# 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/T0373/ # command:# Making conformation for sequence T0373 numbered 1 through 147 Created new target T0373 from T0373.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0373/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0373//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0373/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0373//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0373/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0373/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0373/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hw5A expands to /projects/compbio/data/pdb/1hw5.pdb.gz 1hw5A:Skipped atom 179, because occupancy 0.5 <= existing 0.500 in 1hw5A Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 310, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1007, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1375, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1474, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1480, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1482, because occupancy 0.500 <= existing 0.500 in 1hw5A # T0373 read from 1hw5A/merged-good-all-a2m # 1hw5A read from 1hw5A/merged-good-all-a2m # adding 1hw5A to template set # found chain 1hw5A in template set Warning: unaligning (T0373)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0373)S64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0373 8 :QLAAHLRSQVTTLTRRLRR 1hw5A 111 :DILMRLSAQMARRLQVLAE # choosing archetypes in rotamer library T0373 27 :EAQADPVQFSQLVVLGAIDRLGG 1hw5A 133 :NLAFLDVTGRIAQTLLNLAKQPD T0373 50 :D 1hw5A 160 :P T0373 51 :VTPSELAAAERM 1hw5A 167 :ITRQEIGQIVGC T0373 65 :SNLAALLRELERGGLIV 1hw5A 181 :ETVGRILKMLEDQNLIS Number of specific fragments extracted= 5 number of extra gaps= 1 total=5 Number of alignments=1 # 1hw5A read from 1hw5A/merged-good-all-a2m # found chain 1hw5A in template set Warning: unaligning (T0373)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0373)S64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0373 4 :NQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLG 1hw5A 110 :PDILMRLSAQMARRLQVLAEKVGNLAFLDVTGRIAQTLLNLAKQP T0373 51 :VTPSELAAAERM 1hw5A 167 :ITRQEIGQIVGC T0373 65 :SNLAALLRELERGGLIVR 1hw5A 181 :ETVGRILKMLEDQNLISA Number of specific fragments extracted= 3 number of extra gaps= 1 total=8 Number of alignments=2 # 1hw5A read from 1hw5A/merged-good-all-a2m # found chain 1hw5A in template set Warning: unaligning (T0373)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0373)S64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0373 4 :NQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 1hw5A 110 :PDILMRLSAQMARRLQVLAEKVGNLAFLDVTGRIAQTLLNLAKQPD T0373 51 :VTPSELAAAERM 1hw5A 167 :ITRQEIGQIVGC T0373 65 :SNLAALLRELERGGLIVRH 1hw5A 181 :ETVGRILKMLEDQNLISAH Number of specific fragments extracted= 3 number of extra gaps= 1 total=11 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2eshA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2eshA expands to /projects/compbio/data/pdb/2esh.pdb.gz 2eshA:Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 401, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 643, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 645, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 788, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 790, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 792, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 794, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 796, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 969, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 971, because occupancy 0.500 <= existing 0.500 in 2eshA # T0373 read from 2eshA/merged-good-all-a2m # 2eshA read from 2eshA/merged-good-all-a2m # adding 2eshA to template set # found chain 2eshA in template set Warning: unaligning (T0373)P2 because first residue in template chain is (2eshA)R4 Warning: unaligning (T0373)Q8 because of BadResidue code BAD_PEPTIDE in next template residue (2eshA)G11 Warning: unaligning (T0373)L9 because of BadResidue code BAD_PEPTIDE at template residue (2eshA)G11 Warning: unaligning (T0373)Q34 because of BadResidue code BAD_PEPTIDE in next template residue (2eshA)I43 Warning: unaligning (T0373)L47 because of BadResidue code BAD_PEPTIDE at template residue (2eshA)I43 Warning: unaligning (T0373)T52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eshA)H48 Warning: unaligning (T0373)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)H48 Warning: unaligning (T0373)S64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)M49 Warning: unaligning (T0373)S65 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)G50 Warning: unaligning (T0373)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)N51 Warning: unaligning (T0373)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eshA)L56 Warning: unaligning (T0373)L71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)L56 Warning: unaligning (T0373)S97 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2eshA)P84 Warning: unaligning (T0373)S98 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2eshA)P84 T0373 3 :TNQDL 2eshA 5 :GGRGF T0373 10 :AAHLRSQVTTLTR 2eshA 12 :WWLASTILLLVAE T0373 23 :RLRREAQADPV 2eshA 31 :ELAERLAEFGI T0373 48 :GG 2eshA 44 :PG T0373 51 :V 2eshA 46 :I T0373 67 :LAA 2eshA 52 :IYR T0373 72 :RELERGGLIVRHADPQ 2eshA 57 :ADLEESGFLSTEWDTT T0373 88 :DGRRTRVSL 2eshA 74 :SPPRKIYRI T0373 99 :EGRRNLYGNRAKREE 2eshA 85 :QGKLYLREILRSLED T0373 115 :LVRAM 2eshA 100 :MKRRI T0373 129 :ALLAA 2eshA 105 :ETLEE T0373 137 :LLTR 2eshA 110 :RIKR Number of specific fragments extracted= 12 number of extra gaps= 5 total=23 Number of alignments=4 # 2eshA read from 2eshA/merged-good-all-a2m # found chain 2eshA in template set Warning: unaligning (T0373)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eshA)H48 Warning: unaligning (T0373)S64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)H48 Warning: unaligning (T0373)S65 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)G50 Warning: unaligning (T0373)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)N51 Warning: unaligning (T0373)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eshA)L56 Warning: unaligning (T0373)L71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)L56 Warning: unaligning (T0373)S97 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2eshA)P84 Warning: unaligning (T0373)S98 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2eshA)P84 T0373 35 :FSQLVVLGAIDR 2eshA 13 :WLASTILLLVAE T0373 49 :GDVTPSELAAAE 2eshA 25 :KPSHGYELAERL T0373 61 :RM 2eshA 45 :GI T0373 67 :LAA 2eshA 52 :IYR T0373 72 :RELERGGLIVRHADPQ 2eshA 57 :ADLEESGFLSTEWDTT T0373 88 :DGRRTRVSL 2eshA 74 :SPPRKIYRI T0373 99 :EGRRNLYGNRAKREEWLVRAM 2eshA 85 :QGKLYLREILRSLEDMKRRIE T0373 130 :LLAA 2eshA 106 :TLEE T0373 137 :LLT 2eshA 110 :RIK Number of specific fragments extracted= 9 number of extra gaps= 4 total=32 Number of alignments=5 # 2eshA read from 2eshA/merged-good-all-a2m # found chain 2eshA in template set Warning: unaligning (T0373)Q8 because of BadResidue code BAD_PEPTIDE in next template residue (2eshA)G11 Warning: unaligning (T0373)L9 because of BadResidue code BAD_PEPTIDE at template residue (2eshA)G11 Warning: unaligning (T0373)Q34 because of BadResidue code BAD_PEPTIDE in next template residue (2eshA)I43 Warning: unaligning (T0373)G48 because of BadResidue code BAD_PEPTIDE at template residue (2eshA)I43 Warning: unaligning (T0373)T52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eshA)H48 Warning: unaligning (T0373)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)H48 Warning: unaligning (T0373)S64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)M49 Warning: unaligning (T0373)S65 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)G50 Warning: unaligning (T0373)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)N51 Warning: unaligning (T0373)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eshA)L56 Warning: unaligning (T0373)L71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)L56 Warning: unaligning (T0373)S97 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2eshA)P84 Warning: unaligning (T0373)S98 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2eshA)P84 T0373 10 :AAHLRSQVTTLT 2eshA 12 :WWLASTILLLVA T0373 22 :RRLRREAQADPV 2eshA 30 :YELAERLAEFGI T0373 49 :GDV 2eshA 44 :PGI T0373 67 :LAA 2eshA 52 :IYR T0373 72 :RELERGGLIVRHADPQ 2eshA 57 :ADLEESGFLSTEWDTT T0373 88 :DGRRTRVSL 2eshA 74 :SPPRKIYRI T0373 99 :EGRRNLYGNRAKREEWLVR 2eshA 85 :QGKLYLREILRSLEDMKRR T0373 128 :RALLAAAGPL 2eshA 104 :IETLEERIKR Number of specific fragments extracted= 8 number of extra gaps= 5 total=40 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r1tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0373 read from 1r1tA/merged-good-all-a2m # 1r1tA read from 1r1tA/merged-good-all-a2m # found chain 1r1tA in training set T0373 18 :TTLTRRLRREAQ 1r1tA 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1r1tA 45 :DPNRLRLLSLLAR T0373 48 :GG 1r1tA 58 :SE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1r1tA 60 :LCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ T0373 89 :GRRTRVSLS 1r1tA 95 :GRHVYYQLQ T0373 98 :SEGRRNLYGNRAK 1r1tA 105 :HHIVALYQNALDH Number of specific fragments extracted= 6 number of extra gaps= 0 total=46 Number of alignments=7 # 1r1tA read from 1r1tA/merged-good-all-a2m # found chain 1r1tA in training set T0373 1 :MPTNQDL 1r1tA 26 :QAIAPEV T0373 18 :TTLTRRLRREAQ 1r1tA 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1r1tA 45 :DPNRLRLLSLLAR T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1r1tA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ T0373 89 :GRRTRVSLS 1r1tA 95 :GRHVYYQLQ T0373 98 :SEGRRNLYGNRAK 1r1tA 105 :HHIVALYQNALDH Number of specific fragments extracted= 6 number of extra gaps= 0 total=52 Number of alignments=8 # 1r1tA read from 1r1tA/merged-good-all-a2m # found chain 1r1tA in training set T0373 18 :TTLTRRLRREAQ 1r1tA 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1r1tA 45 :DPNRLRLLSLLAR T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHA 1r1tA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK T0373 88 :DGRRTRVSLSSE 1r1tA 94 :QGRHVYYQLQDH T0373 106 :GNRAKREEWLVR 1r1tA 106 :HIVALYQNALDH Number of specific fragments extracted= 5 number of extra gaps= 0 total=57 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a61A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a61A expands to /projects/compbio/data/pdb/2a61.pdb.gz 2a61A:Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2a61A # T0373 read from 2a61A/merged-good-all-a2m # 2a61A read from 2a61A/merged-good-all-a2m # adding 2a61A to template set # found chain 2a61A in template set Warning: unaligning (T0373)T3 because first residue in template chain is (2a61A)K5 T0373 4 :NQDLQL 2a61A 6 :QPFERI T0373 13 :LRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 2a61A 12 :LREICFMVKVEGRKVLRDFGITPAQFDILQKIYFEGP T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 2a61A 49 :KRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERREN T0373 115 :LVRAMHACLDESERALLAAAGPLLTRLAQ 2a61A 112 :FIEKITSDLGKEKSSKILDYLKELKGVME Number of specific fragments extracted= 4 number of extra gaps= 0 total=61 Number of alignments=10 # 2a61A read from 2a61A/merged-good-all-a2m # found chain 2a61A in template set Warning: unaligning (T0373)D6 because first residue in template chain is (2a61A)K5 T0373 7 :LQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 2a61A 6 :QPFERILREICFMVKVEGRKVLRDFGITPAQFDILQKIYF T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 2a61A 46 :EGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERRENFIEKIT T0373 121 :ACLDESERALLAAAGPLLTRLAQF 2a61A 118 :SDLGKEKSSKILDYLKELKGVMER Number of specific fragments extracted= 3 number of extra gaps= 0 total=64 Number of alignments=11 # 2a61A read from 2a61A/merged-good-all-a2m # found chain 2a61A in template set T0373 11 :AHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 2a61A 10 :RILREICFMVKVEGRKVLRDFGITPAQFDILQKIYF T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 2a61A 46 :EGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERRENFIEK T0373 119 :MHACLDESERALLAAAGPLLTRLAQ 2a61A 116 :ITSDLGKEKSSKILDYLKELKGVME Number of specific fragments extracted= 3 number of extra gaps= 0 total=67 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1smtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1smtA expands to /projects/compbio/data/pdb/1smt.pdb.gz 1smtA:# T0373 read from 1smtA/merged-good-all-a2m # 1smtA read from 1smtA/merged-good-all-a2m # adding 1smtA to template set # found chain 1smtA in template set T0373 18 :TTLTRRLRREAQ 1smtA 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1smtA 45 :DPNRLRLLSLLAR T0373 48 :GG 1smtA 58 :SE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1smtA 60 :LCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ T0373 89 :GRRTRVSLS 1smtA 95 :GRHVYYQLQ T0373 98 :SEGRRNLYGNRAKREE 1smtA 105 :HHIVALYQNALDHLQE Number of specific fragments extracted= 6 number of extra gaps= 0 total=73 Number of alignments=13 # 1smtA read from 1smtA/merged-good-all-a2m # found chain 1smtA in template set T0373 2 :PTNQDL 1smtA 27 :AIAPEV T0373 18 :TTLTRRLRREAQ 1smtA 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAID 1smtA 45 :DPNRLRLLSLLA T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1smtA 57 :RSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ T0373 89 :GRRTRVSLS 1smtA 95 :GRHVYYQLQ T0373 98 :SEGRRNLYGNRAKREE 1smtA 105 :HHIVALYQNALDHLQE Number of specific fragments extracted= 6 number of extra gaps= 0 total=79 Number of alignments=14 # 1smtA read from 1smtA/merged-good-all-a2m # found chain 1smtA in template set T0373 18 :TTLTRRLRREAQ 1smtA 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1smtA 45 :DPNRLRLLSLLAR T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1smtA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQG T0373 90 :RRTRVSLSSE 1smtA 96 :RHVYYQLQDH T0373 106 :GNRAKREEWLVR 1smtA 106 :HIVALYQNALDH T0373 119 :MHA 1smtA 118 :LQE Number of specific fragments extracted= 6 number of extra gaps= 0 total=85 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1smtB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1smtB expands to /projects/compbio/data/pdb/1smt.pdb.gz 1smtB:# T0373 read from 1smtB/merged-good-all-a2m # 1smtB read from 1smtB/merged-good-all-a2m # adding 1smtB to template set # found chain 1smtB in template set T0373 18 :TTLTRRLRREAQ 1smtB 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1smtB 45 :DPNRLRLLSLLAR T0373 48 :GG 1smtB 58 :SE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1smtB 60 :LCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQG T0373 90 :RRTRVSLS 1smtB 96 :RHVYYQLQ T0373 98 :SEGRRNLYGNRAKR 1smtB 105 :HHIVALYQNALDHL Number of specific fragments extracted= 6 number of extra gaps= 0 total=91 Number of alignments=16 # 1smtB read from 1smtB/merged-good-all-a2m # found chain 1smtB in template set T0373 1 :MPTNQDL 1smtB 26 :QAIAPEV T0373 18 :TTLTRRLRREAQ 1smtB 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAID 1smtB 45 :DPNRLRLLSLLA T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1smtB 57 :RSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQG T0373 90 :RRTRVSLS 1smtB 96 :RHVYYQLQ T0373 98 :SEGRRNLYGNRAKR 1smtB 105 :HHIVALYQNALDHL Number of specific fragments extracted= 6 number of extra gaps= 0 total=97 Number of alignments=17 # 1smtB read from 1smtB/merged-good-all-a2m # found chain 1smtB in template set T0373 18 :TTLTRRLRREAQ 1smtB 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1smtB 45 :DPNRLRLLSLLAR T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1smtB 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ T0373 89 :GRRTRVSLSSE 1smtB 95 :GRHVYYQLQDH T0373 106 :GNRAKREEWLVR 1smtB 106 :HIVALYQNALDH Number of specific fragments extracted= 5 number of extra gaps= 0 total=102 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bi0/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bi0 expands to /projects/compbio/data/pdb/1bi0.pdb.gz 1bi0:Warning: there is no chain 1bi0 will retry with 1bi0A # T0373 read from 1bi0/merged-good-all-a2m # 1bi0 read from 1bi0/merged-good-all-a2m # adding 1bi0 to template set # found chain 1bi0 in template set Warning: unaligning (T0373)L131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bi0)R103 Warning: unaligning (T0373)A133 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bi0)R103 T0373 36 :SQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1bi0 10 :MYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVA T0373 87 :QDGR 1bi0 58 :SDRS T0373 94 :VSLSSEGRRNLYGNRAKRE 1bi0 62 :LQMTPTGRTLATAVMRKHR T0373 115 :LVRAMHAC 1bi0 81 :LAERLLTD T0373 123 :LD 1bi0 92 :LD T0373 125 :ESERAL 1bi0 95 :NKVHDE T0373 134 :AG 1bi0 104 :WE T0373 136 :PLLTRLAQFEEP 1bi0 111 :EVERRLVKVLKD Number of specific fragments extracted= 8 number of extra gaps= 0 total=110 Number of alignments=19 # 1bi0 read from 1bi0/merged-good-all-a2m # found chain 1bi0 in template set Warning: unaligning (T0373)L131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bi0)R103 Warning: unaligning (T0373)A133 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bi0)R103 T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 1bi0 9 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVV T0373 85 :DPQDG 1bi0 57 :ASDRS T0373 94 :VSLSSEGRRNLYGNRAKREEWLVRAM 1bi0 62 :LQMTPTGRTLATAVMRKHRLAERLLT T0373 121 :ACLD 1bi0 88 :DIIG T0373 125 :ESERAL 1bi0 95 :NKVHDE T0373 134 :AG 1bi0 104 :WE T0373 136 :PLLTRLAQFEEP 1bi0 111 :EVERRLVKVLKD Number of specific fragments extracted= 7 number of extra gaps= 0 total=117 Number of alignments=20 # 1bi0 read from 1bi0/merged-good-all-a2m # found chain 1bi0 in template set T0373 36 :SQLVVLGAIDR 1bi0 10 :MYLRTIYELEE T0373 48 :GGD 1bi0 21 :EGV T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1bi0 25 :PLRARIAERLEQSGPTVSQTVARMERDGLVVVASDR T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVRA 1bi0 61 :SLQMTPTGRTLATAVMRKHRLAERLL T0373 119 :MHACLDES 1bi0 88 :DIIGLDIN Number of specific fragments extracted= 5 number of extra gaps= 0 total=122 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xmaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xmaA expands to /projects/compbio/data/pdb/1xma.pdb.gz 1xmaA:Skipped atom 237, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 239, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 241, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 243, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 245, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 436, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 438, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 440, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 722, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 724, because occupancy 0.350 <= existing 0.650 in 1xmaA # T0373 read from 1xmaA/merged-good-all-a2m # 1xmaA read from 1xmaA/merged-good-all-a2m # adding 1xmaA to template set # found chain 1xmaA in template set Warning: unaligning (T0373)P86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmaA)K72 Warning: unaligning (T0373)G89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmaA)K72 Warning: unaligning (T0373)D124 because last residue in template chain is (1xmaA)K106 T0373 35 :FSQLVVLGAIDR 1xmaA 10 :YVDTIILSLLIE T0373 48 :GG 1xmaA 22 :GD T0373 51 :VTPSELAAAER 1xmaA 24 :SYGYEISKNIR T0373 62 :MRSSNLAALLRELERGGLIVRHA 1xmaA 43 :IKETTLYSAFARLEKNGYIKSYY T0373 85 :D 1xmaA 68 :E T0373 90 :RRTRVSLSSEGRRNLYGNRAKREE 1xmaA 73 :RRTYYRITPEGIKYYKQKCEEWEL T0373 115 :LVRAMHACL 1xmaA 97 :TKKVINKFV Number of specific fragments extracted= 7 number of extra gaps= 0 total=129 Number of alignments=22 # 1xmaA read from 1xmaA/merged-good-all-a2m # found chain 1xmaA in template set Warning: unaligning (T0373)P86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmaA)K72 Warning: unaligning (T0373)G89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmaA)K72 Warning: unaligning (T0373)D124 because last residue in template chain is (1xmaA)K106 T0373 35 :FSQLVVLGAIDR 1xmaA 10 :YVDTIILSLLIE T0373 49 :GDVTPSELAAAER 1xmaA 22 :GDSYGYEISKNIR T0373 62 :MRSSNLAALLRELERGGLIVRHA 1xmaA 43 :IKETTLYSAFARLEKNGYIKSYY T0373 85 :D 1xmaA 68 :E T0373 90 :RRTRVSLSSEGRRNLYGNRAKREEWLVRAM 1xmaA 73 :RRTYYRITPEGIKYYKQKCEEWELTKKVIN T0373 121 :ACL 1xmaA 103 :KFV Number of specific fragments extracted= 6 number of extra gaps= 0 total=135 Number of alignments=23 # 1xmaA read from 1xmaA/merged-good-all-a2m # found chain 1xmaA in template set Warning: unaligning (T0373)P86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmaA)K72 Warning: unaligning (T0373)G89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmaA)K72 Warning: unaligning (T0373)D124 because last residue in template chain is (1xmaA)K106 T0373 35 :FSQLVVLGAIDR 1xmaA 10 :YVDTIILSLLIE T0373 49 :GDVTPSELAAAER 1xmaA 22 :GDSYGYEISKNIR T0373 62 :MRSSNLAALLRELERGGLIVRH 1xmaA 43 :IKETTLYSAFARLEKNGYIKSY T0373 84 :AD 1xmaA 67 :EE T0373 90 :RRTRVSLSSEGRRNLYGNRAKREEWLVR 1xmaA 73 :RRTYYRITPEGIKYYKQKCEEWELTKKV T0373 119 :MHACL 1xmaA 101 :INKFV Number of specific fragments extracted= 6 number of extra gaps= 0 total=141 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c0wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c0wA expands to /projects/compbio/data/pdb/1c0w.pdb.gz 1c0wA:# T0373 read from 1c0wA/merged-good-all-a2m # 1c0wA read from 1c0wA/merged-good-all-a2m # adding 1c0wA to template set # found chain 1c0wA in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1c0wA 9 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVA T0373 87 :QDGR 1c0wA 58 :SDRS T0373 94 :VSLSSEGRRNLYGNRAKR 1c0wA 62 :LQMTPTGRTLATAVMRKH T0373 112 :EE 1c0wA 95 :NK T0373 115 :LVRAMHAC 1c0wA 97 :VHDEACRW T0373 123 :LDES 1c0wA 108 :MSDE T0373 137 :LLTRLAQFEEP 1c0wA 112 :VERRLVKVLKD Number of specific fragments extracted= 7 number of extra gaps= 0 total=148 Number of alignments=25 # 1c0wA read from 1c0wA/merged-good-all-a2m # found chain 1c0wA in template set T0373 32 :PVQFSQLVVLGAIDRL 1c0wA 3 :DLVDTTEMYLRTIYEL T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 1c0wA 22 :GVTPLRARIAERLEQSGPTVSQTVARMERDGLVVV T0373 85 :DPQDG 1c0wA 57 :ASDRS T0373 94 :VSLSSEGRRNLYGNRAKREEWLVRAM 1c0wA 62 :LQMTPTGRTLATAVMRKHRLAERLLT T0373 121 :ACLD 1c0wA 88 :DIIG T0373 125 :ESERALLAAAG 1c0wA 95 :NKVHDEACRWE T0373 136 :PLLTRLAQFEEP 1c0wA 111 :EVERRLVKVLKD Number of specific fragments extracted= 7 number of extra gaps= 0 total=155 Number of alignments=26 # 1c0wA read from 1c0wA/merged-good-all-a2m # found chain 1c0wA in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1c0wA 9 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASD T0373 89 :G 1c0wA 60 :R T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVR 1c0wA 61 :SLQMTPTGRTLATAVMRKHRLAERL T0373 119 :MHACLD 1c0wA 86 :LTDIIG T0373 132 :AAAGPLLTRLA 1c0wA 95 :NKVHDEACRWE Number of specific fragments extracted= 5 number of extra gaps= 0 total=160 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b1bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b1bA expands to /projects/compbio/data/pdb/1b1b.pdb.gz 1b1bA:# T0373 read from 1b1bA/merged-good-all-a2m # 1b1bA read from 1b1bA/merged-good-all-a2m # adding 1b1bA to template set # found chain 1b1bA in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1b1bA 9 :EMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVA T0373 87 :QDGR 1b1bA 58 :GDRH T0373 94 :VSLSSEGRRNLYGNRAKRE 1b1bA 62 :LELTEKGRALAIAVMRKHR T0373 114 :WLVRAMHAC 1b1bA 81 :LAERLLVDV T0373 125 :ESERALLAAA 1b1bA 95 :EEVHAEACRW T0373 136 :PLLTRLAQFEEP 1b1bA 111 :DVERRLVKVLNN Number of specific fragments extracted= 6 number of extra gaps= 0 total=166 Number of alignments=28 # 1b1bA read from 1b1bA/merged-good-all-a2m # found chain 1b1bA in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1b1bA 9 :EMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVA T0373 87 :QDGR 1b1bA 58 :GDRH T0373 94 :VSLSSEGRRNLYGNRAKREEWLVRAM 1b1bA 62 :LELTEKGRALAIAVMRKHRLAERLLV T0373 121 :ACLD 1b1bA 88 :DVIG T0373 125 :ESERALLAAA 1b1bA 95 :EEVHAEACRW T0373 136 :PLLTRLAQFEEP 1b1bA 111 :DVERRLVKVLNN Number of specific fragments extracted= 6 number of extra gaps= 0 total=172 Number of alignments=29 # 1b1bA read from 1b1bA/merged-good-all-a2m # found chain 1b1bA in template set T0373 37 :QLVVLGAIDR 1b1bA 8 :TEMYLRTIYD T0373 47 :LGGD 1b1bA 20 :EEGV T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 1b1bA 25 :PLRARIAERLDQSGPTVSQTVSRMERDGLLRVA T0373 87 :QDG 1b1bA 58 :GDR T0373 93 :RVSLSSEGRRNLYGNRAKR 1b1bA 61 :HLELTEKGRALAIAVMRKH T0373 112 :EEWLVR 1b1bA 98 :HAEACR T0373 119 :MHACLDES 1b1bA 104 :WEHVMSED T0373 130 :LLAAAGP 1b1bA 112 :VERRLVK Number of specific fragments extracted= 8 number of extra gaps= 0 total=180 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f2eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f2eA expands to /projects/compbio/data/pdb/2f2e.pdb.gz 2f2eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 955, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 2f2eA # T0373 read from 2f2eA/merged-good-all-a2m # 2f2eA read from 2f2eA/merged-good-all-a2m # adding 2f2eA to template set # found chain 2f2eA in template set T0373 37 :QLVVLGAIDR 2f2eA 26 :SMLIVRDAFE T0373 48 :GG 2f2eA 36 :GL T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRT 2f2eA 38 :TRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVPAESGSHQE T0373 94 :VSLSSEGR 2f2eA 80 :YRLTDKGR T0373 106 :GNRAKREEWLVRAMHACLDES 2f2eA 88 :ALFPLLVAIRQWGEDYFFAPD Number of specific fragments extracted= 5 number of extra gaps= 0 total=185 Number of alignments=31 # 2f2eA read from 2f2eA/merged-good-all-a2m # found chain 2f2eA in template set T0373 37 :QLVVLGAID 2f2eA 26 :SMLIVRDAF T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRR 2f2eA 35 :EGLTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVPAESGSHQ T0373 93 :RVSLSSEGRRNLYGNRAKREEWLV 2f2eA 79 :EYRLTDKGRALFPLLVAIRQWGED T0373 121 :AC 2f2eA 103 :YF Number of specific fragments extracted= 4 number of extra gaps= 0 total=189 Number of alignments=32 # 2f2eA read from 2f2eA/merged-good-all-a2m # found chain 2f2eA in template set T0373 37 :QLVVLGAIDR 2f2eA 26 :SMLIVRDAFE T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRT 2f2eA 36 :GLTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVPAESGSHQE T0373 94 :VSLSSEGR 2f2eA 80 :YRLTDKGR T0373 106 :GNRAKREEWLVRAMHACLDES 2f2eA 88 :ALFPLLVAIRQWGEDYFFAPD Number of specific fragments extracted= 4 number of extra gaps= 0 total=193 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sd4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sd4A expands to /projects/compbio/data/pdb/1sd4.pdb.gz 1sd4A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 1sd4A/merged-good-all-a2m # 1sd4A read from 1sd4A/merged-good-all-a2m # adding 1sd4A to template set # found chain 1sd4A in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1sd4A)Q5 T0373 31 :DPVQFSQLVVLGAIDRLGG 1sd4A 6 :VEISMAEWDVMNIIWDKKS T0373 51 :VTPSELAAAER 1sd4A 25 :VSANEIVVEIQ T0373 62 :MRSSNLAALLRELERGGLIVRHADPQ 1sd4A 40 :VSDKTIRTLITRLYKKEIIKRYKSEN T0373 91 :RTRVSLS 1sd4A 66 :IYFYSSN T0373 98 :SEGRRNLYGNRAK 1sd4A 76 :DDIKMKTAKTFLN T0373 113 :E 1sd4A 89 :K T0373 114 :WLVRAMHAC 1sd4A 97 :SLVLNFAKN T0373 123 :LDESERALLAA 1sd4A 108 :LNNKEIEELRD T0373 137 :LLTR 1sd4A 119 :ILND Number of specific fragments extracted= 9 number of extra gaps= 0 total=202 Number of alignments=34 # 1sd4A read from 1sd4A/merged-good-all-a2m # found chain 1sd4A in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1sd4A)Q5 T0373 31 :DPVQFSQLVVLGAIDRL 1sd4A 6 :VEISMAEWDVMNIIWDK T0373 49 :GDVTPSELAAAE 1sd4A 23 :KSVSANEIVVEI T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQ 1sd4A 39 :EVSDKTIRTLITRLYKKEIIKRYKSEN T0373 91 :RTRVSLS 1sd4A 66 :IYFYSSN T0373 98 :SEGRRNLYGNR 1sd4A 76 :DDIKMKTAKTF T0373 109 :AKR 1sd4A 96 :KSL T0373 114 :WLVRAMHACLDESERALLAA 1sd4A 99 :VLNFAKNEELNNKEIEELRD T0373 137 :LLTR 1sd4A 119 :ILND Number of specific fragments extracted= 8 number of extra gaps= 0 total=210 Number of alignments=35 # 1sd4A read from 1sd4A/merged-good-all-a2m # found chain 1sd4A in template set T0373 31 :DPVQFSQLVVLGAIDR 1sd4A 6 :VEISMAEWDVMNIIWD T0373 48 :GGDVTPSELAAAER 1sd4A 22 :KKSVSANEIVVEIQ T0373 62 :MRSSNLAALLRELERGGLIVRHADPQ 1sd4A 40 :VSDKTIRTLITRLYKKEIIKRYKSEN T0373 91 :RTRVSLS 1sd4A 66 :IYFYSSN T0373 98 :SEGRRNLYGNR 1sd4A 76 :DDIKMKTAKTF T0373 109 :AKREEWLVR 1sd4A 96 :KSLVLNFAK T0373 120 :HACLDESERALLAAAGPL 1sd4A 105 :NEELNNKEIEELRDILND Number of specific fragments extracted= 7 number of extra gaps= 0 total=217 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fswA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fswA expands to /projects/compbio/data/pdb/2fsw.pdb.gz 2fswA:Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 179, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 326, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 330, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 397, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 399, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 401, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 403, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 405, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 407, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 409, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 411, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 413, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 415, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 417, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 524, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 526, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 694, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 696, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 698, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 894, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 896, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 898, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 900, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 902, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 904, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 906, because occupancy 0.300 <= existing 0.340 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 908, because occupancy 0.400 <= existing 0.600 in 2fswA # T0373 read from 2fswA/merged-good-all-a2m # 2fswA read from 2fswA/merged-good-all-a2m # adding 2fswA to template set # found chain 2fswA in template set T0373 41 :LGAIDRLGGD 2fswA 25 :LLIIFQINRR T0373 51 :VTPSELAAAE 2fswA 36 :IRYGELKRAI T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEG 2fswA 47 :GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLG T0373 105 :YGNRAKREE 2fswA 87 :EKVLPIIDE T0373 115 :LVRAMHA 2fswA 96 :IAKFGME Number of specific fragments extracted= 5 number of extra gaps= 0 total=222 Number of alignments=37 # 2fswA read from 2fswA/merged-good-all-a2m # found chain 2fswA in template set T0373 30 :ADP 2fswA 20 :AGK T0373 36 :SQLVVLGAID 2fswA 23 :WTLLIIFQIN T0373 48 :GGDVTPSELAAAE 2fswA 33 :RRIIRYGELKRAI T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEG 2fswA 47 :GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLG T0373 105 :YGNRAKREEWLVRAM 2fswA 87 :EKVLPIIDEIAKFGM T0373 121 :A 2fswA 102 :E Number of specific fragments extracted= 6 number of extra gaps= 0 total=228 Number of alignments=38 # 2fswA read from 2fswA/merged-good-all-a2m # found chain 2fswA in template set T0373 40 :VLGAIDRLGGD 2fswA 24 :TLLIIFQINRR T0373 51 :VTPSELAAAE 2fswA 36 :IRYGELKRAI T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGR 2fswA 47 :GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLGE T0373 106 :GNRAKREEWLVR 2fswA 88 :KVLPIIDEIAKF T0373 119 :MHA 2fswA 100 :GME Number of specific fragments extracted= 5 number of extra gaps= 0 total=233 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z91A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z91A expands to /projects/compbio/data/pdb/1z91.pdb.gz 1z91A:# T0373 read from 1z91A/merged-good-all-a2m # 1z91A read from 1z91A/merged-good-all-a2m # adding 1z91A to template set # found chain 1z91A in template set Warning: unaligning (T0373)T3 because first residue in template chain is (1z91A)M8 Warning: unaligning (T0373)E146 because last residue in template chain is (1z91A)H144 T0373 4 :NQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 1z91A 9 :KLENQLSFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHET T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRN 1z91A 55 :LTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALL T0373 104 :LYGNRAKREE 1z91A 111 :AVDIPGTILG T0373 120 :HACLDESERALLAA 1z91A 121 :LSKQSGEDLKQLKS T0373 137 :LLTRLAQFE 1z91A 135 :ALYTLLETL Number of specific fragments extracted= 5 number of extra gaps= 0 total=238 Number of alignments=40 # 1z91A read from 1z91A/merged-good-all-a2m # found chain 1z91A in template set Warning: unaligning (T0373)T3 because first residue in template chain is (1z91A)M8 Warning: unaligning (T0373)E146 because last residue in template chain is (1z91A)H144 T0373 4 :NQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRL 1z91A 9 :KLENQLSFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEH T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRN 1z91A 53 :ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALL T0373 104 :LYGNRAKREEW 1z91A 111 :AVDIPGTILGL T0373 121 :ACLDESERALLAA 1z91A 122 :SKQSGEDLKQLKS T0373 137 :LLTRLAQFE 1z91A 135 :ALYTLLETL Number of specific fragments extracted= 5 number of extra gaps= 0 total=243 Number of alignments=41 # 1z91A read from 1z91A/merged-good-all-a2m # found chain 1z91A in template set T0373 11 :AHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 1z91A 16 :FLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRN 1z91A 52 :HETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALL T0373 104 :LYG 1z91A 111 :AVD T0373 111 :REEWLVR 1z91A 114 :IPGTILG T0373 120 :HACLDESERALLAAAGPLLTR 1z91A 121 :LSKQSGEDLKQLKSALYTLLE Number of specific fragments extracted= 5 number of extra gaps= 0 total=248 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zybA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zybA expands to /projects/compbio/data/pdb/1zyb.pdb.gz 1zybA:Skipped atom 11, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 13, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 15, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 1zybA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 223, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 229, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 429, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 431, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 433, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 435, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 1zybA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 938, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 940, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 942, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 972, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 974, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1094, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1138, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1140, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1142, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1144, because occupancy 0.500 <= existing 0.500 in 1zybA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1240, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1242, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1244, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1246, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1280, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1282, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1284, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1286, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1288, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1290, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1382, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1384, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1503, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1505, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1507, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1509, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1511, because occupancy 0.300 <= existing 0.700 in 1zybA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 1zybA/merged-good-all-a2m # 1zybA read from 1zybA/merged-good-all-a2m # adding 1zybA to template set # found chain 1zybA in template set T0373 12 :HLRSQVTTLTRRLRREAQAD 1zybA 124 :IFRLNYMNIVSNRAQNLYSR T0373 32 :PVQFSQLVVLGAIDRL 1zybA 148 :PTLDLKSKIIRFFLSH T0373 48 :GGD 1zybA 168 :QGE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 1zybA 175 :VKMDDLARCLDDTRLNISKTLNELQDNGLIELH T0373 89 :GRRTRV 1zybA 208 :RKEILI Number of specific fragments extracted= 5 number of extra gaps= 0 total=253 Number of alignments=43 # 1zybA read from 1zybA/merged-good-all-a2m # found chain 1zybA in template set T0373 7 :LQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRL 1zybA 123 :DIFRLNYMNIVSNRAQNLYSRLWDEPTLDLKSKIIRFFLSH T0373 48 :GGD 1zybA 168 :QGE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 1zybA 175 :VKMDDLARCLDDTRLNISKTLNELQDNGLIELH T0373 89 :GRRTRV 1zybA 208 :RKEILI Number of specific fragments extracted= 4 number of extra gaps= 0 total=257 Number of alignments=44 # 1zybA read from 1zybA/merged-good-all-a2m # found chain 1zybA in template set T0373 7 :LQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 1zybA 123 :DIFRLNYMNIVSNRAQNLYSRLWDEPTLDLKSKIIRFFLS T0373 48 :GGD 1zybA 168 :QGE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHA 1zybA 175 :VKMDDLARCLDDTRLNISKTLNELQDNGLIELHR T0373 90 :RRTRV 1zybA 209 :KEILI Number of specific fragments extracted= 4 number of extra gaps= 0 total=261 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fxaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fxaA expands to /projects/compbio/data/pdb/2fxa.pdb.gz 2fxaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 461, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 2fxaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 567, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 918, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1117, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1131, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1189, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1191, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1193, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1199, because occupancy 0.500 <= existing 0.500 in 2fxaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1272, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1280, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1282, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1284, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1286, because occupancy 0.500 <= existing 0.500 in 2fxaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 2fxaA/merged-good-all-a2m # 2fxaA read from 2fxaA/merged-good-all-a2m # adding 2fxaA to template set # found chain 2fxaA in template set Warning: unaligning (T0373)T3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fxaA)D9 Warning: unaligning (T0373)N4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fxaA)D9 Warning: unaligning (T0373)D85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fxaA)T102 Warning: unaligning (T0373)T92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0373 2 :P 2fxaA 7 :P T0373 5 :QDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 2fxaA 16 :FTQKMAQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQLNG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHA 2fxaA 61 :ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK T0373 93 :RVSLSSEGRRNLYGNRAK 2fxaA 103 :YVQLTEEGTEVFWSLLEE Number of specific fragments extracted= 4 number of extra gaps= 1 total=265 Number of alignments=46 # 2fxaA read from 2fxaA/merged-good-all-a2m # found chain 2fxaA in template set Warning: unaligning (T0373)T3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fxaA)D9 Warning: unaligning (T0373)N4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fxaA)D9 Warning: unaligning (T0373)D85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fxaA)T102 Warning: unaligning (T0373)T92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0373 1 :MP 2fxaA 6 :PP T0373 5 :QD 2fxaA 10 :VK T0373 7 :LQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 2fxaA 18 :QKMAQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQLNG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHA 2fxaA 61 :ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK T0373 93 :RVSLSSEGRRNLYGNRA 2fxaA 103 :YVQLTEEGTEVFWSLLE T0373 111 :REEW 2fxaA 128 :VFKG T0373 115 :LVRAM 2fxaA 135 :LYHLF T0373 121 :ACLD 2fxaA 140 :GKFP T0373 125 :ESERALLAAAGP 2fxaA 146 :AEMMCMIRHIYG T0373 139 :TRLAQFEE 2fxaA 158 :DDFMEIFE Number of specific fragments extracted= 10 number of extra gaps= 1 total=275 Number of alignments=47 # 2fxaA read from 2fxaA/merged-good-all-a2m # found chain 2fxaA in template set Warning: unaligning (T0373)D85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fxaA)T102 Warning: unaligning (T0373)T92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0373 10 :AAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 2fxaA 21 :AQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQ T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHA 2fxaA 58 :LNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK T0373 93 :RVSLSSEGRRNLYGNRAK 2fxaA 103 :YVQLTEEGTEVFWSLLEE T0373 112 :EEWLVR 2fxaA 133 :QPLYHL T0373 120 :HACLD 2fxaA 139 :FGKFP T0373 125 :ESERALLAA 2fxaA 146 :AEMMCMIRH Number of specific fragments extracted= 6 number of extra gaps= 0 total=281 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dtr/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2dtr expands to /projects/compbio/data/pdb/2dtr.pdb.gz 2dtr:Warning: there is no chain 2dtr will retry with 2dtrA # T0373 read from 2dtr/merged-good-all-a2m # 2dtr read from 2dtr/merged-good-all-a2m # adding 2dtr to template set # found chain 2dtr in template set T0373 36 :SQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 2dtr 10 :MYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVA T0373 87 :QDGR 2dtr 58 :SDRS T0373 94 :VSLSSEGRRNLYGNRAKRE 2dtr 62 :LQMTPTGRTLATAVMRKHR T0373 114 :WLVRAMHAC 2dtr 81 :LAERLLTDI T0373 127 :ERALLAAAG 2dtr 97 :VHDEACRWE T0373 136 :PLLTRLAQFEEP 2dtr 111 :EVERRLVKVLKD Number of specific fragments extracted= 6 number of extra gaps= 0 total=287 Number of alignments=49 # 2dtr read from 2dtr/merged-good-all-a2m # found chain 2dtr in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 2dtr 9 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVV T0373 85 :DPQDG 2dtr 57 :ASDRS T0373 94 :VSLSSEGRRNLYGNRAKREEWLVRAM 2dtr 62 :LQMTPTGRTLATAVMRKHRLAERLLT T0373 121 :ACLD 2dtr 88 :DIIG T0373 125 :ESERALLAAAG 2dtr 95 :NKVHDEACRWE T0373 136 :PLLTRLAQFEEP 2dtr 111 :EVERRLVKVLKD Number of specific fragments extracted= 6 number of extra gaps= 0 total=293 Number of alignments=50 # 2dtr read from 2dtr/merged-good-all-a2m # found chain 2dtr in template set T0373 36 :SQLVVLGAIDR 2dtr 10 :MYLRTIYELEE T0373 48 :GGD 2dtr 21 :EGV T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 2dtr 25 :PLRARIAERLEQSGPTVSQTVARMERDGLVVVASDR T0373 93 :RVSLSSEGRRNLYGNRAKR 2dtr 61 :SLQMTPTGRTLATAVMRKH T0373 112 :EEWLVR 2dtr 98 :HDEACR T0373 119 :MHACLDES 2dtr 104 :WEHVMSDE T0373 130 :LLAAAGP 2dtr 112 :VERRLVK Number of specific fragments extracted= 7 number of extra gaps= 0 total=300 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b0lA expands to /projects/compbio/data/pdb/2b0l.pdb.gz 2b0lA:Skipped atom 32, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 34, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 36, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 38, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 40, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 42, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 44, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 46, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 48, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 50, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 123, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 125, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 127, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 129, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 131, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 133, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 135, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 137, because occupancy 0.200 <= existing 0.800 in 2b0lA # T0373 read from 2b0lA/merged-good-all-a2m # 2b0lA read from 2b0lA/merged-good-all-a2m # adding 2b0lA to template set # found chain 2b0lA in template set Warning: unaligning (T0373)R46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0373)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0373)A69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0373)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0373)I80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0373)H83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0373)A84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0373)P86 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 Warning: unaligning (T0373)G89 because of BadResidue code BAD_PEPTIDE at template residue (2b0lA)M237 Warning: unaligning (T0373)G106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)L256 T0373 7 :L 2b0lA 169 :K T0373 22 :RRLRREAQ 2b0lA 170 :AVVQMAIS T0373 32 :PVQFSQLVVLGAID 2b0lA 178 :SLSYSELEAIEHIF T0373 48 :GGD 2b0lA 195 :DGN T0373 51 :VTPSELAAAERMRSSNLA 2b0lA 201 :LVASKIADRVGITRSVIV T0373 71 :LRELERGGL 2b0lA 221 :LRKLESAGV T0373 82 :R 2b0lA 232 :S T0373 90 :RRTRVSL 2b0lA 238 :KGTYIKV T0373 97 :SSEGRRNLY 2b0lA 246 :NNKFLIELE Number of specific fragments extracted= 9 number of extra gaps= 5 total=309 Number of alignments=52 # 2b0lA read from 2b0lA/merged-good-all-a2m # found chain 2b0lA in template set Warning: unaligning (T0373)R46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0373)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0373)A69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0373)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0373)I80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0373)H83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0373)A84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0373)P86 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 Warning: unaligning (T0373)G89 because of BadResidue code BAD_PEPTIDE at template residue (2b0lA)M237 Warning: unaligning (T0373)G106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)L256 T0373 4 :NQDLQL 2b0lA 166 :HMSKAV T0373 24 :LRREAQ 2b0lA 172 :VQMAIS T0373 32 :PVQFSQLVVLGAID 2b0lA 178 :SLSYSELEAIEHIF T0373 48 :GG 2b0lA 196 :GN T0373 50 :DVTPSELAAAERMRSSNLA 2b0lA 200 :LLVASKIADRVGITRSVIV T0373 71 :LRELERGGL 2b0lA 221 :LRKLESAGV T0373 82 :R 2b0lA 232 :S T0373 90 :RRTRVSLS 2b0lA 238 :KGTYIKVL T0373 98 :SEGRRNLY 2b0lA 247 :NKFLIELE Number of specific fragments extracted= 9 number of extra gaps= 5 total=318 Number of alignments=53 # 2b0lA read from 2b0lA/merged-good-all-a2m # found chain 2b0lA in template set Warning: unaligning (T0373)R46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0373)A69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0373)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0373)I80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0373)H83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0373)A84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0373)P86 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE at template residue (2b0lA)M237 Warning: unaligning (T0373)G106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)L256 T0373 21 :TRRLRREAQ 2b0lA 169 :KAVVQMAIS T0373 32 :PVQFSQLVVLGAID 2b0lA 178 :SLSYSELEAIEHIF T0373 47 :LGGD 2b0lA 194 :LDGN T0373 51 :VTPSELAAAERMRSSNLA 2b0lA 201 :LVASKIADRVGITRSVIV T0373 71 :LRELERGGL 2b0lA 221 :LRKLESAGV T0373 82 :R 2b0lA 232 :S T0373 88 :DGRRTRV 2b0lA 238 :KGTYIKV T0373 96 :LSSEGRRNLY 2b0lA 245 :LNNKFLIELE Number of specific fragments extracted= 8 number of extra gaps= 5 total=326 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z1dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z1dA expands to /projects/compbio/data/pdb/1z1d.pdb.gz 1z1dA:# T0373 read from 1z1dA/merged-good-all-a2m # 1z1dA read from 1z1dA/merged-good-all-a2m # adding 1z1dA to template set # found chain 1z1dA in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1z1dA)A202 T0373 31 :DPVQFSQLVVLGAIDRLGGD 1z1dA 203 :NGLTVAQNQVLNLIKACPRP T0373 51 :VTPSELAAAE 1z1dA 225 :LNFQDLKNQL T0373 61 :RMRSSNLAALLRELERGGLIVRHADP 1z1dA 236 :HMSVSSIKQAVDFLSNEGHIYSTVDD Number of specific fragments extracted= 3 number of extra gaps= 0 total=329 Number of alignments=55 # 1z1dA read from 1z1dA/merged-good-all-a2m # found chain 1z1dA in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1z1dA)A202 T0373 31 :DPVQFSQLVVLGAIDRL 1z1dA 203 :NGLTVAQNQVLNLIKAC T0373 48 :GGDVTPSELAAAE 1z1dA 222 :PEGLNFQDLKNQL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQ 1z1dA 236 :HMSVSSIKQAVDFLSNEGHIYSTVDDD T0373 93 :RVS 1z1dA 263 :HFK Number of specific fragments extracted= 4 number of extra gaps= 0 total=333 Number of alignments=56 # 1z1dA read from 1z1dA/merged-good-all-a2m # found chain 1z1dA in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1z1dA)A202 T0373 31 :DPVQFSQLVVLGAIDRLGGD 1z1dA 203 :NGLTVAQNQVLNLIKACPRP T0373 51 :VTPSELAAAE 1z1dA 225 :LNFQDLKNQL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQ 1z1dA 236 :HMSVSSIKQAVDFLSNEGHIYSTVDDD Number of specific fragments extracted= 3 number of extra gaps= 0 total=336 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2co5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2co5A expands to /projects/compbio/data/pdb/2co5.pdb.gz 2co5A:Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 735, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 737, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2co5A # T0373 read from 2co5A/merged-good-all-a2m # 2co5A read from 2co5A/merged-good-all-a2m # adding 2co5A to template set # found chain 2co5A in template set Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2co5A)P66 Warning: unaligning (T0373)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2co5A)P66 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE at template residue (2co5A)D67 T0373 35 :FSQLVVLGAIDRLGGDV 2co5A 9 :INYYIILKVLVINGSRL T0373 53 :PSELAAAER 2co5A 31 :RSEILKRFD T0373 62 :MRSSNLAALLRELERGGLIVRHA 2co5A 42 :ISDGVLYPLIDSLIDDKILREEE T0373 88 :DG 2co5A 68 :GK T0373 93 :RVSLSSEGRRNLYGNRAKREE 2co5A 70 :VLFLTEKGMKEFEELHEFFKK T0373 115 :LV 2co5A 91 :IV Number of specific fragments extracted= 6 number of extra gaps= 1 total=342 Number of alignments=58 # 2co5A read from 2co5A/merged-good-all-a2m # found chain 2co5A in template set Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2co5A)P66 Warning: unaligning (T0373)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2co5A)P66 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE at template residue (2co5A)D67 T0373 35 :FSQLVVLGAIDRLGGDVT 2co5A 9 :INYYIILKVLVINGSRLE T0373 53 :PSELAAAE 2co5A 31 :RSEILKRF T0373 61 :RMRSSNLAALLRELERGGLIVRHA 2co5A 41 :DISDGVLYPLIDSLIDDKILREEE T0373 88 :DG 2co5A 68 :GK T0373 93 :RVSLSSEGRRNLYGNRAKREEWL 2co5A 70 :VLFLTEKGMKEFEELHEFFKKIV Number of specific fragments extracted= 5 number of extra gaps= 1 total=347 Number of alignments=59 # 2co5A read from 2co5A/merged-good-all-a2m # found chain 2co5A in template set Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2co5A)P66 Warning: unaligning (T0373)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2co5A)P66 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE at template residue (2co5A)D67 T0373 35 :FSQLVVLGAIDRLGGD 2co5A 9 :INYYIILKVLVINGSR T0373 53 :PSELAAAER 2co5A 31 :RSEILKRFD T0373 62 :MRSSNLAALLRELERGGLIVRHA 2co5A 42 :ISDGVLYPLIDSLIDDKILREEE T0373 88 :DG 2co5A 68 :GK T0373 93 :RVSLSSEGRRNLYGNRAKREEWL 2co5A 70 :VLFLTEKGMKEFEELHEFFKKIV Number of specific fragments extracted= 5 number of extra gaps= 1 total=352 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xnpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xnpA expands to Error: no filename for 1xnpA 1xnpA expands to Error: no filename for 1xnpA 1xnpA expands to Error: no filename for 1xnpA # T0373 read from 1xnpA/merged-good-all-a2m # 1xnpA read from 1xnpA/merged-good-all-a2m # adding 1xnpA to template set Error: can't find template for 1xnpA or 1xnpA, so skipping it. # 1xnpA read from 1xnpA/merged-good-all-a2m # adding 1xnpA to template set Error: can't find template for 1xnpA or 1xnpA, so skipping it. # 1xnpA read from 1xnpA/merged-good-all-a2m # adding 1xnpA to template set Error: can't find template for 1xnpA or 1xnpA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z7uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z7uA expands to /projects/compbio/data/pdb/1z7u.pdb.gz 1z7uA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 60, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 1z7uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 259, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 263, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 297, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 299, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 301, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 303, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 305, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 307, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 309, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 311, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 313, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 315, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 317, because occupancy 0.400 <= existing 0.600 in 1z7uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 596, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 911, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 921, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 923, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 927, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 929, because occupancy 0.500 <= existing 0.500 in 1z7uA # T0373 read from 1z7uA/merged-good-all-a2m # 1z7uA read from 1z7uA/merged-good-all-a2m # adding 1z7uA to template set # found chain 1z7uA in template set T0373 36 :SQLVVLGAIDR 1z7uA 20 :WKLSLMDELFQ T0373 48 :GG 1z7uA 31 :GT T0373 51 :VTPSELAAAE 1z7uA 33 :KRNGELMRAL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 1z7uA 44 :GITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALYDALSSLCHW T0373 115 :LVRAMHA 1z7uA 97 :GETFAQK Number of specific fragments extracted= 5 number of extra gaps= 0 total=357 Number of alignments=61 # 1z7uA read from 1z7uA/merged-good-all-a2m # found chain 1z7uA in template set T0373 6 :DLQL 1z7uA 6 :QTSI T0373 22 :RRLRREAQ 1z7uA 10 :NLALSTIN T0373 35 :FSQLVVLGAIDR 1z7uA 19 :KWKLSLMDELFQ T0373 49 :GDVTPSELAAAE 1z7uA 31 :GTKRNGELMRAL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAMH 1z7uA 44 :GITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALYDALSSLCHWGETFAQK Number of specific fragments extracted= 5 number of extra gaps= 0 total=362 Number of alignments=62 # 1z7uA read from 1z7uA/merged-good-all-a2m # found chain 1z7uA in template set T0373 25 :RREAQADPVQFSQLVVLGAIDR 1z7uA 9 :INLALSTINGKWKLSLMDELFQ T0373 49 :GDVTPSELAAAE 1z7uA 31 :GTKRNGELMRAL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 1z7uA 44 :GITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALYDALSSLCHWGETF T0373 119 :MHA 1z7uA 101 :AQK Number of specific fragments extracted= 4 number of extra gaps= 0 total=366 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fbhA expands to /projects/compbio/data/pdb/2fbh.pdb.gz 2fbhA:Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 286, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 484, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 486, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 488, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 847, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 849, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1004, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1006, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1008, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 2fbhA # T0373 read from 2fbhA/merged-good-all-a2m # 2fbhA read from 2fbhA/merged-good-all-a2m # adding 2fbhA to template set # found chain 2fbhA in template set Warning: unaligning (T0373)S36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbhA)R37 Warning: unaligning (T0373)Q37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbhA)R37 Warning: unaligning (T0373)E60 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0373)R61 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0373 12 :HLRSQVTTLTRRLRREAQADPVQF 2fbhA 12 :LLAQTSRAWRAELDRRLSHLGLSQ T0373 38 :LVVLGAIDRLGGDVTPSELAAA 2fbhA 38 :WLVLLHLARHRDSPTQRELAQS T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIADIEAIAAS T0373 115 :LVRAMHACLDESERALLAA 2fbhA 114 :VRNDVLTGIDESEQALCQQ T0373 137 :LLTRLAQF 2fbhA 133 :VLLRILAN Number of specific fragments extracted= 5 number of extra gaps= 2 total=371 Number of alignments=64 # 2fbhA read from 2fbhA/merged-good-all-a2m # found chain 2fbhA in template set Warning: unaligning (T0373)S36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbhA)R37 Warning: unaligning (T0373)Q37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbhA)R37 Warning: unaligning (T0373)E60 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0373)R61 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0373 12 :HLRSQVTTLTRRLRREAQADPVQF 2fbhA 12 :LLAQTSRAWRAELDRRLSHLGLSQ T0373 38 :LVVLGAIDRLGGDVTPSELAAA 2fbhA 38 :WLVLLHLARHRDSPTQRELAQS T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIADIEAIAASVRNDVL T0373 121 :ACLDESERALLAA 2fbhA 120 :TGIDESEQALCQQ T0373 137 :LLTRLAQF 2fbhA 133 :VLLRILAN Number of specific fragments extracted= 5 number of extra gaps= 2 total=376 Number of alignments=65 # 2fbhA read from 2fbhA/merged-good-all-a2m # found chain 2fbhA in template set Warning: unaligning (T0373)S36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbhA)R37 Warning: unaligning (T0373)Q37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbhA)R37 Warning: unaligning (T0373)E60 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0373)R61 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0373 13 :LRSQVTTLTRRLRREAQADPVQF 2fbhA 13 :LAQTSRAWRAELDRRLSHLGLSQ T0373 38 :LVVLGAIDRLGGDVTPSELAAA 2fbhA 38 :WLVLLHLARHRDSPTQRELAQS T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIADIEAIAASVRND T0373 119 :MHACLDESERALLAAAGPLLTRLAQF 2fbhA 118 :VLTGIDESEQALCQQVLLRILANLEN Number of specific fragments extracted= 4 number of extra gaps= 2 total=380 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bjaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bjaA expands to /projects/compbio/data/pdb/1bja.pdb.gz 1bjaA:# T0373 read from 1bjaA/merged-good-all-a2m # 1bjaA read from 1bjaA/merged-good-all-a2m # adding 1bjaA to template set # found chain 1bjaA in template set T0373 23 :RLRREAQAD 1bjaA 6 :YIIKASNDV T0373 33 :VQFSQLVVLGAIDRLGG 1bjaA 15 :LNEKTATILITIAKKDF T0373 51 :VTPSELAAA 1bjaA 32 :ITAAEVREV T0373 60 :ERMRSSNLAALLRELERGGLIVRH 1bjaA 42 :PDLGNAVVNSNIGVLIKKGLVEKS T0373 87 :QD 1bjaA 66 :GD T0373 93 :RVSLSSEGRRNLYGNRAKREE 1bjaA 68 :GLIITGEAQDIISNAATLYAQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=386 Number of alignments=67 # 1bjaA read from 1bjaA/merged-good-all-a2m # found chain 1bjaA in template set T0373 22 :RRLRREAQAD 1bjaA 5 :TYIIKASNDV T0373 33 :VQFSQLVVLGAIDRLGG 1bjaA 15 :LNEKTATILITIAKKDF T0373 51 :VTPSELAAAE 1bjaA 32 :ITAAEVREVH T0373 61 :RMRSSNLAALLRELERGGLIVR 1bjaA 43 :DLGNAVVNSNIGVLIKKGLVEK T0373 85 :DPQ 1bjaA 65 :SGD T0373 93 :RVSLSSEGRRNLYGNRAKREE 1bjaA 68 :GLIITGEAQDIISNAATLYAQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=392 Number of alignments=68 # 1bjaA read from 1bjaA/merged-good-all-a2m # found chain 1bjaA in template set T0373 32 :PVQFSQLVVLGAIDR 1bjaA 14 :VLNEKTATILITIAK T0373 48 :GGDVTPSELAAAE 1bjaA 29 :KDFITAAEVREVH T0373 61 :RMRSSNLAALLRELERGGLIVRHAD 1bjaA 43 :DLGNAVVNSNIGVLIKKGLVEKSGD T0373 93 :RVSLSSEGRRNLYGNRAKREEW 1bjaA 68 :GLIITGEAQDIISNAATLYAQE Number of specific fragments extracted= 4 number of extra gaps= 0 total=396 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mkmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mkmA expands to /projects/compbio/data/pdb/1mkm.pdb.gz 1mkmA:# T0373 read from 1mkmA/merged-good-all-a2m # 1mkmA read from 1mkmA/merged-good-all-a2m # adding 1mkmA to template set # found chain 1mkmA in template set T0373 38 :LVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1mkmA 8 :FEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK T0373 87 :QDGRRTR 1mkmA 54 :KDKRYVP T0373 109 :AKREE 1mkmA 62 :YKLIE T0373 115 :LVRAMHACLD 1mkmA 67 :YGSFVLRRFN T0373 127 :ERALLAA 1mkmA 77 :IRDIAHD T0373 137 :LLTRLAQFEE 1mkmA 84 :HLVDIMKRTG Number of specific fragments extracted= 6 number of extra gaps= 0 total=402 Number of alignments=70 # 1mkmA read from 1mkmA/merged-good-all-a2m # found chain 1mkmA in template set T0373 36 :SQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1mkmA 6 :KAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK T0373 87 :QDGR 1mkmA 54 :KDKR T0373 94 :VSLSSEGRRNLYG 1mkmA 58 :YVPGYKLIEYGSF T0373 107 :NRAKREEWLVRAM 1mkmA 77 :IRDIAHDHLVDIM T0373 121 :AC 1mkmA 90 :KR Number of specific fragments extracted= 5 number of extra gaps= 0 total=407 Number of alignments=71 # 1mkmA read from 1mkmA/merged-good-all-a2m # found chain 1mkmA in template set T0373 37 :QLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1mkmA 7 :AFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK T0373 87 :QDGRRTR 1mkmA 54 :KDKRYVP T0373 110 :KREEWLVR 1mkmA 63 :KLIEYGSF T0373 119 :MHACLD 1mkmA 71 :VLRRFN T0373 127 :ERALLAAAGPLLTRLA 1mkmA 77 :IRDIAHDHLVDIMKRT Number of specific fragments extracted= 5 number of extra gaps= 0 total=412 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ethA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ethA expands to /projects/compbio/data/pdb/2eth.pdb.gz 2ethA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1046, because occupancy 0.500 <= existing 0.500 in 2ethA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 2ethA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 2ethA # T0373 read from 2ethA/merged-good-all-a2m # 2ethA read from 2ethA/merged-good-all-a2m # adding 2ethA to template set # found chain 2ethA in template set Warning: unaligning (T0373)P2 because first residue in template chain is (2ethA)H0 T0373 3 :TNQDLQL 2ethA 1 :MDALEIF T0373 18 :TTLTRRLRREAQADP 2ethA 8 :KTLFSLVMRFSSYLP T0373 33 :VQFSQLVVLGAIDRLGG 2ethA 30 :MKTTELYAFLYVALFGP T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 2ethA 47 :KKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGEILSNFES T0373 115 :LVRAMHACLDESERALLAA 2ethA 110 :LLKSVLEKFSEEDFKVVSE T0373 137 :LLTRLAQF 2ethA 129 :GFNRMVEA Number of specific fragments extracted= 6 number of extra gaps= 0 total=418 Number of alignments=73 # 2ethA read from 2ethA/merged-good-all-a2m # found chain 2ethA in template set Warning: unaligning (T0373)P2 because first residue in template chain is (2ethA)H0 T0373 3 :TNQDLQL 2ethA 1 :MDALEIF T0373 18 :TTLTRRLRREAQADP 2ethA 8 :KTLFSLVMRFSSYLP T0373 33 :VQFSQLVVLGAIDRL 2ethA 30 :MKTTELYAFLYVALF T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 2ethA 45 :GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGEILSNFESLLKSVL T0373 121 :ACLDESERALLAA 2ethA 116 :EKFSEEDFKVVSE T0373 137 :LLTRLAQF 2ethA 129 :GFNRMVEA Number of specific fragments extracted= 6 number of extra gaps= 0 total=424 Number of alignments=74 # 2ethA read from 2ethA/merged-good-all-a2m # found chain 2ethA in template set Warning: unaligning (T0373)F144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ethA)E140 Warning: unaligning (T0373)E145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ethA)E140 T0373 19 :TLTRRLRREAQADP 2ethA 6 :IFKTLFSLVMRFSS T0373 33 :VQFSQLVVLGAIDR 2ethA 30 :MKTTELYAFLYVAL T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 2ethA 44 :FGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGEILSNFESLLKS T0373 119 :MHACLDESERALLAAAGPLLTRLAQ 2ethA 114 :VLEKFSEEDFKVVSEGFNRMVEALS Number of specific fragments extracted= 4 number of extra gaps= 1 total=428 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lj9A expands to /projects/compbio/data/pdb/1lj9.pdb.gz 1lj9A:# T0373 read from 1lj9A/merged-good-all-a2m # 1lj9A read from 1lj9A/merged-good-all-a2m # adding 1lj9A to template set # found chain 1lj9A in template set Warning: unaligning (T0373)T3 because first residue in template chain is (1lj9A)T2 T0373 4 :NQDLQL 1lj9A 3 :DILREI T0373 14 :RSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 1lj9A 9 :GMIARALDSISNIEFKELSLTRGQYLYLVRVCENPG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 1lj9A 45 :IIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQH T0373 115 :LVRAMHACLDESERALLAA 1lj9A 108 :SNQVALQGLSEVEISQLAD T0373 137 :LLTRLAQF 1lj9A 127 :YLVRMRKN Number of specific fragments extracted= 5 number of extra gaps= 0 total=433 Number of alignments=76 # 1lj9A read from 1lj9A/merged-good-all-a2m # found chain 1lj9A in template set T0373 5 :Q 1lj9A 4 :I T0373 10 :AAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 1lj9A 5 :LREIGMIARALDSISNIEFKELSLTRGQYLYLVRVCENPG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 1lj9A 45 :IIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQHSNQVAL T0373 121 :ACLDESERALLAA 1lj9A 114 :QGLSEVEISQLAD T0373 137 :LLTRLAQF 1lj9A 127 :YLVRMRKN Number of specific fragments extracted= 5 number of extra gaps= 0 total=438 Number of alignments=77 # 1lj9A read from 1lj9A/merged-good-all-a2m # found chain 1lj9A in template set T0373 11 :AHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 1lj9A 6 :REIGMIARALDSISNIEFKELSLTRGQYLYLVRVCE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 1lj9A 42 :NPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQHSNQV T0373 119 :MHACLDESERALLAAAGPLLTRL 1lj9A 112 :ALQGLSEVEISQLADYLVRMRKN Number of specific fragments extracted= 3 number of extra gaps= 0 total=441 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dpuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dpuA expands to /projects/compbio/data/pdb/1dpu.pdb.gz 1dpuA:# T0373 read from 1dpuA/merged-good-all-a2m # 1dpuA read from 1dpuA/merged-good-all-a2m # adding 1dpuA to template set # found chain 1dpuA in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1dpuA)A202 T0373 31 :DPVQFSQLVVLGAIDRLGGD 1dpuA 203 :NGLTVAQNQVLNLIKACPRP T0373 51 :VTPSELAAAE 1dpuA 225 :LNFQDLKNQL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQ 1dpuA 236 :HMSVSSIKQAVDFLSNEGHIYSTVDDD T0373 93 :RVSLSS 1dpuA 263 :HFKSTD Number of specific fragments extracted= 4 number of extra gaps= 0 total=445 Number of alignments=79 # 1dpuA read from 1dpuA/merged-good-all-a2m # found chain 1dpuA in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1dpuA)A202 T0373 31 :DPVQFSQLVVLGAIDRLGGD 1dpuA 203 :NGLTVAQNQVLNLIKACPRP T0373 51 :VTPSELAAAE 1dpuA 225 :LNFQDLKNQL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQ 1dpuA 236 :HMSVSSIKQAVDFLSNEGHIYSTVDDD T0373 93 :RVSLSS 1dpuA 263 :HFKSTD Number of specific fragments extracted= 4 number of extra gaps= 0 total=449 Number of alignments=80 # 1dpuA read from 1dpuA/merged-good-all-a2m # found chain 1dpuA in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1dpuA)A202 T0373 31 :DPVQFSQLVVLGAIDRLGGD 1dpuA 203 :NGLTVAQNQVLNLIKACPRP T0373 51 :VTPSELAAAE 1dpuA 225 :LNFQDLKNQL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQ 1dpuA 236 :HMSVSSIKQAVDFLSNEGHIYSTVDDD T0373 93 :RVSLS 1dpuA 263 :HFKST Number of specific fragments extracted= 4 number of extra gaps= 0 total=453 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yg2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yg2A expands to /projects/compbio/data/pdb/1yg2.pdb.gz 1yg2A:# T0373 read from 1yg2A/merged-good-all-a2m # 1yg2A read from 1yg2A/merged-good-all-a2m # adding 1yg2A to template set # found chain 1yg2A in template set Warning: unaligning (T0373)D85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yg2A)V68 Warning: unaligning (T0373)R93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yg2A)V68 T0373 36 :SQLVVLGAIDR 1yg2A 3 :LPHVILTVLST T0373 48 :GG 1yg2A 14 :RD T0373 51 :VTPSELAAAER 1yg2A 16 :ATGYDITKEFS T0373 62 :MRSSNLAALLRELERGGLIVRHA 1yg2A 35 :ASHQQVYRELNKMGEQGLVTCVL T0373 94 :VSLSSEGRRNLYGNRA 1yg2A 69 :YSITQAGRSALGEWFD T0373 113 :E 1yg2A 95 :E T0373 115 :LVRAMHAC 1yg2A 96 :FSAKLMAC T0373 125 :ESERALLAAAGPLLTRLAQF 1yg2A 109 :EPYRLQLAELVEESRKLVAH Number of specific fragments extracted= 8 number of extra gaps= 0 total=461 Number of alignments=82 # 1yg2A read from 1yg2A/merged-good-all-a2m # found chain 1yg2A in template set Warning: unaligning (T0373)D85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yg2A)V68 Warning: unaligning (T0373)R93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yg2A)V68 T0373 36 :SQLVVLGAIDR 1yg2A 3 :LPHVILTVLST T0373 49 :GDVTPSELAAAER 1yg2A 14 :RDATGYDITKEFS T0373 62 :MRSSNLAALLRELERGGLIVRHA 1yg2A 35 :ASHQQVYRELNKMGEQGLVTCVL T0373 94 :VSLSSEGRRNLYGNRA 1yg2A 69 :YSITQAGRSALGEWFD T0373 110 :KREEWLVRA 1yg2A 95 :EFSAKLMAC T0373 121 :ACLD 1yg2A 104 :SVQS T0373 125 :ESERALLAAAGPLLTRLAQF 1yg2A 109 :EPYRLQLAELVEESRKLVAH Number of specific fragments extracted= 7 number of extra gaps= 0 total=468 Number of alignments=83 # 1yg2A read from 1yg2A/merged-good-all-a2m # found chain 1yg2A in template set Warning: unaligning (T0373)D85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yg2A)V68 Warning: unaligning (T0373)R93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yg2A)V68 T0373 37 :QLVVLGAIDR 1yg2A 4 :PHVILTVLST T0373 49 :GDVTPSELAAAER 1yg2A 14 :RDATGYDITKEFS T0373 62 :MRSSNLAALLRELERGGLIVRHA 1yg2A 35 :ASHQQVYRELNKMGEQGLVTCVL T0373 94 :VSLSSEGRRNLYGNRA 1yg2A 69 :YSITQAGRSALGEWFD T0373 110 :KREEWLVR 1yg2A 95 :EFSAKLMA T0373 119 :M 1yg2A 103 :C T0373 121 :ACLD 1yg2A 104 :SVQS T0373 125 :ESERALLAAAGPLLTRLAQ 1yg2A 109 :EPYRLQLAELVEESRKLVA Number of specific fragments extracted= 8 number of extra gaps= 0 total=476 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1okrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1okrA expands to /projects/compbio/data/pdb/1okr.pdb.gz 1okrA:# T0373 read from 1okrA/merged-good-all-a2m # 1okrA read from 1okrA/merged-good-all-a2m # adding 1okrA to template set # found chain 1okrA in template set Warning: unaligning (T0373)D31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)Y6 Warning: unaligning (T0373)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1okrA)K65 Warning: unaligning (T0373)Q87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)K65 T0373 32 :PVQFSQLVVLGAIDRLGG 1okrA 7 :EISSAEWEVMNIIWMKKY T0373 51 :VTPSELAAAER 1okrA 25 :ASANNIIEEIQ T0373 62 :MRSSNLAALLRELERGGLIVRHAD 1okrA 40 :WSPKTIRTLITRLYKKGFIDRKKD T0373 91 :RTRVSLS 1okrA 66 :IFQYYSL T0373 98 :SEGRRNLYGNRAKR 1okrA 76 :SDIKYKTSKNFINK T0373 113 :EWLVRAMHAC 1okrA 96 :NSLVLNFVEK T0373 123 :LDESERALLAA 1okrA 108 :LSQDEIEELRN T0373 137 :L 1okrA 119 :I Number of specific fragments extracted= 8 number of extra gaps= 2 total=484 Number of alignments=85 # 1okrA read from 1okrA/merged-good-all-a2m # found chain 1okrA in template set Warning: unaligning (T0373)D31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)Y6 Warning: unaligning (T0373)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1okrA)K65 Warning: unaligning (T0373)Q87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)K65 T0373 32 :PVQFSQLVVLGAIDRL 1okrA 7 :EISSAEWEVMNIIWMK T0373 49 :GDVTPSELAAAE 1okrA 23 :KYASANNIIEEI T0373 61 :RMRSSNLAALLRELERGGLIVRHAD 1okrA 39 :DWSPKTIRTLITRLYKKGFIDRKKD T0373 91 :RTRVSLS 1okrA 66 :IFQYYSL T0373 98 :SEGRRNLYGNR 1okrA 76 :SDIKYKTSKNF T0373 109 :AKREEWLVRA 1okrA 96 :NSLVLNFVEK T0373 121 :ACLDESERALLAA 1okrA 106 :EDLSQDEIEELRN Number of specific fragments extracted= 7 number of extra gaps= 2 total=491 Number of alignments=86 # 1okrA read from 1okrA/merged-good-all-a2m # found chain 1okrA in template set Warning: unaligning (T0373)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1okrA)K65 Warning: unaligning (T0373)Q87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)K65 T0373 32 :PVQFSQLVVLGAIDR 1okrA 7 :EISSAEWEVMNIIWM T0373 48 :GGDVTPSELAAAER 1okrA 22 :KKYASANNIIEEIQ T0373 62 :MRSSNLAALLRELERGGLIVRHAD 1okrA 40 :WSPKTIRTLITRLYKKGFIDRKKD T0373 91 :RTRVSLS 1okrA 66 :IFQYYSL T0373 98 :SEGRRNLYGNR 1okrA 76 :SDIKYKTSKNF T0373 109 :AKREEWLVR 1okrA 96 :NSLVLNFVE T0373 120 :HACLDESERALLAAA 1okrA 105 :KEDLSQDEIEELRNI Number of specific fragments extracted= 7 number of extra gaps= 1 total=498 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lnwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lnwA expands to /projects/compbio/data/pdb/1lnw.pdb.gz 1lnwA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 1lnwA/merged-good-all-a2m # 1lnwA read from 1lnwA/merged-good-all-a2m # adding 1lnwA to template set # found chain 1lnwA in template set T0373 2 :PTNQDLQLAAHLRSQVTTLTRRLRRE 1lnwA 6 :NPDLMPALMAVFQHVRTRIQSELDCQ T0373 30 :ADPVQFSQLVVLGAIDRLGG 1lnwA 32 :RLDLTPPDVHVLKLIDEQRG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 1lnwA 52 :LNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQHAEAIMSR T0373 115 :LVRAMHACLDESERALLAA 1lnwA 115 :VHDELFAPLTPVEQATLVH T0373 137 :LLTRLAQF 1lnwA 134 :LLDQCLAA Number of specific fragments extracted= 5 number of extra gaps= 0 total=503 Number of alignments=88 # 1lnwA read from 1lnwA/merged-good-all-a2m # found chain 1lnwA in template set Warning: unaligning (T0373)E145 because last residue in template chain is (1lnwA)Q142 T0373 1 :MPTNQDLQLAAHLRSQVTTLTRRLRRE 1lnwA 5 :VNPDLMPALMAVFQHVRTRIQSELDCQ T0373 30 :ADPVQFSQLVVLGAIDRLGG 1lnwA 32 :RLDLTPPDVHVLKLIDEQRG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 1lnwA 52 :LNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQHAEAIMSRVHDELF T0373 121 :ACLDESERALLAA 1lnwA 121 :APLTPVEQATLVH T0373 137 :LLTRLAQF 1lnwA 134 :LLDQCLAA Number of specific fragments extracted= 5 number of extra gaps= 0 total=508 Number of alignments=89 # 1lnwA read from 1lnwA/merged-good-all-a2m # found chain 1lnwA in template set T0373 14 :RSQVTTLTRRLRREAQADP 1lnwA 14 :MAVFQHVRTRIQSELDCQR T0373 33 :VQFSQLVVLGAIDR 1lnwA 35 :LTPPDVHVLKLIDE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 1lnwA 49 :QRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQHAEAIMSRVHDE T0373 119 :MHACLDESERALLAAAGPL 1lnwA 119 :LFAPLTPVEQATLVHLLDQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=512 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fu4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fu4A expands to /projects/compbio/data/pdb/2fu4.pdb.gz 2fu4A:Skipped atom 148, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 156, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 2fu4A # T0373 read from 2fu4A/merged-good-all-a2m # 2fu4A read from 2fu4A/merged-good-all-a2m # adding 2fu4A to template set # found chain 2fu4A in template set T0373 27 :EAQADPV 2fu4A 7 :ALKKAGL T0373 34 :QFSQLVVLGAIDR 2fu4A 16 :TLPRLKILEVLQE T0373 48 :GG 2fu4A 29 :PD T0373 50 :DVTPSELAAAE 2fu4A 33 :HVSAEDLYKRL T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDGRR 2fu4A 50 :IGLATVYRVLNQFDDAGIVTRHNFEGGKSV T0373 94 :VSL 2fu4A 80 :FEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=518 Number of alignments=91 # 2fu4A read from 2fu4A/merged-good-all-a2m # found chain 2fu4A in template set Warning: unaligning (T0373)S97 because last residue in template chain is (2fu4A)T83 T0373 26 :REAQADPV 2fu4A 6 :TALKKAGL T0373 34 :QFSQLVVLGAIDR 2fu4A 16 :TLPRLKILEVLQE T0373 48 :GG 2fu4A 29 :PD T0373 50 :DVTPSELAAAE 2fu4A 33 :HVSAEDLYKRL T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDGRR 2fu4A 50 :IGLATVYRVLNQFDDAGIVTRHNFEGGKSV T0373 94 :VSL 2fu4A 80 :FEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=524 Number of alignments=92 # 2fu4A read from 2fu4A/merged-good-all-a2m # found chain 2fu4A in template set T0373 27 :EAQADPV 2fu4A 7 :ALKKAGL T0373 34 :QFSQLVVLGAIDR 2fu4A 16 :TLPRLKILEVLQE T0373 48 :GG 2fu4A 29 :PD T0373 51 :VTPSELAAAE 2fu4A 34 :VSAEDLYKRL T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDGRRTR 2fu4A 50 :IGLATVYRVLNQFDDAGIVTRHNFEGGKSVFE Number of specific fragments extracted= 5 number of extra gaps= 0 total=529 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jgsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jgsA expands to /projects/compbio/data/pdb/1jgs.pdb.gz 1jgsA:# T0373 read from 1jgsA/merged-good-all-a2m # 1jgsA read from 1jgsA/merged-good-all-a2m # adding 1jgsA to template set # found chain 1jgsA in template set T0373 2 :PTNQDLQL 1jgsA 11 :IIPLGRLI T0373 14 :RSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 1jgsA 19 :HMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRCAAC T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAMHAC 1jgsA 55 :ITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQCHQLVGQDLHQELTKN T0373 126 :SERALLAA 1jgsA 133 :ATLEYLLK T0373 143 :QFE 1jgsA 141 :KVL Number of specific fragments extracted= 5 number of extra gaps= 0 total=534 Number of alignments=94 # 1jgsA read from 1jgsA/merged-good-all-a2m # found chain 1jgsA in template set Warning: unaligning (T0373)P2 because first residue in template chain is (1jgsA)L7 Warning: unaligning (T0373)E146 because last residue in template chain is (1jgsA)P144 T0373 3 :TNQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRL 1jgsA 8 :FNEIIPLGRLIHMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRCA T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 1jgsA 53 :ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQCHQLVGQDLHQEL T0373 120 :HACLDESERALLAA 1jgsA 127 :LTADEVATLEYLLK T0373 143 :QFE 1jgsA 141 :KVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=538 Number of alignments=95 # 1jgsA read from 1jgsA/merged-good-all-a2m # found chain 1jgsA in template set T0373 2 :PTNQDLQ 1jgsA 11 :IIPLGRL T0373 13 :LRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 1jgsA 18 :IHMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRC T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAMHACLDESERALLAAAGP 1jgsA 52 :AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQCHQLVGQDLHQELTKNLTADEVATLEYLLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=541 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ub9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ub9A expands to /projects/compbio/data/pdb/1ub9.pdb.gz 1ub9A:# T0373 read from 1ub9A/merged-good-all-a2m # 1ub9A read from 1ub9A/merged-good-all-a2m # adding 1ub9A to template set # found chain 1ub9A in template set T0373 34 :QFSQLVVLGAIDRLGG 1ub9A 15 :NPVRLGIMIFLLPRRK T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 1ub9A 31 :APFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFLSSLKA T0373 115 :LVRAM 1ub9A 94 :VIDGL Number of specific fragments extracted= 3 number of extra gaps= 0 total=544 Number of alignments=97 # 1ub9A read from 1ub9A/merged-good-all-a2m # found chain 1ub9A in template set T0373 34 :QFSQLVVLGAIDRL 1ub9A 15 :NPVRLGIMIFLLPR T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRA 1ub9A 29 :RKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFLSSLKAVIDGL Number of specific fragments extracted= 2 number of extra gaps= 0 total=546 Number of alignments=98 # 1ub9A read from 1ub9A/merged-good-all-a2m # found chain 1ub9A in template set T0373 34 :QFSQLVVLGAIDR 1ub9A 15 :NPVRLGIMIFLLP T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 1ub9A 28 :RRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFLSSLKAVIDG T0373 119 :M 1ub9A 98 :L Number of specific fragments extracted= 3 number of extra gaps= 0 total=549 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yyvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yyvA expands to /projects/compbio/data/pdb/1yyv.pdb.gz 1yyvA:Skipped atom 310, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 312, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 314, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 316, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 318, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 320, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 322, because occupancy 0.490 <= existing 0.510 in 1yyvA Bad short name: CH1 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: CH1 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 637, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 639, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 641, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 643, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 645, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 647, because occupancy 0.460 <= existing 0.540 in 1yyvA Bad short name: CH1 for alphabet: pdb_atoms # T0373 read from 1yyvA/merged-good-all-a2m # 1yyvA read from 1yyvA/merged-good-all-a2m # adding 1yyvA to template set # found chain 1yyvA in template set Warning: unaligning (T0373)A58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M55 Warning: unaligning (T0373)E60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0373)S64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0373)N66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0373)I80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yyvA)N77 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0373)Y105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0373)N107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 T0373 26 :REAQ 1yyvA 27 :KHVT T0373 34 :QFSQLVVLGAID 1yyvA 31 :SRWGVLILVALR T0373 48 :GGDVTPSELA 1yyvA 43 :DGTHRFSDLR T0373 61 :RMR 1yyvA 57 :GVS T0373 67 :LAALLRELERGGL 1yyvA 63 :LAQSLQALEQDGF T0373 82 :RHADPQDGRRTRVSLSSEGRRNL 1yyvA 78 :RVSYPVVPPHVEYSLTPLGEQVS T0373 108 :RAKREEWLVRA 1yyvA 104 :AALADWIELNL Number of specific fragments extracted= 7 number of extra gaps= 1 total=556 Number of alignments=100 # 1yyvA read from 1yyvA/merged-good-all-a2m # found chain 1yyvA in template set Warning: unaligning (T0373)A58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M55 Warning: unaligning (T0373)E60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0373)S64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0373)N66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0373)I80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yyvA)N77 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0373)Y105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0373)N107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 T0373 7 :L 1yyvA 23 :R T0373 19 :TLTRRLR 1yyvA 24 :EVLKHVT T0373 34 :QFSQLVVLGAID 1yyvA 31 :SRWGVLILVALR T0373 48 :GGDVTPSELA 1yyvA 43 :DGTHRFSDLR T0373 61 :RMR 1yyvA 57 :GVS T0373 67 :LAALLRELERGGL 1yyvA 63 :LAQSLQALEQDGF T0373 82 :RHADPQDGRRTRVSLSSEGRRNL 1yyvA 78 :RVSYPVVPPHVEYSLTPLGEQVS T0373 108 :RAKREEWLVRAM 1yyvA 104 :AALADWIELNLP Number of specific fragments extracted= 8 number of extra gaps= 1 total=564 Number of alignments=101 # 1yyvA read from 1yyvA/merged-good-all-a2m # found chain 1yyvA in template set Warning: unaligning (T0373)A58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M55 Warning: unaligning (T0373)E60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0373)S64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0373)N66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0373)I80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yyvA)N77 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0373)Y105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0373)N107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 Warning: unaligning (T0373)D124 because last residue in template chain is (1yyvA)E122 T0373 23 :RLRREAQ 1yyvA 24 :EVLKHVT T0373 34 :QFSQLVVLGAIDR 1yyvA 31 :SRWGVLILVALRD T0373 49 :GDVTPSELA 1yyvA 44 :GTHRFSDLR T0373 61 :RMR 1yyvA 57 :GVS T0373 67 :LAALLRELERGGL 1yyvA 63 :LAQSLQALEQDGF T0373 82 :RHADPQDGRRTRVSLSSEGRRNL 1yyvA 78 :RVSYPVVPPHVEYSLTPLGEQVS T0373 108 :RAKREEWLVRA 1yyvA 104 :AALADWIELNL T0373 119 :MHACL 1yyvA 117 :VLAQR Number of specific fragments extracted= 8 number of extra gaps= 1 total=572 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g7uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2g7uA expands to /projects/compbio/data/pdb/2g7u.pdb.gz 2g7uA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 2g7uA/merged-good-all-a2m # 2g7uA read from 2g7uA/merged-good-all-a2m # adding 2g7uA to template set # found chain 2g7uA in template set T0373 2 :PTNQDLQLAAHLRS 2g7uA 7 :DYIQSIERGFAVLL T0373 47 :LGGD 2g7uA 22 :FDAQ T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 2g7uA 29 :PTLAELATEAGLSRPAVRRILLTLQKLGYVAGS T0373 86 :PQ 2g7uA 62 :GG T0373 93 :RVSLSSEGRRN 2g7uA 64 :RWSLTPRVLSI T0373 105 :YGNRAKREE 2g7uA 75 :GQHYSESHA T0373 115 :LVRAMHA 2g7uA 84 :LIEAAMP T0373 137 :LLTRLAQF 2g7uA 91 :RLLEVAEK Number of specific fragments extracted= 8 number of extra gaps= 0 total=580 Number of alignments=103 # 2g7uA read from 2g7uA/merged-good-all-a2m # found chain 2g7uA in template set T0373 1 :MPTNQDLQLAAHLRS 2g7uA 6 :RDYIQSIERGFAVLL T0373 29 :Q 2g7uA 23 :D T0373 48 :GG 2g7uA 24 :AQ T0373 50 :DVTPSELAAAERMRSSNLAALLRELERGGLIVRH 2g7uA 28 :NPTLAELATEAGLSRPAVRRILLTLQKLGYVAGS T0373 86 :PQ 2g7uA 62 :GG T0373 93 :RVSLSSEGRRN 2g7uA 64 :RWSLTPRVLSI T0373 105 :YGNRAKREEWLVRAM 2g7uA 75 :GQHYSESHALIEAAM T0373 136 :PLLTRLAQF 2g7uA 90 :PRLLEVAEK Number of specific fragments extracted= 8 number of extra gaps= 0 total=588 Number of alignments=104 # 2g7uA read from 2g7uA/merged-good-all-a2m # found chain 2g7uA in template set T0373 1 :MPTNQDLQLAAHLRSQ 2g7uA 6 :RDYIQSIERGFAVLLA T0373 47 :LGGD 2g7uA 22 :FDAQ T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 2g7uA 29 :PTLAELATEAGLSRPAVRRILLTLQKLGYVAGSGG T0373 93 :RVSLSSEGRRNL 2g7uA 64 :RWSLTPRVLSIG T0373 121 :ACLD 2g7uA 76 :QHYS T0373 125 :ESERALLAAAGPLLTRLAQ 2g7uA 82 :HALIEAAMPRLLEVAEKTQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=594 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cfxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cfxA expands to /projects/compbio/data/pdb/2cfx.pdb.gz 2cfxA:# T0373 read from 2cfxA/merged-good-all-a2m # 2cfxA read from 2cfxA/merged-good-all-a2m # adding 2cfxA to template set # found chain 2cfxA in template set Warning: unaligning (T0373)S64 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0373)S65 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 Warning: unaligning (T0373)A84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfxA)L54 Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cfxA)L54 T0373 32 :PVQFSQLVVLGAIDR 2cfxA 2 :KLDQIDLNIIEELKK T0373 48 :GGDVTPSELAAAERMR 2cfxA 17 :DSRLSMRELGRKIKLS T0373 66 :NLAALLRELERGGLIVRH 2cfxA 35 :SVTERVRQLESFGIIKQY T0373 86 :PQDGRRTRVSLS 2cfxA 61 :LGLPVSCIVEAT T0373 98 :SEGRRNLYGN 2cfxA 79 :ERFKSYIQTL T0373 108 :RAKREE 2cfxA 112 :LEAVED T0373 115 :LVRAMHA 2cfxA 118 :FINKTSP Number of specific fragments extracted= 7 number of extra gaps= 2 total=601 Number of alignments=106 # 2cfxA read from 2cfxA/merged-good-all-a2m # found chain 2cfxA in template set Warning: unaligning (T0373)D31 because first residue in template chain is (2cfxA)M1 Warning: unaligning (T0373)S64 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0373)S65 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfxA)L54 Warning: unaligning (T0373)R82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cfxA)L54 T0373 32 :PVQFSQLVVLGAIDR 2cfxA 2 :KLDQIDLNIIEELKK T0373 48 :GGDVTPSELAAAERMR 2cfxA 17 :DSRLSMRELGRKIKLS T0373 66 :NLAALLRELERGGLI 2cfxA 35 :SVTERVRQLESFGII T0373 83 :HAD 2cfxA 55 :EVD T0373 86 :PQDGRRTRVSLS 2cfxA 61 :LGLPVSCIVEAT T0373 98 :SEGRRNLYGN 2cfxA 79 :ERFKSYIQTL T0373 108 :RAKREEWLVRA 2cfxA 112 :LEAVEDFINKT Number of specific fragments extracted= 7 number of extra gaps= 2 total=608 Number of alignments=107 # 2cfxA read from 2cfxA/merged-good-all-a2m # found chain 2cfxA in template set Warning: unaligning (T0373)S64 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0373)S65 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 T0373 32 :PVQFSQLVVLGAIDR 2cfxA 2 :KLDQIDLNIIEELKK T0373 48 :GGDVTPSELAAAERMR 2cfxA 17 :DSRLSMRELGRKIKLS T0373 66 :NLAALLRELERGGLIVRH 2cfxA 35 :SVTERVRQLESFGIIKQY T0373 85 :DPQDGRRTRVSLS 2cfxA 60 :KLGLPVSCIVEAT T0373 98 :SEGRRNLYGN 2cfxA 79 :ERFKSYIQTL Number of specific fragments extracted= 5 number of extra gaps= 1 total=613 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tbxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tbxA expands to /projects/compbio/data/pdb/1tbx.pdb.gz 1tbxA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 1tbxA/merged-good-all-a2m # 1tbxA read from 1tbxA/merged-good-all-a2m # adding 1tbxA to template set # found chain 1tbxA in template set T0373 36 :SQLVVLGAIDRLGG 1tbxA 9 :PEAIVLAYLYDNEG T0373 51 :VTPSELAAAER 1tbxA 23 :IATYDLYKKVN T0373 62 :MRSSNLAALLRELERGGLIVRHADPQ 1tbxA 38 :MSTATFYDAKKFLIQEGFVKERQERG T0373 91 :RTRVSLSSEGRRNLYGNRAKREE 1tbxA 64 :EKRLYLTEKGKLFAISLKTAIET T0373 115 :LVRAMHA 1tbxA 87 :YKQIKKR Number of specific fragments extracted= 5 number of extra gaps= 0 total=618 Number of alignments=109 # 1tbxA read from 1tbxA/merged-good-all-a2m # found chain 1tbxA in template set T0373 36 :SQLVVLGAIDRLGG 1tbxA 9 :PEAIVLAYLYDNEG T0373 51 :VTPSELAAAER 1tbxA 23 :IATYDLYKKVN T0373 62 :MRSSNLAALLRELERGGLIVRHADPQ 1tbxA 38 :MSTATFYDAKKFLIQEGFVKERQERG T0373 91 :RTRVSLSSEGRRNLYGNRAKREEWLVRAM 1tbxA 64 :EKRLYLTEKGKLFAISLKTAIETYKQIKK T0373 121 :A 1tbxA 93 :R Number of specific fragments extracted= 5 number of extra gaps= 0 total=623 Number of alignments=110 # 1tbxA read from 1tbxA/merged-good-all-a2m # found chain 1tbxA in template set T0373 36 :SQLVVLGAIDR 1tbxA 9 :PEAIVLAYLYD T0373 48 :GGDVTPSELAAAER 1tbxA 20 :NEGIATYDLYKKVN T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDG 1tbxA 38 :MSTATFYDAKKFLIQEGFVKERQERGEK T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVR 1tbxA 66 :RLYLTEKGKLFAISLKTAIETYKQI T0373 119 :MHACL 1tbxA 91 :KKRHH Number of specific fragments extracted= 5 number of extra gaps= 0 total=628 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ddnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ddnA expands to /projects/compbio/data/pdb/1ddn.pdb.gz 1ddnA:# T0373 read from 1ddnA/merged-good-all-a2m # 1ddnA read from 1ddnA/merged-good-all-a2m # adding 1ddnA to template set # found chain 1ddnA in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1ddnA 9 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVA T0373 87 :QDGR 1ddnA 58 :SDRS T0373 94 :VSLSSEGRRNLYGNRAKRE 1ddnA 62 :LQMTPTGRTLATAVMRKHR T0373 114 :WLVRAMHAC 1ddnA 81 :LAERLLTDI T0373 123 :LDESERALLAA 1ddnA 108 :MSDEVERRLVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=633 Number of alignments=112 # 1ddnA read from 1ddnA/merged-good-all-a2m # found chain 1ddnA in template set Warning: unaligning (T0373)E145 because last residue in template chain is (1ddnA)L120 T0373 34 :QFSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1ddnA 8 :TEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVA T0373 87 :QDGR 1ddnA 58 :SDRS T0373 94 :VSLSSEGRRNLYGNRAKR 1ddnA 62 :LQMTPTGRTLATAVMRKH T0373 113 :EWLVRAMHA 1ddnA 80 :RLAERLLTD T0373 122 :CLD 1ddnA 91 :GLD T0373 125 :ESERALLAAAG 1ddnA 95 :NKVHDEADRWE T0373 136 :PLLTRLAQF 1ddnA 111 :EVERRLVKV Number of specific fragments extracted= 7 number of extra gaps= 0 total=640 Number of alignments=113 # 1ddnA read from 1ddnA/merged-good-all-a2m # found chain 1ddnA in template set T0373 35 :FSQLVVLGAIDR 1ddnA 9 :EMYLRTIYELEE T0373 48 :GGD 1ddnA 21 :EGV T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1ddnA 25 :PLRARIAERLEQSGPTVSQTVARMERDGLVVVASDR T0373 93 :RVSLSSEGRRNLYGNRAKRE 1ddnA 61 :SLQMTPTGRTLATAVMRKHR T0373 114 :WLVRAMHA 1ddnA 81 :LAERLLTD T0373 122 :CLDESERALLAA 1ddnA 107 :VMSDEVERRLVK Number of specific fragments extracted= 6 number of extra gaps= 0 total=646 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r1uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r1uA expands to /projects/compbio/data/pdb/1r1u.pdb.gz 1r1uA:# T0373 read from 1r1uA/merged-good-all-a2m # 1r1uA read from 1r1uA/merged-good-all-a2m # adding 1r1uA to template set # found chain 1r1uA in template set T0373 19 :TLTRRLRREAQ 1r1uA 14 :ERVTEIFKALG T0373 34 :QFSQLVVLGAIDR 1r1uA 25 :DYNRIRIMELLSV T0373 48 :GG 1r1uA 38 :SE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQ 1r1uA 40 :ASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQ T0373 91 :RTRVSLSS 1r1uA 77 :SMIYSLDD T0373 99 :EGRRNLYGNRAK 1r1uA 86 :HVATMLKQAIHH Number of specific fragments extracted= 6 number of extra gaps= 0 total=652 Number of alignments=115 # 1r1uA read from 1r1uA/merged-good-all-a2m # found chain 1r1uA in template set T0373 18 :TTLTRRLRREAQA 1r1uA 13 :LERVTEIFKALGD T0373 35 :FSQLVVLGAIDR 1r1uA 26 :YNRIRIMELLSV T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQ 1r1uA 38 :SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQ T0373 91 :RTRVSLSS 1r1uA 77 :SMIYSLDD T0373 99 :EGRRNLYGNRA 1r1uA 86 :HVATMLKQAIH T0373 117 :R 1r1uA 97 :H Number of specific fragments extracted= 6 number of extra gaps= 0 total=658 Number of alignments=116 # 1r1uA read from 1r1uA/merged-good-all-a2m # found chain 1r1uA in template set T0373 22 :RRLRREAQADPVQFSQLVVLGAIDR 1r1uA 13 :LERVTEIFKALGDYNRIRIMELLSV T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQ 1r1uA 38 :SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQ T0373 91 :RTRVSLSSE 1r1uA 77 :SMIYSLDDI T0373 106 :GNRAKREEWLVR 1r1uA 86 :HVATMLKQAIHH T0373 119 :M 1r1uA 98 :A Number of specific fragments extracted= 5 number of extra gaps= 0 total=663 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u2wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u2wA expands to /projects/compbio/data/pdb/1u2w.pdb.gz 1u2wA:# T0373 read from 1u2wA/merged-good-all-a2m # 1u2wA read from 1u2wA/merged-good-all-a2m # adding 1u2wA to template set # found chain 1u2wA in template set Warning: unaligning (T0373)H83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 Warning: unaligning (T0373)R91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u2wA)L94 T0373 21 :TRRLRREAQ 1u2wA 32 :VSQILKAIA T0373 35 :FSQLVVLGAIDRLGG 1u2wA 42 :ENRAKITYALCQDEE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVR 1u2wA 57 :LCVCDIANILGVTIANASHHLRTLYKQGVVNF T0373 92 :TRVSLS 1u2wA 95 :ALYSLG T0373 98 :SEGRRNLYGNRAK 1u2wA 102 :EHIRQIMMIALAH Number of specific fragments extracted= 5 number of extra gaps= 0 total=668 Number of alignments=118 # 1u2wA read from 1u2wA/merged-good-all-a2m # found chain 1u2wA in template set Warning: unaligning (T0373)H83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 Warning: unaligning (T0373)R91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u2wA)L94 T0373 2 :PTNQDLQLAAHLRS 1u2wA 12 :YDEEKVNRIQGDLQ T0373 21 :TRRLRREAQA 1u2wA 32 :VSQILKAIAD T0373 35 :FSQLVVLGAIDR 1u2wA 42 :ENRAKITYALCQ T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 1u2wA 54 :DEELCVCDIANILGVTIANASHHLRTLYKQGVVNF T0373 92 :TRVSLS 1u2wA 95 :ALYSLG T0373 98 :SEGRRNLYGNRAK 1u2wA 102 :EHIRQIMMIALAH Number of specific fragments extracted= 6 number of extra gaps= 0 total=674 Number of alignments=119 # 1u2wA read from 1u2wA/merged-good-all-a2m # found chain 1u2wA in template set Warning: unaligning (T0373)H83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 Warning: unaligning (T0373)R91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u2wA)L94 T0373 21 :TRRLRREAQ 1u2wA 32 :VSQILKAIA T0373 34 :QFSQLVVLGAIDR 1u2wA 41 :DENRAKITYALCQ T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 1u2wA 54 :DEELCVCDIANILGVTIANASHHLRTLYKQGVVNF T0373 92 :TRVSLS 1u2wA 95 :ALYSLG T0373 98 :SEGRRNLYGNRAK 1u2wA 102 :EHIRQIMMIALAH Number of specific fragments extracted= 5 number of extra gaps= 0 total=679 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s3jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1s3jA expands to /projects/compbio/data/pdb/1s3j.pdb.gz 1s3jA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 993, because occupancy 0.400 <= existing 0.600 in 1s3jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 995, because occupancy 0.400 <= existing 0.600 in 1s3jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 997, because occupancy 0.350 <= existing 0.530 in 1s3jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 999, because occupancy 0.400 <= existing 0.600 in 1s3jA # T0373 read from 1s3jA/merged-good-all-a2m # 1s3jA read from 1s3jA/merged-good-all-a2m # adding 1s3jA to template set # found chain 1s3jA in template set T0373 4 :NQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 1s3jA 6 :QLMSDIQLSLQALFQKIQPEMLESMEKQGVTPAQLFVLASLKKHGS T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 1s3jA 52 :LKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEEVLAGRKA T0373 115 :LVRAMHACLDESERALLAAAGPLLTRL 1s3jA 115 :IMARYLSFLTEEEMLQAAHITAKLAQA Number of specific fragments extracted= 3 number of extra gaps= 0 total=682 Number of alignments=121 # 1s3jA read from 1s3jA/merged-good-all-a2m # found chain 1s3jA in template set Warning: unaligning (T0373)E145 because last residue in template chain is (1s3jA)D145 T0373 3 :TNQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRL 1s3jA 5 :DQLMSDIQLSLQALFQKIQPEMLESMEKQGVTPAQLFVLASLKKH T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 1s3jA 50 :GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEEVLAGRKAIMARYL T0373 121 :ACLDESERALLAAAGPLLTRLAQF 1s3jA 121 :SFLTEEEMLQAAHITAKLAQAAET Number of specific fragments extracted= 3 number of extra gaps= 0 total=685 Number of alignments=122 # 1s3jA read from 1s3jA/merged-good-all-a2m # found chain 1s3jA in template set Warning: unaligning (T0373)E145 because last residue in template chain is (1s3jA)D145 T0373 8 :QLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 1s3jA 10 :DIQLSLQALFQKIQPEMLESMEKQGVTPAQLFVLASLKK T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 1s3jA 49 :HGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEEVLAGRKAIMAR T0373 119 :MHACLDESERALLAAAGPLLTRLAQF 1s3jA 119 :YLSFLTEEEMLQAAHITAKLAQAAET Number of specific fragments extracted= 3 number of extra gaps= 0 total=688 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1on2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0373 read from 1on2A/merged-good-all-a2m # 1on2A read from 1on2A/merged-good-all-a2m # found chain 1on2A in training set T0373 35 :FSQLVVLGAIDRLGG 1on2A 8 :MYIEQIYMLIEEKGY T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 1on2A 23 :ARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE T0373 87 :QDG 1on2A 56 :KYR T0373 93 :RVSLSSEGRRNLYGNRAKRE 1on2A 59 :GLVLTSKGKKIGKRLVYRHE T0373 114 :WLVRAM 1on2A 79 :LLEQFL T0373 120 :HACLDESER 1on2A 86 :IIGVDEEKI T0373 129 :ALLAA 1on2A 111 :DRIGD T0373 137 :LLTRL 1on2A 116 :LVQYF Number of specific fragments extracted= 8 number of extra gaps= 0 total=696 Number of alignments=124 # 1on2A read from 1on2A/merged-good-all-a2m # found chain 1on2A in training set Warning: unaligning (T0373)V33 because first residue in template chain is (1on2A)T2 T0373 34 :QFSQLVVLGAIDRL 1on2A 3 :TPSMEMYIEQIYML T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1on2A 20 :KGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE T0373 86 :PQD 1on2A 56 :KYR T0373 93 :RVSLSSEGRRNLYGNRAKR 1on2A 59 :GLVLTSKGKKIGKRLVYRH T0373 113 :EWLVRAM 1on2A 78 :ELLEQFL T0373 121 :ACLDESERALLAA 1on2A 103 :HHLSWNSIDRIGD T0373 137 :LLTRLA 1on2A 116 :LVQYFE Number of specific fragments extracted= 7 number of extra gaps= 0 total=703 Number of alignments=125 # 1on2A read from 1on2A/merged-good-all-a2m # found chain 1on2A in training set T0373 35 :FSQLVVLGAIDR 1on2A 8 :MYIEQIYMLIEE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1on2A 20 :KGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYR T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVRAMHACLDESER 1on2A 59 :GLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKI T0373 129 :ALLAAAGPLLT 1on2A 111 :DRIGDLVQYFE Number of specific fragments extracted= 4 number of extra gaps= 0 total=707 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sfxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0373 read from 1sfxA/merged-good-all-a2m # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0373 2 :PTNQDLQL 1sfxA 1 :MSNPLGEL T0373 25 :RREAQADPVQFSQLVVLGAIDRLGG 1sfxA 9 :VKALEKLSFKPSDVRIYSLLLERGG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSE 1sfxA 34 :MRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKP T0373 102 :RNLYGNRAKREEWLVRAMHACLD 1sfxA 83 :EKVLKEFKSSILGEIERIEKMFT Number of specific fragments extracted= 4 number of extra gaps= 0 total=711 Number of alignments=127 # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0373 1 :MPTNQDLQLA 1sfxA 0 :HMSNPLGELV T0373 26 :REAQADPVQFSQLVVLGAIDRLGG 1sfxA 10 :KALEKLSFKPSDVRIYSLLLERGG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSE 1sfxA 34 :MRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKP T0373 102 :RNLYGNRAKREEWLVRAMHACLD 1sfxA 83 :EKVLKEFKSSILGEIERIEKMFT Number of specific fragments extracted= 4 number of extra gaps= 0 total=715 Number of alignments=128 # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0373 22 :RRLRREAQADPVQFSQLVVLGAIDR 1sfxA 6 :GELVKALEKLSFKPSDVRIYSLLLE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSE 1sfxA 31 :RGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKP T0373 102 :RNLYGNRAKREEWLVRAMHACLDE 1sfxA 83 :EKVLKEFKSSILGEIERIEKMFTD Number of specific fragments extracted= 3 number of extra gaps= 0 total=718 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ulyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ulyA expands to /projects/compbio/data/pdb/1uly.pdb.gz 1ulyA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 1ulyA/merged-good-all-a2m # 1ulyA read from 1ulyA/merged-good-all-a2m # adding 1ulyA to template set # found chain 1ulyA in template set T0373 35 :FSQLVVLGAIDR 1ulyA 20 :DTRRKILKLLRN T0373 48 :GG 1ulyA 32 :KE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1ulyA 34 :MTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTE T0373 87 :QDGRRTRVSLS 1ulyA 72 :GNLVEKYYGRT T0373 98 :SEGRRNLYGNRAKREE 1ulyA 95 :EELRYIARSRLKTKID T0373 115 :LVRA 1ulyA 111 :IFKR T0373 125 :ESERALLAA 1ulyA 122 :NELLNIMDR T0373 137 :LLTRLAQ 1ulyA 131 :MSQKEFD Number of specific fragments extracted= 8 number of extra gaps= 0 total=726 Number of alignments=130 # 1ulyA read from 1ulyA/merged-good-all-a2m # found chain 1ulyA in template set T0373 6 :DLQLAAHLR 1ulyA 10 :DPEVIKVML T0373 34 :QFSQLVVLGAID 1ulyA 19 :EDTRRKILKLLR T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1ulyA 31 :NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTE T0373 87 :QDGRRTRVSLS 1ulyA 72 :GNLVEKYYGRT T0373 98 :SEGRRNLYGNRAKREEWLVRAM 1ulyA 95 :EELRYIARSRLKTKIDIFKRLG T0373 121 :ACLD 1ulyA 117 :YQFE T0373 125 :ESERALLAAAG 1ulyA 122 :NELLNIMDRMS T0373 136 :PLLTRLAQ 1ulyA 141 :RISKYIEE Number of specific fragments extracted= 8 number of extra gaps= 0 total=734 Number of alignments=131 # 1ulyA read from 1ulyA/merged-good-all-a2m # found chain 1ulyA in template set T0373 35 :FSQLVVLGAIDR 1ulyA 20 :DTRRKILKLLRN T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1ulyA 32 :KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTE T0373 87 :QDGRRTRVSLS 1ulyA 72 :GNLVEKYYGRT T0373 98 :SEGRRNLYGNRAKREEWLVR 1ulyA 95 :EELRYIARSRLKTKIDIFKR T0373 121 :ACLD 1ulyA 115 :LGYQ T0373 125 :ESERALLAAAGPLLTR 1ulyA 122 :NELLNIMDRMSQKEFD Number of specific fragments extracted= 6 number of extra gaps= 0 total=740 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p4xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1p4xA expands to /projects/compbio/data/pdb/1p4x.pdb.gz 1p4xA:# T0373 read from 1p4xA/merged-good-all-a2m # 1p4xA read from 1p4xA/merged-good-all-a2m # adding 1p4xA to template set # found chain 1p4xA in template set T0373 2 :PTNQDLQLAAHLR 1p4xA 5 :NHDKIRDFIIIEA T0373 20 :LTRRLRREAQ 1p4xA 18 :YMFRFKKKVK T0373 30 :ADPVQFSQLVVLGAIDRLGGD 1p4xA 29 :EVDMTIKEFILLTYLFHQQEN T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAMHAC 1p4xA 51 :LPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAERVTLFDQIIKQFNLAD T0373 128 :RALLAAAG 1p4xA 133 :SKEFLNLM T0373 136 :PLLTRLAQ 1p4xA 144 :MYFKNIIK Number of specific fragments extracted= 6 number of extra gaps= 0 total=746 Number of alignments=133 # 1p4xA read from 1p4xA/merged-good-all-a2m # found chain 1p4xA in template set T0373 2 :PTNQDLQLAAHLRSQVTTLTRRLR 1p4xA 4 :NNHDKIRDFIIIEAYMFRFKKKVK T0373 29 :QADPVQFSQLVVLGAIDRLGG 1p4xA 28 :PEVDMTIKEFILLTYLFHQQE T0373 50 :DVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAMHAC 1p4xA 50 :TLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAERVTLFDQIIKQFNLAD T0373 123 :LD 1p4xA 124 :SE T0373 126 :SERALLAAAGPLLTRLAQ 1p4xA 134 :KEFLNLMMYTMYFKNIIK Number of specific fragments extracted= 5 number of extra gaps= 0 total=751 Number of alignments=134 # 1p4xA read from 1p4xA/merged-good-all-a2m # found chain 1p4xA in template set T0373 2 :PTNQDLQLAAHLRSQVTTLTRRLRR 1p4xA 4 :NNHDKIRDFIIIEAYMFRFKKKVKP T0373 30 :ADPVQFSQLVVLGAIDRLGGD 1p4xA 29 :EVDMTIKEFILLTYLFHQQEN T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAMHAC 1p4xA 51 :LPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAERVTLFDQIIKQFNLAD Number of specific fragments extracted= 3 number of extra gaps= 0 total=754 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dbbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2dbbA expands to /projects/compbio/data/pdb/2dbb.pdb.gz 2dbbA:# T0373 read from 2dbbA/merged-good-all-a2m # 2dbbA read from 2dbbA/merged-good-all-a2m # adding 2dbbA to template set # found chain 2dbbA in template set Warning: unaligning (T0373)P32 because first residue in template chain is (2dbbA)K6 T0373 33 :VQFSQLVVLGAIDR 2dbbA 7 :LDRVDMQLVKILSE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLI 2dbbA 21 :NSRLTYRELADILNTTRQRIARRIDKLKKLGII T0373 81 :VRHADPQDGRRTRVSLS 2dbbA 57 :TIIPDIDKLGYMYAIVL T0373 107 :NRAKREE 2dbbA 78 :VPSDADK T0373 115 :LVRAMHAC 2dbbA 85 :VISEISDI T0373 124 :DESERALLAA 2dbbA 116 :DIKDAENLIS T0373 140 :RLAQFEEP 2dbbA 126 :EFLQRIKN Number of specific fragments extracted= 7 number of extra gaps= 0 total=761 Number of alignments=136 # 2dbbA read from 2dbbA/merged-good-all-a2m # found chain 2dbbA in template set Warning: unaligning (T0373)P32 because first residue in template chain is (2dbbA)K6 T0373 33 :VQFSQLVVLGAIDRLGG 2dbbA 7 :LDRVDMQLVKILSENSR T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLI 2dbbA 24 :LTYRELADILNTTRQRIARRIDKLKKLGII T0373 81 :VRHADPQDGRRTRVSLS 2dbbA 57 :TIIPDIDKLGYMYAIVL T0373 98 :SEGRRNLYGN 2dbbA 83 :DKVISEISDI T0373 109 :AKREEWLVRAM 2dbbA 118 :KDAENLISEFL T0373 121 :ACLD 2dbbA 129 :QRIK Number of specific fragments extracted= 6 number of extra gaps= 0 total=767 Number of alignments=137 # 2dbbA read from 2dbbA/merged-good-all-a2m # found chain 2dbbA in template set Warning: unaligning (T0373)P32 because first residue in template chain is (2dbbA)K6 T0373 33 :VQFSQLVVLGAIDR 2dbbA 7 :LDRVDMQLVKILSE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLI 2dbbA 21 :NSRLTYRELADILNTTRQRIARRIDKLKKLGII T0373 81 :VRHADPQDGRRTRVSL 2dbbA 57 :TIIPDIDKLGYMYAIV T0373 98 :SEGRRNLYGN 2dbbA 83 :DKVISEISDI T0373 108 :RAKREEWLVR 2dbbA 117 :IKDAENLISE T0373 119 :MHACLDE 2dbbA 127 :FLQRIKN Number of specific fragments extracted= 6 number of extra gaps= 0 total=773 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r7jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0373 read from 1r7jA/merged-good-all-a2m # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set T0373 38 :LVVLGAID 1r7jA 11 :QAILEACK T0373 48 :GG 1r7jA 19 :SG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 1r7jA 21 :SPKTRIMYGANLSYALTGRYIKMLMDLEIIRQE T0373 86 :PQ 1r7jA 54 :GK T0373 93 :RVSLSSEGRRNLYGNRAKREE 1r7jA 56 :QYMLTKKGEELLEDIRKFNEM T0373 115 :LVRA 1r7jA 77 :RKNM T0373 129 :ALLAA 1r7jA 81 :DQLKE T0373 140 :RLAQF 1r7jA 86 :KINSV Number of specific fragments extracted= 8 number of extra gaps= 0 total=781 Number of alignments=139 # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set Warning: unaligning (T0373)E146 because last residue in template chain is (1r7jA)S92 T0373 36 :SQLVVLGAID 1r7jA 9 :IIQAILEACK T0373 48 :GG 1r7jA 19 :SG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 1r7jA 21 :SPKTRIMYGANLSYALTGRYIKMLMDLEIIRQE T0373 86 :PQ 1r7jA 54 :GK T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVRAM 1r7jA 56 :QYMLTKKGEELLEDIRKFNEMRKNMDQ T0373 137 :LLTRLAQFE 1r7jA 83 :LKEKINSVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=787 Number of alignments=140 # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set T0373 42 :GAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1r7jA 12 :AILEACKSGSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEGK T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVRAMHA 1r7jA 56 :QYMLTKKGEELLEDIRKFNEMRKNMDQLK T0373 133 :A 1r7jA 85 :E Number of specific fragments extracted= 3 number of extra gaps= 0 total=790 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f5tA expands to /projects/compbio/data/pdb/1f5t.pdb.gz 1f5tA:# T0373 read from 1f5tA/merged-good-all-a2m # 1f5tA read from 1f5tA/merged-good-all-a2m # adding 1f5tA to template set # found chain 1f5tA in template set T0373 36 :SQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1f5tA 1010 :MYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVA T0373 87 :QDGR 1f5tA 1058 :SDRS T0373 94 :VSLSSEGRRNLYGNRAKRE 1f5tA 1062 :LQMTPTGRTLATAVMRKHR T0373 114 :WLVRAMHAC 1f5tA 1081 :LAERLLTDI T0373 123 :LDESERALLAA 1f5tA 1108 :MSDEVERRLVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=795 Number of alignments=142 # 1f5tA read from 1f5tA/merged-good-all-a2m # found chain 1f5tA in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 1f5tA 1009 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVV T0373 85 :DPQDG 1f5tA 1057 :ASDRS T0373 94 :VSLSSEGRRNLYGNRAKR 1f5tA 1062 :LQMTPTGRTLATAVMRKH T0373 113 :EWLVRAMHACLD 1f5tA 1080 :RLAERLLTDIIG T0373 125 :ESERALLAA 1f5tA 1098 :HDEADRWEH T0373 136 :PLLTRLAQ 1f5tA 1111 :EVERRLVK Number of specific fragments extracted= 6 number of extra gaps= 0 total=801 Number of alignments=143 # 1f5tA read from 1f5tA/merged-good-all-a2m # found chain 1f5tA in template set T0373 35 :FSQLVVLGAIDR 1f5tA 1009 :EMYLRTIYELEE T0373 48 :GGD 1f5tA 1021 :EGV T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1f5tA 1025 :PLRARIAERLEQSGPTVSQTVARMERDGLVVVASDR T0373 93 :RVSLSSEGRRNLYGNRAKR 1f5tA 1061 :SLQMTPTGRTLATAVMRKH T0373 113 :EWLVRAMHA 1f5tA 1080 :RLAERLLTD T0373 122 :CLDESERALLAA 1f5tA 1107 :VMSDEVERRLVK Number of specific fragments extracted= 6 number of extra gaps= 0 total=807 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fbiA expands to /projects/compbio/data/pdb/2fbi.pdb.gz 2fbiA:Skipped atom 2, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 443, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 445, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 447, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 831, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 833, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 835, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 837, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 839, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 895, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1099, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1101, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 2fbiA # T0373 read from 2fbiA/merged-good-all-a2m # 2fbiA read from 2fbiA/merged-good-all-a2m # adding 2fbiA to template set # found chain 2fbiA in template set Warning: unaligning (T0373)P2 because first residue in template chain is (2fbiA)R5 Warning: unaligning (T0373)P32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbiA)L32 Warning: unaligning (T0373)V33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbiA)L32 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0373)D88 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0373 3 :TNQDLQLA 2fbiA 6 :PSLTLTLL T0373 15 :SQVTTLTRRLRREAQAD 2fbiA 14 :QAREAAMSFFRPSLNQH T0373 34 :QFSQLVVLGAIDRLGG 2fbiA 33 :TEQQWRVIRILRQQGE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 2fbiA 49 :MESYQLANQACILRPSMTGVLARLERDGIVRRWKAP T0373 89 :GRRTRVSLSSEGRRNLYGNRAKREE 2fbiA 87 :QRRVYVNLTEKGQQCFVSMSGDMEK T0373 115 :LVRAMHACLDESERALLAA 2fbiA 112 :NYQRIQERFGEEKLAQLLE T0373 137 :LLTRLAQF 2fbiA 131 :LLNELKKI Number of specific fragments extracted= 7 number of extra gaps= 2 total=814 Number of alignments=145 # 2fbiA read from 2fbiA/merged-good-all-a2m # found chain 2fbiA in template set Warning: unaligning (T0373)P2 because first residue in template chain is (2fbiA)R5 Warning: unaligning (T0373)P32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbiA)L32 Warning: unaligning (T0373)V33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbiA)L32 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0373)D88 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0373 3 :TNQDLQL 2fbiA 6 :PSLTLTL T0373 14 :RSQVTTLTRRLRREAQAD 2fbiA 13 :LQAREAAMSFFRPSLNQH T0373 34 :QFSQLVVLGAIDRL 2fbiA 33 :TEQQWRVIRILRQQ T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 2fbiA 47 :GEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAP T0373 89 :GRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 2fbiA 87 :QRRVYVNLTEKGQQCFVSMSGDMEKNYQRIQ T0373 121 :ACLDESERALLAA 2fbiA 118 :ERFGEEKLAQLLE T0373 137 :LLTRLAQFE 2fbiA 131 :LLNELKKIK Number of specific fragments extracted= 7 number of extra gaps= 2 total=821 Number of alignments=146 # 2fbiA read from 2fbiA/merged-good-all-a2m # found chain 2fbiA in template set Warning: unaligning (T0373)P32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbiA)L32 Warning: unaligning (T0373)V33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbiA)L32 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0373)D88 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0373 14 :RSQVTTLTRRLRREAQAD 2fbiA 13 :LQAREAAMSFFRPSLNQH T0373 34 :QFSQLVVLGAIDR 2fbiA 33 :TEQQWRVIRILRQ T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 2fbiA 46 :QGEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAP T0373 89 :GRRTRVSLSSEGRRNLYGNRAKREEWLVR 2fbiA 87 :QRRVYVNLTEKGQQCFVSMSGDMEKNYQR T0373 119 :MHACLDESERALLAAAGPL 2fbiA 116 :IQERFGEEKLAQLLELLNE Number of specific fragments extracted= 5 number of extra gaps= 2 total=826 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fx7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fx7A expands to /projects/compbio/data/pdb/1fx7.pdb.gz 1fx7A:Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1fx7A # T0373 read from 1fx7A/merged-good-all-a2m # 1fx7A read from 1fx7A/merged-good-all-a2m # adding 1fx7A to template set # found chain 1fx7A in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1fx7A 9 :EMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVA T0373 87 :QDGR 1fx7A 58 :GDRH T0373 94 :VSLSSEGRRNLYGNRAKR 1fx7A 62 :LELTEKGRALAIAVMRKH T0373 112 :EE 1fx7A 95 :EE T0373 115 :LVRAMHAC 1fx7A 97 :VHAEACRW T0373 123 :LDES 1fx7A 108 :MSED T0373 137 :LLTRLAQFEEP 1fx7A 112 :VERRLVKVLNN Number of specific fragments extracted= 7 number of extra gaps= 0 total=833 Number of alignments=148 # 1fx7A read from 1fx7A/merged-good-all-a2m # found chain 1fx7A in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 1fx7A 9 :EMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRV T0373 85 :DPQ 1fx7A 57 :AGD T0373 89 :GR 1fx7A 60 :RH T0373 94 :VSLSSEGRRNLYGNRAKREEWLVRAM 1fx7A 62 :LELTEKGRALAIAVMRKHRLAERLLV T0373 121 :ACLD 1fx7A 88 :DVIG T0373 125 :ESERALLAAA 1fx7A 95 :EEVHAEACRW T0373 135 :GPLLTRLAQFEE 1fx7A 110 :EDVERRLVKVLN Number of specific fragments extracted= 7 number of extra gaps= 0 total=840 Number of alignments=149 # 1fx7A read from 1fx7A/merged-good-all-a2m # found chain 1fx7A in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1fx7A 9 :EMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVA T0373 87 :QDG 1fx7A 58 :GDR T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVR 1fx7A 61 :HLELTEKGRALAIAVMRKHRLAERL T0373 119 :MHACLD 1fx7A 86 :LVDVIG Number of specific fragments extracted= 4 number of extra gaps= 0 total=844 Number of alignments=150 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0373//projects/compbio/experiments/protein-predict/casp7/T0373/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0373//projects/compbio/experiments/protein-predict/casp7/T0373/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0373/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0373/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0373)A57.CB, (T0373)L67.CB) [> 2.9525 = 4.9208 < 6.3971] w=1.0000 to align # Constraint # added constraint: constraint((T0373)P53.CB, (T0373)L67.CB) [> 3.6143 = 6.0238 < 7.8310] w=0.9785 to align # Constraint # added constraint: constraint((T0373)L56.CB, (T0373)L67.CB) [> 3.3702 = 5.6171 < 7.3022] w=0.9784 to align # Constraint # added constraint: constraint((T0373)L71.CB, (T0373)I80.CB) [> 3.8642 = 6.4404 < 8.3725] w=0.9714 to align # Constraint # added constraint: constraint((T0373)P53.CB, (T0373)L71.CB) [> 4.0359 = 6.7265 < 8.7445] w=0.9066 to align # Constraint # added constraint: constraint((T0373)R82.CB, (T0373)V94.CB) [> 3.5168 = 5.8613 < 7.6197] w=0.9064 to align # Constraint # added constraint: constraint((T0373)A43.CB, (T0373)A59.CB) [> 3.6089 = 6.0148 < 7.8192] w=0.9022 to align # Constraint # added constraint: constraint((T0373)Q37.CB, (T0373)L70.CB) [> 3.5035 = 5.8392 < 7.5910] w=0.8994 to align # Constraint # added constraint: constraint((T0373)L71.CB, (T0373)V94.CB) [> 3.8752 = 6.4587 < 8.3963] w=0.8852 to align # Constraint # added constraint: constraint((T0373)V51.CB, (T0373)V94.CB) [> 3.3026 = 5.5043 < 7.1555] w=0.8850 to align # Constraint # added constraint: constraint((T0373)V81.CB, (T0373)S95.CB) [> 3.1515 = 5.2525 < 6.8282] w=0.8705 to align # Constraint # added constraint: constraint((T0373)I80.CB, (T0373)S95.CB) [> 4.1009 = 6.8348 < 8.8852] w=0.8705 to align # Constraint # added constraint: constraint((T0373)I80.CB, (T0373)L96.CB) [> 3.7259 = 6.2098 < 8.0727] w=0.8633 to align # Constraint # added constraint: constraint((T0373)L79.CB, (T0373)L96.CB) [> 4.1815 = 6.9692 < 9.0599] w=0.8632 to align # Constraint # added constraint: constraint((T0373)L79.CB, (T0373)S97.CB) [> 3.5127 = 5.8545 < 7.6108] w=0.8492 to align # Constraint # added constraint: constraint((T0373)G78.CA, (T0373)S97.CB) [> 3.2654 = 5.4422 < 7.0749] w=0.8492 to align # Constraint # added constraint: constraint((T0373)V81.CB, (T0373)V94.CB) [> 4.3916 = 7.3194 < 9.5152] w=0.8489 to align # Constraint # added constraint: constraint((T0373)T52.CB, (T0373)V94.CB) [> 4.3579 = 7.2632 < 9.4422] w=0.8429 to align # Constraint # added constraint: constraint((T0373)A43.CB, (T0373)L56.CB) [> 3.6686 = 6.1143 < 7.9485] w=0.8400 to align # Constraint # added constraint: constraint((T0373)P53.CB, (T0373)A68.CB) [> 3.7840 = 6.3066 < 8.1986] w=0.8294 to align # Constraint # added constraint: constraint((T0373)V81.CB, (T0373)S97.CB) [> 3.4734 = 5.7890 < 7.5258] w=0.8277 to align # Constraint # added constraint: constraint((T0373)V40.CB, (T0373)E60.CB) [> 4.0076 = 6.6793 < 8.6831] w=0.8275 to align # Constraint # added constraint: constraint((T0373)V40.CB, (T0373)L74.CB) [> 4.0499 = 6.7498 < 8.7747] w=0.8256 to align # Constraint # added constraint: constraint((T0373)I80.CB, (T0373)S97.CB) [> 3.8038 = 6.3397 < 8.2416] w=0.8061 to align # Constraint # added constraint: constraint((T0373)V40.CB, (T0373)L70.CB) [> 3.4034 = 5.6723 < 7.3740] w=0.8041 to align # Constraint # added constraint: constraint((T0373)R82.CB, (T0373)R93.CB) [> 4.2069 = 7.0115 < 9.1150] w=0.7908 to align # Constraint # added constraint: constraint((T0373)L41.CB, (T0373)L79.CB) [> 3.9648 = 6.6080 < 8.5904] w=0.7825 to align # Constraint # added constraint: constraint((T0373)V40.CB, (T0373)L71.CB) [> 4.2013 = 7.0021 < 9.1027] w=0.7775 to align # Constraint # added constraint: constraint((T0373)I44.CB, (T0373)V94.CB) [> 3.6825 = 6.1376 < 7.9788] w=0.7735 to align # Constraint # added constraint: constraint((T0373)H83.CB, (T0373)S95.CB) [> 3.8001 = 6.3336 < 8.2337] w=0.7677 to align # Constraint # added constraint: constraint((T0373)L79.CB, (T0373)G100.CA) [> 2.7794 = 4.6323 < 6.0221] w=0.7641 to align # Constraint # added constraint: constraint((T0373)I44.CB, (T0373)I80.CB) [> 4.0164 = 6.6940 < 8.7022] w=0.7541 to align # Constraint # added constraint: constraint((T0373)H83.CB, (T0373)R93.CB) [> 3.2643 = 5.4404 < 7.0725] w=0.7476 to align # Constraint # added constraint: constraint((T0373)V39.CB, (T0373)E60.CB) [> 3.6188 = 6.0313 < 7.8407] w=0.7466 to align # Constraint # added constraint: constraint((T0373)V40.CB, (T0373)L67.CB) [> 4.3315 = 7.2192 < 9.3850] w=0.7464 to align # Constraint # added constraint: constraint((T0373)L41.CB, (T0373)L74.CB) [> 4.2159 = 7.0265 < 9.1345] w=0.7396 to align # Constraint # added constraint: constraint((T0373)L41.CB, (T0373)L96.CB) [> 3.9833 = 6.6388 < 8.6304] w=0.7339 to align # Constraint # added constraint: constraint((T0373)S36.CB, (T0373)L70.CB) [> 3.4786 = 5.7976 < 7.5370] w=0.7325 to align # Constraint # added constraint: constraint((T0373)I44.CB, (T0373)L96.CB) [> 3.1187 = 5.1978 < 6.7571] w=0.7321 to align # Constraint # added constraint: constraint((T0373)L41.CB, (T0373)L104.CB) [> 3.3849 = 5.6414 < 7.3339] w=0.6924 to align # Constraint # added constraint: constraint((T0373)P53.CB, (T0373)S64.CB) [> 3.7895 = 6.3158 < 8.2106] w=0.6910 to align # Constraint # added constraint: constraint((T0373)Q37.CB, (T0373)E73.CB) [> 4.1693 = 6.9488 < 9.0334] w=0.6896 to align # Constraint # added constraint: constraint((T0373)D45.CB, (T0373)L96.CB) [> 3.6678 = 6.1130 < 7.9469] w=0.6883 to align # Constraint # added constraint: constraint((T0373)G78.CA, (T0373)G100.CA) [> 4.3174 = 7.1957 < 9.3544] w=0.6550 to align # Constraint # added constraint: constraint((T0373)L79.CB, (T0373)E99.CB) [> 3.5801 = 5.9668 < 7.7568] w=0.6549 to align # Constraint # added constraint: constraint((T0373)G78.CA, (T0373)E99.CB) [> 3.4720 = 5.7867 < 7.5228] w=0.6549 to align # Constraint # added constraint: constraint((T0373)I44.CB, (T0373)S95.CB) [> 3.9893 = 6.6489 < 8.6435] w=0.6326 to align # Constraint # added constraint: constraint((T0373)S54.CB, (T0373)S64.CB) [> 3.9810 = 6.6351 < 8.6256] w=0.6284 to align # Constraint # added constraint: constraint((T0373)R82.CB, (T0373)S95.CB) [> 4.5094 = 7.5157 < 9.7704] w=0.6280 to align # Constraint # added constraint: constraint((T0373)L71.CB, (T0373)R82.CB) [> 4.1660 = 6.9434 < 9.0264] w=0.6193 to align # Constraint # added constraint: constraint((T0373)L41.CB, (T0373)I80.CB) [> 4.4354 = 7.3923 < 9.6100] w=0.6108 to align # Constraint # added constraint: constraint((T0373)R82.CB, (T0373)T92.CB) [> 3.1775 = 5.2958 < 6.8845] w=0.5985 to align # Constraint # added constraint: constraint((T0373)S36.CB, (T0373)M62.CB) [> 3.9435 = 6.5725 < 8.5442] w=0.5948 to align # Constraint # added constraint: constraint((T0373)V81.CB, (T0373)L96.CB) [> 4.5810 = 7.6351 < 9.9256] w=0.5765 to align # Constraint # added constraint: constraint((T0373)T52.CB, (T0373)R91.CB) [> 3.3672 = 5.6121 < 7.2957] w=0.5700 to align # Constraint # added constraint: constraint((T0373)H83.CB, (T0373)T92.CB) [> 4.1888 = 6.9814 < 9.0758] w=0.5697 to align # Constraint # added constraint: constraint((T0373)D45.CB, (T0373)L104.CB) [> 3.2816 = 5.4693 < 7.1101] w=0.5538 to align # Constraint # added constraint: constraint((T0373)L38.CB, (T0373)N107.CB) [> 3.6989 = 6.1649 < 8.0143] w=0.5402 to align # Constraint # added constraint: constraint((T0373)L41.CB, (T0373)G100.CA) [> 4.0881 = 6.8135 < 8.8576] w=0.5251 to align # Constraint # added constraint: constraint((T0373)P53.CB, (T0373)T92.CB) [> 3.7452 = 6.2420 < 8.1146] w=0.5197 to align # Constraint # added constraint: constraint((T0373)D45.CB, (T0373)R101.CB) [> 4.1371 = 6.8951 < 8.9637] w=0.5179 to align # Constraint # added constraint: constraint((T0373)S36.CB, (T0373)N66.CB) [> 4.0815 = 6.8025 < 8.8433] w=0.4943 to align # Constraint # added constraint: constraint((T0373)D50.CB, (T0373)V94.CB) [> 4.0420 = 6.7366 < 8.7576] w=0.4830 to align # Constraint # added constraint: constraint((T0373)A57.CB, (T0373)N66.CB) [> 4.4709 = 7.4515 < 9.6870] w=0.4577 to align # Constraint # added constraint: constraint((T0373)D50.CB, (T0373)S95.CB) [> 3.0366 = 5.0610 < 6.5793] w=0.4542 to align # Constraint # added constraint: constraint((T0373)D50.CB, (T0373)R93.CB) [> 3.0310 = 5.0517 < 6.5672] w=0.4456 to align # Constraint # added constraint: constraint((T0373)A84.CB, (T0373)R93.CB) [> 4.3216 = 7.2027 < 9.3635] w=0.4364 to align # Constraint # added constraint: constraint((T0373)L41.CB, (T0373)N103.CB) [> 4.1413 = 6.9021 < 8.9727] w=0.3943 to align # Constraint # added constraint: constraint((T0373)L38.CB, (T0373)L104.CB) [> 3.7524 = 6.2539 < 8.1301] w=0.3817 to align # Constraint # added constraint: constraint((T0373)G42.CA, (T0373)R108.CB) [> 4.0875 = 6.8124 < 8.8562] w=0.3676 to align # Constraint # added constraint: constraint((T0373)V40.CB, (T0373)I80.CB) [> 4.6279 = 7.7132 < 10.0271] w=0.3598 to align # Constraint # added constraint: constraint((T0373)A28.CB, (T0373)L38.CB) [> 3.7979 = 6.3298 < 8.2287] w=0.3400 to align # Constraint # added constraint: constraint((T0373)L41.CB, (T0373)N107.CB) [> 4.1105 = 6.8508 < 8.9060] w=0.3375 to align # Constraint # added constraint: constraint((T0373)P53.CB, (T0373)R91.CB) [> 4.3756 = 7.2927 < 9.4805] w=0.2807 to align # Constraint # added constraint: constraint((T0373)Q34.CB, (T0373)L70.CB) [> 4.1867 = 6.9778 < 9.0711] w=0.2647 to align # Constraint # added constraint: constraint((T0373)A43.CB, (T0373)E55.CB) [> 4.2322 = 7.0536 < 9.1697] w=0.2382 to align # Constraint # added constraint: constraint((T0373)D50.CB, (T0373)H83.CB) [> 4.2013 = 7.0022 < 9.1029] w=0.2374 to align # Constraint # added constraint: constraint((T0373)E75.CB, (T0373)V94.CB) [> 4.5946 = 7.6576 < 9.9549] w=0.2347 to align # Constraint # added constraint: constraint((T0373)L38.CB, (T0373)R111.CB) [> 4.0888 = 6.8146 < 8.8590] w=0.2236 to align # Constraint # added constraint: constraint((T0373)P53.CB, (T0373)R82.CB) [> 4.5331 = 7.5551 < 9.8217] w=0.2193 to align # Constraint # added constraint: constraint((T0373)G42.CA, (T0373)L96.CB) [> 4.3668 = 7.2780 < 9.4614] w=0.2081 to align # Constraint # added constraint: constraint((T0373)E27.CB, (T0373)K110.CB) [> 3.3915 = 5.6526 < 7.3483] w=0.1944 to align # Constraint # added constraint: constraint((T0373)G48.CA, (T0373)L96.CB) [> 4.1577 = 6.9295 < 9.0084] w=0.1943 to align # Constraint # added constraint: constraint((T0373)V40.CB, (T0373)V94.CB) [> 4.5284 = 7.5473 < 9.8115] w=0.1939 to align # Constraint # added constraint: constraint((T0373)A28.CB, (T0373)N107.CB) [> 4.2752 = 7.1253 < 9.2628] w=0.1800 to align # Constraint # added constraint: constraint((T0373)S54.CB, (T0373)R91.CB) [> 4.2583 = 7.0972 < 9.2264] w=0.1797 to align # Constraint # added constraint: constraint((T0373)D31.CB, (T0373)N103.CB) [> 3.9376 = 6.5626 < 8.5314] w=0.1728 to align # Constraint # added constraint: constraint((T0373)R25.CB, (T0373)F35.CB) [> 4.0294 = 6.7158 < 8.7305] w=0.1728 to align # Constraint # added constraint: constraint((T0373)T52.CB, (T0373)R90.CB) [> 3.5127 = 5.8545 < 7.6108] w=0.1704 to align # Constraint # added constraint: constraint((T0373)L24.CB, (T0373)L38.CB) [> 4.2427 = 7.0711 < 9.1925] w=0.1655 to align # Constraint # added constraint: constraint((T0373)I44.CB, (T0373)L74.CB) [> 4.6593 = 7.7654 < 10.0951] w=0.1632 to align # Constraint # added constraint: constraint((T0373)G42.CA, (T0373)R111.CB) [> 4.1352 = 6.8920 < 8.9596] w=0.1517 to align # Constraint # added constraint: constraint((T0373)V33.CB, (T0373)N103.CB) [> 4.2918 = 7.1530 < 9.2989] w=0.1512 to align # Constraint # added constraint: constraint((T0373)V33.CB, (T0373)L79.CB) [> 4.3889 = 7.3148 < 9.5092] w=0.1511 to align # Constraint # added constraint: constraint((T0373)L74.CB, (T0373)G100.CA) [> 4.7221 = 7.8701 < 10.2312] w=0.1506 to align # Constraint # added constraint: constraint((T0373)L47.CB, (T0373)A59.CB) [> 4.5711 = 7.6185 < 9.9040] w=0.1409 to align # Constraint # added constraint: constraint((T0373)V39.CB, (T0373)R111.CB) [> 4.1697 = 6.9496 < 9.0344] w=0.1386 to align # Constraint # added constraint: constraint((T0373)Q37.CB, (T0373)L71.CB) [> 4.3250 = 7.2084 < 9.3709] w=0.1385 to align # Constraint # added constraint: constraint((T0373)L24.CB, (T0373)R111.CB) [> 3.5762 = 5.9603 < 7.7484] w=0.1368 to align # Constraint # added constraint: constraint((T0373)E27.CB, (T0373)G77.CA) [> 3.7410 = 6.2350 < 8.1054] w=0.1313 to align # Constraint # added constraint: constraint((T0373)A57.CB, (T0373)A68.CB) [> 4.5573 = 7.5955 < 9.8742] w=0.1294 to align # Constraint # added constraint: constraint((T0373)V39.CB, (T0373)N107.CB) [> 2.9255 = 4.8758 < 6.3385] w=0.1233 to align # Constraint # added constraint: constraint((T0373)T21.CB, (T0373)F35.CB) [> 3.9174 = 6.5290 < 8.4877] w=0.1224 to align # Constraint # added constraint: constraint((T0373)L41.CB, (T0373)V94.CB) [> 3.2925 = 5.4875 < 7.1337] w=0.1170 to align # Constraint # added constraint: constraint((T0373)V39.CB, (T0373)L104.CB) [> 3.4325 = 5.7208 < 7.4370] w=0.1170 to align # Constraint # added constraint: constraint((T0373)L24.CB, (T0373)F35.CB) [> 3.6602 = 6.1002 < 7.9303] w=0.1152 to align # Constraint # added constraint: constraint((T0373)E27.CB, (T0373)N107.CB) [> 3.6780 = 6.1299 < 7.9689] w=0.1152 to align # Constraint # added constraint: constraint((T0373)V51.CB, (T0373)R90.CB) [> 3.6246 = 6.0410 < 7.8533] w=0.1129 to align # Constraint # added constraint: constraint((T0373)F35.CB, (T0373)N107.CB) [> 3.1498 = 5.2497 < 6.8246] w=0.1096 to align # Constraint # added constraint: constraint((T0373)V33.CB, (T0373)N107.CB) [> 3.9174 = 6.5290 < 8.4877] w=0.1080 to align # Constraint # added constraint: constraint((T0373)G42.CA, (T0373)N107.CB) [> 3.4492 = 5.7488 < 7.4734] w=0.0996 to align # Constraint # added constraint: constraint((T0373)A118.CB, (T0373)L131.CB) [> 3.6804 = 6.1340 < 7.9742] w=0.0947 to align # Constraint # added constraint: constraint((T0373)L20.CB, (T0373)L115.CB) [> 4.0807 = 6.8012 < 8.8416] w=0.0936 to align # Constraint # added constraint: constraint((T0373)D50.CB, (T0373)L96.CB) [> 4.1373 = 6.8955 < 8.9641] w=0.0935 to align # Constraint # added constraint: constraint((T0373)R111.CB, (T0373)L131.CB) [> 3.7111 = 6.1852 < 8.0407] w=0.0898 to align # Constraint # added constraint: constraint((T0373)E27.CB, (T0373)W114.CB) [> 3.5371 = 5.8952 < 7.6637] w=0.0864 to align # Constraint # added constraint: constraint((T0373)E27.CB, (T0373)R111.CB) [> 3.6501 = 6.0835 < 7.9085] w=0.0864 to align # Constraint # added constraint: constraint((T0373)L47.CB, (T0373)L56.CB) [> 4.3197 = 7.1996 < 9.3594] w=0.0863 to align # Constraint # added constraint: constraint((T0373)R82.CB, (T0373)R91.CB) [> 3.9852 = 6.6420 < 8.6346] w=0.0862 to align # Constraint # added constraint: constraint((T0373)M119.CB, (T0373)R128.CB) [> 3.6621 = 6.1035 < 7.9345] w=0.0861 to align # Constraint # added constraint: constraint((T0373)D50.CB, (T0373)R90.CB) [> 2.9276 = 4.8794 < 6.3432] w=0.0841 to align # Constraint # added constraint: constraint((T0373)A43.CB, (T0373)R108.CB) [> 4.5533 = 7.5889 < 9.8655] w=0.0834 to align # Constraint # added constraint: constraint((T0373)W114.CB, (T0373)L131.CB) [> 3.1952 = 5.3254 < 6.9230] w=0.0809 to align # Constraint # added constraint: constraint((T0373)L41.CB, (T0373)R111.CB) [> 3.8434 = 6.4056 < 8.3273] w=0.0798 to align # Constraint # added constraint: constraint((T0373)D31.CB, (T0373)K110.CB) [> 4.1006 = 6.8344 < 8.8847] w=0.0792 to align # Constraint # added constraint: constraint((T0373)L24.CB, (T0373)W114.CB) [> 3.6055 = 6.0092 < 7.8120] w=0.0792 to align # Constraint # added constraint: constraint((T0373)E27.CB, (T0373)L115.CB) [> 3.6205 = 6.0342 < 7.8445] w=0.0792 to align # Constraint # added constraint: constraint((T0373)E27.CB, (T0373)L74.CB) [> 3.5728 = 5.9547 < 7.7411] w=0.0791 to align # Constraint # added constraint: constraint((T0373)V51.CB, (T0373)R91.CB) [> 3.8062 = 6.3436 < 8.2467] w=0.0790 to align # Constraint # added constraint: constraint((T0373)L41.CB, (T0373)R101.CB) [> 4.5927 = 7.6544 < 9.9508] w=0.0790 to align # Constraint # added constraint: constraint((T0373)R72.CB, (T0373)R82.CB) [> 4.6572 = 7.7621 < 10.0907] w=0.0790 to align # Constraint # added constraint: constraint((T0373)K110.CB, (T0373)L138.CB) [> 3.6930 = 6.1550 < 8.0015] w=0.0742 to align # Constraint # added constraint: constraint((T0373)L115.CB, (T0373)R128.CB) [> 3.8178 = 6.3630 < 8.2719] w=0.0736 to align # Constraint # added constraint: constraint((T0373)A28.CB, (T0373)K110.CB) [> 4.2425 = 7.0709 < 9.1922] w=0.0720 to align # Constraint # added constraint: constraint((T0373)L71.CB, (T0373)T92.CB) [> 4.3654 = 7.2757 < 9.4585] w=0.0719 to align # Constraint # added constraint: constraint((T0373)L24.CB, (T0373)K110.CB) [> 3.8539 = 6.4232 < 8.3502] w=0.0648 to align # Constraint # added constraint: constraint((T0373)L20.CB, (T0373)W114.CB) [> 3.8357 = 6.3928 < 8.3106] w=0.0648 to align # Constraint # added constraint: constraint((T0373)V33.CB, (T0373)L74.CB) [> 4.6631 = 7.7719 < 10.1034] w=0.0648 to align # Constraint # added constraint: constraint((T0373)D50.CB, (T0373)D85.CB) [> 4.1622 = 6.9371 < 9.0182] w=0.0647 to align # Constraint # added constraint: constraint((T0373)V116.CB, (T0373)R128.CB) [> 3.8671 = 6.4451 < 8.3787] w=0.0624 to align # Constraint # added constraint: constraint((T0373)A118.CB, (T0373)L130.CB) [> 3.8760 = 6.4601 < 8.3981] w=0.0593 to align # Constraint # added constraint: constraint((T0373)K110.CB, (T0373)L123.CB) [> 2.9615 = 4.9358 < 6.4165] w=0.0593 to align # Constraint # added constraint: constraint((T0373)L20.CB, (T0373)R111.CB) [> 3.8751 = 6.4585 < 8.3960] w=0.0576 to align # Constraint # added constraint: constraint((T0373)R23.CB, (T0373)G77.CA) [> 3.9949 = 6.6582 < 8.6557] w=0.0575 to align # Constraint # added constraint: constraint((T0373)L47.CB, (T0373)V94.CB) [> 4.0098 = 6.6830 < 8.6879] w=0.0575 to align # Constraint # added constraint: constraint((T0373)R117.CB, (T0373)L141.CB) [> 3.9143 = 6.5238 < 8.4809] w=0.0574 to align # Constraint # added constraint: constraint((T0373)R111.CB, (T0373)A134.CB) [> 4.5347 = 7.5578 < 9.8251] w=0.0544 to align # Constraint # added constraint: constraint((T0373)K110.CB, (T0373)A134.CB) [> 4.3260 = 7.2099 < 9.3729] w=0.0544 to align # Constraint # added constraint: constraint((T0373)R111.CB, (T0373)A132.CB) [> 3.9679 = 6.6132 < 8.5972] w=0.0535 to align # Constraint # added constraint: constraint((T0373)C122.CB, (T0373)F144.CB) [> 4.4571 = 7.4285 < 9.6571] w=0.0520 to align # Constraint # added constraint: constraint((T0373)L38.CB, (T0373)K110.CB) [> 4.5069 = 7.5114 < 9.7649] w=0.0504 to align # Constraint # added constraint: constraint((T0373)M119.CB, (T0373)L131.CB) [> 3.9586 = 6.5977 < 8.5770] w=0.0479 to align # Constraint # added constraint: constraint((T0373)W114.CB, (T0373)L138.CB) [> 3.4064 = 5.6773 < 7.3805] w=0.0473 to align # Constraint # added constraint: constraint((T0373)W114.CB, (T0373)L130.CB) [> 4.5082 = 7.5136 < 9.7677] w=0.0452 to align # Constraint # added constraint: constraint((T0373)V81.CB, (T0373)R93.CB) [> 3.1246 = 5.2077 < 6.7701] w=0.0431 to align # Constraint # added constraint: constraint((T0373)V81.CB, (T0373)T92.CB) [> 3.8714 = 6.4523 < 8.3880] w=0.0431 to align # Constraint # added constraint: constraint((T0373)I80.CB, (T0373)R93.CB) [> 3.8535 = 6.4226 < 8.3493] w=0.0431 to align # Constraint # added constraint: constraint((T0373)I80.CB, (T0373)T92.CB) [> 3.5644 = 5.9406 < 7.7228] w=0.0431 to align # Constraint # added constraint: constraint((T0373)L13.CB, (T0373)L74.CB) [> 4.0545 = 6.7574 < 8.7847] w=0.0429 to align # Constraint # added constraint: constraint((T0373)K110.CB, (T0373)G135.CA) [> 2.8179 = 4.6965 < 6.1054] w=0.0407 to align # Constraint # added constraint: constraint((T0373)W114.CB, (T0373)L141.CB) [> 3.1681 = 5.2802 < 6.8643] w=0.0398 to align # Constraint # added constraint: constraint((T0373)L7.CB, (T0373)T19.CB) [> 4.0107 = 6.6845 < 8.6898] w=0.0365 to align # Constraint # added constraint: constraint((T0373)D50.CB, (T0373)R91.CB) [> 3.0081 = 5.0135 < 6.5175] w=0.0360 to align # Constraint # added constraint: constraint((T0373)A118.CB, (T0373)L137.CB) [> 4.0950 = 6.8250 < 8.8724] w=0.0359 to align # Constraint # added constraint: constraint((T0373)M119.CB, (T0373)L130.CB) [> 3.6384 = 6.0640 < 7.8832] w=0.0338 to align # Constraint # added constraint: constraint((T0373)W114.CB, (T0373)A142.CB) [> 4.0845 = 6.8075 < 8.8497] w=0.0329 to align # Constraint # added constraint: constraint((T0373)W114.CB, (T0373)A134.CB) [> 2.5465 = 4.2442 < 5.5174] w=0.0308 to align # Constraint # added constraint: constraint((T0373)G78.CA, (T0373)N107.CB) [> 3.4365 = 5.7274 < 7.4456] w=0.0288 to align # Constraint # added constraint: constraint((T0373)D50.CB, (T0373)R101.CB) [> 4.5846 = 7.6409 < 9.9332] w=0.0288 to align # Constraint # added constraint: constraint((T0373)T92.CB, (T0373)R111.CB) [> 3.6242 = 6.0404 < 7.8525] w=0.0288 to align # Constraint # added constraint: constraint((T0373)A118.CB, (T0373)L138.CB) [> 3.3164 = 5.5273 < 7.1855] w=0.0288 to align # Constraint # added constraint: constraint((T0373)M119.CB, (T0373)L137.CB) [> 3.6459 = 6.0764 < 7.8994] w=0.0279 to align # Constraint # added constraint: constraint((T0373)L115.CB, (T0373)A134.CB) [> 2.6916 = 4.4860 < 5.8318] w=0.0260 to align # Constraint # added constraint: constraint((T0373)D50.CB, (T0373)G89.CA) [> 3.6824 = 6.1373 < 7.9785] w=0.0242 to align # Constraint # added constraint: constraint((T0373)S98.CB, (T0373)N107.CB) [> 3.3053 = 5.5089 < 7.1616] w=0.0222 to align # Constraint # added constraint: constraint((T0373)L20.CB, (T0373)A121.CB) [> 4.0167 = 6.6946 < 8.7029] w=0.0216 to align # Constraint # added constraint: constraint((T0373)F35.CB, (T0373)A69.CB) [> 4.6589 = 7.7648 < 10.0942] w=0.0216 to align # Constraint # added constraint: constraint((T0373)G77.CA, (T0373)N107.CB) [> 3.7381 = 6.2303 < 8.0993] w=0.0216 to align # Constraint # added constraint: constraint((T0373)L9.CB, (T0373)E27.CB) [> 3.3896 = 5.6494 < 7.3442] w=0.0216 to align # Constraint # added constraint: constraint((T0373)D50.CB, (T0373)T92.CB) [> 3.6275 = 6.0458 < 7.8595] w=0.0216 to align # Constraint # added constraint: constraint((T0373)I44.CB, (T0373)N107.CB) [> 3.4238 = 5.7064 < 7.4183] w=0.0216 to align # Constraint # added constraint: constraint((T0373)A43.CB, (T0373)L74.CB) [> 3.9472 = 6.5787 < 8.5524] w=0.0216 to align # Constraint # added constraint: constraint((T0373)A43.CB, (T0373)L70.CB) [> 3.5078 = 5.8464 < 7.6003] w=0.0216 to align # Constraint # added constraint: constraint((T0373)H120.CB, (T0373)L138.CB) [> 3.4488 = 5.7481 < 7.4725] w=0.0216 to align # Constraint # added constraint: constraint((T0373)I44.CB, (T0373)R93.CB) [> 3.6368 = 6.0613 < 7.8797] w=0.0216 to align # Constraint # added constraint: constraint((T0373)L9.CB, (T0373)M62.CB) [> 3.6346 = 6.0576 < 7.8748] w=0.0215 to align # Constraint # added constraint: constraint((T0373)L9.CB, (T0373)N66.CB) [> 3.8872 = 6.4787 < 8.4223] w=0.0215 to align # Constraint # added constraint: constraint((T0373)L9.CB, (T0373)L67.CB) [> 4.7513 = 7.9188 < 10.2945] w=0.0215 to align # Constraint # added constraint: constraint((T0373)A10.CB, (T0373)L70.CB) [> 3.2560 = 5.4267 < 7.0547] w=0.0215 to align # Constraint # added constraint: constraint((T0373)A10.CB, (T0373)L74.CB) [> 3.9521 = 6.5869 < 8.5629] w=0.0215 to align # Constraint # added constraint: constraint((T0373)R14.CB, (T0373)L96.CB) [> 4.3413 = 7.2355 < 9.4062] w=0.0215 to align # Constraint # added constraint: constraint((T0373)R14.CB, (T0373)L79.CB) [> 4.0322 = 6.7203 < 8.7364] w=0.0215 to align # Constraint # added constraint: constraint((T0373)L13.CB, (T0373)L71.CB) [> 3.9369 = 6.5615 < 8.5299] w=0.0215 to align # Constraint # added constraint: constraint((T0373)L13.CB, (T0373)L67.CB) [> 3.4929 = 5.8215 < 7.5679] w=0.0215 to align # Constraint # added constraint: constraint((T0373)L13.CB, (T0373)M62.CB) [> 4.4280 = 7.3800 < 9.5940] w=0.0215 to align # Constraint # added constraint: constraint((T0373)L13.CB, (T0373)L56.CB) [> 3.6143 = 6.0238 < 7.8309] w=0.0215 to align # Constraint # added constraint: constraint((T0373)H12.CB, (T0373)M62.CB) [> 3.9516 = 6.5859 < 8.5617] w=0.0215 to align # Constraint # added constraint: constraint((T0373)E27.CB, (T0373)S36.CB) [> 3.1215 = 5.2024 < 6.7632] w=0.0215 to align # Constraint # added constraint: constraint((T0373)E27.CB, (T0373)V39.CB) [> 3.1029 = 5.1716 < 6.7230] w=0.0215 to align # Constraint # added constraint: constraint((T0373)E27.CB, (T0373)V40.CB) [> 4.7633 = 7.9389 < 10.3206] w=0.0215 to align # Constraint # added constraint: constraint((T0373)W114.CB, (T0373)E127.CB) [> 3.6800 = 6.1334 < 7.9735] w=0.0209 to align # Constraint # added constraint: constraint((T0373)D6.CB, (T0373)L20.CB) [> 3.7928 = 6.3214 < 8.2178] w=0.0150 to align # Constraint # added constraint: constraint((T0373)D50.CB, (T0373)S97.CB) [> 4.4964 = 7.4941 < 9.7423] w=0.0144 to align # Constraint # added constraint: constraint((T0373)L13.CB, (T0373)L138.CB) [> 4.7752 = 7.9587 < 10.3463] w=0.0144 to align # Constraint # added constraint: constraint((T0373)T19.CB, (T0373)W114.CB) [> 3.9780 = 6.6301 < 8.6191] w=0.0144 to align # Constraint # added constraint: constraint((T0373)Q16.CB, (T0373)C122.CB) [> 4.7783 = 7.9639 < 10.3531] w=0.0144 to align # Constraint # added constraint: constraint((T0373)V39.CB, (T0373)V51.CB) [> 4.6651 = 7.7752 < 10.1078] w=0.0144 to align # Constraint # added constraint: constraint((T0373)Q37.CB, (T0373)G100.CA) [> 3.8429 = 6.4048 < 8.3263] w=0.0144 to align # Constraint # added constraint: constraint((T0373)S36.CB, (T0373)L74.CB) [> 3.9834 = 6.6391 < 8.6308] w=0.0144 to align # Constraint # added constraint: constraint((T0373)L20.CB, (T0373)K110.CB) [> 4.7519 = 7.9198 < 10.2957] w=0.0144 to align # Constraint # added constraint: constraint((T0373)Q8.CB, (T0373)E27.CB) [> 3.8648 = 6.4413 < 8.3737] w=0.0144 to align # Constraint # added constraint: constraint((T0373)L9.CB, (T0373)M119.CB) [> 4.1173 = 6.8621 < 8.9207] w=0.0144 to align # Constraint # added constraint: constraint((T0373)L41.CB, (T0373)K110.CB) [> 4.3185 = 7.1975 < 9.3568] w=0.0144 to align # Constraint # added constraint: constraint((T0373)V81.CB, (T0373)R91.CB) [> 4.0433 = 6.7387 < 8.7604] w=0.0144 to align # Constraint # added constraint: constraint((T0373)D50.CB, (T0373)A84.CB) [> 4.4228 = 7.3713 < 9.5827] w=0.0144 to align # Constraint # added constraint: constraint((T0373)L9.CB, (T0373)G78.CA) [> 4.1621 = 6.9368 < 9.0179] w=0.0144 to align # Constraint # added constraint: constraint((T0373)L131.CB, (T0373)R140.CB) [> 3.2721 = 5.4535 < 7.0896] w=0.0144 to align # Constraint # added constraint: constraint((T0373)E27.CB, (T0373)R46.CB) [> 3.8694 = 6.4490 < 8.3837] w=0.0143 to align # Constraint # added constraint: constraint((T0373)V17.CB, (T0373)N107.CB) [> 4.4360 = 7.3933 < 9.6113] w=0.0141 to align # Constraint # added constraint: constraint((T0373)V17.CB, (T0373)L104.CB) [> 3.5055 = 5.8425 < 7.5953] w=0.0141 to align # Constraint # added constraint: constraint((T0373)V17.CB, (T0373)I80.CB) [> 4.5697 = 7.6161 < 9.9010] w=0.0141 to align # Constraint # added constraint: constraint((T0373)V17.CB, (T0373)L74.CB) [> 3.6934 = 6.1557 < 8.0024] w=0.0141 to align # Constraint # added constraint: constraint((T0373)Q16.CB, (T0373)L74.CB) [> 4.1342 = 6.8903 < 8.9574] w=0.0141 to align # Constraint # added constraint: constraint((T0373)L123.CB, (T0373)L137.CB) [> 3.1695 = 5.2825 < 6.8673] w=0.0129 to align # Constraint # added constraint: constraint((T0373)L123.CB, (T0373)L138.CB) [> 3.7732 = 6.2886 < 8.1752] w=0.0129 to align # Constraint # added constraint: constraint((T0373)Q16.CB, (T0373)L131.CB) [> 4.6668 = 7.7780 < 10.1114] w=0.0072 to align # Constraint # added constraint: constraint((T0373)A10.CB, (T0373)G135.CA) [> 3.4634 = 5.7723 < 7.5040] w=0.0072 to align # Constraint # added constraint: constraint((T0373)H12.CB, (T0373)T21.CB) [> 3.7637 = 6.2728 < 8.1546] w=0.0072 to align # Constraint # added constraint: constraint((T0373)H12.CB, (T0373)A134.CB) [> 2.9688 = 4.9480 < 6.4324] w=0.0072 to align # Constraint # added constraint: constraint((T0373)L9.CB, (T0373)L141.CB) [> 4.7675 = 7.9458 < 10.3295] w=0.0072 to align # Constraint # added constraint: constraint((T0373)S15.CB, (T0373)A118.CB) [> 4.5612 = 7.6021 < 9.8827] w=0.0072 to align # Constraint # added constraint: constraint((T0373)Q16.CB, (T0373)R111.CB) [> 4.2228 = 7.0379 < 9.1493] w=0.0072 to align # Constraint # added constraint: constraint((T0373)A10.CB, (T0373)E27.CB) [> 4.3590 = 7.2650 < 9.4445] w=0.0072 to align # Constraint # added constraint: constraint((T0373)A10.CB, (T0373)A28.CB) [> 3.5211 = 5.8685 < 7.6291] w=0.0072 to align # Constraint # added constraint: constraint((T0373)E75.CB, (T0373)S97.CB) [> 4.4417 = 7.4028 < 9.6236] w=0.0072 to align # Constraint # added constraint: constraint((T0373)A11.CB, (T0373)N103.CB) [> 4.6955 = 7.8259 < 10.1736] w=0.0072 to align # Constraint # added constraint: constraint((T0373)V94.CB, (T0373)W114.CB) [> 4.7707 = 7.9512 < 10.3366] w=0.0072 to align # Constraint # added constraint: constraint((T0373)C122.CB, (T0373)L141.CB) [> 3.8566 = 6.4276 < 8.3559] w=0.0072 to align # Constraint # added constraint: constraint((T0373)Q16.CB, (T0373)L56.CB) [> 2.8149 = 4.6915 < 6.0989] w=0.0072 to align # Constraint # added constraint: constraint((T0373)Q16.CB, (T0373)E55.CB) [> 4.6733 = 7.7888 < 10.1254] w=0.0072 to align # Constraint # added constraint: constraint((T0373)L74.CB, (T0373)T92.CB) [> 4.5487 = 7.5812 < 9.8555] w=0.0072 to align # Constraint # added constraint: constraint((T0373)N107.CB, (T0373)A133.CB) [> 4.3730 = 7.2883 < 9.4747] w=0.0069 to align # Constraint # added constraint: constraint((T0373)N107.CB, (T0373)A142.CB) [> 3.1417 = 5.2362 < 6.8071] w=0.0063 to align # Constraint # added constraint: constraint((T0373)K110.CB, (T0373)L141.CB) [> 4.3479 = 7.2465 < 9.4205] w=0.0063 to align # Constraint # added constraint: constraint((T0373)K110.CB, (T0373)A142.CB) [> 2.6491 = 4.4151 < 5.7396] w=0.0063 to align # Constraint # added constraint: constraint((T0373)R111.CB, (T0373)T139.CB) [> 4.1729 = 6.9549 < 9.0413] w=0.0063 to align # Constraint # added constraint: constraint((T0373)R111.CB, (T0373)L141.CB) [> 4.6064 = 7.6773 < 9.9805] w=0.0063 to align # Constraint # added constraint: constraint((T0373)W114.CB, (T0373)L137.CB) [> 4.4021 = 7.3368 < 9.5379] w=0.0063 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0373/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0373/decoys/ # ReadConformPDB reading from PDB file chimera-1-2a61A.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera-2-2a61A.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-1-1jgsA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-1-1jgsA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-1-1lnwA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-1-1lnwA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-1-2a61A.pdb.gz looking for chain 'A' model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-1-2a61A # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-1-2fbhA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-1-2fbhA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-6-1jgsA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-6-1jgsA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-6-1lnwA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-6-1lnwA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-6-2a61A.pdb.gz looking for chain 'A' model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-6-2a61A # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-6-2fbhA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-6-2fbhA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-7-1jgsA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-7-1jgsA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-7-1lnwA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-7-1lnwA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-7-2a61A.pdb.gz looking for chain 'A' model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-7-2a61A # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-7-2fbhA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-7-2fbhA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-chimera-1-2a61A.pdb.gz looking for chain 'A' model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-chimera-1-2a61A # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 7 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 134, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 136, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 422, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 426, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 428, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 446, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 448, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 450, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 452, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 516, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 Skipped atom 555, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 332, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 450, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 452, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 454, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 456, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 534, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 536, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 134, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 136, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 422, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 426, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 428, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 446, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 448, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 450, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 452, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 516, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 Skipped atom 555, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 332, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 450, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 452, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 454, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 456, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 534, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 536, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 53 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 16 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 134, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 136, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 422, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 426, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 428, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 446, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 448, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 450, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 452, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 516, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 60 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 145 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 2 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 49 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 32 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 Skipped atom 326, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 332, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 446, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 448, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 450, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 452, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 134, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 136, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 422, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 426, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 428, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 446, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 448, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 450, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 452, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 516, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 Skipped atom 547, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 Skipped atom 110, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 112, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 114, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 116, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 422, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 426, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 428, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 478, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 480, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 482, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 484, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 516, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 Skipped atom 179, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 267, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 269, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 271, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 273, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 Skipped atom 231, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 Skipped atom 151, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 428, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 430, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 432, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 434, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 133 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 Skipped atom 547, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 134, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 136, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 422, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 426, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 428, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 446, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 448, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 450, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 452, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 516, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 332, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 450, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 452, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 454, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 456, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 534, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 536, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 26 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/panther3_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0373)D45.N and (T0373)A57.N only 0.000 apart, marking (T0373)A57.N as missing WARNING: atoms too close: (T0373)D45.CA and (T0373)A57.CA only 0.000 apart, marking (T0373)A57.CA as missing WARNING: atoms too close: (T0373)D45.CB and (T0373)A57.CB only 0.000 apart, marking (T0373)A57.CB as missing WARNING: atoms too close: (T0373)D45.O and (T0373)A57.O only 0.000 apart, marking (T0373)A57.O as missing WARNING: atoms too close: (T0373)D45.C and (T0373)A57.C only 0.000 apart, marking (T0373)A57.C as missing WARNING: atoms too close: (T0373)A57.N and (T0373)A58.N only 0.000 apart, marking (T0373)A57.N as missing WARNING: atoms too close: (T0373)D45.N and (T0373)A58.N only 0.000 apart, marking (T0373)A58.N as missing WARNING: atoms too close: (T0373)A57.CA and (T0373)A58.CA only 0.000 apart, marking (T0373)A58.CA as missing WARNING: atoms too close: (T0373)D45.CA and (T0373)A58.CA only 0.000 apart, marking (T0373)A58.CA as missing WARNING: atoms too close: (T0373)A57.CB and (T0373)A58.CB only 0.000 apart, marking (T0373)A58.CB as missing WARNING: atoms too close: (T0373)D45.CB and (T0373)A58.CB only 0.000 apart, marking (T0373)A58.CB as missing WARNING: atoms too close: (T0373)A57.O and (T0373)A58.O only 0.000 apart, marking (T0373)A58.O as missing WARNING: atoms too close: (T0373)D45.O and (T0373)A58.O only 0.000 apart, marking (T0373)A58.O as missing WARNING: atoms too close: (T0373)A57.C and (T0373)A58.C only 0.000 apart, marking (T0373)A58.C as missing WARNING: atoms too close: (T0373)D45.C and (T0373)A58.C only 0.000 apart, marking (T0373)A58.C as missing WARNING: atoms too close: (T0373)A58.N and (T0373)A59.N only 0.000 apart, marking (T0373)A58.N as missing WARNING: atoms too close: (T0373)A57.N and (T0373)A59.N only 0.000 apart, marking (T0373)A57.N as missing WARNING: atoms too close: (T0373)D45.N and (T0373)A59.N only 0.000 apart, marking (T0373)A59.N as missing WARNING: atoms too close: (T0373)A58.CA and (T0373)A59.CA only 0.000 apart, marking (T0373)A59.CA as missing WARNING: atoms too close: (T0373)A57.CA and (T0373)A59.CA only 0.000 apart, marking (T0373)A59.CA as missing WARNING: atoms too close: (T0373)D45.CA and (T0373)A59.CA only 0.000 apart, marking (T0373)A59.CA as missing WARNING: atoms too close: (T0373)A58.CB and (T0373)A59.CB only 0.000 apart, marking (T0373)A59.CB as missing WARNING: atoms too close: (T0373)A57.CB and (T0373)A59.CB only 0.000 apart, marking (T0373)A59.CB as missing WARNING: atoms too close: (T0373)D45.CB and (T0373)A59.CB only 0.000 apart, marking (T0373)A59.CB as missing WARNING: atoms too close: (T0373)A58.O and (T0373)A59.O only 0.000 apart, marking (T0373)A59.O as missing WARNING: atoms too close: (T0373)A57.O and (T0373)A59.O only 0.000 apart, marking (T0373)A59.O as missing WARNING: atoms too close: (T0373)D45.O and (T0373)A59.O only 0.000 apart, marking (T0373)A59.O as missing WARNING: atoms too close: (T0373)A58.C and (T0373)A59.C only 0.000 apart, marking (T0373)A59.C as missing WARNING: atoms too close: (T0373)A57.C and (T0373)A59.C only 0.000 apart, marking (T0373)A59.C as missing WARNING: atoms too close: (T0373)D45.C and (T0373)A59.C only 0.000 apart, marking (T0373)A59.C as missing # WARNING: incomplete conformation T0373 can't currently be optimized by undertaker # naming current conformation panther3_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.5128 model score -0.5232 model score 0.5718 model score 0.5718 model score 0.5718 model score 0.5718 model score -0.5014 model score -0.5014 model score -0.5015 model score -0.5015 model score -0.4756 model score -0.4756 model score -0.4755 model score -0.4756 model score -0.5128 model score -0.2166 model score -0.2166 model score -0.2166 model score -0.2166 model score -0.2166 model score -0.2166 model score -0.2166 model score -0.5557 model score -0.3024 model score -0.4509 model score -0.4500 model score -0.3366 model score 0.7234 model score 1.2804 model score 1.1546 model score 1.2068 model score 1.4572 model score -0.5037 model score -0.4872 model score -0.4200 model score -0.4080 model score -0.5279 model score -0.4412 model score -0.5063 model score -0.4991 model score -0.4751 model score -0.5004 model score -0.3485 model score -0.5257 model score -0.4896 model score -0.5057 model score -0.4932 model score -0.2557 model score 1.2797 model score 1.2687 model score 1.2552 model score 1.2773 model score 1.2547 model score -0.5461 model score -0.5327 model score -0.4532 model score -0.5555 model score -0.4496 model score -0.5064 model score -0.4751 model score -0.4365 model score -0.5004 model score -0.4991 model score -0.5791 model score -0.5557 model score -0.4500 model score -0.4341 model score -0.4459 model score 1.2552 model score 1.2537 model score 1.2532 model score 1.2531 model score 1.2540 model score 1.2552 model score 1.2537 model score 1.2532 model score 1.2531 model score 1.2540 model score 1.6079 model score 1.7598 model score 1.9239 model score 2.1654 model score 1.8036 model score -0.5009 model score -0.4944 model score -0.4895 model score -0.3023 model score -0.4361 model score 1.2552 model score 1.2556 model score 1.2547 model score 1.2537 model score 1.2546 model score -0.4790 model score -0.4365 model score -0.4079 model score -0.5180 model score -0.4426 model score -0.4655 model score -0.4221 model score -0.3785 model score -0.4836 model score -0.5165 model score -0.4916 model score -0.4799 model score -0.5286 model score -0.5261 model score -0.4740 model score -0.5504 model score -0.4915 model score -0.5001 model score 0.0507 model score -0.2196 model score 0.1033 model score -0.2467 model score -0.3069 model score -0.5292 model score -0.4667 model score -0.4159 model score -0.4078 model score -0.1654 model score 1.2537 model score -0.4979 model score -0.4928 model score -0.5026 model score -0.5627 model score -0.5470 model score -0.4928 model score -0.4880 model score -0.5026 model score -0.4910 model score -0.5627 model score -0.5958 model score -0.6007 model score -0.6029 model score -0.5292 model score 1.2924 model score 1.2627 model score 1.2857 model score 1.2901 model score 1.2606 model score -0.5236 model score -0.5086 model score -0.4966 model score -0.5312 model score -0.5344 model score -0.4817 model score -0.4855 model score -0.5009 model score -0.4554 model score -0.5139 model score -0.4765 model score -0.5175 model score -0.4561 model score -0.4561 model score -0.4561 model score -0.4561 model score -0.5194 model score -0.5059 model score -0.4386 model score -0.3829 model score -0.4900 model score -0.4662 model score -0.5346 model score -0.4700 model score -0.4688 model score -0.5352 model score -0.4583 model score -0.5024 model score -0.1829 model score -0.4921 model score -0.4411 model score -0.5143 model score -0.4901 model score -0.2290 model score -0.5014 model score -0.4551 model score -0.5144 model score -0.5147 model score -0.5059 model score -0.5072 model score -0.3829 model score -0.4555 model score -0.3880 model score -0.4848 model score -0.5229 model score -0.4173 model score 1.2531 model score 1.2552 model score 1.2532 model score 1.2538 model score 1.2536 model score 1.2543 model score 1.2531 model score 1.2541 model score 1.2533 model score 1.2544 model score -0.5034 model score -0.2276 model score -0.0621 model score -0.4466 model score -0.0090 model score -0.4911 model score -0.5096 model score -0.5243 model score -0.3826 model score -0.4889 model score -0.4759 model score -0.5184 model score -0.5139 model score -0.4161 model score -0.4937 model score -0.4911 model score -0.5243 model score -0.5096 model score -0.4233 model score -0.4934 model score 1.2532 model score 1.2556 model score 1.2552 model score 1.2537 model score 1.2531 model score -0.3835 model score 1.2532 model score 1.2556 model score 1.2552 model score 1.2537 model score 1.2531 model score -0.5834 model score -0.5855 model score -0.5788 model score -0.5932 model score -0.6107 model score -0.4815 model score -0.4794 model score 1.2556 model score 1.2537 model score 1.2547 model score 1.2538 model score 1.2551 model score -0.4987 model score -0.5583 model score -0.5450 model score -0.4814 model score -0.4941 model score -0.4950 model score -0.5039 model score -0.2209 model score -0.1234 model score -0.1908 model score -0.4827 model score -0.3986 model score -0.4959 model score -0.4980 model score -0.4817 model score -0.5741 model score -0.3539 model score -0.4535 model score -0.3720 model score -0.4909 model 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cost: -0.1908 min: -0.6107 max: 2.1654 USE_META, weight: 0.9585 cost: -0.4827 min: -0.6107 max: 2.1654 USE_META, weight: 0.9313 cost: -0.3986 min: -0.6107 max: 2.1654 USE_META, weight: 0.9628 cost: -0.4959 min: -0.6107 max: 2.1654 USE_META, weight: 0.9635 cost: -0.4980 min: -0.6107 max: 2.1654 USE_META, weight: 0.9582 cost: -0.4817 min: -0.6107 max: 2.1654 USE_META, weight: 0.9881 cost: -0.5741 min: -0.6107 max: 2.1654 USE_META, weight: 0.9167 cost: -0.3539 min: -0.6107 max: 2.1654 USE_META, weight: 0.9491 cost: -0.4535 min: -0.6107 max: 2.1654 USE_META, weight: 0.9226 cost: -0.3720 min: -0.6107 max: 2.1654 USE_META, weight: 0.9612 cost: -0.4909 min: -0.6107 max: 2.1654 USE_META, weight: 0.9124 cost: -0.3406 min: -0.6107 max: 2.1654 USE_META, weight: 0.8902 cost: -0.2721 min: -0.6107 max: 2.1654 USE_META, weight: 0.7451 cost: 0.1755 min: -0.6107 max: 2.1654 USE_META, weight: 0.9703 cost: -0.5191 min: -0.6107 max: 2.1654 USE_EVALUE, weight: 0.9958 eval: 0.0004 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9958 eval: 0.0004 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9958 eval: 0.0004 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9808 eval: 0.0018 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9808 eval: 0.0018 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9808 eval: 0.0018 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9816 eval: 0.0018 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9816 eval: 0.0018 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9816 eval: 0.0018 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.1000 eval: 0.0862 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.1000 eval: 0.0862 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.1000 eval: 0.0862 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.5392 eval: 0.0441 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.5392 eval: 0.0441 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.5392 eval: 0.0441 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9971 eval: 0.0003 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9971 eval: 0.0003 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9971 eval: 0.0003 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.8759 eval: 0.0119 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.8759 eval: 0.0119 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.8759 eval: 0.0119 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9535 eval: 0.0045 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9535 eval: 0.0045 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9535 eval: 0.0045 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9960 eval: 0.0004 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9960 eval: 0.0004 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9960 eval: 0.0004 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9947 eval: 0.0005 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9947 eval: 0.0005 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9947 eval: 0.0005 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9989 eval: 0.0001 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9989 eval: 0.0001 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9989 eval: 0.0001 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.8996 eval: 0.0096 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.8996 eval: 0.0096 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.8996 eval: 0.0096 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9959 eval: 0.0004 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9959 eval: 0.0004 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9959 eval: 0.0004 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9968 eval: 0.0003 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9968 eval: 0.0003 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9968 eval: 0.0003 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9972 eval: 0.0003 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9972 eval: 0.0003 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9972 eval: 0.0003 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9953 eval: 0.0004 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9953 eval: 0.0004 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9953 eval: 0.0004 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9973 eval: 0.0003 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9973 eval: 0.0003 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9973 eval: 0.0003 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.7910 eval: 0.0200 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.7910 eval: 0.0200 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.7910 eval: 0.0200 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9995 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9995 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9995 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9995 eval: 0.0001 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9995 eval: 0.0001 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9995 eval: 0.0001 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9988 eval: 0.0001 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9988 eval: 0.0001 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9988 eval: 0.0001 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9547 eval: 0.0043 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9547 eval: 0.0043 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9547 eval: 0.0043 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9177 eval: 0.0079 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9177 eval: 0.0079 min: 0.0000 max: 0.0862 USE_EVALUE, weight: 0.9177 eval: 0.0079 min: 0.0000 max: 0.0862 Number of contacts in models: 264 Number of contacts in alignments: 150 NUMB_ALIGNS: 150 Adding 2921 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -232.4586, CN propb: -232.4586 weights: 0.3149 constraints: 239 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 239 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 239 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 2682 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 2682 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 2921 # command: