0A 613 :SDRLYFEP T0333 286 :GGGTVMTAIDAGIP 1cs0A 622 :TLEDVLEIVRIEKP T0333 300 :QLLAPDPRD 1cs0A 637 :GVIVQYGGQ T0333 309 :QFQHTAR 1cs0A 647 :PLKLARA T0333 318 :VSRRGIGLV 1cs0A 654 :LEAAGVPVI T0333 327 :ST 1cs0A 664 :TS T0333 334 :ADLLRRLIG 1cs0A 666 :PDAIDRAED T0333 347 :RTAAREVREE 1cs0A 675 :RERFQHAVER T0333 363 :PAETVRRIVERIS 1cs0A 697 :AIEMAVEKAKEIG Number of specific fragments extracted= 27 number of extra gaps= 1 total=3126 Number of alignments=157 # 1cs0A read from 1cs0A/merged-good-all-a2m # found chain 1cs0A in template set Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1cs0A)D558 Warning: unaligning (T0333)R354 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cs0A)V750 Warning: unaligning (T0333)E355 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cs0A)V750 T0333 2 :LFVSSPGI 1cs0A 12 :ILGAGPIV T0333 10 :GHL 1cs0A 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHADRAAAAG 1cs0A 28 :YSGAQACKALREEGYRVILVNSNPATIMTDPE T0333 45 :LEVVDVAPDYS 1cs0A 61 :ADATYIEPIHW T0333 98 :DGTMALVDDYRPDLVVYEQGATVGLLAADRA 1cs0A 72 :EVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1cs0A 112 :GVT T0333 135 :RNQSA 1cs0A 115 :MIGAT T0333 140 :WRTRGMHRSIASFLTDLM 1cs0A 479 :VGITGLNADFLRQLKRKG T0333 188 :FMRWVP 1cs0A 525 :VYKRVD T0333 198 :AVLGDR 1cs0A 531 :TCAAEF T0333 205 :PPVP 1cs0A 537 :ATDT T0333 210 :RPEVAITMGTIELQAFGIGA 1cs0A 559 :REKIMVLGGGPNRIGQGIEF T0333 230 :VEPIIAAAGEVDADFVLALGDLDI 1cs0A 582 :CVHASLALREDGYETIMVNCNPET T0333 261 :RNVRAVGWT 1cs0A 614 :DRLYFEPVT T0333 271 :LHTLLR 1cs0A 626 :VLEIVR T0333 277 :TCTAVVHHGGGGTVM 1cs0A 634 :KPKGVIVQYGGQTPL T0333 292 :TAIDAGIPQLLAPDPR 1cs0A 653 :ALEAAGVPVIGTSPDA T0333 308 :DQF 1cs0A 674 :DRE T0333 313 :TAREAVSRRG 1cs0A 677 :RFQHAVERLK T0333 323 :IGLVST 1cs0A 691 :ANATVT T0333 330 :DKVD 1cs0A 697 :AIEM T0333 334 :ADLLRRL 1cs0A 702 :VEKAKEI T0333 342 :GDESLRTAAREV 1cs0A 729 :YDEADLRRYFQT T0333 361 :P 1cs0A 799 :Y T0333 362 :TPAETVRRIVERIS 1cs0A 801 :LSQEIQDVMRQQVQ Number of specific fragments extracted= 25 number of extra gaps= 2 total=3151 Number of alignments=158 # 1cs0A read from 1cs0A/merged-good-all-a2m # found chain 1cs0A in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1cs0A)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1cs0A)D558 T0333 1 :MLFVSSPGI 1cs0A 10 :ILILGAGPI T0333 10 :GH 1cs0A 21 :GQ T0333 12 :LFPLIQLAWGFRTAGHDVLIAV 1cs0A 27 :DYSGAQACKALREEGYRVILVN T0333 34 :AEHA 1cs0A 51 :PATI T0333 40 :A 1cs0A 55 :M T0333 45 :LEVVDVAPDY 1cs0A 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1cs0A 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GV 1cs0A 112 :GV T0333 137 :QSAWRTRGMHRSIASFL 1cs0A 114 :TMIGATADAIDKAEDRR T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1cs0A 508 :VREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEEC T0333 203 :RLPPV 1cs0A 552 :EANPS T0333 210 :RPEVAITMGTIELQAFGIGAVEPIIA 1cs0A 559 :REKIMVLGGGPNRIGQGIEFDYCCVH T0333 236 :AAGEVDADFVLALGD 1cs0A 588 :ALREDGYETIMVNCN T0333 251 :LDISPLGTLPR 1cs0A 604 :ETVSTDYDTSD T0333 279 :TAVVHHGGGGTVMTAIDAGIP 1cs0A 615 :RLYFEPVTLEDVLEIVRIEKP T0333 300 :QLLAP 1cs0A 637 :GVIVQ T0333 305 :DPRDQFQHTAREAVSRRGIGL 1cs0A 643 :GGQTPLKLARALEAAGVPVIG T0333 329 :SD 1cs0A 665 :SP T0333 335 :DLLRRLIGDESLRTAAREV 1cs0A 667 :DAIDRAEDRERFQHAVERL T0333 360 :LPTPAETVRRIVER 1cs0A 695 :VTAIEMAVEKAKEI Number of specific fragments extracted= 20 number of extra gaps= 1 total=3171 Number of alignments=159 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uqtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1uqtA expands to /projects/compbio/data/pdb/1uqt.pdb.gz 1uqtA:# T0333 read from 1uqtA/merged-good-all-a2m # 1uqtA read from 1uqtA/merged-good-all-a2m # adding 1uqtA to template set # found chain 1uqtA in template set Warning: unaligning (T0333)P7 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uqtA)S19 Warning: unaligning (T0333)F22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1uqtA)G35 Warning: unaligning (T0333)D28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uqtA)G35 Warning: unaligning (T0333)E115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1uqtA)D130 Warning: unaligning (T0333)G218 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1uqtA)R262 Warning: unaligning (T0333)T219 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1uqtA)R262 T0333 8 :GIGHLFPLIQLAWG 1uqtA 20 :AGGLAVGILGALKA T0333 29 :VLIAV 1uqtA 36 :GLWFG T0333 34 :AEH 1uqtA 45 :TGN T0333 41 :AAAGLEVVD 1uqtA 48 :EDQPLKKVK T0333 51 :APDYSAVKVF 1uqtA 57 :KGNITWASFN T0333 61 :EQVAKDNP 1uqtA 69 :EQDLDEYY T0333 69 :RFAETVA 1uqtA 90 :YRLDLVQ T0333 81 :DLEEWGVQIAAVNRP 1uqtA 97 :FQRPAWDGYLRVNAL T0333 100 :TMALVDDY 1uqtA 112 :LADKLLPL T0333 108 :R 1uqtA 123 :D T0333 110 :DLVVY 1uqtA 124 :DIIWI T0333 116 :QGATVGLLAADRAGV 1uqtA 131 :YHLLPFAHELRKRGV T0333 131 :PAVQRNQSAW 1uqtA 148 :RIGFFLHIPF T0333 145 :MHRSIASFLTDLMDKHQVSL 1uqtA 185 :QTENDRLAFLDCLSNLTRVT T0333 165 :P 1uqtA 206 :R T0333 176 :PSLLLEAEPEGWFMR 1uqtA 207 :SAKSHTAWGKAFRTE T0333 192 :VPYGGGAV 1uqtA 222 :VYPIGIEP T0333 200 :LGDRL 1uqtA 247 :LKAEL T0333 209 :ARPEVAITM 1uqtA 252 :KNVQNIFSV T0333 220 :IELQAFGIGAVEPIIAAAGEV 1uqtA 263 :LDYSKGLPERFLAYEALLEKY T0333 242 :ADFVLALGDLD 1uqtA 290 :IRYTQIAPTSR T0333 254 :SPL 1uqtA 327 :LGW T0333 261 :RNVRAV 1uqtA 330 :TPLYYL T0333 267 :GWTPLHTLLRT 1uqtA 337 :QHFDRKLLMKI T0333 278 :CTAVVHHG 1uqtA 351 :SDVGLVTP T0333 286 :GG 1uqtA 362 :GM T0333 288 :GTVMTAIDAG 1uqtA 365 :LVAKEYVAAQ T0333 298 :IPQLLAPDPRDQFQHTAR 1uqtA 379 :PGVLVLSQFAGAANELTS T0333 324 :G 1uqtA 397 :A T0333 325 :LV 1uqtA 399 :IV T0333 327 :STSDKV 1uqtA 403 :YDRDEV T0333 334 :ADLLRRLIG 1uqtA 409 :AAALDRALT T0333 344 :ESLRTAAREVREEMVALP 1uqtA 421 :AERISRHAEMLDVIVKND T0333 364 :AETVRR 1uqtA 439 :INHWQE T0333 370 :IVERI 1uqtA 446 :FISDL Number of specific fragments extracted= 35 number of extra gaps= 3 total=3206 Number of alignments=160 # 1uqtA read from 1uqtA/merged-good-all-a2m # found chain 1uqtA in template set Warning: unaligning (T0333)P7 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uqtA)S19 Warning: unaligning (T0333)F22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1uqtA)G35 Warning: unaligning (T0333)D28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uqtA)G35 Warning: unaligning (T0333)Y114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1uqtA)D130 Warning: unaligning (T0333)E115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uqtA)D130 Warning: unaligning (T0333)G218 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1uqtA)R262 Warning: unaligning (T0333)T219 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1uqtA)R262 T0333 8 :GIGHLFPLIQLAWG 1uqtA 20 :AGGLAVGILGALKA T0333 29 :VLIAV 1uqtA 36 :GLWFG T0333 34 :AEHADRA 1uqtA 45 :TGNEDQP T0333 41 :AAAGLEVVDVAPDYSAVK 1uqtA 56 :KKGNITWASFNLSEQDLD T0333 59 :VFEQVAKDNPRFAETVATRPAIDLEEWGVQIAAVNR 1uqtA 75 :YYNQFSNAVLWPAFHYRLDLVQFQRPAWDGYLRVNA T0333 99 :GTMALVDD 1uqtA 111 :LLADKLLP T0333 107 :YRPDLVV 1uqtA 122 :DDDIIWI T0333 116 :QGATVGLLAADRAGVP 1uqtA 131 :YHLLPFAHELRKRGVN T0333 132 :AVQRNQSA 1uqtA 149 :IGFFLHIP T0333 140 :WRTRGMHRSIASFLTDL 1uqtA 163 :FNALPTYDTLLEQLCDY T0333 158 :DKHQVSLPEPVATIE 1uqtA 180 :DLLGFQTENDRLAFL T0333 173 :SFPP 1uqtA 199 :NLTR T0333 180 :LEAEPE 1uqtA 203 :VTTRSA T0333 186 :GWFMRWVPYGGGAVLG 1uqtA 214 :WGKAFRTEVYPIGIEP T0333 205 :PPVP 1uqtA 238 :GPLP T0333 209 :ARPEVAITM 1uqtA 252 :KNVQNIFSV T0333 220 :IE 1uqtA 263 :LD T0333 223 :QAFGIGAVEPIIAAAGEV 1uqtA 265 :YSKGLPERFLAYEALLEK T0333 241 :DADFVLALG 1uqtA 289 :KIRYTQIAP T0333 250 :DLDI 1uqtA 300 :RGDV T0333 254 :SP 1uqtA 328 :GW T0333 261 :RNVRAVGWT 1uqtA 330 :TPLYYLNQH T0333 270 :PLHTLLR 1uqtA 340 :DRKLLMK T0333 277 :TCTAVVHHG 1uqtA 350 :YSDVGLVTP T0333 286 :GGGTVMTAIDA 1uqtA 363 :MNLVAKEYVAA T0333 297 :GIPQLLAPDPR 1uqtA 378 :NPGVLVLSQFA T0333 308 :DQF 1uqtA 392 :NEL T0333 322 :GIGLVSTS 1uqtA 395 :TSALIVNP T0333 330 :DKVD 1uqtA 404 :DRDE T0333 334 :ADLLRRLIG 1uqtA 409 :AAALDRALT T0333 343 :DESLRTAAREVREEMVAL 1uqtA 420 :LAERISRHAEMLDVIVKN T0333 362 :TPAETVRRIVERIS 1uqtA 438 :DINHWQECFISDLK Number of specific fragments extracted= 32 number of extra gaps= 3 total=3238 Number of alignments=161 # 1uqtA read from 1uqtA/merged-good-all-a2m # found chain 1uqtA in template set Warning: unaligning (T0333)Y114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1uqtA)D130 Warning: unaligning (T0333)E115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uqtA)D130 Warning: unaligning (T0333)G218 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1uqtA)R262 Warning: unaligning (T0333)T219 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1uqtA)R262 T0333 48 :VDVAPDYSAVKVF 1uqtA 63 :ASFNLSEQDLDEY T0333 64 :AKDNPRFA 1uqtA 88 :FHYRLDLV T0333 73 :TVATRPAIDLEEWGVQIAAVNRPLVD 1uqtA 96 :QFQRPAWDGYLRVNALLADKLLPLLQ T0333 107 :YRPDLVV 1uqtA 122 :DDDIIWI T0333 116 :QGATVGLLAADRAGV 1uqtA 131 :YHLLPFAHELRKRGV T0333 131 :PAVQRNQSAWRTRGMHRSIASFLT 1uqtA 148 :RIGFFLHIPFPTPEIFNALPTYDT T0333 185 :EGWFMRWVPYGGGA 1uqtA 214 :WGKAFRTEVYPIGI T0333 199 :VLGDRL 1uqtA 239 :PLPPKL T0333 205 :PP 1uqtA 249 :AE T0333 208 :PARPEVAITM 1uqtA 251 :LKNVQNIFSV T0333 220 :IELQAFGIGAVEPIIAAAGEVD 1uqtA 263 :LDYSKGLPERFLAYEALLEKYP T0333 242 :ADFVLALGDLD 1uqtA 290 :IRYTQIAPTSR T0333 254 :SPL 1uqtA 301 :GDV T0333 264 :RAVGWTPLHTLL 1uqtA 333 :YYLNQHFDRKLL T0333 276 :RTCTAVVHH 1uqtA 349 :RYSDVGLVT T0333 285 :GGGGTVMTAIDA 1uqtA 362 :GMNLVAKEYVAA T0333 298 :IPQLLAPDP 1uqtA 379 :PGVLVLSQF T0333 318 :VSRRGIGLVSTSDKVDADLLRRLIG 1uqtA 393 :ELTSALIVNPYDRDEVAAALDRALT T0333 344 :ESLRTAAREVREEMVAL 1uqtA 421 :AERISRHAEMLDVIVKN T0333 362 :TPAETVRRIVERI 1uqtA 438 :DINHWQECFISDL Number of specific fragments extracted= 20 number of extra gaps= 2 total=3258 Number of alignments=162 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jixA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0333 read from 1jixA/merged-good-all-a2m # 1jixA read from 1jixA/merged-good-all-a2m # found chain 1jixA in training set T0333 1 :M 1jixA 1 :M T0333 2 :LFVSSPGI 1jixA 3 :IAIINMGN T0333 11 :HLFPLIQLAWGFRTAGHDVLIAVAEH 1jixA 19 :PSSETIYLFKVISEMGLNVDIISLKN T0333 45 :LEVVDVAPDYSAVKVF 1jixA 45 :GVYTKSFDEVDVNDYD T0333 110 :DLVVYEQGA 1jixA 61 :RLIVVNSSI T0333 120 :VGLLAADRAGVPAVQRNQSAW 1jixA 82 :SAQKFMAKYKSKIYYLFTDIR T0333 143 :RGMH 1jixA 138 :GINL T0333 151 :SFLTDLMDK 1jixA 142 :DIAKAAHKK T0333 164 :LPEPVATIESFPPSLLLEAEPEGWFMR 1jixA 151 :VDNVIEFEYFPIEQYKIHMNDFQLSKP T0333 209 :ARPEVAITMGTIELQAFGIGAV 1jixA 178 :TKKTLDVIYGGSFRSGQRESKM T0333 234 :IAAAGEVDADFVLA 1jixA 200 :VEFLFDTGLNIEFF T0333 249 :GDLDISPLGT 1jixA 214 :GNAREKQFKN T0333 259 :LPRNVRAVGWTPLHTLLRT 1jixA 228 :WTKAPVFTGKIPMNMVSEK T0333 278 :CTAVVHHG 1jixA 250 :AIAALIIG T0333 288 :GTVMTAIDAGIPQLLA 1jixA 268 :LRVWETMASDAVMLID T0333 315 :R 1jixA 291 :R T0333 325 :LV 1jixA 292 :II T0333 327 :STSDKV 1jixA 301 :NNRAEL T0333 334 :ADLLRRLIGDES 1jixA 307 :IDRVNELKHSDV T0333 346 :LRTAAREVREEMVALPTPAETVRRIVERI 1jixA 320 :RKEMLSIQHDILNKTRAKKAEWQDAFKKA Number of specific fragments extracted= 20 number of extra gaps= 0 total=3278 Number of alignments=163 # 1jixA read from 1jixA/merged-good-all-a2m # found chain 1jixA in training set T0333 10 :GHLFPLIQLAWGFRTAGHDVLIAVAE 1jixA 18 :VPSSETIYLFKVISEMGLNVDIISLK T0333 65 :KD 1jixA 44 :NG T0333 72 :ETVATRPAIDLEE 1jixA 46 :VYTKSFDEVDVND T0333 109 :P 1jixA 59 :Y T0333 110 :DLVVYE 1jixA 61 :RLIVVN T0333 117 :GA 1jixA 77 :NL T0333 119 :TVGLLAADRAGVPAVQRNQSA 1jixA 81 :LSAQKFMAKYKSKIYYLFTDI T0333 140 :WRTRGM 1jixA 116 :PWAYLY T0333 158 :DKHQVSLPEPVATIE 1jixA 131 :PIKVISQGINLDIAK T0333 173 :SFPPS 1jixA 149 :KKVDN T0333 191 :WVPYGGGAVLG 1jixA 154 :VIEFEYFPIEQ T0333 202 :DRLPPVP 1jixA 170 :NDFQLSK T0333 209 :ARPEVAITMGTIE 1jixA 179 :KKTLDVIYGGSFR T0333 223 :QAFGIGAVEPIIAAA 1jixA 192 :SGQRESKMVEFLFDT T0333 241 :DADFVLALG 1jixA 207 :GLNIEFFGN T0333 250 :DLDISPLGTLP 1jixA 217 :REKQFKNPKYP T0333 261 :RNVRAVGWTPLHTLLR 1jixA 230 :KAPVFTGKIPMNMVSE T0333 277 :TCTAVVHHG 1jixA 249 :QAIAALIIG T0333 286 :GGGTVMTAIDAGIPQLLA 1jixA 266 :ITLRVWETMASDAVMLID T0333 304 :PDPR 1jixA 294 :NDAR T0333 325 :LVST 1jixA 298 :FYVN T0333 330 :DKVD 1jixA 302 :NRAE T0333 334 :ADLLRRLIGDESLRTAAREVREEMVALP 1jixA 307 :IDRVNELKHSDVLRKEMLSIQHDILNKT T0333 362 :TPAETVRRIVERIS 1jixA 337 :KKAEWQDAFKKAID Number of specific fragments extracted= 24 number of extra gaps= 0 total=3302 Number of alignments=164 # 1jixA read from 1jixA/merged-good-all-a2m # found chain 1jixA in training set T0333 1 :MLFVSSPG 1jixA 3 :IAIINMGN T0333 11 :HLFPLIQLAWGFRTAGHDVLIAV 1jixA 19 :PSSETIYLFKVISEMGLNVDIIS T0333 44 :GLEVVDVAPDYSAVKVF 1jixA 44 :NGVYTKSFDEVDVNDYD T0333 110 :DLVVYEQ 1jixA 61 :RLIVVNS T0333 117 :GATVGLLAADRAGVPAVQRNQSAWRTRGMHRSIASFLT 1jixA 79 :AILSAQKFMAKYKSKIYYLFTDIRLPFSQSWPNVKNRP T0333 155 :DLMDKHQVSLPEPVATIESFPP 1jixA 119 :YLYTEEELLIKSPIKVISQGIN T0333 182 :AEPEGWFMRWVPYGGGA 1jixA 148 :HKKVDNVIEFEYFPIEQ T0333 199 :VLGDRLPPVPARPEVAITMGTIELQAFGIGA 1jixA 168 :HMNDFQLSKPTKKTLDVIYGGSFRSGQRESK T0333 233 :IIAAAGEVDADFVLA 1jixA 199 :MVEFLFDTGLNIEFF T0333 249 :GDLDISPL 1jixA 214 :GNAREKQF T0333 257 :GTLPRNVRAVGWTPLHTLL 1jixA 226 :YPWTKAPVFTGKIPMNMVS T0333 276 :RTCTAVVHHGG 1jixA 248 :SQAIAALIIGD T0333 287 :GGTVMTAIDAGIPQLLA 1jixA 267 :TLRVWETMASDAVMLID T0333 324 :GL 1jixA 291 :RI T0333 327 :STSDKVDADLLRRLIGD 1jixA 300 :VNNRAELIDRVNELKHS T0333 344 :ESLRTAAREVREEMVALP 1jixA 318 :VLRKEMLSIQHDILNKTR T0333 362 :TPAETVRRIVERIS 1jixA 337 :KKAEWQDAFKKAID Number of specific fragments extracted= 17 number of extra gaps= 0 total=3319 Number of alignments=165 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rzuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rzuA expands to /projects/compbio/data/pdb/1rzu.pdb.gz 1rzuA:# T0333 read from 1rzuA/merged-good-all-a2m # 1rzuA read from 1rzuA/merged-good-all-a2m # adding 1rzuA to template set # found chain 1rzuA in template set T0333 1 :M 1rzuA 1 :M T0333 2 :LFVSS 1rzuA 3 :VLSVS T0333 8 :GIGHLFPLIQLAWGFRTAGHDVLIAVAEHADRAAAA 1rzuA 16 :TGGLADVVGALPIALEAHGVRTRTLIPGYPAVKAAV T0333 51 :APDYSAVKVFEQVAKDNPRFAETVATRP 1rzuA 75 :HERLDLLILDAPAYYERSGGPYLGQTGK T0333 81 :DLEEWGVQIAAVNRPLV 1rzuA 103 :DYPDNWKRFAALSLAAA T0333 102 :ALVDDY 1rzuA 120 :RIGAGV T0333 108 :RPDLVVYE 1rzuA 130 :RPDMVHAH T0333 116 :QGATVGLLAADRAG 1rzuA 139 :WQAAMTPVYMRYAE T0333 130 :VPAVQRNQSAW 1rzuA 156 :IPSLLTIHNIA T0333 141 :RTRGMHRSIASFLTDL 1rzuA 222 :LTAEFGMGLEGVIGSR T0333 161 :Q 1rzuA 238 :A T0333 166 :EPVATIESFPPSLLLEAEPEGWFMRWVPYGGGAV 1rzuA 239 :HVLHGIVNGIDADVWNPATDHLIHDNYSAANLKN T0333 200 :LGDRLPPVPARPEVAITMGTIELQAF 1rzuA 280 :VAEHFRIDDDGSPLFCVISRLTWQKG T0333 230 :VEPIIAAAG 1rzuA 306 :IDLMAEAVD T0333 239 :EVDADFVLALGDLD 1rzuA 318 :SLGGRLVVLGAGDV T0333 253 :ISPLG 1rzuA 341 :ASRHH T0333 261 :RNVRAV 1rzuA 346 :GRVGVA T0333 267 :GWT 1rzuA 353 :GYN T0333 270 :PLHTLLRT 1rzuA 357 :PLSHLMQA T0333 278 :CTAVVHHG 1rzuA 366 :CDAIIIPS T0333 286 :G 1rzuA 379 :G T0333 288 :GTVMTAIDAGIPQLLAPDPR 1rzuA 380 :LTQLYALRYGCIPVVARTGG T0333 308 :DQFQHTAREAVSRRGIG 1rzuA 402 :DTVIDANHAALASKAAT T0333 325 :LV 1rzuA 420 :VQ T0333 327 :STSDKV 1rzuA 425 :VTLDGL T0333 334 :ADLLRRLI 1rzuA 431 :KQAIRRTV T0333 342 :GDESLRTAA 1rzuA 442 :HDPKLWTQM T0333 354 :REEMVALPTPAETVRRIVERI 1rzuA 451 :QKLGMKSDVSWEKSAGLYAAL Number of specific fragments extracted= 28 number of extra gaps= 0 total=3347 Number of alignments=166 # 1rzuA read from 1rzuA/merged-good-all-a2m # found chain 1rzuA in template set T0333 1 :M 1rzuA 1 :M T0333 2 :LFV 1rzuA 3 :VLS T0333 5 :SSPGIGHLFPLIQLAWGFRTAGHDVLIAVAEHADRAAA 1rzuA 13 :LIKTGGLADVVGALPIALEAHGVRTRTLIPGYPAVKAA T0333 43 :AGLEVVDVAPDY 1rzuA 76 :ERLDLLILDAPA T0333 65 :KDNPRFAETVATRPAIDLEEWGVQIAAVN 1rzuA 88 :YYERSGGPYLGQTGKDYPDNWKRFAALSL T0333 99 :GTMALVDD 1rzuA 117 :AAARIGAG T0333 107 :YRPDLVVYE 1rzuA 129 :WRPDMVHAH T0333 116 :QGATVGLLAADRAG 1rzuA 139 :WQAAMTPVYMRYAE T0333 130 :VPAVQRNQSA 1rzuA 156 :IPSLLTIHNI T0333 149 :IASFLTDLMDKHQVSLPEPVATIE 1rzuA 199 :FLKGGLQTATALSTVSPSYAEEIL T0333 173 :SFPPS 1rzuA 235 :GSRAH T0333 191 :WVPYGGGAVLGDRLPPVP 1rzuA 240 :VLHGIVNGIDADVWNPAT T0333 209 :ARPEVAITMGTIE 1rzuA 289 :DGSPLFCVISRLT T0333 223 :QAFGIGAVEPIIAAAGEVDADFVLALGDLDI 1rzuA 302 :WQKGIDLMAEAVDEIVSLGGRLVVLGAGDVA T0333 254 :SPLG 1rzuA 342 :SRHH T0333 261 :RNVRA 1rzuA 346 :GRVGV T0333 266 :VGWT 1rzuA 352 :IGYN T0333 270 :PLHTLLR 1rzuA 357 :PLSHLMQ T0333 277 :TCTAVVHHG 1rzuA 365 :GCDAIIIPS T0333 286 :GGGTVMTAIDAGIPQLLAPDPR 1rzuA 378 :CGLTQLYALRYGCIPVVARTGG T0333 314 :AREAVSR 1rzuA 400 :LADTVID T0333 323 :IGLVSTS 1rzuA 418 :TGVQFSP T0333 330 :DKVD 1rzuA 426 :TLDG T0333 334 :ADLLRRLIG 1rzuA 431 :KQAIRRTVR T0333 343 :DESLRTAAREVR 1rzuA 443 :DPKLWTQMQKLG T0333 358 :VALP 1rzuA 455 :MKSD T0333 362 :TPAETVRRIVERIS 1rzuA 460 :SWEKSAGLYAALYS Number of specific fragments extracted= 27 number of extra gaps= 0 total=3374 Number of alignments=167 # 1rzuA read from 1rzuA/merged-good-all-a2m # found chain 1rzuA in template set T0333 1 :MLFVSSPGI 1rzuA 3 :VLSVSSEIY T0333 10 :GHLFPLIQLAWGFRTAGHDVLIAV 1rzuA 18 :GLADVVGALPIALEAHGVRTRTLI T0333 34 :AEHADRA 1rzuA 45 :PAVKAAV T0333 65 :KDNPRFAETVATRPAIDLEEWGVQIAAVNRPLVD 1rzuA 94 :GPYLGQTGKDYPDNWKRFAALSLAAARIGAGVLP T0333 106 :DYRPDLVVYEQGAT 1rzuA 128 :GWRPDMVHAHDWQA T0333 120 :VGLLAADRAG 1rzuA 143 :MTPVYMRYAE T0333 130 :VPAVQRNQSAWRTRGMHRSIASFLT 1rzuA 156 :IPSLLTIHNIAFQGQFGANIFSKLA T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPY 1rzuA 228 :MGLEGVIGSRAHVLHGIVNGIDADVWNPATDHLIHDNYSA T0333 199 :VLGDRLPPVPARPEVAITMGTIELQ 1rzuA 279 :AVAEHFRIDDDGSPLFCVISRLTWQ T0333 225 :FGIGAVEPIIAAAGEVDADFVLALGD 1rzuA 304 :KGIDLMAEAVDEIVSLGGRLVVLGAG T0333 256 :L 1rzuA 333 :L T0333 257 :GTLPRNVRAVGWTP 1rzuA 342 :SRHHGRVGVAIGYN T0333 271 :LHTLL 1rzuA 358 :LSHLM T0333 276 :RTCTAVVHH 1rzuA 364 :AGCDAIIIP T0333 285 :GG 1rzuA 378 :CG T0333 288 :GTVMTAIDAGIPQLLAP 1rzuA 380 :LTQLYALRYGCIPVVAR T0333 317 :AVSRRGIGLV 1rzuA 412 :LASKAATGVQ T0333 327 :STSDKVDADLLRRLIG 1rzuA 424 :PVTLDGLKQAIRRTVR T0333 343 :DESL 1rzuA 443 :DPKL T0333 350 :AREVREEMVALP 1rzuA 447 :WTQMQKLGMKSD T0333 362 :TPAETVRRIVERI 1rzuA 460 :SWEKSAGLYAALY Number of specific fragments extracted= 21 number of extra gaps= 0 total=3395 Number of alignments=168 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cs0C/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cs0C expands to /projects/compbio/data/pdb/1cs0.pdb.gz 1cs0C:Skipped atom 15065, because occupancy 0.500 <= existing 0.500 in 1cs0C Skipped atom 15067, because occupancy 0.500 <= existing 0.500 in 1cs0C Skipped atom 15069, because occupancy 0.500 <= existing 0.500 in 1cs0C Skipped atom 15071, because occupancy 0.500 <= existing 0.500 in 1cs0C Skipped atom 15073, because occupancy 0.500 <= existing 0.500 in 1cs0C Skipped atom 18590, because occupancy 0.500 <= existing 0.500 in 1cs0C Skipped atom 18592, because occupancy 0.500 <= existing 0.500 in 1cs0C Skipped atom 18594, because occupancy 0.500 <= existing 0.500 in 1cs0C Skipped atom 18740, because occupancy 0.500 <= existing 0.500 in 1cs0C Skipped atom 18742, because occupancy 0.500 <= existing 0.500 in 1cs0C Skipped atom 18744, because occupancy 0.500 <= existing 0.500 in 1cs0C Skipped atom 18746, because occupancy 0.500 <= existing 0.500 in 1cs0C Skipped atom 18748, because occupancy 0.500 <= existing 0.500 in 1cs0C # T0333 read from 1cs0C/merged-good-all-a2m # 1cs0C read from 1cs0C/merged-good-all-a2m # adding 1cs0C to template set # found chain 1cs0C in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1cs0C)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1cs0C)D558 T0333 2 :LFVSSPGI 1cs0C 10 :ILILGAGP T0333 10 :GHL 1cs0C 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1cs0C 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEHADRAAAA 1cs0C 51 :PATIMTDPEM T0333 45 :LEVVDVAP 1cs0C 61 :ADATYIEP T0333 93 :NRPL 1cs0C 70 :HWEV T0333 100 :TMALVDDYRPDLVVYEQGATVGLLAADRA 1cs0C 74 :VRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1cs0C 112 :GVT T0333 135 :RNQSA 1cs0C 115 :MIGAT T0333 141 :RTRGMHRSIASFLTDL 1cs0C 505 :LAGVREAEIRKLRDQY T0333 165 :PEPVATI 1cs0C 521 :DLHPVYK T0333 172 :ESFPPSLL 1cs0C 529 :VDTCAAEF T0333 200 :LGDR 1cs0C 547 :YEEE T0333 204 :LPPV 1cs0C 553 :ANPS T0333 210 :RPEVAITMG 1cs0C 559 :REKIMVLGG T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1cs0C 572 :IGQGIEFDYCCVHASLALREDGYETIMVNCNPE T0333 275 :LRTCTAVVHHG 1cs0C 610 :YDTSDRLYFEP T0333 286 :GGGTVMTAIDAGIP 1cs0C 622 :TLEDVLEIVRIEKP T0333 300 :QLLAPDPRD 1cs0C 637 :GVIVQYGGQ T0333 309 :QFQHTAR 1cs0C 647 :PLKLARA T0333 318 :VSRRGIGLV 1cs0C 654 :LEAAGVPVI T0333 327 :ST 1cs0C 664 :TS T0333 334 :ADLLRRLIG 1cs0C 666 :PDAIDRAED T0333 347 :RTAAREVREE 1cs0C 675 :RERFQHAVER T0333 363 :PAETVRRIVERIS 1cs0C 697 :AIEMAVEKAKEIG Number of specific fragments extracted= 25 number of extra gaps= 1 total=3420 Number of alignments=169 # 1cs0C read from 1cs0C/merged-good-all-a2m # found chain 1cs0C in template set Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1cs0C)D558 Warning: unaligning (T0333)R354 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cs0C)V750 Warning: unaligning (T0333)E355 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cs0C)V750 T0333 2 :LFVSSPGI 1cs0C 12 :ILGAGPIV T0333 10 :GHL 1cs0C 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHADRAAAAG 1cs0C 28 :YSGAQACKALREEGYRVILVNSNPATIMTDPE T0333 45 :LEVVDVAPDY 1cs0C 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1cs0C 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1cs0C 112 :GVT T0333 135 :RNQSA 1cs0C 115 :MIGAT T0333 140 :WRTRGMHRSIASFLTDLM 1cs0C 479 :VGITGLNADFLRQLKRKG T0333 198 :AVLGDR 1cs0C 531 :TCAAEF T0333 205 :PPVP 1cs0C 537 :ATDT T0333 210 :RPEVAITMG 1cs0C 559 :REKIMVLGG T0333 219 :TIE 1cs0C 571 :RIG T0333 225 :FGIGA 1cs0C 574 :QGIEF T0333 230 :VEPIIAAAGEVDADFVLALGDLDI 1cs0C 582 :CVHASLALREDGYETIMVNCNPET T0333 261 :RNVRAVGWT 1cs0C 614 :DRLYFEPVT T0333 271 :LHTLLR 1cs0C 626 :VLEIVR T0333 277 :TCTAVVHHGGGGTVM 1cs0C 634 :KPKGVIVQYGGQTPL T0333 292 :TAIDAGIPQLLAPDPR 1cs0C 653 :ALEAAGVPVIGTSPDA T0333 308 :DQF 1cs0C 674 :DRE T0333 313 :TAREAVSRRG 1cs0C 677 :RFQHAVERLK T0333 323 :IGLVST 1cs0C 691 :ANATVT T0333 330 :DKVD 1cs0C 697 :AIEM T0333 334 :ADLLRRL 1cs0C 702 :VEKAKEI T0333 342 :GDESLRTAAREV 1cs0C 729 :YDEADLRRYFQT T0333 361 :P 1cs0C 799 :Y T0333 362 :TPAETVRRIVERIS 1cs0C 801 :LSQEIQDVMRQQVQ Number of specific fragments extracted= 26 number of extra gaps= 2 total=3446 Number of alignments=170 # 1cs0C read from 1cs0C/merged-good-all-a2m # found chain 1cs0C in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1cs0C)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1cs0C)D558 T0333 1 :MLFVSSPGI 1cs0C 10 :ILILGAGPI T0333 10 :GH 1cs0C 21 :GQ T0333 12 :LFPLIQLAWGFRTAGHDVLIAV 1cs0C 27 :DYSGAQACKALREEGYRVILVN T0333 34 :AEHA 1cs0C 51 :PATI T0333 45 :LEVVDVAPDY 1cs0C 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1cs0C 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GV 1cs0C 112 :GV T0333 136 :N 1cs0C 114 :T T0333 138 :SAWRTRGMHRSIASFLT 1cs0C 115 :MIGATADAIDKAEDRRR T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1cs0C 508 :VREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEEC T0333 203 :RLPPV 1cs0C 552 :EANPS T0333 210 :RPEVAITMGTIELQAFGIGAVEPII 1cs0C 559 :REKIMVLGGGPNRIGQGIEFDYCCV T0333 235 :AAAGEVDADFVLALGD 1cs0C 587 :LALREDGYETIMVNCN T0333 252 :DISPLG 1cs0C 605 :TVSTDY T0333 276 :RTC 1cs0C 611 :DTS T0333 279 :TAVVHHGGGGTVMTAIDAGIP 1cs0C 615 :RLYFEPVTLEDVLEIVRIEKP T0333 300 :QLLAP 1cs0C 637 :GVIVQ T0333 305 :DPRDQFQHTAREAVSRRGIGL 1cs0C 643 :GGQTPLKLARALEAAGVPVIG T0333 329 :SD 1cs0C 665 :SP T0333 335 :DLLRRLIGDESLRTAAREV 1cs0C 667 :DAIDRAEDRERFQHAVERL T0333 360 :LPTPAETVRRIVER 1cs0C 695 :VTAIEMAVEKAKEI Number of specific fragments extracted= 21 number of extra gaps= 1 total=3467 Number of alignments=171 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p3dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0333 read from 1p3dA/merged-good-all-a2m # 1p3dA read from 1p3dA/merged-good-all-a2m # found chain 1p3dA in training set Warning: unaligning (T0333)A132 because of BadResidue code BAD_PEPTIDE in next template residue (1p3dA)T148 Warning: unaligning (T0333)V133 because of BadResidue code BAD_PEPTIDE at template residue (1p3dA)T148 T0333 3 :FVSSPGIGHL 1p3dA 21 :IHFIGIGGAG T0333 15 :LIQLAWGFRTAGHDVLIAV 1p3dA 31 :MSGIAEILLNEGYQISGSD T0333 34 :AEHADRAAAAGLEVVD 1p3dA 53 :GVVTQRLAQAGAKIYI T0333 50 :VAPDYSAVKVFEQVAKDN 1p3dA 74 :HIEGASVVVVSSAIKDDN T0333 84 :EWGVQIAAV 1p3dA 92 :PELVTSKQK T0333 93 :NRPLVDGT 1p3dA 107 :RAQMLAEI T0333 104 :VDDYR 1p3dA 115 :MRFRH T0333 110 :DLVVYEQGA 1p3dA 120 :GIAVAGTHG T0333 119 :TVGLLAADRAGVP 1p3dA 134 :AMISMIYTQAKLD T0333 134 :QRNQSAW 1p3dA 149 :FVNGGLV T0333 200 :LGDRLP 1p3dA 360 :AREGWG T0333 209 :ARPEVAITMGTIELQ 1p3dA 366 :DKRIVMIFQPHRYSR T0333 226 :GIGAVEPIIAAAGEVDADFVLALGDLDISP 1p3dA 381 :TRDLFDDFVQVLSQVDALIMLDVYAAGEAP T0333 305 :DPR 1p3dA 411 :IVG T0333 308 :DQFQHTAR 1p3dA 415 :DSKSLCRS T0333 318 :VSRRGIG 1p3dA 423 :IRNLGKV T0333 325 :LV 1p3dA 432 :IL T0333 327 :STSDKV 1p3dA 435 :SDTSQL T0333 334 :ADLLRRLI 1p3dA 441 :GDVLDQII T0333 346 :LRTAAREVREE 1p3dA 462 :VSKISRGLAES Number of specific fragments extracted= 20 number of extra gaps= 1 total=3487 Number of alignments=172 # 1p3dA read from 1p3dA/merged-good-all-a2m # found chain 1p3dA in training set Warning: unaligning (T0333)A132 because of BadResidue code BAD_PEPTIDE in next template residue (1p3dA)T148 Warning: unaligning (T0333)V133 because of BadResidue code BAD_PEPTIDE at template residue (1p3dA)T148 T0333 7 :PGIGHL 1p3dA 25 :GIGGAG T0333 15 :LIQLAWGFRTAGHDVLIAV 1p3dA 31 :MSGIAEILLNEGYQISGSD T0333 34 :AE 1p3dA 51 :AD T0333 38 :DRAAAAGLEVVDVAPDY 1p3dA 57 :QRLAQAGAKIYIGHAEE T0333 56 :AV 1p3dA 74 :HI T0333 65 :KDNPRFAETVATRPAIDLEEWGVQ 1p3dA 76 :EGASVVVVSSAIKDDNPELVTSKQ T0333 89 :IAA 1p3dA 107 :RAQ T0333 99 :GTMALVDDYR 1p3dA 110 :MLAEIMRFRH T0333 110 :DLVVYEQGA 1p3dA 120 :GIAVAGTHG T0333 119 :TVGLLAADRAGVP 1p3dA 134 :AMISMIYTQAKLD T0333 134 :QRNQSA 1p3dA 149 :FVNGGL T0333 140 :WRTRGMHRSIASFLTDLM 1p3dA 200 :DTYEGDFEKMKATYVKFL T0333 158 :DKHQVSLPEPVATIE 1p3dA 225 :LAVMCADDPVLMELV T0333 173 :SFPP 1p3dA 241 :KVGR T0333 191 :WVPYGGGA 1p3dA 245 :QVITYGFS T0333 205 :PPVP 1p3dA 253 :EQAD T0333 209 :ARPE 1p3dA 336 :PNGK T0333 213 :VAITMGTIE 1p3dA 341 :RLVDDYGHH T0333 223 :Q 1p3dA 350 :P T0333 225 :FGIGAVEPIIAAAGE 1p3dA 351 :TEVGVTIKAAREGWG T0333 241 :DADFVLALGDLDI 1p3dA 366 :DKRIVMIFQPHRY T0333 271 :LHTLLRTCTAVVHHG 1p3dA 388 :FVQVLSQVDALIMLD T0333 286 :GG 1p3dA 407 :GE T0333 304 :PDPR 1p3dA 410 :PIVG T0333 308 :DQF 1p3dA 415 :DSK T0333 313 :TAREAVSRRGIG 1p3dA 418 :SLCRSIRNLGKV T0333 325 :LVST 1p3dA 432 :ILVS T0333 330 :DKVD 1p3dA 436 :DTSQ T0333 334 :ADLLRRLIG 1p3dA 441 :GDVLDQIIQ T0333 359 :AL 1p3dA 450 :DG T0333 361 :PTPAETVRRIVER 1p3dA 460 :GSVSKISRGLAES Number of specific fragments extracted= 31 number of extra gaps= 1 total=3518 Number of alignments=173 # 1p3dA read from 1p3dA/merged-good-all-a2m # found chain 1p3dA in training set Warning: unaligning (T0333)A132 because of BadResidue code BAD_PEPTIDE in next template residue (1p3dA)T148 Warning: unaligning (T0333)V133 because of BadResidue code BAD_PEPTIDE at template residue (1p3dA)T148 Warning: unaligning (T0333)I374 because last residue in template chain is (1p3dA)W473 T0333 1 :MLFVSSPGIG 1p3dA 21 :IHFIGIGGAG T0333 15 :LIQLAWGFRTAGHDVLIAV 1p3dA 31 :MSGIAEILLNEGYQISGSD T0333 34 :AEHADRAAAAGLEVVDVAPDYSAVKVF 1p3dA 53 :GVVTQRLAQAGAKIYIGHAEEHIEGAS T0333 61 :EQVAKDNPRF 1p3dA 95 :VTSKQKRIPV T0333 96 :LVDGTMALVDDYRPDLVVYEQGATVGL 1p3dA 107 :RAQMLAEIMRFRHGIAVAGTHGKTTTT T0333 123 :LAADRAGVP 1p3dA 138 :MIYTQAKLD T0333 134 :QRNQSAWRTRGMHRSIASFLT 1p3dA 149 :FVNGGLVKSAGKNAHLGASRY T0333 155 :DLMDKHQVSLPEPVATIESFPPSL 1p3dA 311 :EAILEALADFQGAGRRFDQLGEFI T0333 184 :PEGWFMRWVPYGGGA 1p3dA 335 :RPNGKVRLVDDYGHH T0333 207 :VPARPEVAITMGTIELQ 1p3dA 364 :WGDKRIVMIFQPHRYSR T0333 226 :GIGAVEPIIAAAGEVDADFVLALGDLDISPLG 1p3dA 381 :TRDLFDDFVQVLSQVDALIMLDVYAAGEAPIV T0333 306 :PRDQFQHTAREAVSRRGIGLVSTSDKVDADLLRRLIGD 1p3dA 413 :GADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQD T0333 360 :LPTPAETVRRIVER 1p3dA 459 :AGSVSKISRGLAES Number of specific fragments extracted= 13 number of extra gaps= 1 total=3531 Number of alignments=174 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f48A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f48A expands to /projects/compbio/data/pdb/1f48.pdb.gz 1f48A:# T0333 read from 1f48A/merged-good-all-a2m # 1f48A read from 1f48A/merged-good-all-a2m # adding 1f48A to template set # found chain 1f48A in template set Warning: unaligning (T0333)E185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f48A)R309 Warning: unaligning (T0333)A198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f48A)R309 Warning: unaligning (T0333)C278 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f48A)T480 T0333 2 :LFVSS 1f48A 11 :LFFTG T0333 7 :PGIGHLFPLIQLAWGFRTAGHDVLIAVAEHADRAAAA 1f48A 17 :GGVGKTSISCATAIRLAEQGKRVLLVSTDPASNVGQV T0333 44 :GLEVVDVAP 1f48A 59 :GNTIQAIAS T0333 53 :DYS 1f48A 70 :GLS T0333 58 :KVFEQVAKDNP 1f48A 152 :LLQLPGAWSSF T0333 69 :RFAETVATRPAIDL 1f48A 168 :EGASCLGPMAGLEK T0333 94 :RPLVDGTMALVD 1f48A 183 :REQYAYAVEALS T0333 106 :DYRPDLVVYEQGA 1f48A 196 :PKRTRLVLVARLQ T0333 119 :TVGLLAADRA 1f48A 210 :STLQEVARTH T0333 129 :GVP 1f48A 226 :GLK T0333 132 :AVQRNQSAW 1f48A 231 :YLVINGVLP T0333 141 :RTRGMHRSIASFLTDLMDKHQVSLPEPVATIESFPPSLL 1f48A 244 :ANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNM T0333 180 :LEAEP 1f48A 291 :LLSTQ T0333 199 :V 1f48A 310 :P T0333 200 :LGD 1f48A 322 :IAR T0333 209 :ARPEVAITMGTIELQ 1f48A 325 :NEHGLIMLMGKGGVG T0333 226 :GIGAVEPIIAAAGEVDADFVLALGDLD 1f48A 340 :KTTMAAAIAVRLADMGFDVHLTTSDPA T0333 253 :ISPLG 1f48A 436 :IREAG T0333 261 :RNVRAVGWTP 1f48A 441 :KRFVVMDTAP T0333 271 :LHTLLRT 1f48A 454 :TLLLLDA T0333 297 :GIPQLLAPDP 1f48A 490 :RTKVLLVTLP T0333 308 :DQFQHTAR 1f48A 506 :EAANLQAD T0333 318 :VSRRGIG 1f48A 514 :LERAGIH T0333 325 :LV 1f48A 522 :WG T0333 327 :STSDKV 1f48A 535 :TRSPLL T0333 334 :ADLLRRL 1f48A 541 :RMRAQQE T0333 347 :RTAAREVREE 1f48A 548 :LPQIESVKRQ T0333 357 :MVALPTPAETVRRIV 1f48A 568 :LASEPTGIDKLKQLA Number of specific fragments extracted= 28 number of extra gaps= 0 total=3559 Number of alignments=175 # 1f48A read from 1f48A/merged-good-all-a2m # found chain 1f48A in template set T0333 2 :LFVSSPGI 1f48A 11 :LFFTGKGG T0333 10 :GHLFPLIQLAWGFRTAGHDVLIAVAEHADRAAA 1f48A 20 :GKTSISCATAIRLAEQGKRVLLVSTDPASNVGQ T0333 43 :AGLEVVDVAPDYSAVKVFEQVAKDNP 1f48A 69 :PGLSALEIDPQAAAQQYRARIVDPIK T0333 78 :PAIDLEEWGVQ 1f48A 95 :GVLPDDVVSSI T0333 89 :IAAVNRPLVD 1f48A 120 :FDEFTGLLTD T0333 99 :GTMAL 1f48A 131 :SLLTR T0333 109 :PDLVVYEQGA 1f48A 136 :FDHIIFDTAP T0333 119 :TVGLLAAD 1f48A 147 :GHTIRLLQ T0333 136 :NQ 1f48A 155 :LP T0333 140 :WRTRGMHRSIASFLTD 1f48A 180 :EKQREQYAYAVEALSD T0333 156 :LMDKHQVSLPE 1f48A 198 :RTRLVLVARLQ T0333 167 :PVATIE 1f48A 211 :TLQEVA T0333 173 :SFP 1f48A 226 :GLK T0333 191 :WVPYGGGAVLGDRLPPVP 1f48A 229 :NQYLVINGVLPKTEAAND T0333 209 :ARPEVAITMGTIE 1f48A 325 :NEHGLIMLMGKGG T0333 223 :QAF 1f48A 338 :VGK T0333 228 :GAVEPIIAAAGEV 1f48A 341 :TTMAAAIAVRLAD T0333 241 :DADFVLALGDLDI 1f48A 355 :GFDVHLTTSDPAA T0333 254 :SPLGTLP 1f48A 437 :REAGKRF T0333 271 :LHTLLR 1f48A 481 :PMMLLQ T0333 277 :TCTAVVHHG 1f48A 490 :RTKVLLVTL T0333 286 :GGGTVMTAI 1f48A 500 :ETTPVLEAA T0333 313 :TAREAVSRRG 1f48A 509 :NLQADLERAG T0333 323 :IGLVSTS 1f48A 561 :RVALVPV T0333 330 :DKVD 1f48A 570 :SEPT T0333 334 :ADLLRRLI 1f48A 575 :IDKLKQLA Number of specific fragments extracted= 26 number of extra gaps= 0 total=3585 Number of alignments=176 # 1f48A read from 1f48A/merged-good-all-a2m # found chain 1f48A in template set Warning: unaligning (T0333)E185 because of BadResidue code BAD_PEPTIDE in next template residue (1f48A)P167 Warning: unaligning (T0333)G186 because of BadResidue code BAD_PEPTIDE at template residue (1f48A)P167 T0333 1 :MLFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAV 1f48A 11 :LFFTGKGGVGKTSISCATAIRLAEQGKRVLLVS T0333 34 :AEHADRAAA 1f48A 47 :ASNVGQVFS T0333 43 :AGLEVVDVAPDYSAVKVF 1f48A 69 :PGLSALEIDPQAAAQQYR T0333 61 :EQVAKDNPRFAETVATRPAIDLEEWGVQIAAVNRPLVDGTMA 1f48A 88 :RIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTD T0333 103 :LVD 1f48A 132 :LLT T0333 108 :RPDLVVYEQGAT 1f48A 135 :RFDHIIFDTAPT T0333 120 :VGLLAA 1f48A 149 :TIRLLQ T0333 174 :FPPSLLLEAEP 1f48A 155 :LPGAWSSFIDS T0333 187 :WFMRWVPYGGGA 1f48A 168 :EGASCLGPMAGL T0333 199 :VLGDRLPPVPARPEVAITMGTIE 1f48A 187 :AYAVEALSDPKRTRLVLVARLQK T0333 222 :LQAFGIGAVEPIIAA 1f48A 211 :TLQEVARTHLELAAI T0333 239 :EVDADFVLALGDLDISPL 1f48A 226 :GLKNQYLVINGVLPKTEA T0333 257 :GTLPRNV 1f48A 261 :ANLPADL T0333 267 :GWTPLHTLL 1f48A 311 :DIPSLSALV T0333 276 :RTCTAVVHHG 1f48A 325 :NEHGLIMLMG T0333 286 :GGGTVMTAI 1f48A 339 :GKTTMAAAI T0333 313 :TAREAVSRRGIGL 1f48A 348 :AVRLADMGFDVHL T0333 327 :STSDKVDADL 1f48A 384 :RIDPHEETER T0333 346 :LRTAA 1f48A 394 :YRQHV T0333 351 :REVREEMVALPTPAETV 1f48A 411 :KRLLEEDLRSPCTEEIA Number of specific fragments extracted= 20 number of extra gaps= 1 total=3605 Number of alignments=177 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l2lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1l2lA expands to /projects/compbio/data/pdb/1l2l.pdb.gz 1l2lA:# T0333 read from 1l2lA/merged-good-all-a2m # 1l2lA read from 1l2lA/merged-good-all-a2m # adding 1l2lA to template set # found chain 1l2lA in template set Warning: unaligning (T0333)H160 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1l2lA)E175 Warning: unaligning (T0333)P165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1l2lA)E175 T0333 14 :PLIQLAWGFRTA 1l2lA 10 :LYEKALDKVEAS T0333 26 :GHD 1l2lA 24 :KVR T0333 29 :VLIAV 1l2lA 28 :VLLAY T0333 35 :EHADRAAAAG 1l2lA 46 :DLEKRIEKVG T0333 57 :VKVFEQVAKDNPRFAE 1l2lA 56 :KEEVLRYSEELPKEIE T0333 81 :DLEEWGVQIAAVNRP 1l2lA 72 :TIPQLLGSILWSIKR T0333 98 :DGTMALVDDYRPD 1l2lA 97 :REVREYMRKWGWD T0333 119 :TVGLLAADRA 1l2lA 115 :GQVGIMANLL T0333 129 :GVPAVQRNQSAW 1l2lA 129 :GIPVIAHVPQLS T0333 149 :IA 1l2lA 167 :PR T0333 159 :K 1l2lA 169 :E T0333 166 :EPVATIESFPPSLLLEAEPEGW 1l2lA 176 :DCIHYIYEFPRNFKVLDFEAPR T0333 200 :LG 1l2lA 225 :IA T0333 209 :ARPEVAITMGTIELQA 1l2lA 227 :KRSELAIISGLHPLTQ T0333 225 :FGIGAVEPIIAAAGEVDADFVLALGDLDISPLG 1l2lA 247 :KPIKLVREHLKILNDLGIRAHLEFAFTPDEVVR T0333 269 :TPLHTLLRTCTAVVHH 1l2lA 280 :LEIVKLLKHFYSVGLN T0333 334 :ADLLRRLI 1l2lA 296 :EVELASVV T0333 342 :GDESLRTAARE 1l2lA 307 :GEKELAERIIS T0333 358 :VALP 1l2lA 318 :KDPA T0333 363 :PAETVRRIVERI 1l2lA 322 :DPIAVIEGLLKL Number of specific fragments extracted= 20 number of extra gaps= 0 total=3625 Number of alignments=178 # 1l2lA read from 1l2lA/merged-good-all-a2m # found chain 1l2lA in template set T0333 13 :FPLIQLAWGFRTA 1l2lA 9 :SLYEKALDKVEAS T0333 26 :GHDVLIAVAEHA 1l2lA 24 :KVRGVLLAYNTN T0333 50 :VAPDYSAVKVFEQVAKDNP 1l2lA 41 :YLKREDLEKRIEKVGKEEV T0333 69 :RFAETVATRPAIDLEEWGVQIAAVNR 1l2lA 61 :RYSEELPKEIETIPQLLGSILWSIKR T0333 95 :PLVDGTMALVDDYRPD 1l2lA 94 :VVSREVREYMRKWGWD T0333 115 :EQGATVGLLAADRAGVPAVQRNQSA 1l2lA 115 :GQVGIMANLLGGVYGIPVIAHVPQL T0333 142 :TRGMHRSIASF 1l2lA 212 :LYVREEWIERF T0333 153 :LTDLMDKHQVS 1l2lA 225 :IAKRSELAIIS T0333 195 :GGGAVLGDR 1l2lA 236 :GLHPLTQEN T0333 223 :QAFGIGAVEPIIAAAGEVDADFVLALGDLDI 1l2lA 245 :HGKPIKLVREHLKILNDLGIRAHLEFAFTPD T0333 271 :LHTLLRTCTAVVHH 1l2lA 282 :IVKLLKHFYSVGLN T0333 306 :PR 1l2lA 296 :EV T0333 313 :TAREAVSRRGI 1l2lA 298 :ELASVVSVMGE T0333 344 :ESLRTAARE 1l2lA 309 :KELAERIIS T0333 358 :VALPTPAETVR 1l2lA 318 :KDPADPIAVIE T0333 369 :RIVERI 1l2lA 332 :KLIKET Number of specific fragments extracted= 16 number of extra gaps= 0 total=3641 Number of alignments=179 # 1l2lA read from 1l2lA/merged-good-all-a2m # found chain 1l2lA in template set Warning: unaligning (T0333)H160 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1l2lA)E175 Warning: unaligning (T0333)P165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1l2lA)E175 T0333 2 :LFVSSPG 1l2lA 28 :VLLAYNT T0333 28 :DVLIAV 1l2lA 35 :NIDAIK T0333 34 :AEHADRAAAAG 1l2lA 45 :EDLEKRIEKVG T0333 57 :VKVFEQVAKDNPRFAETV 1l2lA 56 :KEEVLRYSEELPKEIETI T0333 83 :EEWGVQIAAVNRPL 1l2lA 74 :PQLLGSILWSIKRG T0333 98 :DGTMALVDDYRPD 1l2lA 97 :REVREYMRKWGWD T0333 115 :EQGATVGLLAADRAGVPAVQR 1l2lA 115 :GQVGIMANLLGGVYGIPVIAH T0333 138 :SA 1l2lA 136 :VP T0333 141 :RTRGMHRSIASFLT 1l2lA 138 :QLSELQASLFLDGP T0333 155 :DLMDK 1l2lA 165 :IHPRE T0333 166 :EPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1l2lA 176 :DCIHYIYEFPRNFKVLDFEAPRENRFIGAADDY T0333 199 :VLGDRLPPVPARPEVAITMGTIE 1l2lA 217 :EWIERFEEIAKRSELAIISGLHP T0333 222 :LQAFGIGAVEPIIAAAGEVDADFVLALGDLDISPL 1l2lA 244 :NHGKPIKLVREHLKILNDLGIRAHLEFAFTPDEVV T0333 272 :HTLLRTCTAVVH 1l2lA 283 :VKLLKHFYSVGL T0333 329 :SDKVDADLL 1l2lA 295 :NEVELASVV T0333 339 :RLIGDESLRTAARE 1l2lA 304 :SVMGEKELAERIIS T0333 358 :VALPTPAETVR 1l2lA 318 :KDPADPIAVIE T0333 369 :RIVERIS 1l2lA 332 :KLIKETG Number of specific fragments extracted= 18 number of extra gaps= 0 total=3659 Number of alignments=180 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jbwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jbwA expands to /projects/compbio/data/pdb/1jbw.pdb.gz 1jbwA:Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms # T0333 read from 1jbwA/merged-good-all-a2m # 1jbwA read from 1jbwA/merged-good-all-a2m # adding 1jbwA to template set # found chain 1jbwA in template set Warning: unaligning (T0333)W268 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jbwA)R386 T0333 3 :FVSSPGIGHLFPLIQLAWGFRTAGHDVLIAVAEHADRAAAA 1jbwA 42 :IHVTGTNGKGSAANAIAHVLEASGLTVGLYTSPFIMRFNER T0333 57 :VKVFEQVAKDN 1jbwA 83 :IMIDHEPIPDA T0333 81 :DLEEWGVQIAAVNRPLVDG 1jbwA 94 :ALVNAVAFVRAALERLQQQ T0333 105 :DDYRPD 1jbwA 114 :ADFNVT T0333 117 :GATVGLLAADRAGVPAVQRNQSAW 1jbwA 124 :ITALAYWYFRQRQVDVAVIEVGIG T0333 141 :RTRGMHRSIASFLTD 1jbwA 280 :EWPLTPQNIRQGLAA T0333 167 :P 1jbwA 295 :S T0333 184 :PEGWFMRWVP 1jbwA 296 :HWPARLEKIS T0333 209 :ARPEVAITMGT 1jbwA 306 :DTPLIVIDGAH T0333 226 :GIGAVEPIIAAAGEV 1jbwA 317 :NPDGINGLITALKQL T0333 241 :DADFVLALGDLD 1jbwA 335 :PITVIAGILADK T0333 269 :T 1jbwA 387 :L T0333 270 :PLHTLLRT 1jbwA 390 :SWQEALAA T0333 278 :CTAVVHHG 1jbwA 405 :QPIVITGS T0333 306 :PR 1jbwA 413 :LY T0333 312 :HTAR 1jbwA 415 :LASA T0333 318 :VS 1jbwA 419 :VR Number of specific fragments extracted= 17 number of extra gaps= 0 total=3676 Number of alignments=181 # 1jbwA read from 1jbwA/merged-good-all-a2m # found chain 1jbwA in template set Warning: unaligning (T0333)F152 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jbwA)A186 Warning: unaligning (T0333)T154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jbwA)A186 Warning: unaligning (T0333)V358 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jbwA)R386 T0333 3 :FVSSPGIGHLFPLIQLAWGFRTAGHDVLIAVAE 1jbwA 42 :IHVTGTNGKGSAANAIAHVLEASGLTVGLYTSP T0333 65 :KDNPRFAETVATRPAIDLEEWGVQIA 1jbwA 75 :FIMRFNERIMIDHEPIPDAALVNAVA T0333 99 :GTMALVDD 1jbwA 101 :FVRAALER T0333 107 :YRP 1jbwA 116 :FNV T0333 116 :QGATVGLLAADRAGVPAVQRNQSA 1jbwA 123 :FITALAYWYFRQRQVDVAVIEVGI T0333 140 :WRTRGMHRSIAS 1jbwA 172 :KLLGHTITAIAK T0333 155 :DLM 1jbwA 187 :GII T0333 158 :DKHQVSLPEPVATIE 1jbwA 194 :PVVTGNLVPDAAAVV T0333 173 :SF 1jbwA 216 :GS T0333 191 :WVPYGGGAVLGDRLPPVP 1jbwA 218 :QWLRFDRDFSVPKAKLHG T0333 209 :ARPEVAITMGTIE 1jbwA 306 :DTPLIVIDGAHNP T0333 225 :FGIGAVEPIIAAAGEVDADFVLALGDLDI 1jbwA 319 :DGINGLITALKQLFSQPITVIAGILADKD T0333 313 :TAREAVSR 1jbwA 350 :AMADRLTA T0333 321 :RGIGLVSTS 1jbwA 359 :FSTVYLVPV T0333 359 :ALPTPAETVRRIVE 1jbwA 387 :LKDSWQEALAASLN Number of specific fragments extracted= 15 number of extra gaps= 0 total=3691 Number of alignments=182 # 1jbwA read from 1jbwA/merged-good-all-a2m # found chain 1jbwA in template set Warning: unaligning (T0333)S329 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jbwA)R386 Warning: unaligning (T0333)V358 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jbwA)R386 T0333 2 :LFVSSPGIGHLFPLIQLAWGFRTAGHDVLIAV 1jbwA 41 :YIHVTGTNGKGSAANAIAHVLEASGLTVGLYT T0333 52 :PDYSAVKVF 1jbwA 74 :PFIMRFNER T0333 83 :EEWGVQIAAVNRPLVDGTMALVDDYRPD 1jbwA 92 :DAALVNAVAFVRAALERLQQQQADFNVT T0333 116 :QGATVGLLAADRAGVPAVQRNQSAWRTRGMHRSIASFLT 1jbwA 123 :FITALAYWYFRQRQVDVAVIEVGIGGDTDSTNVITPVVS T0333 155 :D 1jbwA 296 :H T0333 175 :PPSLLLEAEPEGWFMRWVPY 1jbwA 297 :WPARLEKISDTPLIVIDGAH T0333 226 :GIGAVEPIIAAAGEV 1jbwA 317 :NPDGINGLITALKQL T0333 241 :DADFVLALGD 1jbwA 335 :PITVIAGILA T0333 306 :PRDQFQHTAREAVSRRGIGLV 1jbwA 345 :DKDYAAMADRLTAAFSTVYLV T0333 327 :ST 1jbwA 368 :PG T0333 359 :ALPTPAETVRRIVE 1jbwA 387 :LKDSWQEALAASLN Number of specific fragments extracted= 11 number of extra gaps= 0 total=3702 Number of alignments=183 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c3oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c3oA expands to /projects/compbio/data/pdb/1c3o.pdb.gz 1c3oA:Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 285, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 591, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 2557, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 2559, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 2561, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 2563, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 5050, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 5052, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 5054, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 5056, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 5058, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 5060, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 5062, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 7269, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 7271, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 7273, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 7275, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 7277, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 7279, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 7281, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 7550, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 7552, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 7554, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 7556, because occupancy 0.500 <= existing 0.500 in 1c3oA Skipped atom 7558, because occupancy 0.500 <= existing 0.500 in 1c3oA # T0333 read from 1c3oA/merged-good-all-a2m # 1c3oA read from 1c3oA/merged-good-all-a2m # adding 1c3oA to template set # found chain 1c3oA in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1c3oA)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1c3oA)D558 T0333 2 :LFVSSPGI 1c3oA 10 :ILILGAGP T0333 10 :GHL 1c3oA 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1c3oA 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEH 1c3oA 51 :PAT T0333 37 :ADR 1c3oA 58 :PEM T0333 45 :LEVVDVAP 1c3oA 61 :ADATYIEP T0333 94 :RPL 1c3oA 71 :WEV T0333 100 :TMALVDDYRPDLVVYEQGATVGLLAADRA 1c3oA 74 :VRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1c3oA 112 :GVT T0333 135 :RNQSA 1c3oA 115 :MIGAT T0333 141 :RTRGMHRSIASFLTDL 1c3oA 505 :LAGVREAEIRKLRDQY T0333 165 :PEPVATIESFPPSLL 1c3oA 521 :DLHPVYKRVDTCAAE T0333 184 :PEGWFMRWVPYGGGAV 1c3oA 536 :FATDTAYMYSTYEEEC T0333 204 :LPPV 1c3oA 553 :ANPS T0333 210 :RPEVAITMGT 1c3oA 559 :REKIMVLGGG T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1c3oA 572 :IGQGIEFDYCCVHASLALREDGYETIMVNCNPE T0333 275 :LRTCTAVVHHG 1c3oA 610 :YDTSDRLYFEP T0333 286 :GGGTVMTAIDAGIP 1c3oA 622 :TLEDVLEIVRIEKP T0333 300 :QLLAPDPRD 1c3oA 637 :GVIVQYGGQ T0333 309 :QFQHTAR 1c3oA 647 :PLKLARA T0333 318 :VSRRGIG 1c3oA 654 :LEAAGVP T0333 325 :LVST 1c3oA 662 :IGTS T0333 334 :ADLLRRLIG 1c3oA 666 :PDAIDRAED T0333 347 :RTAAREVREE 1c3oA 675 :RERFQHAVER T0333 363 :PAETVRRIVERI 1c3oA 697 :AIEMAVEKAKEI Number of specific fragments extracted= 25 number of extra gaps= 1 total=3727 Number of alignments=184 # 1c3oA read from 1c3oA/merged-good-all-a2m # found chain 1c3oA in template set T0333 2 :LFVSSPGI 1c3oA 12 :ILGAGPIV T0333 10 :GHL 1c3oA 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHADRAA 1c3oA 28 :YSGAQACKALREEGYRVILVNSNPATIMT T0333 67 :NPRFAETVATRPAI 1c3oA 57 :DPEMADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1c3oA 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1c3oA 112 :GVT T0333 135 :RNQSA 1c3oA 115 :MIGAT T0333 140 :WRTRGMHRSIASFLT 1c3oA 800 :TLSQEIQDVMRQQVQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=3735 Number of alignments=185 # 1c3oA read from 1c3oA/merged-good-all-a2m # found chain 1c3oA in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1c3oA)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1c3oA)D558 T0333 1 :MLFVSSPGI 1c3oA 10 :ILILGAGPI T0333 10 :GHL 1c3oA 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1c3oA 28 :YSGAQACKALREEGYRVILVN T0333 34 :A 1c3oA 51 :P T0333 45 :LEVVDVAPDY 1c3oA 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1c3oA 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GV 1c3oA 112 :GV T0333 137 :QSAWRTRGMHRSIASFLT 1c3oA 114 :TMIGATADAIDKAEDRRR T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1c3oA 508 :VREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEEC T0333 203 :RLPPV 1c3oA 552 :EANPS T0333 210 :RPEVAITMGTIELQAFGIGAVEPII 1c3oA 559 :REKIMVLGGGPNRIGQGIEFDYCCV T0333 235 :AAAGEVDADFVLALGD 1c3oA 587 :LALREDGYETIMVNCN T0333 251 :LDISPL 1c3oA 608 :TDYDTS T0333 279 :TAVVHHGGGGTVMTAIDAGIP 1c3oA 615 :RLYFEPVTLEDVLEIVRIEKP T0333 300 :QLLAP 1c3oA 637 :GVIVQ T0333 305 :DPRDQFQHTAREAVSRRGIGL 1c3oA 643 :GGQTPLKLARALEAAGVPVIG T0333 329 :SD 1c3oA 665 :SP T0333 335 :DLLRRLIGDESLRTAAREV 1c3oA 667 :DAIDRAEDRERFQHAVERL T0333 360 :LPTPAETVRRIVER 1c3oA 695 :VTAIEMAVEKAKEI Number of specific fragments extracted= 19 number of extra gaps= 1 total=3754 Number of alignments=186 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c3oC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c3oC expands to /projects/compbio/data/pdb/1c3o.pdb.gz 1c3oC:Skipped atom 11156, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 11158, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 11160, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 11162, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 11164, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 11315, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 11317, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 14278, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 14280, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 14282, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 14284, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 14286, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 14853, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 14855, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 14857, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 14859, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 14861, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 14863, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 14865, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 15096, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 15098, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 15100, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 15102, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 15104, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 17255, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 17257, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 17259, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 17261, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 17263, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 18626, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 18628, because occupancy 0.500 <= existing 0.500 in 1c3oC Skipped atom 18630, because occupancy 0.500 <= existing 0.500 in 1c3oC # T0333 read from 1c3oC/merged-good-all-a2m # 1c3oC read from 1c3oC/merged-good-all-a2m # adding 1c3oC to template set # found chain 1c3oC in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1c3oC)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1c3oC)D558 T0333 2 :LFVSSPGI 1c3oC 10 :ILILGAGP T0333 10 :GHL 1c3oC 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAV 1c3oC 28 :YSGAQACKALREEGYRVILVN T0333 34 :AEHADRAAAA 1c3oC 51 :PATIMTDPEM T0333 45 :LEVVDVAP 1c3oC 61 :ADATYIEP T0333 93 :NRPL 1c3oC 70 :HWEV T0333 100 :TMALVDDYRPDLVVYEQGATVGLLAADRA 1c3oC 74 :VRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1c3oC 112 :GVT T0333 136 :NQSAW 1c3oC 115 :MIGAT T0333 141 :RTRGMHRSIASFLTDL 1c3oC 505 :LAGVREAEIRKLRDQY T0333 165 :PEPVATIESFPPSLL 1c3oC 521 :DLHPVYKRVDTCAAE T0333 184 :PEGWFMRWVPYGGGAV 1c3oC 536 :FATDTAYMYSTYEEEC T0333 204 :LPPV 1c3oC 553 :ANPS T0333 210 :RPEVAITMGT 1c3oC 559 :REKIMVLGGG T0333 220 :IELQAFGIGAVEPIIAAAGEVDADFVLALGDLD 1c3oC 572 :IGQGIEFDYCCVHASLALREDGYETIMVNCNPE T0333 275 :LRTCTAVVHHG 1c3oC 610 :YDTSDRLYFEP T0333 286 :GGGTVMTAIDAGIP 1c3oC 622 :TLEDVLEIVRIEKP T0333 300 :QLLAPDPRD 1c3oC 637 :GVIVQYGGQ T0333 309 :QFQHTAR 1c3oC 647 :PLKLARA T0333 318 :VSRRGIG 1c3oC 654 :LEAAGVP T0333 325 :LVST 1c3oC 662 :IGTS T0333 334 :ADLLRRLIG 1c3oC 666 :PDAIDRAED T0333 347 :RTAAREVREE 1c3oC 675 :RERFQHAVER T0333 363 :PAETVRRIVERI 1c3oC 697 :AIEMAVEKAKEI Number of specific fragments extracted= 24 number of extra gaps= 1 total=3778 Number of alignments=187 # 1c3oC read from 1c3oC/merged-good-all-a2m # found chain 1c3oC in template set T0333 2 :LFVSSPGI 1c3oC 12 :ILGAGPIV T0333 10 :GHL 1c3oC 21 :GQA T0333 13 :FPLIQLAWGFRTAGHDVLIAVAEHADRAAAAG 1c3oC 28 :YSGAQACKALREEGYRVILVNSNPATIMTDPE T0333 45 :LEVVDVAPDY 1c3oC 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1c3oC 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GVP 1c3oC 112 :GVT T0333 135 :RNQSA 1c3oC 115 :MIGAT T0333 140 :WRTRGMHRSIASFLTDLM 1c3oC 800 :TLSQEIQDVMRQQVQKLA T0333 168 :VATI 1c3oC 874 :LAEQ T0333 173 :SFPPSLLL 1c3oC 878 :GVTKEVIP T0333 186 :GWFMRWVPYGGGAVLGDRLPPVP 1c3oC 886 :PYYSVKEVVLPFNKFPGVDPLLG T0333 209 :ARPEVAITM 1c3oC 941 :KHGRALLSV T0333 223 :QAFGIGAVEPIIAAAGEVDADFVL 1c3oC 950 :REGDKERVVDLAAKLLKQGFELDA T0333 255 :PLG 1c3oC 983 :EAG T0333 261 :RNVRAVGWT 1c3oC 986 :INPRLVNKV T0333 271 :LHTLLR 1c3oC 1001 :IQDRIK T0333 277 :TCTAVVHHG 1c3oC 1009 :EYTYIINTT T0333 286 :GGGTVMTAIDAGIPQ 1c3oC 1026 :SRVIRRSALQYKVHY Number of specific fragments extracted= 18 number of extra gaps= 0 total=3796 Number of alignments=188 # 1c3oC read from 1c3oC/merged-good-all-a2m # found chain 1c3oC in template set Warning: unaligning (T0333)P208 because of BadResidue code BAD_PEPTIDE in next template residue (1c3oC)D558 Warning: unaligning (T0333)A209 because of BadResidue code BAD_PEPTIDE at template residue (1c3oC)D558 T0333 1 :MLFVSSPGI 1c3oC 10 :ILILGAGPI T0333 10 :GH 1c3oC 21 :GQ T0333 12 :LFPLIQLAWGFRTAGHDVLIAV 1c3oC 27 :DYSGAQACKALREEGYRVILVN T0333 34 :AEHA 1c3oC 51 :PATI T0333 45 :LEVVDVAPDY 1c3oC 61 :ADATYIEPIH T0333 97 :VDGTMALVDDYRPDLVVYEQGATVGLLAADRA 1c3oC 71 :WEVVRKIIEKERPDAVLPTMGGQTALNCALEL T0333 129 :GV 1c3oC 112 :GV T0333 136 :NQ 1c3oC 114 :TM T0333 139 :AWRTRGMHRSIASFLT 1c3oC 116 :IGATADAIDKAEDRRR T0333 155 :DLMDKHQVSLPEPVATIESFPPSLLLEAEPEGWFMRWVPYGGGA 1c3oC 508 :VREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEEC T0333 204 :LPPV 1c3oC 553 :ANPS T0333 210 :RPEVAITMGTIELQAFGIGAVEPII 1c3oC 559 :REKIMVLGGGPNRIGQGIEFDYCCV T0333 235 :AAAGEVDADFVLALGD 1c3oC 587 :LALREDGYETIMVNCN T0333 251 :LDISPL 1c3oC 608 :TDYDTS T0333 262 :NVRAVGWTPLHTLL 1c3oC 614 :DRLYFEPVTLEDVL T0333 276 :RTCTAVVHHGGGGTVM 1c3oC 633 :EKPKGVIVQYGGQTPL T0333 311 :QHTAREAVSRRGIGL 1c3oC 649 :KLARALEAAGVPVIG T0333 329 :SD 1c3oC 665 :SP T0333 335 :DLLRRLIGDESLRTAAREV 1c3oC 667 :DAIDRAEDRERFQHAVERL T0333 360 :LPTPAETVRRIVER 1c3oC 695 :VTAIEMAVEKAKEI Number of specific fragments extracted= 20 number of extra gaps= 1 total=3816 Number of alignments=189 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 189 Done printing distance constraints # command: