# 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/T0317/ # command:# Making conformation for sequence T0317 numbered 1 through 163 Created new target T0317 from T0317.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0317/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0317//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0317/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0317//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0317/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0317/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0317/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wrmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wrmA expands to /projects/compbio/data/pdb/1wrm.pdb.gz 1wrmA:# T0317 read from 1wrmA/merged-good-all-a2m # 1wrmA read from 1wrmA/merged-good-all-a2m # adding 1wrmA to template set # found chain 1wrmA in template set T0317 9 :PPFARVAPALFIGNARAAGATELLVRAGITLCVNVS 1wrmA 3 :NGMNKILPGLYIGNFKDARDAEQLSKNKVTHILSVH # choosing archetypes in rotamer library T0317 46 :QQPGPRAPGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1wrmA 39 :DSARPMLEGVKYLCIPAADSPSQNLTRHFKESIKFIHECRLRGESCLVHCLAGVSRSVTLVIAYIMTVTDFGWEDALHTVRAGRSCANPNVGFQRQLQEFEK T0317 148 :TLQA 1wrmA 145 :QYRQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Number of alignments=1 # 1wrmA read from 1wrmA/merged-good-all-a2m # found chain 1wrmA in template set T0317 9 :PPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGP 1wrmA 3 :NGMNKILPGLYIGNFKDARDAEQLSKNKVTHILSVHDSARPM T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQT 1wrmA 45 :LEGVKYLCIPAADSPSQNLTRHFKESIKFIHECRLRGESCLVHCLAGVSRSVTLVIAYIMTVTDFGWEDALHTVRAGRSCANPNVGFQRQLQEFEKH Number of specific fragments extracted= 2 number of extra gaps= 0 total=5 Number of alignments=2 # 1wrmA read from 1wrmA/merged-good-all-a2m # found chain 1wrmA in template set T0317 6 :AAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQP 1wrmA -1 :PMGNGMNKILPGLYIGNFKDARDAEQLSKNKVTHILSVHDSAR T0317 50 :PRAPGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQT 1wrmA 43 :PMLEGVKYLCIPAADSPSQNLTRHFKESIKFIHECRLRGESCLVHCLAGVSRSVTLVIAYIMTVTDFGWEDALHTVRAGRSCANPNVGFQRQLQEFEKH Number of specific fragments extracted= 2 number of extra gaps= 0 total=7 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bzlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bzlA expands to /projects/compbio/data/pdb/2bzl.pdb.gz 2bzlA:Skipped atom 1123, because occupancy 0.3 <= existing 0.700 in 2bzlA Skipped atom 1127, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1129, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1131, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1133, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1135, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1137, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1139, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1756, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1808, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1812, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1814, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2115, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2119, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2121, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2123, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2125, because occupancy 0.500 <= existing 0.500 in 2bzlA # T0317 read from 2bzlA/merged-good-all-a2m # 2bzlA read from 2bzlA/merged-good-all-a2m # adding 2bzlA to template set # found chain 2bzlA in template set Warning: unaligning (T0317)R51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bzlA)K1029 Warning: unaligning (T0317)A153 because last residue in template chain is (2bzlA)S1184 T0317 18 :LFIGNARAAGA 2bzlA 981 :ATQGPLPHTCH T0317 29 :TELLVRAGITLCVNVS 2bzlA 994 :WQMVWEQGVNVIAMVT T0317 49 :GP 2bzlA 1023 :WP T0317 54 :GVAELRVP 2bzlA 1071 :HLQYTDWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 2bzlA 1079 :DHGCPEDVQGFLSYLEEIQSVRR T0317 87 :DG 2bzlA 1108 :EG T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2bzlA 1115 :PPIVVHCSAGVGRTGVLILSELMIY T0317 114 :RG 2bzlA 1143 :HN T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 2bzlA 1147 :VEVPMMLRLLREQRMFMIQTIAQYKFVYQVLIQFLQN Number of specific fragments extracted= 9 number of extra gaps= 0 total=16 Number of alignments=4 # 2bzlA read from 2bzlA/merged-good-all-a2m # found chain 2bzlA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (2bzlA)S1184 T0317 18 :LFIGNARAAGA 2bzlA 981 :ATQGPLPHTCH T0317 29 :TELLVRAGITLCVNVS 2bzlA 994 :WQMVWEQGVNVIAMVT T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAV 2bzlA 1067 :RTVWHLQYTDWPDHGCPEDVQGFLSYLEEIQSVR T0317 87 :DG 2bzlA 1108 :EG T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2bzlA 1115 :PPIVVHCSAGVGRTGVLILSELMIY T0317 114 :RG 2bzlA 1143 :HN T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 2bzlA 1147 :VEVPMMLRLLREQRMFMIQTIAQYKFVYQVLIQFLQN Number of specific fragments extracted= 7 number of extra gaps= 0 total=23 Number of alignments=5 # 2bzlA read from 2bzlA/merged-good-all-a2m # found chain 2bzlA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (2bzlA)S1184 T0317 18 :LFIGNARAAGA 2bzlA 981 :ATQGPLPHTCH T0317 29 :TELLVRAGITLCVNVSRQ 2bzlA 994 :WQMVWEQGVNVIAMVTAE T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 2bzlA 1069 :VWHLQYTDWPDHGCPEDVQGFLSYLEEIQSVRR T0317 87 :DG 2bzlA 1108 :EG T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2bzlA 1115 :PPIVVHCSAGVGRTGVLILSELMIY T0317 114 :RG 2bzlA 1143 :HN T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 2bzlA 1147 :VEVPMMLRLLREQRMFMIQTIAQYKFVYQVLIQFLQN Number of specific fragments extracted= 7 number of extra gaps= 0 total=30 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bijA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bijA expands to /projects/compbio/data/pdb/2bij.pdb.gz 2bijA:Skipped atom 617, because occupancy 0.350 <= existing 0.650 in 2bijA Skipped atom 618, because occupancy 0.350 <= existing 0.650 in 2bijA Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 2bijA Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2bijA Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 2bijA Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 2bijA Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 2bijA # T0317 read from 2bijA/merged-good-all-a2m # 2bijA read from 2bijA/merged-good-all-a2m # adding 2bijA to template set # found chain 2bijA in template set Warning: unaligning (T0317)Q46 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bijA)K383 Warning: unaligning (T0317)A132 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)I515 Warning: unaligning (T0317)E133 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)I515 Warning: unaligning (T0317)L155 because last residue in template chain is (2bijA)H537 T0317 11 :FARVAPALFI 2bijA 337 :GYGGEEKVYI T0317 21 :GNARA 2bijA 350 :GPIVS T0317 26 :AGATEL 2bijA 356 :VADFWR T0317 32 :LVRAGITLCVNVS 2bijA 363 :VWQEHTPIIVMIT T0317 47 :QPGPRAP 2bijA 384 :CTEYWPE T0317 54 :GVAELRVP 2bijA 429 :HYWFTSWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVRDG 2bijA 437 :DQKTPDRAPPLLHLVREVEEAAQQE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 2bijA 466 :APIIVHCSAGIGRTGCFIATS T0317 110 :LMRHRGH 2bijA 491 :QLRQEGV T0317 117 :SLDRAFQMVKSARPV 2bijA 499 :DILKTTCQLRQDRGG T0317 134 :PNLGFWAQLQKYEQTLQAQAI 2bijA 516 :QTCEQYQFVHHVMSLYEKQLS Number of specific fragments extracted= 11 number of extra gaps= 1 total=41 Number of alignments=7 # 2bijA read from 2bijA/merged-good-all-a2m # found chain 2bijA in template set Warning: unaligning (T0317)A132 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)I515 Warning: unaligning (T0317)E133 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)I515 T0317 12 :ARVAPALFI 2bijA 338 :YGGEEKVYI T0317 21 :GNARAAGA 2bijA 350 :GPIVSTVA T0317 29 :TELLVRAGITLCVNVS 2bijA 360 :WRMVWQEHTPIIVMIT T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDG 2bijA 425 :RGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQQE T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2bijA 466 :APIIVHCSAGIGRTGCFIATSICCQ T0317 114 :RG 2bijA 495 :EG T0317 116 :HSLDRAFQMVKSARPV 2bijA 498 :VDILKTTCQLRQDRGG T0317 134 :PNLGFWAQLQKYEQTLQAQAI 2bijA 516 :QTCEQYQFVHHVMSLYEKQLS Number of specific fragments extracted= 8 number of extra gaps= 1 total=49 Number of alignments=8 # 2bijA read from 2bijA/merged-good-all-a2m # found chain 2bijA in template set Warning: unaligning (T0317)P48 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bijA)K383 Warning: unaligning (T0317)A52 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bijA)K383 Warning: unaligning (T0317)A132 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)I515 Warning: unaligning (T0317)E133 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)I515 T0317 18 :LFIGNARAAGA 2bijA 347 :ATQGPIVSTVA T0317 29 :TELLVRAGITLCVNVSRQQ 2bijA 360 :WRMVWQEHTPIIVMITNIE T0317 53 :P 2bijA 384 :C T0317 54 :GVAELRV 2bijA 426 :GLKHYWF T0317 61 :PVFDDPAEDLLTHLEPTCAAMEAAVRDGGS 2bijA 434 :SWPDQKTPDRAPPLLHLVREVEEAAQQEGP T0317 91 :CLVYCKNGRSRSAAVCTAYL 2bijA 468 :IIVHCSAGIGRTGCFIATSI T0317 111 :MRHRG 2bijA 492 :LRQEG T0317 116 :HSLDRAFQMVKSARPV 2bijA 498 :VDILKTTCQLRQDRGG T0317 134 :PNLGFWAQLQKY 2bijA 516 :QTCEQYQFVHHV Number of specific fragments extracted= 9 number of extra gaps= 1 total=58 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xriA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xriA expands to /projects/compbio/data/pdb/1xri.pdb.gz 1xriA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0317 read from 1xriA/merged-good-all-a2m # 1xriA read from 1xriA/merged-good-all-a2m # adding 1xriA to template set # found chain 1xriA in template set T0317 5 :EAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPG 1xriA 53 :LIPPLNFSMVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYP T0317 54 :GVAELRVPVFDDPAEDL 1xriA 108 :GIRLFQFGIEGNKEPFV T0317 71 :LTHLEPTCAAM 1xriA 128 :DHKIRMALKVL T0317 85 :VRDG 1xriA 139 :LDEK T0317 89 :GSCLVYCKNGRSRSAAVCTA 1xriA 144 :HPVLIHCKRGKHRTGCLVGC T0317 110 :LMRHRGHSLDRAFQMVKSAR 1xriA 164 :LRKLQKWCLTSIFDEYQRFA T0317 131 :VAEPNLGFWAQLQ 1xriA 184 :AAKARVSDQRFME Number of specific fragments extracted= 7 number of extra gaps= 0 total=65 Number of alignments=10 # 1xriA read from 1xriA/merged-good-all-a2m # found chain 1xriA in template set Warning: unaligning (T0317)S4 because first residue in template chain is (1xriA)H52 T0317 5 :EAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPR 1xriA 53 :LIPPLNFSMVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYPES T0317 53 :PGVAELRVPVFDDPAE 1xriA 107 :NGIRLFQFGIEGNKEP T0317 69 :DL 1xriA 127 :PD T0317 72 :THLEPTCAAM 1xriA 129 :HKIRMALKVL T0317 85 :VRDG 1xriA 139 :LDEK T0317 89 :GSCLVYCKNGRSRSAAVCTA 1xriA 144 :HPVLIHCKRGKHRTGCLVGC T0317 110 :LMRHRGHSLDRAFQMVKSAR 1xriA 164 :LRKLQKWCLTSIFDEYQRFA T0317 131 :VAEPNLGFWAQLQ 1xriA 184 :AAKARVSDQRFME Number of specific fragments extracted= 8 number of extra gaps= 0 total=73 Number of alignments=11 # 1xriA read from 1xriA/merged-good-all-a2m # found chain 1xriA in template set T0317 5 :EAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPG 1xriA 53 :LIPPLNFSMVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYP T0317 54 :GVAELRVPVFDDPAEDL 1xriA 108 :GIRLFQFGIEGNKEPFV T0317 71 :LTHLEPTCAAME 1xriA 128 :DHKIRMALKVLL T0317 89 :GSCLVYCKNGRSRSAAVCTA 1xriA 144 :HPVLIHCKRGKHRTGCLVGC T0317 110 :LMRHRGHSLDRAFQMVKSARP 1xriA 164 :LRKLQKWCLTSIFDEYQRFAA T0317 132 :AEPNLGFWAQLQ 1xriA 185 :AKARVSDQRFME Number of specific fragments extracted= 6 number of extra gaps= 0 total=79 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f46A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f46A expands to /projects/compbio/data/pdb/2f46.pdb.gz 2f46A:Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 6, because occupancy 0.500 <= existing 0.500 in 2f46A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 10, because occupancy 0.500 <= existing 0.500 in 2f46A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2f46A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2f46A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 257, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 390, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 729, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 784, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 786, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 788, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 790, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 792, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 794, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 796, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 804, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 806, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 808, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 810, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 812, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 814, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 816, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 847, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 849, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 851, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 853, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 855, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 857, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 859, because occupancy 0.200 <= existing 0.800 in 2f46A Skipped atom 861, because occupancy 0.200 <= existing 0.800 in 2f46A Skipped atom 863, because occupancy 0.200 <= existing 0.800 in 2f46A Skipped atom 865, because occupancy 0.200 <= existing 0.800 in 2f46A Skipped atom 867, because occupancy 0.200 <= existing 0.800 in 2f46A Skipped atom 869, because occupancy 0.200 <= existing 0.800 in 2f46A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 991, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 993, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 995, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 997, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 999, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1001, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1003, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1005, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1007, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1025, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1027, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1029, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1031, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1033, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1035, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1037, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1039, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1041, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1043, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1045, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1115, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1117, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1119, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 2f46A # T0317 read from 2f46A/merged-good-all-a2m # 2f46A read from 2f46A/merged-good-all-a2m # adding 2f46A to template set # found chain 2f46A in template set Warning: unaligning (T0317)P8 because first residue in template chain is (2f46A)K13 Warning: unaligning (T0317)P9 because of BadResidue code BAD_PEPTIDE at template residue (2f46A)M14 Warning: unaligning (T0317)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2f46A)T81 Warning: unaligning (T0317)F63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2f46A)T81 T0317 10 :PFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPRAP 2f46A 15 :AILKLDEHLYISPQLTKADAEQIAQLGIKTIICNRPDREEESQP T0317 54 :GV 2f46A 71 :GV T0317 56 :AELRVP 2f46A 74 :GFHHQP T0317 64 :DDPAED 2f46A 82 :ARDIQK T0317 72 :THLEPTCAAME 2f46A 88 :HDVETFRQLIG T0317 88 :G 2f46A 99 :Q T0317 89 :GSCLVYCKNGR 2f46A 102 :YPVLAYCRTGT T0317 102 :SAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWA 2f46A 113 :RCSLLWGFRRAAEGMPVDEIIRRAQAAGVNLENFRERLD Number of specific fragments extracted= 8 number of extra gaps= 1 total=87 Number of alignments=13 # 2f46A read from 2f46A/merged-good-all-a2m # found chain 2f46A in template set Warning: unaligning (T0317)P8 because first residue in template chain is (2f46A)K13 Warning: unaligning (T0317)P9 because of BadResidue code BAD_PEPTIDE at template residue (2f46A)M14 Warning: unaligning (T0317)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2f46A)T81 Warning: unaligning (T0317)F63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2f46A)T81 T0317 10 :PFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPR 2f46A 15 :AILKLDEHLYISPQLTKADAEQIAQLGIKTIICNRPDREEES T0317 52 :APGVAELRVP 2f46A 70 :AGVTGFHHQP T0317 64 :DDPAED 2f46A 82 :ARDIQK T0317 72 :THLEPTCAAM 2f46A 88 :HDVETFRQLI T0317 86 :R 2f46A 98 :G T0317 88 :G 2f46A 99 :Q T0317 89 :GSCLVYCKNGR 2f46A 102 :YPVLAYCRTGT T0317 101 :RSAA 2f46A 113 :RCSL T0317 106 :CTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWA 2f46A 117 :LWGFRRAAEGMPVDEIIRRAQAAGVNLENFRERLD Number of specific fragments extracted= 9 number of extra gaps= 1 total=96 Number of alignments=14 # 2f46A read from 2f46A/merged-good-all-a2m # found chain 2f46A in template set Warning: unaligning (T0317)P8 because first residue in template chain is (2f46A)K13 Warning: unaligning (T0317)P9 because of BadResidue code BAD_PEPTIDE at template residue (2f46A)M14 Warning: unaligning (T0317)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2f46A)T81 Warning: unaligning (T0317)F63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2f46A)T81 T0317 10 :PFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPRAP 2f46A 15 :AILKLDEHLYISPQLTKADAEQIAQLGIKTIICNRPDREEESQP T0317 54 :GVAELRVP 2f46A 72 :VTGFHHQP T0317 64 :DDPAED 2f46A 82 :ARDIQK T0317 72 :THLEPTCAAME 2f46A 88 :HDVETFRQLIG T0317 87 :D 2f46A 99 :Q T0317 88 :GGSCLVYCKNGRS 2f46A 101 :EYPVLAYCRTGTR T0317 103 :AAVCTAYLMRHRGHSLDRAFQMVKSARPVA 2f46A 114 :CSLLWGFRRAAEGMPVDEIIRRAQAAGVNL T0317 136 :LGFWAQLQK 2f46A 144 :ENFRERLDN Number of specific fragments extracted= 8 number of extra gaps= 1 total=104 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yz4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yz4A expands to /projects/compbio/data/pdb/1yz4.pdb.gz 1yz4A:# T0317 read from 1yz4A/merged-good-all-a2m # 1yz4A read from 1yz4A/merged-good-all-a2m # adding 1yz4A to template set # found chain 1yz4A in template set T0317 7 :APPPFARVAPALFIGNARAAGATELLVRAGITLCVNVS 1yz4A 1 :MGNGMTKVLPGLYLGNFIDAKDLDQLGRNKITHIISIH T0317 46 :QQPGPRAPGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1yz4A 39 :ESPQPLLQDITYLRIPVADTPEVPIKKHFKECINFIHCCRLNGGNCLVHSFAGISRSTTIVTAYVMTVTGLGWRDVLEAIKATRPIANPNPGFRQQLEEFGW T0317 148 :TLQA 1yz4A 145 :KLRR Number of specific fragments extracted= 3 number of extra gaps= 0 total=107 Number of alignments=16 # 1yz4A read from 1yz4A/merged-good-all-a2m # found chain 1yz4A in template set T0317 7 :APPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGP 1yz4A 1 :MGNGMTKVLPGLYLGNFIDAKDLDQLGRNKITHIISIHESPQPL T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1yz4A 45 :LQDITYLRIPVADTPEVPIKKHFKECINFIHCCRLNGGNCLVHSFAGISRSTTIVTAYVMTVTGLGWRDVLEAIKATRPIANPNPGFRQQLEEFGW T0317 148 :TLQ 1yz4A 145 :KLR Number of specific fragments extracted= 3 number of extra gaps= 0 total=110 Number of alignments=17 # 1yz4A read from 1yz4A/merged-good-all-a2m # found chain 1yz4A in template set T0317 5 :EAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSR 1yz4A -1 :SHMGNGMTKVLPGLYLGNFIDAKDLDQLGRNKITHIISIHE T0317 47 :QPGPRAPGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1yz4A 40 :SPQPLLQDITYLRIPVADTPEVPIKKHFKECINFIHCCRLNGGNCLVHSFAGISRSTTIVTAYVMTVTGLGWRDVLEAIKATRPIANPNPGFRQQLEEFGW Number of specific fragments extracted= 2 number of extra gaps= 0 total=112 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aax/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aax expands to /projects/compbio/data/pdb/1aax.pdb.gz 1aax:Warning: there is no chain 1aax will retry with 1aaxA # T0317 read from 1aax/merged-good-all-a2m # 1aax read from 1aax/merged-good-all-a2m # adding 1aax to template set # found chain 1aax in template set T0317 18 :LFIGNARAAGA 1aax 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1aax 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1aax 126 :PQKEEKE T0317 54 :GVAELRVP 1aax 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEAA 1aax 181 :DFGVPESPASFLNFLFKVRES T0317 85 :VRDG 1aax 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1aax 209 :GPVVVHSSAGIGRSGTFCLAD T0317 110 :LMRHRG 1aax 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAI 1aax 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIM Number of specific fragments extracted= 9 number of extra gaps= 0 total=121 Number of alignments=19 # 1aax read from 1aax/merged-good-all-a2m # found chain 1aax in template set T0317 18 :LFIGNARAAGA 1aax 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1aax 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1aax 126 :PQKEEKE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAA 1aax 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRES T0317 85 :VRDG 1aax 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1aax 209 :GPVVVHSSAGIGRSGTFCLAD T0317 110 :LMRHRG 1aax 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 1aax 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=129 Number of alignments=20 # 1aax read from 1aax/merged-good-all-a2m # found chain 1aax in template set T0317 18 :LFIGNARAAGA 1aax 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 1aax 96 :WEMVWEQKSRGVVMLNR T0317 46 :QQPGP 1aax 123 :QYWPQ T0317 54 :GVAELRVPVFDDPAEDLL 1aax 171 :ILHFHYTTWPDFGVPESP T0317 75 :EPTCAAMEAAVRDG 1aax 189 :ASFLNFLFKVRESG T0317 89 :GSCLVYCKNGRSRSAAVCTA 1aax 209 :GPVVVHSSAGIGRSGTFCLA T0317 109 :YLMRHRG 1aax 233 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKY 1aax 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLA Number of specific fragments extracted= 8 number of extra gaps= 0 total=137 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wchA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wchA expands to /projects/compbio/data/pdb/1wch.pdb.gz 1wchA:Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 614, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 616, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1069, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1071, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1921, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1923, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1925, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1985, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1987, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2164, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2166, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2168, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2170, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2200, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2202, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2204, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2206, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2371, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2373, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2375, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2377, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2379, because occupancy 0.500 <= existing 0.500 in 1wchA # T0317 read from 1wchA/merged-good-all-a2m # 1wchA read from 1wchA/merged-good-all-a2m # adding 1wchA to template set # found chain 1wchA in template set T0317 18 :LFIGNARA 1wchA 2281 :ACQGPLPT T0317 26 :AGATEL 1wchA 2290 :VGDFWQ T0317 32 :LVRAGITLCVNVS 1wchA 2297 :IWEQKSTVIAMMT T0317 46 :QQPGPRAP 1wchA 2320 :QRYWPNIL T0317 54 :GVAELRVP 1wchA 2367 :HISHLNFT T0317 62 :VFDDPAEDLLTHLEPTCAAMEAA 1wchA 2376 :WPDHDTPSQPDDLLTFISYMRHI T0317 86 :RDGGSCLVYCKNGRSRSAAVCTAYLM 1wchA 2399 :HRSGPIITHCSAGIGRSGTLICIDVV T0317 112 :RHRG 1wchA 2428 :ISQD T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 1wchA 2434 :FDISDLVRCMRLQRHGMVQTEDQYIFCYQVILYVLTR Number of specific fragments extracted= 9 number of extra gaps= 0 total=146 Number of alignments=22 # 1wchA read from 1wchA/merged-good-all-a2m # found chain 1wchA in template set T0317 18 :LFIGNARAAGA 1wchA 2281 :ACQGPLPTTVG T0317 29 :TELLVRAGITLCVNVS 1wchA 2294 :WQMIWEQKSTVIAMMT T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAV 1wchA 2366 :RHISHLNFTAWPDHDTPSQPDDLLTFISYMRHIH T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRH 1wchA 2400 :RSGPIITHCSAGIGRSGTLICIDVVLG T0317 114 :RG 1wchA 2430 :QD T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQ 1wchA 2434 :FDISDLVRCMRLQRHGMVQTEDQYIFCYQVILYVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=152 Number of alignments=23 # 1wchA read from 1wchA/merged-good-all-a2m # found chain 1wchA in template set T0317 17 :ALFIGNARAAGA 1wchA 2280 :IACQGPLPTTVG T0317 29 :TELLVRAGITLCVNVSRQ 1wchA 2294 :WQMIWEQKSTVIAMMTQE T0317 47 :QPGPR 1wchA 2322 :YWPNI T0317 54 :GVAELRVP 1wchA 2367 :HISHLNFT T0317 62 :VFDDPAEDLLTHLEPTCAAMEAA 1wchA 2376 :WPDHDTPSQPDDLLTFISYMRHI T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHR 1wchA 2400 :RSGPIITHCSAGIGRSGTLICIDVVLGL T0317 115 :G 1wchA 2431 :D T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKY 1wchA 2434 :FDISDLVRCMRLQRHGMVQTEDQYIFCYQV Number of specific fragments extracted= 8 number of extra gaps= 0 total=160 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rpmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rpmA expands to /projects/compbio/data/pdb/1rpm.pdb.gz 1rpmA:# T0317 read from 1rpmA/merged-good-all-a2m # 1rpmA read from 1rpmA/merged-good-all-a2m # adding 1rpmA to template set # found chain 1rpmA in template set T0317 18 :LFIGNARA 1rpmA 970 :ATQGPMQE T0317 26 :AGA 1rpmA 979 :IYD T0317 29 :TELLVRAGITLCVNVS 1rpmA 983 :WRMVWHENTASIIMVT T0317 46 :QQP 1rpmA 1012 :WPD T0317 54 :GVAELRVP 1rpmA 1055 :QFHFTGWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVRDG 1rpmA 1063 :DHGVPYHATGLLGFVRQVKSKSPPS T0317 89 :GSCLVYCKNGRSRSAAVCTAYLM 1rpmA 1089 :GPLVVHCSAGAGRTGCFIVIDIM T0317 112 :RHRG 1rpmA 1116 :EREG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTL 1rpmA 1121 :VDIYNCVRELRSRRVNMVQTEEQYVFIHDAILEA Number of specific fragments extracted= 9 number of extra gaps= 0 total=169 Number of alignments=25 # 1rpmA read from 1rpmA/merged-good-all-a2m # found chain 1rpmA in template set T0317 15 :APALFIGNARAAGATELL 1rpmA 965 :PNHYIATQGPMQETIYDF T0317 33 :VRAGITLCVNVS 1rpmA 987 :WHENTASIIMVT T0317 45 :RQ 1rpmA 1009 :CK T0317 47 :QPGP 1rpmA 1012 :WPDD T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDG 1rpmA 1051 :REIRQFHFTGWPDHGVPYHATGLLGFVRQVKSKSPPS T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1rpmA 1089 :GPLVVHCSAGAGRTGCFIVIDIMLD T0317 114 :RG 1rpmA 1118 :EG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTL 1rpmA 1121 :VDIYNCVRELRSRRVNMVQTEEQYVFIHDAILEA Number of specific fragments extracted= 8 number of extra gaps= 0 total=177 Number of alignments=26 # 1rpmA read from 1rpmA/merged-good-all-a2m # found chain 1rpmA in template set T0317 16 :PALFIGNARAAGA 1rpmA 966 :NHYIATQGPMQET T0317 29 :TELLVRAGITLCVNVSRQ 1rpmA 983 :WRMVWHENTASIIMVTNL T0317 47 :QPGPRAP 1rpmA 1008 :CCKYWPD T0317 54 :GVAELRVPVFDDPAE 1rpmA 1052 :EIRQFHFTGWPDHGV T0317 71 :LTHLEPTCAAMEAAVR 1rpmA 1067 :PYHATGLLGFVRQVKS T0317 87 :D 1rpmA 1087 :S T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1rpmA 1089 :GPLVVHCSAGAGRTGCFIVIDIMLD T0317 114 :RG 1rpmA 1118 :EG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQK 1rpmA 1121 :VDIYNCVRELRSRRVNMVQTEEQYVFIHD Number of specific fragments extracted= 9 number of extra gaps= 0 total=186 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rxdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rxdA expands to /projects/compbio/data/pdb/1rxd.pdb.gz 1rxdA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0317 read from 1rxdA/merged-good-all-a2m # 1rxdA read from 1rxdA/merged-good-all-a2m # adding 1rxdA to template set # found chain 1rxdA in template set Warning: unaligning (T0317)V62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rxdA)G72 Warning: unaligning (T0317)P66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rxdA)G72 T0317 20 :IGNARA 1rxdA 21 :THNPTN T0317 26 :AGATELLVRAGITLCVNVSRQQPGPR 1rxdA 30 :NKFIEELKKYGVTTIVRVCEATYDTT T0317 54 :GVAELRVP 1rxdA 61 :GIHVLDWP T0317 67 :AEDLLTHLEPTCAAMEAAVR 1rxdA 73 :APPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLM 1rxdA 95 :PGCCIAVHCVAGLGRAPVLVALALI T0317 113 :HRGHSLDRAFQMVKSARPVAE 1rxdA 120 :EGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1rxdA 141 :NSKQLLYLEK Number of specific fragments extracted= 7 number of extra gaps= 0 total=193 Number of alignments=28 # 1rxdA read from 1rxdA/merged-good-all-a2m # found chain 1rxdA in template set Warning: unaligning (T0317)V62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rxdA)G72 Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rxdA)G72 T0317 18 :LFIGNARAAG 1rxdA 19 :LITHNPTNAT T0317 29 :TELLVRAGITLCVNVSRQQPGPR 1rxdA 33 :IEELKKYGVTTIVRVCEATYDTT T0317 52 :APGVAELRVP 1rxdA 59 :KEGIHVLDWP T0317 66 :PAEDL 1rxdA 73 :APPSN T0317 72 :THLEPTCAAMEAAVR 1rxdA 78 :QIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTA 1rxdA 95 :PGCCIAVHCVAGLGRAPVLVAL T0317 110 :LMRHRGHSLDRAFQMVKSARPVAE 1rxdA 117 :ALIEGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1rxdA 141 :NSKQLLYLEK T0317 154 :ILPRE 1rxdA 151 :YRPKM Number of specific fragments extracted= 9 number of extra gaps= 0 total=202 Number of alignments=29 # 1rxdA read from 1rxdA/merged-good-all-a2m # found chain 1rxdA in template set Warning: unaligning (T0317)V62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rxdA)G72 Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rxdA)G72 T0317 16 :PALFIGNARAAGA 1rxdA 17 :RFLITHNPTNATL T0317 29 :TELLVRAGITLCVNVSRQQPG 1rxdA 33 :IEELKKYGVTTIVRVCEATYD T0317 54 :GVAELRVP 1rxdA 61 :GIHVLDWP T0317 67 :AEDLLTHLEPTCAAMEAAVR 1rxdA 73 :APPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMR 1rxdA 95 :PGCCIAVHCVAGLGRAPVLVALALIE T0317 114 :RGHSLDRAFQMVKSARPVA 1rxdA 121 :GGMKYEDAVQFIRQKRRGA T0317 134 :PNLGFWAQLQ 1rxdA 140 :FNSKQLLYLE T0317 152 :QAILPREP 1rxdA 150 :KYRPKMRL Number of specific fragments extracted= 8 number of extra gaps= 0 total=210 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yfoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yfoA expands to /projects/compbio/data/pdb/1yfo.pdb.gz 1yfoA:# T0317 read from 1yfoA/merged-good-all-a2m # 1yfoA read from 1yfoA/merged-good-all-a2m # adding 1yfoA to template set # found chain 1yfoA in template set Warning: unaligning (T0317)Q152 because last residue in template chain is (1yfoA)Y495 T0317 18 :LFIGNARA 1yfoA 303 :AAQGPKEE T0317 26 :AGA 1yfoA 312 :VND T0317 29 :TELLVRAGITLCVNVS 1yfoA 316 :WRMIWEQNTATIVMVT T0317 45 :RQQPGPR 1yfoA 346 :PDQGCWT T0317 54 :GVAELRVP 1yfoA 393 :QFHFTSWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVRDG 1yfoA 401 :DFGVPFTPIGMLKFLKKVKACNPQY T0317 89 :GSCLVYCKNGRSRSAAVCTAYLM 1yfoA 427 :GAIVVHCSAGVGRTGTFVVIDAM T0317 112 :RHRGH 1yfoA 453 :MHSER T0317 117 :SLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 1yfoA 460 :DVYGFVSRIRAQRCQMVQTDMQYVFIYQALLEHYL Number of specific fragments extracted= 9 number of extra gaps= 0 total=219 Number of alignments=31 # 1yfoA read from 1yfoA/merged-good-all-a2m # found chain 1yfoA in template set T0317 14 :VAPA 1yfoA 297 :EKNK T0317 18 :LFIGNARAAGA 1yfoA 303 :AAQGPKEETVN T0317 29 :TELLVRAGITLCVNVS 1yfoA 316 :WRMIWEQNTATIVMVT T0317 45 :RQQPGPR 1yfoA 343 :QYWPDQG T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDG 1yfoA 389 :RLITQFHFTSWPDFGVPFTPIGMLKFLKKVKACNPQY T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1yfoA 427 :GAIVVHCSAGVGRTGTFVVIDAMLD T0317 114 :RG 1yfoA 456 :ER T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQ 1yfoA 459 :VDVYGFVSRIRAQRCQMVQTDMQYVFIYQALLEHY Number of specific fragments extracted= 8 number of extra gaps= 0 total=227 Number of alignments=32 # 1yfoA read from 1yfoA/merged-good-all-a2m # found chain 1yfoA in template set T0317 16 :PALFI 1yfoA 299 :NKFIA T0317 21 :GNARAAGA 1yfoA 306 :GPKEETVN T0317 29 :TELLVRAGITLCVNVSR 1yfoA 316 :WRMIWEQNTATIVMVTN T0317 46 :QQPGPRAP 1yfoA 342 :AQYWPDQG T0317 54 :GVAELRVPVFDDPAEDL 1yfoA 391 :ITQFHFTSWPDFGVPFT T0317 74 :LEPTCAAMEAAVR 1yfoA 408 :PIGMLKFLKKVKA T0317 87 :DG 1yfoA 424 :QY T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHR 1yfoA 427 :GAIVVHCSAGVGRTGTFVVIDAMLDM T0317 115 :G 1yfoA 457 :R T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQK 1yfoA 459 :VDVYGFVSRIRAQRCQMVQTDMQYVFIYQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=237 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u24A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u24A expands to /projects/compbio/data/pdb/1u24.pdb.gz 1u24A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0317 read from 1u24A/merged-good-all-a2m # 1u24A read from 1u24A/merged-good-all-a2m # adding 1u24A to template set # found chain 1u24A in template set T0317 4 :SEAAPPPFARVAPALFIGNARAAGATELL 1u24A 169 :VYIAPLGKHKLPEGGEVRRVQKVQTEQEV T0317 33 :VRAGITL 1u24A 199 :EAAGMRY T0317 58 :LRVPVFDDPAE 1u24A 206 :FRIAATDHVWP T0317 70 :LLTHLEPTCAAMEA 1u24A 217 :TPENIDRFLAFYRT T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRH 1u24A 233 :QDAWLHFHCEAGVGRTTAFMVMTDMLK T0317 114 :RGHSLDRAFQMVKSAR 1u24A 261 :PSVSLKDILYRQHEIG T0317 132 :AE 1u24A 285 :IK T0317 136 :LGFWAQLQKYEQTLQAQAILP 1u24A 302 :IVMIEQFYRYVQENRADGYQT Number of specific fragments extracted= 8 number of extra gaps= 0 total=245 Number of alignments=34 # 1u24A read from 1u24A/merged-good-all-a2m # found chain 1u24A in template set T0317 3 :TSEAAPPPFARVAPALFIGNARAAGATELL 1u24A 168 :TVYIAPLGKHKLPEGGEVRRVQKVQTEQEV T0317 33 :VRAGITL 1u24A 199 :EAAGMRY T0317 58 :LRVPVFDDPAEDL 1u24A 206 :FRIAATDHVWPTP T0317 72 :THLEPTCAAMEAA 1u24A 219 :ENIDRFLAFYRTL T0317 86 :RDGGSCLVYCKNGRSRSAAVCTAYLMRH 1u24A 232 :PQDAWLHFHCEAGVGRTTAFMVMTDMLK T0317 114 :RGHSLDRAFQMVKSARPV 1u24A 261 :PSVSLKDILYRQHEIGGF T0317 136 :LGFWAQLQKYEQTLQAQAILP 1u24A 302 :IVMIEQFYRYVQENRADGYQT Number of specific fragments extracted= 7 number of extra gaps= 0 total=252 Number of alignments=35 # 1u24A read from 1u24A/merged-good-all-a2m # found chain 1u24A in template set T0317 17 :ALFIGNARAAGA 1u24A 90 :HISGSSAFTPAQ T0317 29 :TELLVRA 1u24A 106 :AAKLREK T0317 36 :GITLCVNVSRQQ 1u24A 115 :GPIYDVDLRQES T0317 54 :GVAELRVPVFD 1u24A 202 :GMRYFRIAATD T0317 66 :PAEDLLTHLEPTCAAMEA 1u24A 213 :HVWPTPENIDRFLAFYRT T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRH 1u24A 233 :QDAWLHFHCEAGVGRTTAFMVMTDMLK T0317 114 :RGHSLDRAFQMVKSARPVA 1u24A 261 :PSVSLKDILYRQHEIGGFY Number of specific fragments extracted= 7 number of extra gaps= 0 total=259 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zckA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zckA expands to /projects/compbio/data/pdb/1zck.pdb.gz 1zckA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0317 read from 1zckA/merged-good-all-a2m # 1zckA read from 1zckA/merged-good-all-a2m # adding 1zckA to template set # found chain 1zckA in template set Warning: unaligning (T0317)V62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zckA)G73 Warning: unaligning (T0317)P66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zckA)G73 T0317 19 :FIGNARA 1zckA 21 :ITHNPTN T0317 26 :AGATELLVRAGITLCVNVSRQQPGPR 1zckA 31 :NKFIEELKKYGVTTIVRVCEATYDTT T0317 54 :GVAELRVP 1zckA 62 :GIHVLDWP T0317 67 :AEDLLTHLEPTCAAMEAAVR 1zckA 74 :APPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLM 1zckA 96 :PGCCIAVHCVAGLGRAPVLVALALI T0317 113 :HRGHSLDRAFQMVKSARPVAE 1zckA 121 :EGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1zckA 142 :NSKQLLYLEK Number of specific fragments extracted= 7 number of extra gaps= 0 total=266 Number of alignments=37 # 1zckA read from 1zckA/merged-good-all-a2m # found chain 1zckA in template set Warning: unaligning (T0317)V62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zckA)G73 Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zckA)G73 T0317 18 :LFIGNARAAG 1zckA 20 :LITHNPTNAT T0317 29 :TELLVRAGITLCVNVSRQQPGPR 1zckA 34 :IEELKKYGVTTIVRVCEATYDTT T0317 52 :APGVAELRVP 1zckA 60 :KEGIHVLDWP T0317 66 :PAEDL 1zckA 74 :APPSN T0317 72 :THLEPTCAAMEAAVR 1zckA 79 :QIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTA 1zckA 96 :PGCCIAVHCVAGLGRAPVLVAL T0317 110 :LMRHRGHSLDRAFQMVKSARPVAE 1zckA 118 :ALIEGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1zckA 142 :NSKQLLYLEK T0317 154 :ILPRE 1zckA 152 :YRPKM Number of specific fragments extracted= 9 number of extra gaps= 0 total=275 Number of alignments=38 # 1zckA read from 1zckA/merged-good-all-a2m # found chain 1zckA in template set Warning: unaligning (T0317)V62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zckA)G73 Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zckA)G73 T0317 16 :PALFIGNARAAGA 1zckA 18 :RFLITHNPTNATL T0317 29 :TELLVRAGITLCVNVSRQQPG 1zckA 34 :IEELKKYGVTTIVRVCEATYD T0317 54 :GVAELRVP 1zckA 62 :GIHVLDWP T0317 67 :AEDLLTHLEPTCAAMEAAVR 1zckA 74 :APPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMR 1zckA 96 :PGCCIAVHCVAGLGRAPVLVALALIE T0317 114 :RGHSLDRAFQMVKSARPVA 1zckA 122 :GGMKYEDAVQFIRQKRRGA T0317 134 :PNLGFWAQLQ 1zckA 141 :FNSKQLLYLE T0317 152 :QAILPREP 1zckA 151 :KYRPKMRL Number of specific fragments extracted= 8 number of extra gaps= 0 total=283 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1larA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1larA expands to /projects/compbio/data/pdb/1lar.pdb.gz 1larA:# T0317 read from 1larA/merged-good-all-a2m # 1larA read from 1larA/merged-good-all-a2m # adding 1larA to template set # found chain 1larA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (1larA)F1876 T0317 18 :LFIGNARA 1larA 1685 :ATQGPLAE T0317 26 :AGATEL 1larA 1694 :TEDFWR T0317 32 :LVRAGITLCVNVS 1larA 1701 :LWEHNSTIIVMLT T0317 46 :QQP 1larA 1727 :WPA T0317 54 :GVAELRVP 1larA 1771 :QFQFTDWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 1larA 1779 :EQGVPKTGEGFIDFIGQVHKTKE T0317 87 :DG 1larA 1803 :FG T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1larA 1807 :GPITVHCSAGVGRTGVFITLS T0317 110 :LMRHRG 1larA 1832 :RMRYEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 1larA 1839 :VDMFQTVKTLRTQRPAMVQTEDQYQLCYRAALEYLGS Number of specific fragments extracted= 10 number of extra gaps= 0 total=293 Number of alignments=40 # 1larA read from 1larA/merged-good-all-a2m # found chain 1larA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (1larA)F1876 T0317 18 :LFIGNARAAGATE 1larA 1683 :YIATQGPLAESTE T0317 31 :LLVRAGITLCVNVS 1larA 1700 :MLWEHNSTIIVMLT T0317 47 :QPGPR 1larA 1727 :WPAER T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1larA 1767 :RTIRQFQFTDWPEQGVPKTGEGFIDFIGQVHKTKE T0317 87 :DG 1larA 1803 :FG T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1larA 1807 :GPITVHCSAGVGRTGVFITLS T0317 110 :LMRHRG 1larA 1832 :RMRYEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 1larA 1839 :VDMFQTVKTLRTQRPAMVQTEDQYQLCYRAALEYLGS Number of specific fragments extracted= 8 number of extra gaps= 0 total=301 Number of alignments=41 # 1larA read from 1larA/merged-good-all-a2m # found chain 1larA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (1larA)F1876 T0317 2 :GTSEAAPPPFARVAPA 1larA 1662 :GVEGSDYINASFLDGY T0317 18 :LFIGNARAAGA 1larA 1685 :ATQGPLAESTE T0317 29 :TELLVRAGITLCVNVSR 1larA 1698 :WRMLWEHNSTIIVMLTK T0317 46 :QQPGPRAP 1larA 1724 :HQYWPAER T0317 54 :GVAELRVP 1larA 1763 :DGQSRTIR T0317 62 :VFDDPAEDLLTHLEPTCAAMEAAVR 1larA 1774 :FTDWPEQGVPKTGEGFIDFIGQVHK T0317 87 :DG 1larA 1803 :FG T0317 89 :GSCLVYCKNGRSRSAAVCTA 1larA 1807 :GPITVHCSAGVGRTGVFITL T0317 109 :YLMRHRG 1larA 1831 :ERMRYEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 1larA 1839 :VDMFQTVKTLRTQRPAMVQTEDQYQLCYRAALEYLGS Number of specific fragments extracted= 10 number of extra gaps= 0 total=311 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i9sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0317 read from 1i9sA/merged-good-all-a2m # 1i9sA read from 1i9sA/merged-good-all-a2m # found chain 1i9sA in training set Warning: unaligning (T0317)A84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i9sA)P119 Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i9sA)P119 T0317 3 :TSEAAPPPFARVAPA 1i9sA 28 :KTMLGPRYDSQVAEE T0317 21 :GNARAAGATELLVRAGIT 1i9sA 43 :NRFHPSMLSNYLKSLKVK T0317 39 :LCVNVSRQQPGPRAP 1i9sA 63 :LLVDLTNTSRFYDRN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAMEA 1i9sA 83 :GIKYIKLQCKGHGECPTTENTETFIRLCER T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYE 1i9sA 120 :ELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRY T0317 151 :AQAILPREPID 1i9sA 180 :IEEAPPPPVLP Number of specific fragments extracted= 6 number of extra gaps= 0 total=317 Number of alignments=43 # 1i9sA read from 1i9sA/merged-good-all-a2m # found chain 1i9sA in training set Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i9sA)P119 T0317 4 :SEAAPPPFARVAPA 1i9sA 29 :TMLGPRYDSQVAEE T0317 21 :GNARAAGATELLVRAG 1i9sA 43 :NRFHPSMLSNYLKSLK T0317 37 :ITLCVNVSRQQPGPR 1i9sA 61 :MSLLVDLTNTSRFYD T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEA 1i9sA 81 :KEGIKYIKLQCKGHGECPTTENTETFIRLCER T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYE 1i9sA 120 :ELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRY T0317 150 :QAQAILPREPIDPE 1i9sA 178 :GDIEEAPPPPVLPD Number of specific fragments extracted= 6 number of extra gaps= 0 total=323 Number of alignments=44 # 1i9sA read from 1i9sA/merged-good-all-a2m # found chain 1i9sA in training set Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i9sA)P119 T0317 2 :GTSEAAPPPFARVAPALFIGNARA 1i9sA 8 :PRWLNCPRRGQPVAGRFLPLKTML T0317 26 :AGA 1i9sA 33 :PRY T0317 29 :TELLVRAGITL 1i9sA 51 :SNYLKSLKVKM T0317 40 :CVNVSRQQPGPRAP 1i9sA 64 :LVDLTNTSRFYDRN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAME 1i9sA 83 :GIKYIKLQCKGHGECPTTENTETFIRLCE T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYE 1i9sA 120 :ELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRY T0317 150 :QAQAILPREPIDPE 1i9sA 178 :GDIEEAPPPPVLPD Number of specific fragments extracted= 7 number of extra gaps= 0 total=330 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p15A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1p15A expands to /projects/compbio/data/pdb/1p15.pdb.gz 1p15A:# T0317 read from 1p15A/merged-good-all-a2m # 1p15A read from 1p15A/merged-good-all-a2m # adding 1p15A to template set # found chain 1p15A in template set Warning: unaligning (T0317)Q46 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)E629 Warning: unaligning (T0317)Q47 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E629 Warning: unaligning (T0317)P48 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)G631 Warning: unaligning (T0317)G49 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)G631 Warning: unaligning (T0317)P53 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)A636 T0317 13 :RVAPALFIGNARAAGATELL 1p15A 590 :RQKDSYIASQGPLLHTIEDF T0317 33 :VRAGITLCVNVS 1p15A 614 :WEWKSCSIVMLT T0317 50 :PRA 1p15A 632 :QEK T0317 54 :GVAELRVP 1p15A 683 :QFHFHGWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 1p15A 691 :EVGIPSDGKGMINIIAAVQKQQQ T0317 87 :DGGSCLVYCKNGRSRSAAVCTAY 1p15A 716 :GNHPITVHCSAGAGRTGTFCALS T0317 110 :LMRHRGH 1p15A 743 :RVKAEGI T0317 117 :SLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 1p15A 751 :DVFQTVKSLRLQRPHMVQTLEQYEFCYKVVQEYID Number of specific fragments extracted= 8 number of extra gaps= 2 total=338 Number of alignments=46 # 1p15A read from 1p15A/merged-good-all-a2m # found chain 1p15A in template set Warning: unaligning (T0317)Q46 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)E629 Warning: unaligning (T0317)Q47 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E629 Warning: unaligning (T0317)P48 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)G631 Warning: unaligning (T0317)G49 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)G631 Warning: unaligning (T0317)Q152 because last residue in template chain is (1p15A)A786 T0317 13 :RVAPALFIGNARAAGATELL 1p15A 590 :RQKDSYIASQGPLLHTIEDF T0317 33 :VRAGITLCVNVS 1p15A 614 :WEWKSCSIVMLT T0317 45 :R 1p15A 627 :L T0317 50 :PR 1p15A 632 :QE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1p15A 679 :RQIRQFHFHGWPEVGIPSDGKGMINIIAAVQKQQQ T0317 87 :D 1p15A 716 :G T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1p15A 718 :HPITVHCSAGAGRTGTFCALSTVLE T0317 114 :RG 1p15A 747 :EG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 1p15A 750 :LDVFQTVKSLRLQRPHMVQTLEQYEFCYKVVQEYID Number of specific fragments extracted= 9 number of extra gaps= 1 total=347 Number of alignments=47 # 1p15A read from 1p15A/merged-good-all-a2m # found chain 1p15A in template set Warning: unaligning (T0317)Q47 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)E629 Warning: unaligning (T0317)P48 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E629 Warning: unaligning (T0317)G49 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)G631 Warning: unaligning (T0317)P50 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)G631 Warning: unaligning (T0317)Q152 because last residue in template chain is (1p15A)A786 T0317 13 :RVAPALFIGNARAAGATE 1p15A 590 :RQKDSYIASQGPLLHTIE T0317 31 :LLVRAGITLCVNVSRQ 1p15A 612 :MIWEWKSCSIVMLTEL T0317 51 :RAP 1p15A 632 :QEK T0317 54 :GVAELRVPVFDDPAED 1p15A 680 :QIRQFHFHGWPEVGIP T0317 70 :LLTHLEPTCAAMEAAVRD 1p15A 697 :DGKGMINIIAAVQKQQQQ T0317 88 :GGSCLVYCKNGRSRSAAVCTA 1p15A 717 :NHPITVHCSAGAGRTGTFCAL T0317 109 :YLMRHRG 1p15A 742 :ERVKAEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 1p15A 750 :LDVFQTVKSLRLQRPHMVQTLEQYEFCYKVVQEYID Number of specific fragments extracted= 8 number of extra gaps= 1 total=355 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ywfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ywfA expands to /projects/compbio/data/pdb/1ywf.pdb.gz 1ywfA:# T0317 read from 1ywfA/merged-good-all-a2m # 1ywfA read from 1ywfA/merged-good-all-a2m # adding 1ywfA to template set # found chain 1ywfA in template set Warning: unaligning (T0317)A67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywfA)S117 T0317 15 :APA 1ywfA 23 :RPG T0317 18 :LFIGNARA 1ywfA 27 :LFRSSELS T0317 26 :AGATELLVRAGITLCVNVS 1ywfA 38 :DAGRATLRRLGITDVADLR T0317 47 :QPGPRAPGVAELRVPVFDDP 1ywfA 65 :GPGRVPDGIDVHLLPFPDLA T0317 85 :VRDGGSCLVYCKNGRSRSAAVCTAY 1ywfA 150 :LAAGRPVLTHCFAGKDRTGFVVALV T0317 111 :MRHRGHSLDRAFQMVK 1ywfA 175 :LEAVGLDRDVIVADYL T0317 131 :VAEPN 1ywfA 191 :RSNDS T0317 139 :WAQLQKYEQTLQAQAILP 1ywfA 196 :VPQLRARISEMIQQRFDT Number of specific fragments extracted= 8 number of extra gaps= 0 total=363 Number of alignments=49 # 1ywfA read from 1ywfA/merged-good-all-a2m # found chain 1ywfA in template set T0317 14 :VAPA 1ywfA 22 :LRPG T0317 18 :LFIGNARA 1ywfA 27 :LFRSSELS T0317 26 :AGATELLVRAGITLCVNVS 1ywfA 38 :DAGRATLRRLGITDVADLR T0317 47 :QPGPRAPGVAELRVPVFD 1ywfA 65 :GPGRVPDGIDVHLLPFPD T0317 69 :DLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTA 1ywfA 134 :PTRNGAQRALHRVVTLLAAGRPVLTHCFAGKDRTGFVVAL T0317 110 :LMRHRGHSLDRAFQMVKS 1ywfA 174 :VLEAVGLDRDVIVADYLR T0317 132 :AEP 1ywfA 192 :SND T0317 138 :FWAQLQKYEQTLQAQAILPRE 1ywfA 195 :SVPQLRARISEMIQQRFDTEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=371 Number of alignments=50 # 1ywfA read from 1ywfA/merged-good-all-a2m # found chain 1ywfA in template set Warning: unaligning (T0317)A67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywfA)S117 T0317 16 :PALFIGNARAAGA 1ywfA 25 :GRLFRSSELSRLD T0317 29 :TELLVRAGITLCVNVSR 1ywfA 41 :RATLRRLGITDVADLRS T0317 47 :QPGPRAPGVAELRVPVFDDP 1ywfA 65 :GPGRVPDGIDVHLLPFPDLA T0317 87 :DGGSCLVYCKNGRSRSAAVCTA 1ywfA 152 :AGRPVLTHCFAGKDRTGFVVAL T0317 110 :LMRHRGHSLDRAFQMVKSARP 1ywfA 174 :VLEAVGLDRDVIVADYLRSND T0317 138 :FWAQLQKYEQTLQAQAI 1ywfA 195 :SVPQLRARISEMIQQRF Number of specific fragments extracted= 6 number of extra gaps= 0 total=377 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g7fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g7fA expands to /projects/compbio/data/pdb/1g7f.pdb.gz 1g7fA:# T0317 read from 1g7fA/merged-good-all-a2m # 1g7fA read from 1g7fA/merged-good-all-a2m # adding 1g7fA to template set # found chain 1g7fA in template set Warning: unaligning (T0317)G115 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)D240 T0317 18 :LFIGNARAAGA 1g7fA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1g7fA 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1g7fA 126 :PQKEEKE T0317 54 :GVAELRVP 1g7fA 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEAA 1g7fA 181 :DFGVPESPASFLNFLFKVRES T0317 85 :VRDG 1g7fA 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1g7fA 209 :GPVVVHCSAGIGRSGTFCLAD T0317 110 :LMRHR 1g7fA 234 :LMDKR T0317 116 :HSLDRAFQ 1g7fA 244 :VDIKKVLL T0317 125 :VKSARPVAEPNLGFWAQLQKYEQTLQAQAILPRE 1g7fA 253 :MRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSS Number of specific fragments extracted= 10 number of extra gaps= 1 total=387 Number of alignments=52 # 1g7fA read from 1g7fA/merged-good-all-a2m # found chain 1g7fA in template set Warning: unaligning (T0317)G115 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)D240 T0317 18 :LFIGNARAAGA 1g7fA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1g7fA 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1g7fA 126 :PQKEEKE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAA 1g7fA 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRES T0317 85 :VRDG 1g7fA 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1g7fA 209 :GPVVVHCSAGIGRSGTFCLAD T0317 110 :LMRHR 1g7fA 234 :LMDKR T0317 116 :HSLDRAFQ 1g7fA 244 :VDIKKVLL T0317 125 :VKSARPVAEPNLGFWAQLQKYEQTLQA 1g7fA 253 :MRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 1 total=396 Number of alignments=53 # 1g7fA read from 1g7fA/merged-good-all-a2m # found chain 1g7fA in template set Warning: unaligning (T0317)G115 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)D240 T0317 18 :LFIGNARAAGA 1g7fA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 1g7fA 96 :WEMVWEQKSRGVVMLNR T0317 46 :QQPGPR 1g7fA 123 :QYWPQK T0317 54 :GVAELRVPVFDDPAEDLL 1g7fA 171 :ILHFHYTTWPDFGVPESP T0317 75 :EPTCAAMEAAVR 1g7fA 189 :ASFLNFLFKVRE T0317 87 :DGGSCLVYCKNGRSRSAAVCTA 1g7fA 207 :EHGPVVVHCSAGIGRSGTFCLA T0317 109 :YLMRHR 1g7fA 233 :LLMDKR T0317 116 :HSLDRAFQ 1g7fA 244 :VDIKKVLL T0317 125 :VKSARPVAEPNLGFWAQLQ 1g7fA 253 :MRKFRMGLIQTADQLRFSY Number of specific fragments extracted= 9 number of extra gaps= 1 total=405 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d5rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d5rA expands to /projects/compbio/data/pdb/1d5r.pdb.gz 1d5rA:# T0317 read from 1d5rA/merged-good-all-a2m # 1d5rA read from 1d5rA/merged-good-all-a2m # adding 1d5rA to template set # found chain 1d5rA in template set T0317 9 :PPFARVAPALFIGNA 1d5rA 36 :GFPAERLEGVYRNNI T0317 26 :AGATELLVR 1d5rA 51 :DDVVRFLDS T0317 35 :AGITLCVNVS 1d5rA 62 :KNHYKIYNLC T0317 45 :RQQPGPRAPGVAELRVPVFDDPAEDLLT 1d5rA 73 :ERHYDTAKFNCRVAQYPFEDHNPPQLEL T0317 74 :LEPTCAAMEAAVRDG 1d5rA 101 :IKPFCEDLDQWLSED T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRG 1d5rA 118 :HVAAIHCKAGKGRTGVMICAYLLHRGK T0317 116 :HSLDRAFQMVKSAR 1d5rA 146 :LKAQEALDFYGEVR T0317 130 :PVAEPNLGFWAQLQKYEQTLQAQAILPR 1d5rA 163 :KKGVTIPSQRRYVYYYSYLLKNHLDYRP Number of specific fragments extracted= 8 number of extra gaps= 0 total=413 Number of alignments=55 # 1d5rA read from 1d5rA/merged-good-all-a2m # found chain 1d5rA in template set T0317 9 :PPFARVAPALFIGNARA 1d5rA 36 :GFPAERLEGVYRNNIDD T0317 29 :TELLVRA 1d5rA 54 :VRFLDSK T0317 36 :GITLCVNVS 1d5rA 63 :NHYKIYNLC T0317 45 :RQQPGPRAPGVAELRVPVFDDPAEDL 1d5rA 73 :ERHYDTAKFNCRVAQYPFEDHNPPQL T0317 72 :THLEPTCAAMEAAVRDG 1d5rA 99 :ELIKPFCEDLDQWLSED T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRG 1d5rA 118 :HVAAIHCKAGKGRTGVMICAYLLHRGK T0317 116 :HSLDRAFQMVKSARPV 1d5rA 146 :LKAQEALDFYGEVRTR T0317 132 :AEPNLGFWAQLQKYEQTLQAQAILPRE 1d5rA 165 :GVTIPSQRRYVYYYSYLLKNHLDYRPV Number of specific fragments extracted= 8 number of extra gaps= 0 total=421 Number of alignments=56 # 1d5rA read from 1d5rA/merged-good-all-a2m # found chain 1d5rA in template set T0317 3 :TSEAAPPPFARVAPALFIGNARAAGA 1d5rA 17 :QEDGFDLDLTYIYPNIIAMGFPAERL T0317 29 :TELLVRA 1d5rA 50 :IDDVVRF T0317 36 :GITLCVNVSRQQPGPRAP 1d5rA 63 :NHYKIYNLCAERHYDTAK T0317 54 :GVAELRVPVFD 1d5rA 82 :NCRVAQYPFED T0317 66 :PAEDLLTHLEPTCAAMEAAVRDG 1d5rA 93 :HNPPQLELIKPFCEDLDQWLSED T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRG 1d5rA 118 :HVAAIHCKAGKGRTGVMICAYLLHRGK T0317 116 :HSLDRAFQMVKSAR 1d5rA 146 :LKAQEALDFYGEVR T0317 130 :PVAEPNLGFWAQLQKYEQTLQAQAILPRE 1d5rA 163 :KKGVTIPSQRRYVYYYSYLLKNHLDYRPV Number of specific fragments extracted= 8 number of extra gaps= 0 total=429 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ytw/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ytw expands to /projects/compbio/data/pdb/1ytw.pdb.gz 1ytw:Warning: there is no chain 1ytw will retry with 1ytwA Skipped atom 1776, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1778, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1780, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1782, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1784, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1786, because occupancy 0.450 <= existing 0.550 in 1ytw # T0317 read from 1ytw/merged-good-all-a2m # 1ytw read from 1ytw/merged-good-all-a2m # adding 1ytw to template set # found chain 1ytw in template set T0317 25 :AAGATELLVRAGITLCVNVS 1ytw 267 :LESHFRMLAENRTPVLAVLA T0317 45 :RQQPGPRAP 1ytw 296 :FGMPDYFRQ T0317 54 :GVAELRVP 1ytw 340 :GQKTISVP T0317 62 :VFDDPAEDL 1ytw 354 :WPDQTAVSS T0317 72 :THLEPTCAAMEAA 1ytw 363 :EVTKALASLVDQT T0317 86 :RD 1ytw 394 :DS T0317 89 :GSCLVYCKNGRSRSAAVCTAYLM 1ytw 397 :LRPVIHCRAGVGRTAQLIGAMCM T0317 114 :RGHSLDRAFQMVKSAR 1ytw 425 :SQLSVEDMVSQMRVQR T0317 130 :PVAEPNLGFWAQLQKYEQT 1ytw 442 :GIMVQKDEQLDVLIKLAEG T0317 152 :Q 1ytw 461 :Q Number of specific fragments extracted= 10 number of extra gaps= 0 total=439 Number of alignments=58 # 1ytw read from 1ytw/merged-good-all-a2m # found chain 1ytw in template set T0317 25 :AAGATELLVRAGITLCVNVS 1ytw 267 :LESHFRMLAENRTPVLAVLA T0317 45 :RQQPGP 1ytw 299 :PDYFRQ T0317 52 :APGVAELRV 1ytw 343 :TISVPVVHV T0317 61 :PVFDDPAEDL 1ytw 353 :NWPDQTAVSS T0317 72 :THLEPTCAAMEAAV 1ytw 363 :EVTKALASLVDQTA T0317 86 :RDGGSCLVYCKNGRSRSAAVCTAYLMRH 1ytw 394 :DSKLRPVIHCRAGVGRTAQLIGAMCMND T0317 114 :RGHSLDRAFQMVKSARPV 1ytw 425 :SQLSVEDMVSQMRVQRNG T0317 132 :AEPNLGFWAQLQKYEQTL 1ytw 444 :MVQKDEQLDVLIKLAEGQ T0317 154 :ILP 1ytw 462 :GRP Number of specific fragments extracted= 9 number of extra gaps= 0 total=448 Number of alignments=59 # 1ytw read from 1ytw/merged-good-all-a2m # found chain 1ytw in template set T0317 29 :TELLVRAGITLCVNVSR 1ytw 271 :FRMLAENRTPVLAVLAS T0317 46 :QQPGPRAP 1ytw 297 :GMPDYFRQ T0317 54 :GVAELRVP 1ytw 340 :GQKTISVP T0317 62 :VFDDP 1ytw 354 :WPDQT T0317 68 :EDLLTHLEPTCAAMEAAVR 1ytw 359 :AVSSEVTKALASLVDQTAE T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMR 1ytw 397 :LRPVIHCRAGVGRTAQLIGAMCMN T0317 114 :RGHSLDRAFQMVKSAR 1ytw 425 :SQLSVEDMVSQMRVQR T0317 130 :PVAEPNLGFWAQLQKYEQT 1ytw 442 :GIMVQKDEQLDVLIKLAEG Number of specific fragments extracted= 8 number of extra gaps= 0 total=456 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c46A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c46A expands to /projects/compbio/data/pdb/2c46.pdb.gz 2c46A:Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 2c46A # T0317 read from 2c46A/merged-good-all-a2m # 2c46A read from 2c46A/merged-good-all-a2m # adding 2c46A to template set # found chain 2c46A in template set Warning: unaligning (T0317)A84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c46A)P119 Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c46A)P119 T0317 3 :TSEAAPPPFARVAPA 2c46A 28 :KTMLGPRYDSQVAEE T0317 21 :GNARAAGATELLVRAGIT 2c46A 43 :NRFHPSMLSNYLKSLKVK T0317 39 :LCVNVSRQQPGPRAP 2c46A 63 :LLVDLTNTSRFYDRN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAMEA 2c46A 83 :GIKYIKLQCKGHGECPTTENTETFIRLCER T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYE 2c46A 120 :ELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRY T0317 151 :AQAILPREPID 2c46A 180 :IEEAPPPPLLP Number of specific fragments extracted= 6 number of extra gaps= 0 total=462 Number of alignments=61 # 2c46A read from 2c46A/merged-good-all-a2m # found chain 2c46A in template set Warning: unaligning (T0317)A84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c46A)P119 T0317 4 :SEAAPPPFARVAPA 2c46A 29 :TMLGPRYDSQVAEE T0317 21 :GNARAAGATELLVRAGITL 2c46A 43 :NRFHPSMLSNYLKSLKVKM T0317 40 :CVNVSRQQPGPR 2c46A 64 :LVDLTNTSRFYD T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEA 2c46A 81 :KEGIKYIKLQCKGHGECPTTENTETFIRLCER T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYE 2c46A 120 :ELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRY T0317 150 :Q 2c46A 178 :G T0317 151 :AQAILPREPIDP 2c46A 182 :EAPPPPLLPDWC Number of specific fragments extracted= 7 number of extra gaps= 0 total=469 Number of alignments=62 # 2c46A read from 2c46A/merged-good-all-a2m # found chain 2c46A in template set Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c46A)P119 T0317 2 :GTSEAAPPPFARVAPALFIGNA 2c46A 8 :PRWLNCPRRGQPVAGRFLPLKT T0317 29 :TELLVRAGITL 2c46A 51 :SNYLKSLKVKM T0317 40 :CVNVSRQQPGPRAP 2c46A 64 :LVDLTNTSRFYDRN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAME 2c46A 83 :GIKYIKLQCKGHGECPTTENTETFIRLCE T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYE 2c46A 120 :ELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRY T0317 150 :Q 2c46A 178 :G T0317 151 :AQAILPREPI 2c46A 180 :IEEAPPPPLL Number of specific fragments extracted= 7 number of extra gaps= 0 total=476 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g4uS/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g4uS expands to /projects/compbio/data/pdb/1g4u.pdb.gz 1g4uS:# T0317 read from 1g4uS/merged-good-all-a2m # 1g4uS read from 1g4uS/merged-good-all-a2m # adding 1g4uS to template set # found chain 1g4uS in template set Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1g4uS)K474 T0317 21 :GNARA 1g4uS 347 :GSYPK T0317 26 :AGATEL 1g4uS 353 :TPDALE T0317 32 :LVRAGITLCVNVS 1g4uS 364 :LLEKECSCLVVLT T0317 45 :RQQPGPRAP 1g4uS 384 :KQLPPYFRG T0317 54 :GVAELRV 1g4uS 430 :TIPVLHV T0317 62 :VFDDPAEDLLTHLEPTCAAME 1g4uS 439 :WPDHQPLPSTDQLEYLADRVK T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1g4uS 475 :HLPMIHCLGGVGRTGTMAAALVLKD T0317 114 :RGHSLDRAFQMVKSAR 1g4uS 501 :PHSNLEQVRADFRDSR T0317 130 :PVAEPNLGFWAQLQKYEQTLQ 1g4uS 518 :NRMLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 9 number of extra gaps= 0 total=485 Number of alignments=64 # 1g4uS read from 1g4uS/merged-good-all-a2m # found chain 1g4uS in template set Warning: unaligning (T0317)A83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1g4uS)K474 Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1g4uS)K474 T0317 18 :LFIGNARAAGA 1g4uS 344 :ALAGSYPKNTP T0317 29 :TELLVRAGITLCVNVS 1g4uS 361 :MKMLLEKECSCLVVLT T0317 45 :RQQPGP 1g4uS 408 :SASQGE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAME 1g4uS 429 :YTIPVLHVKNWPDHQPLPSTDQLEYLADRVK T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1g4uS 475 :HLPMIHCLGGVGRTGTMAAALVLKD T0317 114 :RGHSLDRAFQMVKSARPV 1g4uS 501 :PHSNLEQVRADFRDSRNN T0317 132 :AEPNLGFWAQLQKYEQTLQ 1g4uS 520 :MLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 7 number of extra gaps= 0 total=492 Number of alignments=65 # 1g4uS read from 1g4uS/merged-good-all-a2m # found chain 1g4uS in template set Warning: unaligning (T0317)A83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1g4uS)K474 Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1g4uS)K474 T0317 19 :FIGNARAAGA 1g4uS 345 :LAGSYPKNTP T0317 29 :TELLVRAGITLCVNVSR 1g4uS 361 :MKMLLEKECSCLVVLTS T0317 46 :QQPGPRAP 1g4uS 385 :QLPPYFRG T0317 54 :GVAELRVP 1g4uS 425 :GEKRYTIP T0317 62 :VFDDPAEDLLTHLEPTCAAME 1g4uS 439 :WPDHQPLPSTDQLEYLADRVK T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1g4uS 475 :HLPMIHCLGGVGRTGTMAAALVLKD T0317 114 :RGHSLDRAFQMVKSAR 1g4uS 501 :PHSNLEQVRADFRDSR T0317 130 :PVAEPNLGFWAQLQKYEQTLQ 1g4uS 518 :NRMLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 8 number of extra gaps= 0 total=500 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2shpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2shpA expands to /projects/compbio/data/pdb/2shp.pdb.gz 2shpA:# T0317 read from 2shpA/merged-good-all-a2m # 2shpA read from 2shpA/merged-good-all-a2m # adding 2shpA to template set # found chain 2shpA in template set Warning: unaligning (T0317)N22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)L334 Warning: unaligning (T0317)A23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)L334 T0317 18 :LFIG 2shpA 329 :ATQG T0317 24 :RA 2shpA 335 :QN T0317 26 :AGATEL 2shpA 338 :VNDFWR T0317 32 :LVRAGITLCVNVS 2shpA 345 :VFQENSRVIVMTT T0317 54 :GVAELRVP 2shpA 417 :QYHFRTWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 2shpA 425 :DHGVPSDPGGVLDFLEEVHHKQE T0317 87 :DG 2shpA 450 :MD T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2shpA 453 :GPVVVHCSAGIGRTGTFIVIDILID T0317 114 :RGHS 2shpA 484 :VDCD T0317 118 :LDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 2shpA 490 :VPKTIQMVRSQRSGMVQTEAQYRSIYMAVQHYIET Number of specific fragments extracted= 10 number of extra gaps= 1 total=510 Number of alignments=67 # 2shpA read from 2shpA/merged-good-all-a2m # found chain 2shpA in template set Warning: unaligning (T0317)V14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2shpA)K324 Warning: unaligning (T0317)A17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)I328 Warning: unaligning (T0317)L18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)I328 Warning: unaligning (T0317)A23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)L334 Warning: unaligning (T0317)R24 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)L334 T0317 15 :AP 2shpA 325 :KS T0317 19 :FIGN 2shpA 329 :ATQG T0317 25 :A 2shpA 335 :Q T0317 26 :AGA 2shpA 337 :TVN T0317 29 :TELLVRAGITLCVNVS 2shpA 342 :WRMVFQENSRVIVMTT T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 2shpA 413 :RTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQE T0317 87 :DG 2shpA 450 :MD T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2shpA 453 :GPVVVHCSAGIGRTGTFIVIDILID T0317 114 :RG 2shpA 484 :VD T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 2shpA 488 :IDVPKTIQMVRSQRSGMVQTEAQYRSIYMAVQHYIET Number of specific fragments extracted= 10 number of extra gaps= 2 total=520 Number of alignments=68 # 2shpA read from 2shpA/merged-good-all-a2m # found chain 2shpA in template set Warning: unaligning (T0317)A17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)I328 Warning: unaligning (T0317)L18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)I328 Warning: unaligning (T0317)A23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)L334 Warning: unaligning (T0317)R24 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)L334 T0317 15 :AP 2shpA 325 :KS T0317 19 :FIGN 2shpA 329 :ATQG T0317 25 :A 2shpA 335 :Q T0317 26 :AGA 2shpA 338 :VND T0317 29 :TELLVRAGITLCVNVSRQ 2shpA 342 :WRMVFQENSRVIVMTTKE T0317 54 :GVAELRVPVFDDPAEDLL 2shpA 415 :VWQYHFRTWPDHGVPSDP T0317 75 :EPTCAAMEAAVR 2shpA 433 :GGVLDFLEEVHH T0317 87 :DG 2shpA 450 :MD T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2shpA 453 :GPVVVHCSAGIGRTGTFIVIDILID T0317 115 :G 2shpA 485 :D T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKY 2shpA 488 :IDVPKTIQMVRSQRSGMVQTEAQYRSIYMA Number of specific fragments extracted= 11 number of extra gaps= 2 total=531 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mkp/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mkp expands to /projects/compbio/data/pdb/1mkp.pdb.gz 1mkp:Warning: there is no chain 1mkp will retry with 1mkpA # T0317 read from 1mkp/merged-good-all-a2m # 1mkp read from 1mkp/merged-good-all-a2m # adding 1mkp to template set # found chain 1mkp in template set Warning: unaligning (T0317)P8 because first residue in template chain is (1mkp)A204 T0317 9 :PPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPRA 1mkp 205 :SFPVEILPFLYLGCAKDSTNLDVLEEFGIKYILNVTPNLPNLFE T0317 53 :PGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1mkp 251 :GEFKYKQIPISDHWSQNLSQFFPEAISFIDEARGKNCGVLVHSLAGISRSVTVTVAYLMQKLNLSMNDAYDIVKMKKSNISPNFNFMGQLLDFER Number of specific fragments extracted= 2 number of extra gaps= 0 total=533 Number of alignments=70 # 1mkp read from 1mkp/merged-good-all-a2m # found chain 1mkp in template set T0317 9 :PPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPR 1mkp 205 :SFPVEILPFLYLGCAKDSTNLDVLEEFGIKYILNVTPNLPNLF T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1mkp 250 :AGEFKYKQIPISDHWSQNLSQFFPEAISFIDEARGKNCGVLVHSLAGISRSVTVTVAYLMQKLNLSMNDAYDIVKMKKSNISPNFNFMGQLLDFER Number of specific fragments extracted= 2 number of extra gaps= 0 total=535 Number of alignments=71 # 1mkp read from 1mkp/merged-good-all-a2m # found chain 1mkp in template set T0317 9 :PPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPRAP 1mkp 205 :SFPVEILPFLYLGCAKDSTNLDVLEEFGIKYILNVTPNLPNLFEN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1mkp 252 :EFKYKQIPISDHWSQNLSQFFPEAISFIDEARGKNCGVLVHSLAGISRSVTVTVAYLMQKLNLSMNDAYDIVKMKKSNISPNFNFMGQLLDFER Number of specific fragments extracted= 2 number of extra gaps= 0 total=537 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f71A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f71A expands to /projects/compbio/data/pdb/2f71.pdb.gz 2f71A:Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 166, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 170, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 172, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 174, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 176, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 178, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 229, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 285, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 293, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 295, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 297, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1059, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1063, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1065, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1067, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1389, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1391, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1517, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1521, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1523, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1525, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1527, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1678, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1682, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1684, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1744, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1752, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1756, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1766, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1770, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1772, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1774, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1776, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1778, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1780, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1782, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1835, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1839, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1867, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1871, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1873, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1908, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1912, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1914, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1977, because occupancy 0.200 <= existing 0.800 in 2f71A Skipped atom 1981, because occupancy 0.200 <= existing 0.800 in 2f71A Skipped atom 1983, because occupancy 0.200 <= existing 0.800 in 2f71A Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2064, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2066, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2068, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2070, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2072, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2195, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2199, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2201, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2203, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2205, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2346, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2350, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2352, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2473, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2477, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2479, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2481, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2493, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2497, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2499, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2501, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2503, because occupancy 0.500 <= existing 0.500 in 2f71A # T0317 read from 2f71A/merged-good-all-a2m # 2f71A read from 2f71A/merged-good-all-a2m # adding 2f71A to template set # found chain 2f71A in template set Warning: unaligning (T0317)I154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f71A)G283 Warning: unaligning (T0317)L155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f71A)G283 T0317 18 :LFIGNARAAGA 2f71A 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 2f71A 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPRA 2f71A 126 :PQKEEKEM T0317 54 :GVAELRVP 2f71A 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEAA 2f71A 181 :DFGVPESPASFLNFLFKVRES T0317 85 :VRDG 2f71A 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 2f71A 209 :GPVVVHCSAGIGRSGTFCLAD T0317 110 :LMRHRG 2f71A 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQA 2f71A 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFI T0317 156 :P 2f71A 284 :D Number of specific fragments extracted= 10 number of extra gaps= 1 total=547 Number of alignments=73 # 2f71A read from 2f71A/merged-good-all-a2m # found chain 2f71A in template set T0317 18 :LFIGNARAAGA 2f71A 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 2f71A 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 2f71A 126 :PQKEEKE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEA 2f71A 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRE T0317 85 :VRDG 2f71A 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 2f71A 209 :GPVVVHCSAGIGRSGTFCLAD T0317 110 :LMRHRG 2f71A 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2f71A 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=555 Number of alignments=74 # 2f71A read from 2f71A/merged-good-all-a2m # found chain 2f71A in template set T0317 18 :LFIGNARAAGA 2f71A 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 2f71A 96 :WEMVWEQKSRGVVMLNR T0317 54 :GVAELRVPVFDDPAEDLL 2f71A 171 :ILHFHYTTWPDFGVPESP T0317 75 :EPTCAAMEAAVRDG 2f71A 189 :ASFLNFLFKVRESG T0317 89 :GSCLVYCKNGRSRSAAVCTA 2f71A 209 :GPVVVHCSAGIGRSGTFCLA T0317 109 :YLMRHRG 2f71A 233 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKY 2f71A 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLA Number of specific fragments extracted= 7 number of extra gaps= 0 total=562 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g4wR/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g4wR expands to /projects/compbio/data/pdb/1g4w.pdb.gz 1g4wR:# T0317 read from 1g4wR/merged-good-all-a2m # 1g4wR read from 1g4wR/merged-good-all-a2m # adding 1g4wR to template set # found chain 1g4wR in template set T0317 19 :FIGNARAAGA 1g4wR 349 :YPKNTPDALE T0317 29 :TELLVRAGITLCVNVS 1g4wR 361 :MKMLLEKECSCLVVLT T0317 45 :RQQPGPRAP 1g4wR 384 :KQLPPYFRG T0317 54 :GVAELRV 1g4wR 430 :TIPVLHV T0317 62 :VFDDPAEDLLTHLEPTCAAME 1g4wR 439 :WPDHQPLPSTDQLEYLADRVK T0317 87 :DG 1g4wR 467 :PG T0317 91 :CLVYCKNGRSRSAAVCTAYLMRH 1g4wR 477 :PMIHCLGGVGRTGTMAAALVLKD T0317 114 :RGHSLDRAFQMVKSAR 1g4wR 501 :PHSNLEQVRADFRDSR T0317 130 :PVAEPNLGFWAQLQKYEQTLQ 1g4wR 518 :NRMLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 9 number of extra gaps= 0 total=571 Number of alignments=76 # 1g4wR read from 1g4wR/merged-good-all-a2m # found chain 1g4wR in template set T0317 19 :FIGNARAAGA 1g4wR 349 :YPKNTPDALE T0317 29 :TELLVRAGITLCVNVS 1g4wR 361 :MKMLLEKECSCLVVLT T0317 45 :RQQPG 1g4wR 384 :KQLPP T0317 52 :APGVAELRV 1g4wR 428 :RYTIPVLHV T0317 61 :PVFDDPAEDLLTHLEPTCAAME 1g4wR 438 :NWPDHQPLPSTDQLEYLADRVK T0317 86 :RDGGSCLVYCKNGRSRSAAVCTAYLMRH 1g4wR 472 :SDKHLPMIHCLGGVGRTGTMAAALVLKD T0317 114 :RGHSLDRAFQMVKSARPV 1g4wR 501 :PHSNLEQVRADFRDSRNN T0317 132 :AEPNLGFWAQLQKYEQTLQ 1g4wR 520 :MLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 8 number of extra gaps= 0 total=579 Number of alignments=77 # 1g4wR read from 1g4wR/merged-good-all-a2m # found chain 1g4wR in template set T0317 18 :LFIGNARAAGA 1g4wR 345 :LAGSYPKNTPD T0317 29 :TELLVRAGITLCVNVSR 1g4wR 361 :MKMLLEKECSCLVVLTS T0317 46 :QQPGPRAP 1g4wR 385 :QLPPYFRG T0317 54 :GVAELRVP 1g4wR 425 :GEKRYTIP T0317 62 :VFDDPAEDLLTHLEPTCAAME 1g4wR 439 :WPDHQPLPSTDQLEYLADRVK T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRH 1g4wR 473 :DKHLPMIHCLGGVGRTGTMAAALVLKD T0317 114 :RGHSLDRAFQMVKSAR 1g4wR 501 :PHSNLEQVRADFRDSR T0317 130 :PVAEPNLGFWAQLQKYEQTLQ 1g4wR 518 :NRMLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 8 number of extra gaps= 0 total=587 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fpzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fpzA expands to /projects/compbio/data/pdb/1fpz.pdb.gz 1fpzA:# T0317 read from 1fpzA/merged-good-all-a2m # 1fpzA read from 1fpzA/merged-good-all-a2m # adding 1fpzA to template set # found chain 1fpzA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (1fpzA)L200 T0317 22 :NARAAGATELLVRAGITLCVNVS 1fpzA 57 :RRNVQKDTEELKSCGIQDIFVFC T0317 45 :RQQP 1fpzA 87 :YRVP T0317 54 :GVAELRVPVFDDPAEDLLT 1fpzA 100 :GIITHHHPIADGGTPDIAS T0317 74 :LEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGH 1fpzA 119 :CCEIMEELTTCLKNYRKTLIHSYGGLGRSCLVAACLLLYLSDT T0317 117 :SLDRAFQMVKSAR 1fpzA 163 :SPEQAIDSLRDLR T0317 130 :PVAEPNLGFWAQLQKYEQTLQAQ 1fpzA 177 :SGAIQTIKQYNYLHEFRDKLAAH Number of specific fragments extracted= 6 number of extra gaps= 0 total=593 Number of alignments=79 # 1fpzA read from 1fpzA/merged-good-all-a2m # found chain 1fpzA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (1fpzA)L200 T0317 15 :APAL 1fpzA 53 :FKDV T0317 22 :NARAAGATELLVRAGITLCVNVS 1fpzA 57 :RRNVQKDTEELKSCGIQDIFVFC T0317 45 :RQQPG 1fpzA 87 :YRVPN T0317 52 :APGVAELRVPVFDDPAEDL 1fpzA 98 :QCGIITHHHPIADGGTPDI T0317 72 :THLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRG 1fpzA 117 :ASCCEIMEELTTCLKNYRKTLIHSYGGLGRSCLVAACLLLYLSD T0317 116 :HSLDRAFQMVKSARPV 1fpzA 162 :ISPEQAIDSLRDLRGS T0317 132 :AEPNLGFWAQLQKYEQTLQAQ 1fpzA 179 :AIQTIKQYNYLHEFRDKLAAH Number of specific fragments extracted= 7 number of extra gaps= 0 total=600 Number of alignments=80 # 1fpzA read from 1fpzA/merged-good-all-a2m # found chain 1fpzA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (1fpzA)L200 T0317 23 :ARAAGATELLVRAGITLCVNVSR 1fpzA 58 :RNVQKDTEELKSCGIQDIFVFCT T0317 54 :GVAELRVPVFDDPAED 1fpzA 100 :GIITHHHPIADGGTPD T0317 71 :LTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRG 1fpzA 116 :IASCCEIMEELTTCLKNYRKTLIHSYGGLGRSCLVAACLLLYLSD T0317 116 :HSLDRAFQMVKSAR 1fpzA 162 :ISPEQAIDSLRDLR T0317 130 :PVAEPNLGFWAQLQKYEQTLQAQ 1fpzA 177 :SGAIQTIKQYNYLHEFRDKLAAH Number of specific fragments extracted= 5 number of extra gaps= 0 total=605 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j4xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0317/1j4xA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0317/1j4xA/merged-good-all-a2m.gz for input Trying 1j4xA/merged-good-all-a2m Error: Couldn't open file 1j4xA/merged-good-all-a2m or 1j4xA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ohcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0317/1ohcA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0317/1ohcA/merged-good-all-a2m.gz for input Trying 1ohcA/merged-good-all-a2m Error: Couldn't open file 1ohcA/merged-good-all-a2m or 1ohcA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cfvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0317/2cfvA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0317/2cfvA/merged-good-all-a2m.gz for input Trying 2cfvA/merged-good-all-a2m Error: Couldn't open file 2cfvA/merged-good-all-a2m or 2cfvA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hnp/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2hnp expands to /projects/compbio/data/pdb/2hnp.pdb.gz 2hnp:Warning: there is no chain 2hnp will retry with 2hnpA # T0317 read from 2hnp/merged-good-all-a2m # 2hnp read from 2hnp/merged-good-all-a2m # adding 2hnp to template set # found chain 2hnp in template set Warning: unaligning (T0317)I154 because last residue in template chain is (2hnp)M282 T0317 18 :LFIGNARAAGA 2hnp 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 2hnp 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGP 2hnp 126 :PQKEEK T0317 54 :GVAELRVP 2hnp 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEA 2hnp 181 :DFGVPESPASFLNFLFKVRE T0317 87 :DG 2hnp 206 :PE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 2hnp 209 :GPVVVHCSAGIGRSGTFCLAD T0317 110 :LM 2hnp 234 :LM T0317 114 :RGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQA 2hnp 242 :SSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFI Number of specific fragments extracted= 9 number of extra gaps= 0 total=614 Number of alignments=82 # 2hnp read from 2hnp/merged-good-all-a2m # found chain 2hnp in template set Warning: unaligning (T0317)I154 because last residue in template chain is (2hnp)M282 T0317 18 :LFIGNARAAGA 2hnp 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 2hnp 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGP 2hnp 126 :PQKEEK T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAV 2hnp 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRESG T0317 87 :DG 2hnp 206 :PE T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2hnp 209 :GPVVVHCSAGIGRSGTFCLADTCLL T0317 114 :RG 2hnp 241 :PS T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQA 2hnp 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFI Number of specific fragments extracted= 8 number of extra gaps= 0 total=622 Number of alignments=83 # 2hnp read from 2hnp/merged-good-all-a2m # found chain 2hnp in template set Warning: unaligning (T0317)Q150 because last residue in template chain is (2hnp)M282 T0317 18 :LFIGNARAAGA 2hnp 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 2hnp 96 :WEMVWEQKSRGVVMLNR T0317 46 :QQPGPR 2hnp 123 :QYWPQK T0317 54 :GVAELRVPVFDDPAEDLL 2hnp 171 :ILHFHYTTWPDFGVPESP T0317 75 :EPTCAAMEAAVRDG 2hnp 189 :ASFLNFLFKVRESG T0317 89 :GSCLVYCKNGRSRSAAVCTA 2hnp 209 :GPVVVHCSAGIGRSGTFCLA T0317 109 :YLMRHRG 2hnp 233 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQ 2hnp 244 :VDIKKVLLEMRKFRMGLIQTADQLRF T0317 142 :LQKYEQTL 2hnp 274 :VIEGAKFI Number of specific fragments extracted= 9 number of extra gaps= 0 total=631 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bv5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bv5A expands to /projects/compbio/data/pdb/2bv5.pdb.gz 2bv5A:Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 110, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 114, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 192, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 603, because occupancy 0.350 <= existing 0.650 in 2bv5A Skipped atom 604, because occupancy 0.350 <= existing 0.650 in 2bv5A Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1243, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1247, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 2bv5A Bad short name: OCD for alphabet: pdb_atoms Bad short name: OCD for alphabet: pdb_atoms Skipped atom 1796, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1797, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1798, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1799, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2041, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2042, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2043, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2045, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2046, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2140, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2141, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2142, because occupancy 0.500 <= existing 0.500 in 2bv5A # T0317 read from 2bv5A/merged-good-all-a2m # 2bv5A read from 2bv5A/merged-good-all-a2m # adding 2bv5A to template set # found chain 2bv5A in template set Warning: unaligning (T0317)F19 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I346 Warning: unaligning (T0317)I20 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I346 Warning: unaligning (T0317)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bv5A)S473 Warning: unaligning (T0317)K96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bv5A)S473 Warning: unaligning (T0317)A132 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I515 Warning: unaligning (T0317)E133 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I515 T0317 11 :FARVAPAL 2bv5A 337 :GYGGEEKV T0317 21 :GNARA 2bv5A 350 :GPIVS T0317 26 :AGATEL 2bv5A 356 :VADFWR T0317 32 :LVRAGITLCVNVS 2bv5A 363 :VWQEHTPIIVMIT T0317 49 :GPR 2bv5A 386 :EYW T0317 54 :GVAELRVP 2bv5A 426 :GLKHYWFT T0317 62 :VFDDPAEDLLTHLEPTCAAMEAAVRDG 2bv5A 435 :WPDQKTPDRAPPLLHLVREVEEAAQQE T0317 89 :GSCLV 2bv5A 466 :APIIV T0317 97 :NGRSRSAAVCTAY 2bv5A 474 :AGIGRTGCFIATS T0317 110 :LMRHRGH 2bv5A 491 :QLRQEGV T0317 117 :SLDRAFQMVKSARPV 2bv5A 499 :DILKTTCQLRQDRGG T0317 134 :PNLGFWAQLQKYEQTLQAQ 2bv5A 516 :QTCEQYQFVHHVMSLYEKQ Number of specific fragments extracted= 12 number of extra gaps= 2 total=643 Number of alignments=85 # 2bv5A read from 2bv5A/merged-good-all-a2m # found chain 2bv5A in template set Warning: unaligning (T0317)F19 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I346 Warning: unaligning (T0317)I20 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I346 Warning: unaligning (T0317)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bv5A)S473 Warning: unaligning (T0317)K96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bv5A)S473 Warning: unaligning (T0317)A132 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I515 Warning: unaligning (T0317)E133 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I515 T0317 11 :FARVAPAL 2bv5A 337 :GYGGEEKV T0317 21 :GNARAAGA 2bv5A 350 :GPIVSTVA T0317 29 :TELLVRAGITLCVNVS 2bv5A 360 :WRMVWQEHTPIIVMIT T0317 45 :RQQPGPR 2bv5A 385 :TEYWPEE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDG 2bv5A 425 :RGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQQE T0317 89 :GSCLV 2bv5A 466 :APIIV T0317 97 :NGRSRSAAVCTAYLMRH 2bv5A 474 :AGIGRTGCFIATSICCQ T0317 114 :RG 2bv5A 495 :EG T0317 116 :HSLDRAFQMVKSARPV 2bv5A 498 :VDILKTTCQLRQDRGG T0317 134 :PNLGFWAQLQKYEQTLQAQ 2bv5A 516 :QTCEQYQFVHHVMSLYEKQ Number of specific fragments extracted= 10 number of extra gaps= 2 total=653 Number of alignments=86 # 2bv5A read from 2bv5A/merged-good-all-a2m # found chain 2bv5A in template set Warning: unaligning (T0317)F19 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I346 Warning: unaligning (T0317)R51 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bv5A)K383 Warning: unaligning (T0317)A52 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bv5A)K383 Warning: unaligning (T0317)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bv5A)S473 Warning: unaligning (T0317)K96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bv5A)S473 Warning: unaligning (T0317)A132 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I515 Warning: unaligning (T0317)E133 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I515 T0317 20 :I 2bv5A 347 :A T0317 21 :GNARAAGA 2bv5A 350 :GPIVSTVA T0317 29 :TELLVRAGITLCVNVSRQQPGP 2bv5A 360 :WRMVWQEHTPIIVMITNIEEMN T0317 53 :P 2bv5A 384 :C T0317 54 :GVAELRVP 2bv5A 426 :GLKHYWFT T0317 62 :VFDDPAEDLLTHLEPTCAAMEAAVRDGGS 2bv5A 435 :WPDQKTPDRAPPLLHLVREVEEAAQQEGP T0317 91 :CLV 2bv5A 468 :IIV T0317 97 :NGRSRSAAVCTAYL 2bv5A 474 :AGIGRTGCFIATSI T0317 111 :MRHRG 2bv5A 492 :LRQEG T0317 116 :HSLDRAFQMVKSARPV 2bv5A 498 :VDILKTTCQLRQDRGG T0317 134 :PNLGFWAQLQK 2bv5A 516 :QTCEQYQFVHH Number of specific fragments extracted= 11 number of extra gaps= 3 total=664 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yn9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0317 read from 1yn9A/merged-good-all-a2m # 1yn9A read from 1yn9A/merged-good-all-a2m # found chain 1yn9A in training set T0317 4 :SEAAPPPFARVA 1yn9A 26 :TPLRPELFAYVT T0317 22 :NARAAGATELLVR 1yn9A 38 :SEEDVWTAEQIVK T0317 35 :AGITLCVNVSRQQPGPRAP 1yn9A 53 :PSIGAIIDLTNTSKYYDGV T0317 54 :GVAELRVPVFDDPAEDLLT 1yn9A 77 :GLLYKKIQVPGQTLPPESI T0317 74 :LEPTCAAMEAAVR 1yn9A 96 :VQEFIDTVKEFTE T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQ 1yn9A 111 :PGMLVGVHCTHGINRTGYMVCRYLMHTLGIAPQEAIDRFEKARGHKIERQNYVQDLL Number of specific fragments extracted= 6 number of extra gaps= 0 total=670 Number of alignments=88 # 1yn9A read from 1yn9A/merged-good-all-a2m # found chain 1yn9A in training set T0317 14 :VAPALF 1yn9A 28 :LRPELF T0317 20 :IGNARAAGATELLVR 1yn9A 36 :VTSEEDVWTAEQIVK T0317 35 :AGITLCVNVSRQQPGPR 1yn9A 53 :PSIGAIIDLTNTSKYYD T0317 52 :APGVAELRVPVFDDPAEDL 1yn9A 75 :RAGLLYKKIQVPGQTLPPE T0317 72 :THLEPTCAAMEAAVR 1yn9A 94 :SIVQEFIDTVKEFTE T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQ 1yn9A 111 :PGMLVGVHCTHGINRTGYMVCRYLMHTLGIAPQEAIDRFEKARGHKIERQNYVQDLL Number of specific fragments extracted= 6 number of extra gaps= 0 total=676 Number of alignments=89 # 1yn9A read from 1yn9A/merged-good-all-a2m # found chain 1yn9A in training set T0317 22 :NARAAGATELLVRA 1yn9A 38 :SEEDVWTAEQIVKQ T0317 36 :GITLCVNVSRQQPGPRAP 1yn9A 54 :SIGAIIDLTNTSKYYDGV T0317 54 :GVAELRVPVFDDPAED 1yn9A 77 :GLLYKKIQVPGQTLPP T0317 71 :LTHLEPTCAAMEAAVR 1yn9A 93 :ESIVQEFIDTVKEFTE T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQ 1yn9A 111 :PGMLVGVHCTHGINRTGYMVCRYLMHTLGIAPQEAIDRFEKARGHKIERQNYVQDLL Number of specific fragments extracted= 5 number of extra gaps= 0 total=681 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oheA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1oheA expands to /projects/compbio/data/pdb/1ohe.pdb.gz 1oheA:# T0317 read from 1oheA/merged-good-all-a2m # 1oheA read from 1oheA/merged-good-all-a2m # adding 1oheA to template set # found chain 1oheA in template set T0317 6 :AAPPPFARVAPA 1oheA 228 :CGPHSRARLESG T0317 20 :IGNARAAGATELLVRAGITLCVNVSRQQPGPR 1oheA 240 :YHQHSPETYIQYFKNHNVTTIIRLNKRMYDAK T0317 52 :APGVAELRVPVFDDPAEDLLT 1oheA 275 :DAGFDHHDLFFADGSTPTDAI T0317 74 :LEPTCAAME 1oheA 296 :VKEFLDICE T0317 88 :GGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAE 1oheA 307 :EGAIAVHSKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPGSV T0317 135 :NLGFWAQLQKYEQTLQAQA 1oheA 353 :IGPQQQFLVMKQTNLWLEG Number of specific fragments extracted= 6 number of extra gaps= 0 total=687 Number of alignments=91 # 1oheA read from 1oheA/merged-good-all-a2m # found chain 1oheA in template set Warning: unaligning (T0317)L155 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1oheA)G380 Warning: unaligning (T0317)P156 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1oheA)G380 T0317 6 :AAPPPFARVAPALFIGNA 1oheA 228 :CGPHSRARLESGYHQHSP T0317 26 :AGATELLVRAGITLCVNVSRQQPGPR 1oheA 246 :ETYIQYFKNHNVTTIIRLNKRMYDAK T0317 52 :APGVAELRVPVFDDPAEDL 1oheA 275 :DAGFDHHDLFFADGSTPTD T0317 72 :THLEPTCAAME 1oheA 294 :AIVKEFLDICE T0317 88 :GGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNL 1oheA 307 :EGAIAVHSKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPGSVIGP T0317 138 :FWAQLQKYEQTLQ 1oheA 356 :QQQFLVMKQTNLW T0317 151 :AQAI 1oheA 375 :RQKL Number of specific fragments extracted= 7 number of extra gaps= 1 total=694 Number of alignments=92 # 1oheA read from 1oheA/merged-good-all-a2m # found chain 1oheA in template set T0317 29 :TELLVRAGITLCVNVSRQQPGP 1oheA 249 :IQYFKNHNVTTIIRLNKRMYDA T0317 54 :GVAELRVPVFD 1oheA 277 :GFDHHDLFFAD T0317 66 :PAEDLLTHLEPTCAAME 1oheA 288 :GSTPTDAIVKEFLDICE T0317 88 :GGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNL 1oheA 307 :EGAIAVHSKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPGSVIGP T0317 138 :FWAQLQKYEQTLQAQA 1oheA 356 :QQQFLVMKQTNLWLEG Number of specific fragments extracted= 5 number of extra gaps= 0 total=699 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fh7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fh7A expands to /projects/compbio/data/pdb/2fh7.pdb.gz 2fh7A:Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 137, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 425, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 429, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1366, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1368, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1370, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1372, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1374, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1794, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1796, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1798, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1800, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1802, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1804, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1806, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1808, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1937, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1941, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1943, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1945, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1947, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1949, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2385, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2387, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2389, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2391, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2393, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2395, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2397, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3718, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3720, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3722, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3724, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3726, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3728, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3730, because occupancy 0.500 <= existing 0.500 in 2fh7A # T0317 read from 2fh7A/merged-good-all-a2m # 2fh7A read from 2fh7A/merged-good-all-a2m # adding 2fh7A to template set # found chain 2fh7A in template set Warning: unaligning (T0317)S44 because of BadResidue code BAD_PEPTIDE in next template residue (2fh7A)K1781 Warning: unaligning (T0317)Q152 because last residue in template chain is (2fh7A)S1942 T0317 18 :LFIGNARA 2fh7A 1752 :ATQGPLAE T0317 26 :AGA 2fh7A 1761 :TED T0317 29 :TELLVRAGITLCVNV 2fh7A 1765 :WRMLWENNSTIVVML T0317 47 :QPGP 2fh7A 1795 :PAER T0317 54 :GVAELRVP 2fh7A 1838 :QFQFTDWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 2fh7A 1846 :EQGVPKSGEGFIDFIGQVHKTKE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 2fh7A 1874 :GPISVHCSAGVGRTGVFITLS T0317 110 :LMRHRG 2fh7A 1899 :RMRYEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2fh7A 1906 :VDIFQTVKMLRTQRPAMVQTEDEYQFCYQAALEYLG Number of specific fragments extracted= 9 number of extra gaps= 1 total=708 Number of alignments=94 # 2fh7A read from 2fh7A/merged-good-all-a2m # found chain 2fh7A in template set Warning: unaligning (T0317)S44 because of BadResidue code BAD_PEPTIDE in next template residue (2fh7A)K1781 Warning: unaligning (T0317)D87 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2fh7A)F1870 Warning: unaligning (T0317)Q152 because last residue in template chain is (2fh7A)S1942 T0317 18 :LFIGNARAAGA 2fh7A 1752 :ATQGPLAETTE T0317 29 :TELLVRAGITLCVNV 2fh7A 1765 :WRMLWENNSTIVVML T0317 47 :QPGPR 2fh7A 1794 :WPAER T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 2fh7A 1834 :RTVRQFQFTDWPEQGVPKSGEGFIDFIGQVHKTKE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 2fh7A 1874 :GPISVHCSAGVGRTGVFITLS T0317 110 :LMRHRG 2fh7A 1899 :RMRYEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2fh7A 1906 :VDIFQTVKMLRTQRPAMVQTEDEYQFCYQAALEYLG Number of specific fragments extracted= 7 number of extra gaps= 2 total=715 Number of alignments=95 # 2fh7A read from 2fh7A/merged-good-all-a2m # found chain 2fh7A in template set Warning: unaligning (T0317)S44 because of BadResidue code BAD_PEPTIDE in next template residue (2fh7A)K1781 Warning: unaligning (T0317)R45 because of BadResidue code BAD_PEPTIDE at template residue (2fh7A)K1781 Warning: unaligning (T0317)D87 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2fh7A)F1870 Warning: unaligning (T0317)Q152 because last residue in template chain is (2fh7A)S1942 T0317 4 :SEAAPPPFARVAPA 2fh7A 1731 :EGSDYINASFIDGY T0317 18 :LFIGNARAAGA 2fh7A 1751 :IATQGPLAETT T0317 29 :TELLVRAGITLCVNV 2fh7A 1765 :WRMLWENNSTIVVML T0317 46 :QQPGPRAP 2fh7A 1791 :HQYWPAER T0317 54 :GVAELRV 2fh7A 1830 :DGQSRTV T0317 61 :PVFDDPAEDLLTHLEPTCAAMEAAVR 2fh7A 1843 :DWPEQGVPKSGEGFIDFIGQVHKTKE T0317 88 :GGSCLVYCKNGRSRSAAVCTA 2fh7A 1873 :DGPISVHCSAGVGRTGVFITL T0317 109 :YLMRHRG 2fh7A 1898 :ERMRYEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2fh7A 1906 :VDIFQTVKMLRTQRPAMVQTEDEYQFCYQAALEYLG Number of specific fragments extracted= 9 number of extra gaps= 2 total=724 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jlnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jlnA expands to /projects/compbio/data/pdb/1jln.pdb.gz 1jlnA:# T0317 read from 1jlnA/merged-good-all-a2m # 1jlnA read from 1jlnA/merged-good-all-a2m # adding 1jlnA to template set # found chain 1jlnA in template set Warning: unaligning (T0317)E158 because last residue in template chain is (1jlnA)V548 T0317 11 :FARVAPA 1jlnA 346 :GYSGKEK T0317 18 :LFIGNARAAGA 1jlnA 356 :ATQGPMINTVN T0317 29 :TELLVRAGITLCVNVS 1jlnA 369 :WQMVWQEDSPVIVMIT T0317 45 :RQQPGPRAP 1jlnA 387 :KEKNEKCVL T0317 54 :GVAELRVP 1jlnA 438 :HYWYTSWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 1jlnA 446 :DHKTPDSAQPLLQLMLDVEEDRL T0317 87 :DG 1jlnA 471 :EG T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1jlnA 474 :GPVVVHCSAGIGRTGCFIATS T0317 110 :LMRHRG 1jlnA 499 :QLKEEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPR 1jlnA 506 :VDALSIVCQLRVDRGGMVQTSEQYEFVHHALCLFESRLSPET Number of specific fragments extracted= 10 number of extra gaps= 0 total=734 Number of alignments=97 # 1jlnA read from 1jlnA/merged-good-all-a2m # found chain 1jlnA in template set Warning: unaligning (T0317)E158 because last residue in template chain is (1jlnA)V548 T0317 10 :PFARVAPA 1jlnA 346 :GYSGKEKA T0317 18 :LFIGNARAAGA 1jlnA 356 :ATQGPMINTVN T0317 29 :TELLVRAGITLCVNVS 1jlnA 369 :WQMVWQEDSPVIVMIT T0317 45 :RQQPGPR 1jlnA 386 :LKEKNEK T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1jlnA 434 :QHVKHYWYTSWPDHKTPDSAQPLLQLMLDVEEDRL T0317 87 :DG 1jlnA 471 :EG T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1jlnA 474 :GPVVVHCSAGIGRTGCFIATS T0317 110 :LMRHRG 1jlnA 499 :QLKEEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPR 1jlnA 506 :VDALSIVCQLRVDRGGMVQTSEQYEFVHHALCLFESRLSPET Number of specific fragments extracted= 9 number of extra gaps= 0 total=743 Number of alignments=98 # 1jlnA read from 1jlnA/merged-good-all-a2m # found chain 1jlnA in template set Warning: unaligning (T0317)E158 because last residue in template chain is (1jlnA)V548 T0317 18 :LFIGNARAAGA 1jlnA 356 :ATQGPMINTVN T0317 29 :TELLVRAGITLCVNVSRQQPGPRAP 1jlnA 369 :WQMVWQEDSPVIVMITKLKEKNEKC T0317 54 :GVAELRV 1jlnA 435 :HVKHYWY T0317 61 :PVFDDPAEDLLTHLEPTCAAMEAAVRD 1jlnA 443 :SWPDHKTPDSAQPLLQLMLDVEEDRLA T0317 88 :G 1jlnA 472 :G T0317 89 :GSCLVYCKNGRSRSAAVCTAYL 1jlnA 474 :GPVVVHCSAGIGRTGCFIATSI T0317 111 :MRHRG 1jlnA 500 :LKEEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPR 1jlnA 506 :VDALSIVCQLRVDRGGMVQTSEQYEFVHHALCLFESRLSPET Number of specific fragments extracted= 8 number of extra gaps= 0 total=751 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c7sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0317/2c7sA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0317/2c7sA/merged-good-all-a2m.gz for input Trying 2c7sA/merged-good-all-a2m Error: Couldn't open file 2c7sA/merged-good-all-a2m or 2c7sA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eeoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1eeoA expands to /projects/compbio/data/pdb/1eeo.pdb.gz 1eeoA:# T0317 read from 1eeoA/merged-good-all-a2m # 1eeoA read from 1eeoA/merged-good-all-a2m # adding 1eeoA to template set # found chain 1eeoA in template set T0317 18 :LFIGNARAAGA 1eeoA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1eeoA 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPG 1eeoA 126 :PQKEE T0317 54 :GVAELRVP 1eeoA 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEAA 1eeoA 181 :DFGVPESPASFLNFLFKVRES T0317 85 :VRDG 1eeoA 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1eeoA 209 :GPVVVHSSAGIGRSGTFCLAD T0317 110 :LMRHRG 1eeoA 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPR 1eeoA 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDS Number of specific fragments extracted= 9 number of extra gaps= 0 total=760 Number of alignments=100 # 1eeoA read from 1eeoA/merged-good-all-a2m # found chain 1eeoA in template set T0317 18 :LFIGNARAAGA 1eeoA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1eeoA 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGP 1eeoA 126 :PQKEEK T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEA 1eeoA 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRE T0317 85 :VRDG 1eeoA 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1eeoA 209 :GPVVVHSSAGIGRSGTFCLAD T0317 110 :LMRHRG 1eeoA 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQA 1eeoA 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFI Number of specific fragments extracted= 8 number of extra gaps= 0 total=768 Number of alignments=101 # 1eeoA read from 1eeoA/merged-good-all-a2m # found chain 1eeoA in template set T0317 18 :LFIGNARAAGA 1eeoA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 1eeoA 96 :WEMVWEQKSRGVVMLNR T0317 54 :GVAELRVP 1eeoA 170 :EILHFHYT T0317 62 :VFDDPAEDLL 1eeoA 179 :WPDFGVPESP T0317 75 :EPTCAAMEAAVRDG 1eeoA 189 :ASFLNFLFKVRESG T0317 89 :GSCLVYCKNGRSRSAAVCTA 1eeoA 209 :GPVVVHSSAGIGRSGTFCLA T0317 109 :YLMRHRG 1eeoA 233 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKY 1eeoA 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLA Number of specific fragments extracted= 8 number of extra gaps= 0 total=776 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lyvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0317 read from 1lyvA/merged-good-all-a2m # 1lyvA read from 1lyvA/merged-good-all-a2m # found chain 1lyvA in training set T0317 26 :AGATELLVRAGITLCVNVS 1lyvA 268 :ESHFRMLAENRTPVLAVLA T0317 45 :RQQPGPRAP 1lyvA 296 :FGMPDYFRQ T0317 54 :GVAELRV 1lyvA 345 :SVPVVHV T0317 62 :VFDDPAEDL 1lyvA 354 :WPDQTAVSS T0317 72 :THLEPTCAAMEAA 1lyvA 363 :EVTKALASLVDQT T0317 86 :RDGGSCLVYCKNGRSRSAAVCTAYLM 1lyvA 394 :DSKLRPVIHSRAGVGRTAQLIGAMCM T0317 114 :RGHSLDRAFQMVKSAR 1lyvA 425 :SQLSVEDMVSQMRVQR T0317 130 :PVAEPNLGFWAQLQKYEQT 1lyvA 442 :GIMVQKDEQLDVLIKLAEG Number of specific fragments extracted= 8 number of extra gaps= 0 total=784 Number of alignments=103 # 1lyvA read from 1lyvA/merged-good-all-a2m # found chain 1lyvA in training set T0317 21 :GNARAAG 1lyvA 261 :YPLQSQL T0317 28 :ATELLVRAGITLCVNVS 1lyvA 270 :HFRMLAENRTPVLAVLA T0317 45 :RQQPGP 1lyvA 299 :PDYFRQ T0317 52 :APGV 1lyvA 342 :KTIS T0317 56 :AELRVPVFDDPAEDL 1lyvA 348 :VVHVGNWPDQTAVSS T0317 72 :THLEPTCAAMEAAV 1lyvA 363 :EVTKALASLVDQTA T0317 86 :RDGGSCLVYCKNGRSRSAAVCTAYLMRH 1lyvA 394 :DSKLRPVIHSRAGVGRTAQLIGAMCMND T0317 114 :RGHSLDRAFQMVKSARPV 1lyvA 425 :SQLSVEDMVSQMRVQRNG T0317 132 :AEPNLGFWAQLQKYEQTL 1lyvA 444 :MVQKDEQLDVLIKLAEGQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=793 Number of alignments=104 # 1lyvA read from 1lyvA/merged-good-all-a2m # found chain 1lyvA in training set T0317 21 :GNARAAGA 1lyvA 261 :YPLQSQLE T0317 29 :TELLVRAGITLCVNVSR 1lyvA 271 :FRMLAENRTPVLAVLAS T0317 46 :QQPGPRAP 1lyvA 297 :GMPDYFRQ T0317 54 :GVAELRVP 1lyvA 340 :GQKTISVP T0317 62 :VFD 1lyvA 354 :WPD T0317 66 :PAEDLLTHLEPTCAAMEAAVR 1lyvA 357 :QTAVSSEVTKALASLVDQTAE T0317 87 :DG 1lyvA 386 :KG T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMR 1lyvA 397 :LRPVIHSRAGVGRTAQLIGAMCMN T0317 114 :RGHSLDRAFQMVKSAR 1lyvA 425 :SQLSVEDMVSQMRVQR T0317 130 :PVAEPNLGFWAQLQKYEQT 1lyvA 442 :GIMVQKDEQLDVLIKLAEG Number of specific fragments extracted= 10 number of extra gaps= 0 total=803 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gwz/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0317/1gwz/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0317/1gwz/merged-good-all-a2m.gz for input Trying 1gwz/merged-good-all-a2m Error: Couldn't open file 1gwz/merged-good-all-a2m or 1gwz/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b49A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b49A expands to /projects/compbio/data/pdb/2b49.pdb.gz 2b49A:Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1158, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1162, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1213, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1217, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1275, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1416, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1420, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1422, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1425, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1429, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1431, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1492, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1494, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1496, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1498, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1562, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1564, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1566, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1568, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1570, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1572, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1574, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1580, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1582, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1584, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1586, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1588, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1614, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1618, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1739, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1975, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1979, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1981, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1983, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1985, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2011, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2015, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2017, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2020, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2024, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2026, because occupancy 0.500 <= existing 0.500 in 2b49A # T0317 read from 2b49A/merged-good-all-a2m # 2b49A read from 2b49A/merged-good-all-a2m # adding 2b49A to template set # found chain 2b49A in template set Warning: unaligning (T0317)Q152 because last residue in template chain is (2b49A)E904 T0317 18 :LFIGNARA 2b49A 716 :ATQGPLPH T0317 26 :AGATELLVRAGITLCVNVS 2b49A 726 :AQFWQVVWDQKLSLIVMLT T0317 49 :GPR 2b49A 758 :WPD T0317 54 :GVAELRVP 2b49A 803 :HLQYVAWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAY 2b49A 811 :DHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHCSAGIGRTGVLVTME T0317 110 :LMRHRGHS 2b49A 860 :CLTERNLP T0317 118 :LDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2b49A 870 :PLDIVRKMRDQRAMMVQTSSQYKFVCEAILRVYE Number of specific fragments extracted= 7 number of extra gaps= 0 total=810 Number of alignments=106 # 2b49A read from 2b49A/merged-good-all-a2m # found chain 2b49A in template set Warning: unaligning (T0317)Q152 because last residue in template chain is (2b49A)E904 T0317 18 :LFIGNARAAGA 2b49A 716 :ATQGPLPHTCA T0317 29 :TELLVRAGITLCVNVS 2b49A 729 :WQVVWDQKLSLIVMLT T0317 45 :RQQPGPR 2b49A 756 :QYWPDPP T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRH 2b49A 799 :HTVTHLQYVAWPDHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHCSAGIGRTGVLVTMETAMC T0317 114 :RG 2b49A 864 :RN T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2b49A 868 :IYPLDIVRKMRDQRAMMVQTSSQYKFVCEAILRVYE Number of specific fragments extracted= 6 number of extra gaps= 0 total=816 Number of alignments=107 # 2b49A read from 2b49A/merged-good-all-a2m # found chain 2b49A in template set Warning: unaligning (T0317)Q152 because last residue in template chain is (2b49A)E904 T0317 18 :LFIGNARAAGA 2b49A 716 :ATQGPLPHTCA T0317 29 :TELLVRAGITLCVNVSR 2b49A 729 :WQVVWDQKLSLIVMLTT T0317 46 :QQPGPRAP 2b49A 755 :HQYWPDPP T0317 54 :GVAEL 2b49A 800 :TVTHL T0317 59 :RVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCT 2b49A 806 :YVAWPDHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHCSAGIGRTGVLVT T0317 108 :AYLMRHRG 2b49A 858 :AMCLTERN T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2b49A 868 :IYPLDIVRKMRDQRAMMVQTSSQYKFVCEAILRVYE Number of specific fragments extracted= 7 number of extra gaps= 0 total=823 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m3gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0317/1m3gA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0317/1m3gA/merged-good-all-a2m.gz for input Trying 1m3gA/merged-good-all-a2m Error: Couldn't open file 1m3gA/merged-good-all-a2m or 1m3gA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zclA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zclA expands to /projects/compbio/data/pdb/1zcl.pdb.gz 1zclA:# T0317 read from 1zclA/merged-good-all-a2m # 1zclA read from 1zclA/merged-good-all-a2m # adding 1zclA to template set # found chain 1zclA in template set T0317 16 :PALFIGNARA 1zclA 18 :RFLITHNPTN T0317 26 :AGATELLVRAGITLCVNVSRQQPGPR 1zclA 31 :NKFIEELKKYGVTTIVRVCEATYDTT T0317 52 :APGVAELRVPVFD 1zclA 60 :KEGIHVLDWPFDD T0317 66 :PAEDLLTHLEPTCAAMEAAVR 1zclA 73 :GAPPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLM 1zclA 96 :PGCCIAVHSVAGLGRAPVLVALALI T0317 113 :HRGHSLDRAFQMVKSARPVAE 1zclA 121 :EGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1zclA 142 :NSKQLLYLEK Number of specific fragments extracted= 7 number of extra gaps= 0 total=830 Number of alignments=109 # 1zclA read from 1zclA/merged-good-all-a2m # found chain 1zclA in template set T0317 15 :APALFIGNARAAG 1zclA 17 :MRFLITHNPTNAT T0317 29 :TELLVRAGITLCVNVSRQQPGPR 1zclA 34 :IEELKKYGVTTIVRVCEATYDTT T0317 52 :APGVAELRVPVFDDPAEDL 1zclA 60 :KEGIHVLDWPFDDGAPPSN T0317 72 :THLEPTCAAMEAAVR 1zclA 79 :QIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLM 1zclA 96 :PGCCIAVHSVAGLGRAPVLVALALI T0317 113 :HRGHSLDRAFQMVKSARPVAE 1zclA 121 :EGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQKY 1zclA 142 :NSKQLLYLEKY T0317 155 :LPREP 1zclA 153 :RPKMR Number of specific fragments extracted= 8 number of extra gaps= 0 total=838 Number of alignments=110 # 1zclA read from 1zclA/merged-good-all-a2m # found chain 1zclA in template set Warning: unaligning (T0317)F11 because first residue in template chain is (1zclA)P9 T0317 12 :ARVA 1zclA 10 :VEVT T0317 16 :PALFIGNARAAGA 1zclA 18 :RFLITHNPTNATL T0317 29 :TELLVRAGITLCVNVSRQQPGP 1zclA 34 :IEELKKYGVTTIVRVCEATYDT T0317 54 :GVAELRVPVFD 1zclA 62 :GIHVLDWPFDD T0317 66 :PAEDLLTHLEPTCAAMEAAVR 1zclA 73 :GAPPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMR 1zclA 96 :PGCCIAVHSVAGLGRAPVLVALALIE T0317 114 :RGHSLDRAFQMVKSARPVA 1zclA 122 :GGMKYEDAVQFIRQKRRGA T0317 134 :PNLGFWAQLQK 1zclA 141 :FNSKQLLYLEK Number of specific fragments extracted= 8 number of extra gaps= 0 total=846 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a5y/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a5y expands to /projects/compbio/data/pdb/1a5y.pdb.gz 1a5y:Warning: there is no chain 1a5y will retry with 1a5yA Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0317 read from 1a5y/merged-good-all-a2m # 1a5y read from 1a5y/merged-good-all-a2m # adding 1a5y to template set # found chain 1a5y in template set Warning: unaligning (T0317)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a5y)S216 Warning: unaligning (T0317)K96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a5y)S216 Warning: unaligning (T0317)R157 because last residue in template chain is (1a5y)S285 T0317 18 :LFIGNARAAGA 1a5y 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1a5y 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGP 1a5y 126 :PQKEEK T0317 54 :GVAELRVP 1a5y 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEA 1a5y 181 :DFGVPESPASFLNFLFKVRE T0317 87 :DG 1a5y 206 :PE T0317 89 :GSCLV 1a5y 209 :GPVVV T0317 97 :NGRSRSAAVCTAY 1a5y 217 :AGIGRSGTFCLAD T0317 110 :LMRHRG 1a5y 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILP 1a5y 244 :VDIKKVLLDMRKFRMGLIATAEQLRFSYLAVIEGAKFIMGD Number of specific fragments extracted= 10 number of extra gaps= 0 total=856 Number of alignments=112 # 1a5y read from 1a5y/merged-good-all-a2m # found chain 1a5y in template set Warning: unaligning (T0317)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a5y)S216 Warning: unaligning (T0317)K96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a5y)S216 Warning: unaligning (T0317)R157 because last residue in template chain is (1a5y)S285 T0317 18 :LFIGNARAAGA 1a5y 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1a5y 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1a5y 126 :PQKEEKE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEA 1a5y 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRE T0317 85 :VRDG 1a5y 204 :LSPE T0317 89 :GSCLV 1a5y 209 :GPVVV T0317 97 :NGRSRSAAVCTAY 1a5y 217 :AGIGRSGTFCLAD T0317 110 :LMRHRG 1a5y 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILP 1a5y 244 :VDIKKVLLDMRKFRMGLIATAEQLRFSYLAVIEGAKFIMGD Number of specific fragments extracted= 9 number of extra gaps= 0 total=865 Number of alignments=113 # 1a5y read from 1a5y/merged-good-all-a2m # found chain 1a5y in template set Warning: unaligning (T0317)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a5y)S216 Warning: unaligning (T0317)K96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a5y)S216 Warning: unaligning (T0317)A153 because last residue in template chain is (1a5y)S285 T0317 18 :LFIGNARAAGA 1a5y 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 1a5y 96 :WEMVWEQKSRGVVMLNR T0317 47 :QPGPR 1a5y 123 :QYWPQ T0317 54 :GVAELRVPVFDDPAEDLL 1a5y 171 :ILHFHYTTWPDFGVPESP T0317 75 :EPTCAAMEAAVRDG 1a5y 189 :ASFLNFLFKVRESG T0317 89 :GSCLV 1a5y 209 :GPVVV T0317 97 :NGRSRSAAVCTA 1a5y 217 :AGIGRSGTFCLA T0317 109 :YLMRHRG 1a5y 233 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQ 1a5y 244 :VDIKKVLLDMRKFRMGLIATAEQLRF T0317 142 :LQKYEQTLQAQ 1a5y 274 :VIEGAKFIMGD Number of specific fragments extracted= 10 number of extra gaps= 0 total=875 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ptvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ptvA expands to /projects/compbio/data/pdb/1ptv.pdb.gz 1ptvA:# T0317 read from 1ptvA/merged-good-all-a2m # 1ptvA read from 1ptvA/merged-good-all-a2m # adding 1ptvA to template set # found chain 1ptvA in template set T0317 18 :LFIGNARAAGA 1ptvA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1ptvA 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPRAP 1ptvA 126 :PQKEEKEMI T0317 54 :GVAELRVP 1ptvA 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEAA 1ptvA 181 :DFGVPESPASFLNFLFKVRES T0317 85 :VRDG 1ptvA 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1ptvA 209 :GPVVVHSSAGIGRSGTFCLAD T0317 110 :LMRHRG 1ptvA 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 1ptvA 244 :VDIKKVLLDMRKFRMGLIQTADQLRFSYLAVIEGAKF Number of specific fragments extracted= 9 number of extra gaps= 0 total=884 Number of alignments=115 # 1ptvA read from 1ptvA/merged-good-all-a2m # found chain 1ptvA in template set T0317 18 :LFIGNARAAGA 1ptvA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1ptvA 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1ptvA 126 :PQKEEKE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEA 1ptvA 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRE T0317 84 :AVRDG 1ptvA 203 :SLSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1ptvA 209 :GPVVVHSSAGIGRSGTFCLAD T0317 110 :LMRHRG 1ptvA 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQ 1ptvA 244 :VDIKKVLLDMRKFRMGLIQTADQLRFSYLAVIEGA Number of specific fragments extracted= 8 number of extra gaps= 0 total=892 Number of alignments=116 # 1ptvA read from 1ptvA/merged-good-all-a2m # found chain 1ptvA in template set T0317 18 :LFIGNARAAGA 1ptvA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 1ptvA 96 :WEMVWEQKSRGVVMLNR T0317 54 :GVAELRVP 1ptvA 170 :EILHFHYT T0317 62 :VFDDPAED 1ptvA 179 :WPDFGVPE T0317 73 :HLEPTCAAMEAAVRDG 1ptvA 187 :SPASFLNFLFKVRESG T0317 89 :GSCLVYCKNGRSRSAAVCTA 1ptvA 209 :GPVVVHSSAGIGRSGTFCLA T0317 109 :YLMRHRG 1ptvA 233 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQK 1ptvA 244 :VDIKKVLLDMRKFRMGLIQTADQLRFSYL Number of specific fragments extracted= 8 number of extra gaps= 0 total=900 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vhrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vhrA expands to /projects/compbio/data/pdb/1vhr.pdb.gz 1vhrA:# T0317 read from 1vhrA/merged-good-all-a2m # 1vhrA read from 1vhrA/merged-good-all-a2m # adding 1vhrA to template set # found chain 1vhrA in template set Warning: unaligning (T0317)R157 because last residue in template chain is (1vhrA)P185 T0317 2 :GTSEAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPRAP 1vhrA 21 :GCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMHVN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1vhrA 82 :GITYLGIKANDTQEFNLSAYFERAADFIDQALA T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSAR 1vhrA 116 :KNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNR T0317 131 :VAEPNLGFWAQLQKYEQTLQAQAILP 1vhrA 159 :EIGPNDGFLAQLCQLNDRLAKEGKLK Number of specific fragments extracted= 4 number of extra gaps= 0 total=904 Number of alignments=118 # 1vhrA read from 1vhrA/merged-good-all-a2m # found chain 1vhrA in template set Warning: unaligning (T0317)R157 because last residue in template chain is (1vhrA)P185 T0317 2 :GTSEAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPR 1vhrA 21 :GCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMH T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1vhrA 80 :DSGITYLGIKANDTQEFNLSAYFERAADFIDQALA T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSAR 1vhrA 116 :KNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNR T0317 131 :VAEPNLGFWAQLQKYEQTLQAQAILP 1vhrA 159 :EIGPNDGFLAQLCQLNDRLAKEGKLK Number of specific fragments extracted= 4 number of extra gaps= 0 total=908 Number of alignments=119 # 1vhrA read from 1vhrA/merged-good-all-a2m # found chain 1vhrA in template set Warning: unaligning (T0317)R157 because last residue in template chain is (1vhrA)P185 T0317 3 :TSEAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPRAP 1vhrA 22 :CYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMHVN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1vhrA 82 :GITYLGIKANDTQEFNLSAYFERAADFIDQALA T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARP 1vhrA 116 :KNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNRE T0317 132 :AEPNLGFWAQLQKYEQTLQAQAILP 1vhrA 160 :IGPNDGFLAQLCQLNDRLAKEGKLK Number of specific fragments extracted= 4 number of extra gaps= 0 total=912 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x24A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x24A expands to /projects/compbio/data/pdb/1x24.pdb.gz 1x24A:# T0317 read from 1x24A/merged-good-all-a2m # 1x24A read from 1x24A/merged-good-all-a2m # adding 1x24A to template set # found chain 1x24A in template set T0317 22 :NARAAGATELLVRAGITLCVNVSRQQPGPR 1x24A 27 :NATLNKFIEELKKYGVTTIVRVCEATYDTT T0317 52 :APGVAELRVPVFD 1x24A 60 :KEGIHVLDWPFDD T0317 66 :PAEDLLTHLEPTCAAMEAAVR 1x24A 73 :GAPPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLM 1x24A 96 :PGCCIAVHCVAGLGRAPVLVALALI T0317 113 :HRGHSLDRAFQMVKSARPVAE 1x24A 121 :EGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1x24A 142 :NSKQLLYLEK Number of specific fragments extracted= 6 number of extra gaps= 0 total=918 Number of alignments=121 # 1x24A read from 1x24A/merged-good-all-a2m # found chain 1x24A in template set T0317 18 :LFIGNARAAG 1x24A 20 :LITHNPTNAT T0317 28 :A 1x24A 31 :N T0317 29 :TELLVRAGITLCVNVSRQQPGPR 1x24A 34 :IEELKKYGVTTIVRVCEATYDTT T0317 52 :APGVAELRVPVFDDPAEDL 1x24A 60 :KEGIHVLDWPFDDGAPPSN T0317 72 :THLEPTCAAMEAAVR 1x24A 79 :QIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTA 1x24A 96 :PGCCIAVHCVAGLGRAPVLVAL T0317 110 :LMRHRGHSLDRAFQMVKSARPVAE 1x24A 118 :ALIEGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1x24A 142 :NSKQLLYLEK T0317 154 :ILPRE 1x24A 152 :YRPKM Number of specific fragments extracted= 9 number of extra gaps= 0 total=927 Number of alignments=122 # 1x24A read from 1x24A/merged-good-all-a2m # found chain 1x24A in template set Warning: unaligning (T0317)F11 because first residue in template chain is (1x24A)P9 T0317 12 :ARVA 1x24A 10 :VEVT T0317 16 :PALFIGNARAAGA 1x24A 18 :RFLITHNPTNATL T0317 29 :TELLVRAGITLCVNVSRQQPG 1x24A 34 :IEELKKYGVTTIVRVCEATYD T0317 54 :GVAELRVPVFD 1x24A 62 :GIHVLDWPFDD T0317 66 :PAEDLLTHLEPTCAAMEAAVR 1x24A 73 :GAPPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLM 1x24A 96 :PGCCIAVHCVAGLGRAPVLVALALI T0317 113 :HRGHSLDRAFQMVKSARP 1x24A 121 :EGGMKYEDAVQFIRQKRR T0317 132 :AEPNLGFWAQLQ 1x24A 139 :GAFNSKQLLYLE T0317 152 :QAILPREP 1x24A 151 :KYRPKMRL Number of specific fragments extracted= 9 number of extra gaps= 0 total=936 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pa1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0317 read from 1pa1A/merged-good-all-a2m # 1pa1A read from 1pa1A/merged-good-all-a2m # found chain 1pa1A in training set Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pa1A)G683 Warning: unaligning (T0317)P66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)G683 T0317 18 :LFIGNARAAGA 1pa1A 583 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1pa1A 596 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPRAP 1pa1A 626 :PQKEEKEMI T0317 54 :GVAELRVP 1pa1A 673 :HFHYTTWP T0317 64 :D 1pa1A 681 :D T0317 67 :AEDLLTHLEPTCAAMEAA 1pa1A 684 :VPESPASFLNFLFKVRES T0317 85 :VRDG 1pa1A 704 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1pa1A 709 :GPVVVHDSAGIGRSGTFCLAD T0317 110 :LMRHRG 1pa1A 734 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPR 1pa1A 744 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDS Number of specific fragments extracted= 10 number of extra gaps= 1 total=946 Number of alignments=124 # 1pa1A read from 1pa1A/merged-good-all-a2m # found chain 1pa1A in training set Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pa1A)G683 Warning: unaligning (T0317)P66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)G683 T0317 18 :LFIGNARAAGA 1pa1A 583 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1pa1A 596 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1pa1A 626 :PQKEEKE T0317 52 :APGVAELRVPVFD 1pa1A 669 :REILHFHYTTWPD T0317 67 :AEDLLTHLEPTCAAMEA 1pa1A 684 :VPESPASFLNFLFKVRE T0317 84 :AVRDG 1pa1A 703 :SLSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1pa1A 709 :GPVVVHDSAGIGRSGTFCLAD T0317 110 :LMRHRG 1pa1A 734 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 1pa1A 744 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 1 total=955 Number of alignments=125 # 1pa1A read from 1pa1A/merged-good-all-a2m # found chain 1pa1A in training set Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pa1A)G683 Warning: unaligning (T0317)P66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)G683 T0317 18 :LFIGNARAAGA 1pa1A 583 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 1pa1A 596 :WEMVWEQKSRGVVMLNR T0317 54 :GVAELRVPVFD 1pa1A 671 :ILHFHYTTWPD T0317 67 :AEDLL 1pa1A 684 :VPESP T0317 75 :EPTCAAMEAAVRDG 1pa1A 689 :ASFLNFLFKVRESG T0317 89 :GSCLVYCKNGRSRSAAVCTA 1pa1A 709 :GPVVVHDSAGIGRSGTFCLA T0317 109 :YLMRHRG 1pa1A 733 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQ 1pa1A 744 :VDIKKVLLEMRKFRMGLIQTADQLRFSY Number of specific fragments extracted= 8 number of extra gaps= 1 total=963 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b3oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b3oA expands to /projects/compbio/data/pdb/2b3o.pdb.gz 2b3oA:# T0317 read from 2b3oA/merged-good-all-a2m # 2b3oA read from 2b3oA/merged-good-all-a2m # adding 2b3oA to template set # found chain 2b3oA in template set Warning: unaligning (T0317)I160 because last residue in template chain is (2b3oA)L526 T0317 5 :EAAPPPFARVAPA 2b3oA 308 :KNQLLGPDENAKT T0317 18 :LFIGNARA 2b3oA 322 :IASQGCLE T0317 26 :AGATELL 2b3oA 332 :VNDFWQM T0317 33 :VRAGITLCVNVS 2b3oA 340 :WQENSRVIVMTT T0317 45 :RQQPGPRA 2b3oA 361 :CVPYWPEV T0317 54 :GVAELRVP 2b3oA 411 :HYQYLSWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 2b3oA 419 :DHGVPSEPGGVLSFLDQINQRQE T0317 87 :DG 2b3oA 444 :PH T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2b3oA 447 :GPIIVHCSAGIGRTGTIIVIDMLME T0317 114 :RGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPREP 2b3oA 480 :CDIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEV Number of specific fragments extracted= 10 number of extra gaps= 0 total=973 Number of alignments=127 # 2b3oA read from 2b3oA/merged-good-all-a2m # found chain 2b3oA in template set Warning: unaligning (T0317)I160 because last residue in template chain is (2b3oA)L526 T0317 5 :EAAPPPFARVAPA 2b3oA 308 :KNQLLGPDENAKT T0317 18 :LFIGNARA 2b3oA 322 :IASQGCLE T0317 26 :AGA 2b3oA 331 :TVN T0317 29 :TELLVRAGITLCVNVS 2b3oA 336 :WQMAWQENSRVIVMTT T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 2b3oA 407 :REIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQE T0317 87 :DG 2b3oA 444 :PH T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2b3oA 447 :GPIIVHCSAGIGRTGTIIVIDMLME T0317 114 :RG 2b3oA 478 :LD T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPREP 2b3oA 482 :IDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEV Number of specific fragments extracted= 9 number of extra gaps= 0 total=982 Number of alignments=128 # 2b3oA read from 2b3oA/merged-good-all-a2m # found chain 2b3oA in template set Warning: unaligning (T0317)I160 because last residue in template chain is (2b3oA)L526 T0317 5 :EAAPPPFARVAPALFI 2b3oA 309 :NQLLGPDENAKTYIAS T0317 21 :GNARAAGA 2b3oA 326 :GCLEATVN T0317 29 :TELLVRAGITLCVNVSRQ 2b3oA 336 :WQMAWQENSRVIVMTTRE T0317 47 :QPGPRAP 2b3oA 361 :CVPYWPE T0317 54 :GVAELRVPVFD 2b3oA 409 :IWHYQYLSWPD T0317 65 :DPAEDLLTHLEPTCAAMEA 2b3oA 424 :SEPGGVLSFLDQINQRQES T0317 87 :DG 2b3oA 444 :PH T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2b3oA 447 :GPIIVHCSAGIGRTGTIIVIDMLME T0317 115 :G 2b3oA 479 :D T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPREP 2b3oA 482 :IDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEV Number of specific fragments extracted= 10 number of extra gaps= 0 total=992 Number of alignments=129 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0317//projects/compbio/experiments/protein-predict/casp7/T0317/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0317//projects/compbio/experiments/protein-predict/casp7/T0317/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0317/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0317/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((T0317)T107.CB, (T0317)V125.CB) [> 3.7407 = 6.2344 < 8.1048] w=1.0000 to align # Constraint # added constraint: constraint((T0317)V93.CB, (T0317)C106.CB) [> 3.6498 = 6.0830 < 7.9078] w=1.0000 to align # Constraint # added constraint: constraint((T0317)V43.CB, (T0317)V93.CB) [> 4.1712 = 6.9519 < 9.0375] w=0.9838 to align # Constraint # added constraint: constraint((T0317)V41.CB, (T0317)V93.CB) [> 2.7673 = 4.6122 < 5.9959] w=0.9838 to align # Constraint # added constraint: constraint((T0317)V41.CB, (T0317)L92.CB) [> 4.2077 = 7.0129 < 9.1167] w=0.9838 to align # Constraint # added constraint: constraint((T0317)V41.CB, (T0317)C91.CB) [> 3.8322 = 6.3870 < 8.3031] w=0.9838 to align # Constraint # added constraint: constraint((T0317)C40.CB, (T0317)L92.CB) [> 2.9167 = 4.8611 < 6.3194] w=0.9838 to align # Constraint # added constraint: constraint((T0317)L39.CB, (T0317)L92.CB) [> 4.2670 = 7.1117 < 9.2452] w=0.9838 to align # Constraint # added constraint: constraint((T0317)L39.CB, (T0317)C91.CB) [> 2.9792 = 4.9652 < 6.4548] w=0.9838 to align # Constraint # added constraint: constraint((T0317)V93.CB, (T0317)S102.CB) [> 2.8272 = 4.7120 < 6.1255] w=0.9838 to align # Constraint # added constraint: constraint((T0317)A103.CB, (T0317)V125.CB) [> 3.5012 = 5.8353 < 7.5859] w=0.9838 to align # Constraint # added constraint: constraint((T0317)V43.CB, (T0317)S102.CB) [> 3.6553 = 6.0922 < 7.9199] w=0.9758 to align # Constraint # added constraint: constraint((T0317)T107.CB, (T0317)A121.CB) [> 3.1203 = 5.2005 < 6.7607] w=0.9758 to align # Constraint # added constraint: constraint((T0317)C106.CB, (T0317)V125.CB) [> 3.7758 = 6.2930 < 8.1810] w=0.9758 to align # Constraint # added constraint: constraint((T0317)V93.CB, (T0317)V105.CB) [> 3.4597 = 5.7662 < 7.4960] w=0.9758 to align # Constraint # added constraint: constraint((T0317)V43.CB, (T0317)R101.CB) [> 2.6430 = 4.4050 < 5.7265] w=0.9677 to align # Constraint # added constraint: constraint((T0317)I37.CB, (T0317)S90.CB) [> 3.3819 = 5.6364 < 7.3274] w=0.9596 to align # Constraint # added constraint: constraint((T0317)V43.CB, (T0317)V105.CB) [> 3.7198 = 6.1996 < 8.0596] w=0.9596 to align # Constraint # added constraint: constraint((T0317)T107.CB, (T0317)F122.CB) [> 3.5823 = 5.9704 < 7.7616] w=0.9515 to align # Constraint # added constraint: constraint((T0317)N42.CB, (T0317)Y94.CB) [> 3.8289 = 6.3815 < 8.2959] w=0.9357 to align # Constraint # added constraint: constraint((T0317)V43.CB, (T0317)Y94.CB) [> 4.2994 = 7.1657 < 9.3154] w=0.9357 to align # Constraint # added constraint: constraint((T0317)V43.CB, (T0317)C95.CB) [> 2.8129 = 4.6882 < 6.0947] w=0.9357 to align # Constraint # added constraint: constraint((T0317)L118.CB, (T0317)L142.CB) [> 3.2869 = 5.4782 < 7.1216] w=0.9354 to align # Constraint # added constraint: constraint((T0317)A104.CB, (T0317)F138.CB) [> 2.9804 = 4.9673 < 6.4575] w=0.9354 to align # Constraint # added constraint: constraint((T0317)T38.CB, (T0317)G89.CA) [> 3.6728 = 6.1214 < 7.9578] w=0.9354 to align # Constraint # added constraint: constraint((T0317)V41.CB, (T0317)V105.CB) [> 3.9956 = 6.6593 < 8.6571] w=0.9354 to align # Constraint # added constraint: constraint((T0317)N42.CB, (T0317)E57.CB) [> 4.0214 = 6.7023 < 8.7130] w=0.9352 to align # Constraint # added constraint: constraint((T0317)I37.CB, (T0317)L92.CB) [> 2.9622 = 4.9370 < 6.4180] w=0.9273 to align # Constraint # added constraint: constraint((T0317)L39.CB, (T0317)V55.CB) [> 3.7194 = 6.1990 < 8.0587] w=0.9271 to align # Constraint # added constraint: constraint((T0317)T107.CB, (T0317)L142.CB) [> 3.2130 = 5.3550 < 6.9615] w=0.9193 to align # Constraint # added constraint: constraint((T0317)A104.CB, (T0317)L142.CB) [> 3.7398 = 6.2330 < 8.1029] w=0.9162 to align # Constraint # added constraint: constraint((T0317)S44.CB, (T0317)K96.CB) [> 3.2370 = 5.3951 < 7.0136] w=0.9115 to align # Constraint # added constraint: constraint((T0317)S44.CB, (T0317)C95.CB) [> 2.9413 = 4.9021 < 6.3728] w=0.9115 to align # Constraint # added constraint: constraint((T0317)L32.CB, (T0317)L92.CB) [> 3.8600 = 6.4334 < 8.3634] w=0.9114 to align # Constraint # added constraint: constraint((T0317)I37.CB, (T0317)C91.CB) [> 4.0752 = 6.7920 < 8.8296] w=0.9111 to align # Constraint # added constraint: constraint((T0317)C40.CB, (T0317)V55.CB) [> 3.7730 = 6.2883 < 8.1748] w=0.9110 to align # Constraint # added constraint: constraint((T0317)C78.CB, (T0317)A108.CB) [> 3.7828 = 6.3047 < 8.1961] w=0.9031 to align # Constraint # added constraint: constraint((T0317)T107.CB, (T0317)L118.CB) [> 4.1139 = 6.8565 < 8.9134] w=0.9031 to align # Constraint # added constraint: constraint((T0317)A104.CB, (T0317)Q141.CB) [> 3.9804 = 6.6340 < 8.6242] w=0.9031 to align # Constraint # added constraint: constraint((T0317)C40.CB, (T0317)C91.CB) [> 4.5473 = 7.5789 < 9.8525] w=0.9031 to align # Constraint # added constraint: constraint((T0317)A108.CB, (T0317)L142.CB) [> 3.7265 = 6.2109 < 8.0742] w=0.9030 to align # Constraint # added constraint: constraint((T0317)R99.CB, (T0317)A132.CB) [> 3.3513 = 5.5855 < 7.2611] w=0.8950 to align # Constraint # added constraint: constraint((T0317)V41.CB, (T0317)Y94.CB) [> 4.4670 = 7.4451 < 9.6786] w=0.8873 to align # Constraint # added constraint: constraint((T0317)F122.CB, (T0317)W139.CB) [> 4.2652 = 7.1086 < 9.2412] w=0.8707 to align # Constraint # added constraint: constraint((T0317)M81.CB, (T0317)C91.CB) [> 3.8761 = 6.4602 < 8.3982] w=0.8691 to align # Constraint # added constraint: constraint((T0317)I37.CB, (T0317)G89.CA) [> 3.7518 = 6.2531 < 8.1290] w=0.8627 to align # Constraint # added constraint: constraint((T0317)A35.CB, (T0317)S90.CB) [> 3.6392 = 6.0654 < 7.8850] w=0.8627 to align # Constraint # added constraint: constraint((T0317)R101.CB, (T0317)F138.CB) [> 4.4724 = 7.4540 < 9.6902] w=0.8546 to align # Constraint # added constraint: constraint((T0317)S100.CB, (T0317)F138.CB) [> 3.3721 = 5.6201 < 7.3061] w=0.8546 to align # Constraint # added constraint: constraint((T0317)R99.CB, (T0317)R129.CB) [> 3.8325 = 6.3875 < 8.3037] w=0.8546 to align # Constraint # added constraint: constraint((T0317)A103.CB, (T0317)A132.CB) [> 2.3576 = 3.9293 < 5.1081] w=0.8465 to align # Constraint # added constraint: constraint((T0317)L74.CB, (T0317)A108.CB) [> 3.7253 = 6.2088 < 8.0715] w=0.8449 to align # Constraint # added constraint: constraint((T0317)S100.CB, (T0317)N135.CB) [> 3.5960 = 5.9933 < 7.7913] w=0.8384 to align # Constraint # added constraint: constraint((T0317)L110.CB, (T0317)A121.CB) [> 3.2954 = 5.4924 < 7.1401] w=0.8384 to align # Constraint # added constraint: constraint((T0317)R99.CB, (T0317)V131.CB) [> 2.9407 = 4.9012 < 6.3716] w=0.8379 to align # Constraint # added constraint: constraint((T0317)S100.CB, (T0317)P134.CB) [> 2.3700 = 3.9501 < 5.1351] w=0.8061 to align # Constraint # added constraint: constraint((T0317)C40.CB, (T0317)Y94.CB) [> 4.4949 = 7.4915 < 9.7389] w=0.8037 to align # Constraint # added constraint: constraint((T0317)N42.CB, (T0317)R59.CB) [> 3.2576 = 5.4294 < 7.0582] w=0.7882 to align # Constraint # added constraint: constraint((T0317)N42.CB, (T0317)L58.CB) [> 3.6298 = 6.0497 < 7.8646] w=0.7882 to align # Constraint # added constraint: constraint((T0317)C40.CB, (T0317)E57.CB) [> 3.2895 = 5.4826 < 7.1273] w=0.7882 to align # Constraint # added constraint: constraint((T0317)C40.CB, (T0317)A56.CB) [> 3.8311 = 6.3851 < 8.3007] w=0.7882 to align # Constraint # added constraint: constraint((T0317)A103.CB, (T0317)E133.CB) [> 2.6490 = 4.4151 < 5.7396] w=0.7819 to align # Constraint # added constraint: constraint((T0317)R99.CB, (T0317)E133.CB) [> 4.2885 = 7.1475 < 9.2917] w=0.7819 to align # Constraint # added constraint: constraint((T0317)R99.CB, (T0317)P134.CB) [> 3.5982 = 5.9969 < 7.7960] w=0.7819 to align # Constraint # added constraint: constraint((T0317)F122.CB, (T0317)A132.CB) [> 3.9749 = 6.6248 < 8.6123] w=0.7819 to align # Constraint # added constraint: constraint((T0317)G21.CA, (T0317)G98.CA) [> 3.6018 = 6.0030 < 7.8039] w=0.7748 to align # Constraint # added constraint: constraint((T0317)C78.CB, (T0317)Y109.CB) [> 3.4307 = 5.7178 < 7.4331] w=0.7722 to align # Constraint # added constraint: constraint((T0317)S44.CB, (T0317)R101.CB) [> 4.1313 = 6.8855 < 8.9511] w=0.7714 to align # Constraint # added constraint: constraint((T0317)L39.CB, (T0317)A84.CB) [> 3.3216 = 5.5361 < 7.1969] w=0.7688 to align # Constraint # added constraint: constraint((T0317)G36.CA, (T0317)G89.CA) [> 3.2015 = 5.3358 < 6.9366] w=0.7657 to align # Constraint # added constraint: constraint((T0317)V41.CB, (T0317)M81.CB) [> 3.7946 = 6.3243 < 8.2216] w=0.7641 to align # Constraint # added constraint: constraint((T0317)G21.CA, (T0317)Y94.CB) [> 2.7819 = 4.6365 < 6.0274] w=0.7590 to align # Constraint # added constraint: constraint((T0317)A103.CB, (T0317)F122.CB) [> 4.4972 = 7.4953 < 9.7439] w=0.7586 to align # Constraint # added constraint: constraint((T0317)F19.CB, (T0317)V93.CB) [> 4.1163 = 6.8605 < 8.9186] w=0.7578 to align # Constraint # added constraint: constraint((T0317)V62.CB, (T0317)R101.CB) [> 3.5061 = 5.8436 < 7.5966] w=0.7563 to align # Constraint # added constraint: constraint((T0317)S44.CB, (T0317)Y94.CB) [> 4.5510 = 7.5849 < 9.8604] w=0.7556 to align # Constraint # added constraint: constraint((T0317)F122.CB, (T0317)L142.CB) [> 4.3738 = 7.2896 < 9.4765] w=0.7536 to align # Constraint # added constraint: constraint((T0317)V43.CB, (T0317)V62.CB) [> 3.4381 = 5.7301 < 7.4492] w=0.7482 to align # Constraint # added constraint: constraint((T0317)T38.CB, (T0317)V55.CB) [> 3.7683 = 6.2805 < 8.1646] w=0.7473 to align # Constraint # added constraint: constraint((T0317)C40.CB, (T0317)V93.CB) [> 4.6709 = 7.7848 < 10.1203] w=0.7467 to align # Constraint # added constraint: constraint((T0317)A108.CB, (T0317)Y145.CB) [> 3.3312 = 5.5521 < 7.2177] w=0.7422 to align # Constraint # added constraint: constraint((T0317)I20.CB, (T0317)Y94.CB) [> 3.6433 = 6.0722 < 7.8938] w=0.7420 to align # Constraint # added constraint: constraint((T0317)A103.CB, (T0317)F138.CB) [> 4.3382 = 7.2304 < 9.3995] w=0.7334 to align # Constraint # added constraint: constraint((T0317)L18.CB, (T0317)V93.CB) [> 3.6695 = 6.1158 < 7.9506] w=0.7166 to align # Constraint # added constraint: constraint((T0317)V41.CB, (T0317)L58.CB) [> 3.3997 = 5.6662 < 7.3660] w=0.7159 to align # Constraint # added constraint: constraint((T0317)F19.CB, (T0317)L92.CB) [> 3.4883 = 5.8137 < 7.5579] w=0.7093 to align # Constraint # added constraint: constraint((T0317)A103.CB, (T0317)P134.CB) [> 4.0585 = 6.7642 < 8.7935] w=0.7091 to align # Constraint # added constraint: constraint((T0317)N42.CB, (T0317)C95.CB) [> 4.5579 = 7.5966 < 9.8755] w=0.7090 to align # Constraint # added constraint: constraint((T0317)N22.CB, (T0317)Y94.CB) [> 4.0740 = 6.7900 < 8.8270] w=0.7038 to align # Constraint # added constraint: constraint((T0317)L39.CB, (T0317)E57.CB) [> 4.3360 = 7.2267 < 9.3947] w=0.6993 to align # Constraint # added constraint: constraint((T0317)T38.CB, (T0317)C91.CB) [> 4.4114 = 7.3523 < 9.5580] w=0.6953 to align # Constraint # added constraint: constraint((T0317)A103.CB, (T0317)R129.CB) [> 4.3389 = 7.2314 < 9.4009] w=0.6848 to align # Constraint # added constraint: constraint((T0317)V43.CB, (T0317)V60.CB) [> 3.4970 = 5.8283 < 7.5768] w=0.6801 to align # Constraint # added constraint: constraint((T0317)A104.CB, (T0317)E133.CB) [> 3.5324 = 5.8873 < 7.6535] w=0.6768 to align # Constraint # added constraint: constraint((T0317)L118.CB, (T0317)E146.CB) [> 3.5981 = 5.9968 < 7.7958] w=0.6752 to align # Constraint # added constraint: constraint((T0317)M111.CB, (T0317)E146.CB) [> 3.6872 = 6.1453 < 7.9889] w=0.6701 to align # Constraint # added constraint: constraint((T0317)M111.CB, (T0317)A121.CB) [> 3.3861 = 5.6436 < 7.3366] w=0.6624 to align # Constraint # added constraint: constraint((T0317)A67.CB, (T0317)G137.CA) [> 3.6553 = 6.0922 < 7.9199] w=0.6610 to align # Constraint # added constraint: constraint((T0317)A35.CB, (T0317)L92.CB) [> 4.4884 = 7.4807 < 9.7249] w=0.6607 to align # Constraint # added constraint: constraint((T0317)V41.CB, (T0317)E57.CB) [> 4.0089 = 6.6815 < 8.6859] w=0.6366 to align # Constraint # added constraint: constraint((T0317)L74.CB, (T0317)Y145.CB) [> 3.6804 = 6.1340 < 7.9742] w=0.6348 to align # Constraint # added constraint: constraint((T0317)T77.CB, (T0317)V105.CB) [> 3.5858 = 5.9763 < 7.7692] w=0.6251 to align # Constraint # added constraint: constraint((T0317)M81.CB, (T0317)Y109.CB) [> 3.6951 = 6.1585 < 8.0061] w=0.6222 to align # Constraint # added constraint: constraint((T0317)G21.CA, (T0317)C95.CB) [> 4.2547 = 7.0912 < 9.2186] w=0.6198 to align # Constraint # added constraint: constraint((T0317)L39.CB, (T0317)M81.CB) [> 3.9427 = 6.5712 < 8.5426] w=0.6187 to align # Constraint # added constraint: constraint((T0317)L71.CB, (T0317)Y145.CB) [> 3.0297 = 5.0495 < 6.5644] w=0.6055 to align # Constraint # added constraint: constraint((T0317)R99.CB, (T0317)P130.CB) [> 4.1160 = 6.8599 < 8.9179] w=0.6032 to align # Constraint # added constraint: constraint((T0317)E82.CB, (T0317)Y109.CB) [> 4.2933 = 7.1555 < 9.3022] w=0.6025 to align # Constraint # added constraint: constraint((T0317)T38.CB, (T0317)G54.CA) [> 3.7597 = 6.2661 < 8.1459] w=0.6011 to align # Constraint # added constraint: constraint((T0317)L71.CB, (T0317)Q141.CB) [> 3.9415 = 6.5691 < 8.5398] w=0.5810 to align # Constraint # added constraint: constraint((T0317)L18.CB, (T0317)C106.CB) [> 3.9987 = 6.6644 < 8.6638] w=0.5793 to align # Constraint # added constraint: constraint((T0317)V41.CB, (T0317)R59.CB) [> 4.5745 = 7.6242 < 9.9114] w=0.5695 to align # Constraint # added constraint: constraint((T0317)L74.CB, (T0317)V105.CB) [> 4.3092 = 7.1820 < 9.3366] w=0.5691 to align # Constraint # added constraint: constraint((T0317)N97.CB, (T0317)V131.CB) [> 4.4386 = 7.3977 < 9.6170] w=0.5632 to align # Constraint # added constraint: constraint((T0317)C40.CB, (T0317)L58.CB) [> 4.1940 = 6.9901 < 9.0871] w=0.5573 to align # Constraint # added constraint: constraint((T0317)G36.CA, (T0317)S90.CB) [> 3.6756 = 6.1260 < 7.9638] w=0.5480 to align # Constraint # added constraint: constraint((T0317)F19.CB, (T0317)Y94.CB) [> 3.3277 = 5.5462 < 7.2100] w=0.5476 to align # Constraint # added constraint: constraint((T0317)S100.CB, (T0317)V131.CB) [> 4.5785 = 7.6308 < 9.9200] w=0.5471 to align # Constraint # added constraint: constraint((T0317)L58.CB, (T0317)A80.CB) [> 3.6943 = 6.1571 < 8.0043] w=0.5412 to align # Constraint # added constraint: constraint((T0317)D64.CB, (T0317)R101.CB) [> 4.1166 = 6.8610 < 8.9193] w=0.5404 to align # Constraint # added constraint: constraint((T0317)V41.CB, (T0317)V60.CB) [> 4.0520 = 6.7533 < 8.7793] w=0.5331 to align # Constraint # added constraint: constraint((T0317)L39.CB, (T0317)L58.CB) [> 4.0820 = 6.8033 < 8.8443] w=0.5331 to align # Constraint # added constraint: constraint((T0317)C78.CB, (T0317)V105.CB) [> 4.1343 = 6.8905 < 8.9576] w=0.5217 to align # Constraint # added constraint: constraint((T0317)T77.CB, (T0317)A108.CB) [> 4.2696 = 7.1161 < 9.2509] w=0.5201 to align # Constraint # added constraint: constraint((T0317)T38.CB, (T0317)A84.CB) [> 4.2879 = 7.1465 < 9.2905] w=0.5182 to align # Constraint # added constraint: constraint((T0317)S100.CB, (T0317)A132.CB) [> 4.5815 = 7.6358 < 9.9266] w=0.5176 to align # Constraint # added constraint: constraint((T0317)S102.CB, (T0317)A132.CB) [> 4.4318 = 7.3863 < 9.6021] w=0.5162 to align # Constraint # added constraint: constraint((T0317)A35.CB, (T0317)G89.CA) [> 3.7003 = 6.1671 < 8.0173] w=0.5152 to align # Constraint # added constraint: constraint((T0317)N42.CB, (T0317)V60.CB) [> 4.3124 = 7.1874 < 9.3436] w=0.5089 to align # Constraint # added constraint: constraint((T0317)V60.CB, (T0317)T77.CB) [> 3.7471 = 6.2451 < 8.1187] w=0.4930 to align # Constraint # added constraint: constraint((T0317)L31.CB, (T0317)L92.CB) [> 4.4452 = 7.4086 < 9.6312] w=0.4905 to align # Constraint # added constraint: constraint((T0317)C78.CB, (T0317)R112.CB) [> 3.5583 = 5.9306 < 7.7097] w=0.4889 to align # Constraint # added constraint: constraint((T0317)T38.CB, (T0317)S90.CB) [> 3.9134 = 6.5224 < 8.4791] w=0.4862 to align # Constraint # added constraint: constraint((T0317)D64.CB, (T0317)K96.CB) [> 4.1844 = 6.9740 < 9.0661] w=0.4842 to align # Constraint # added constraint: constraint((T0317)A67.CB, (T0317)A104.CB) [> 4.4527 = 7.4212 < 9.6476] w=0.4742 to align # Constraint # added constraint: constraint((T0317)T107.CB, (T0317)A132.CB) [> 4.3801 = 7.3001 < 9.4902] w=0.4653 to align # Constraint # added constraint: constraint((T0317)G21.CA, (T0317)K96.CB) [> 3.4917 = 5.8194 < 7.5652] w=0.4582 to align # Constraint # added constraint: constraint((T0317)A103.CB, (T0317)V131.CB) [> 4.4656 = 7.4426 < 9.6754] w=0.4582 to align # Constraint # added constraint: constraint((T0317)S44.CB, (T0317)V62.CB) [> 4.2804 = 7.1340 < 9.2742] w=0.4560 to align # Constraint # added constraint: constraint((T0317)I37.CB, (T0317)V55.CB) [> 3.8962 = 6.4936 < 8.4417] w=0.4523 to align # Constraint # added constraint: constraint((T0317)V60.CB, (T0317)H73.CB) [> 3.4708 = 5.7846 < 7.5200] w=0.4444 to align # Constraint # added constraint: constraint((T0317)E75.CB, (T0317)L149.CB) [> 3.5231 = 5.8719 < 7.6335] w=0.4419 to align # Constraint # added constraint: constraint((T0317)C106.CB, (T0317)A132.CB) [> 4.3577 = 7.2629 < 9.4418] w=0.4411 to align # Constraint # added constraint: constraint((T0317)I20.CB, (T0317)V93.CB) [> 3.6753 = 6.1255 < 7.9631] w=0.4288 to align # Constraint # added constraint: constraint((T0317)D64.CB, (T0317)S100.CB) [> 4.1396 = 6.8994 < 8.9692] w=0.4196 to align # Constraint # added constraint: constraint((T0317)L32.CB, (T0317)V55.CB) [> 3.9968 = 6.6613 < 8.6597] w=0.4119 to align # Constraint # added constraint: constraint((T0317)L18.CB, (T0317)C91.CB) [> 3.5484 = 5.9140 < 7.6883] w=0.4037 to align # Constraint # added constraint: constraint((T0317)C40.CB, (T0317)G54.CA) [> 3.6339 = 6.0565 < 7.8735] w=0.4021 to align # Constraint # added constraint: constraint((T0317)L39.CB, (T0317)G54.CA) [> 4.0133 = 6.6889 < 8.6955] w=0.4021 to align # Constraint # added constraint: constraint((T0317)V41.CB, (T0317)A80.CB) [> 3.9892 = 6.6487 < 8.6434] w=0.3959 to align # Constraint # added constraint: constraint((T0317)N42.CB, (T0317)A56.CB) [> 3.4707 = 5.7845 < 7.5198] w=0.3940 to align # Constraint # added constraint: constraint((T0317)L39.CB, (T0317)V85.CB) [> 3.6374 = 6.0623 < 7.8810] w=0.3923 to align # Constraint # added constraint: constraint((T0317)N22.CB, (T0317)G98.CA) [> 3.5357 = 5.8928 < 7.6607] w=0.3896 to align # Constraint # added constraint: constraint((T0317)A17.CB, (T0317)S90.CB) [> 3.3251 = 5.5418 < 7.2043] w=0.3863 to align # Constraint # added constraint: constraint((T0317)V60.CB, (T0317)P76.CB) [> 3.8771 = 6.4619 < 8.4004] w=0.3794 to align # Constraint # added constraint: constraint((T0317)R45.CB, (T0317)P61.CB) [> 3.3892 = 5.6487 < 7.3433] w=0.3791 to align # Constraint # added constraint: constraint((T0317)V43.CB, (T0317)R59.CB) [> 3.4709 = 5.7848 < 7.5203] w=0.3760 to align # Constraint # added constraint: constraint((T0317)I20.CB, (T0317)S102.CB) [> 3.6129 = 6.0215 < 7.8279] w=0.3722 to align # Constraint # added constraint: constraint((T0317)L110.CB, (T0317)M124.CB) [> 4.0996 = 6.8327 < 8.8825] w=0.3717 to align # Constraint # added constraint: constraint((T0317)A121.CB, (T0317)L142.CB) [> 4.3209 = 7.2015 < 9.3620] w=0.3707 to align # Constraint # added constraint: constraint((T0317)P66.CB, (T0317)F138.CB) [> 4.5197 = 7.5328 < 9.7926] w=0.3637 to align # Constraint # added constraint: constraint((T0317)S44.CB, (T0317)P61.CB) [> 4.0388 = 6.7313 < 8.7507] w=0.3636 to align # Constraint # added constraint: constraint((T0317)D64.CB, (T0317)C95.CB) [> 4.4442 = 7.4070 < 9.6291] w=0.3631 to align # Constraint # added constraint: constraint((T0317)L18.CB, (T0317)S102.CB) [> 2.9885 = 4.9807 < 6.4750] w=0.3528 to align # Constraint # added constraint: constraint((T0317)I20.CB, (T0317)L92.CB) [> 3.9549 = 6.5915 < 8.5689] w=0.3490 to align # Constraint # added constraint: constraint((T0317)L74.CB, (T0317)Q141.CB) [> 4.2745 = 7.1241 < 9.2614] w=0.3456 to align # Constraint # added constraint: constraint((T0317)L18.CB, (T0317)R99.CB) [> 4.1936 = 6.9893 < 9.0861] w=0.3452 to align # Constraint # added constraint: constraint((T0317)L18.CB, (T0317)A103.CB) [> 4.4351 = 7.3918 < 9.6094] w=0.3452 to align # Constraint # added constraint: constraint((T0317)R112.CB, (T0317)L149.CB) [> 3.7478 = 6.2463 < 8.1202] w=0.3386 to align # Constraint # added constraint: constraint((T0317)L18.CB, (T0317)A132.CB) [> 4.4033 = 7.3389 < 9.5405] w=0.3371 to align # Constraint # added constraint: constraint((T0317)E57.CB, (T0317)T77.CB) [> 3.7200 = 6.2000 < 8.0599] w=0.3353 to align # Constraint # added constraint: constraint((T0317)G21.CA, (T0317)S102.CB) [> 4.0409 = 6.7348 < 8.7552] w=0.3331 to align # Constraint # added constraint: constraint((T0317)V62.CB, (T0317)H73.CB) [> 3.6999 = 6.1665 < 8.0165] w=0.3313 to align # Constraint # added constraint: constraint((T0317)V41.CB, (T0317)S102.CB) [> 4.6581 = 7.7635 < 10.0925] w=0.3303 to align # Constraint # added constraint: constraint((T0317)A17.CB, (T0317)C91.CB) [> 3.8489 = 6.4148 < 8.3392] w=0.3297 to align # Constraint # added constraint: constraint((T0317)L39.CB, (T0317)S90.CB) [> 4.3465 = 7.2441 < 9.4174] w=0.3232 to align # Constraint # added constraint: constraint((T0317)L39.CB, (T0317)G89.CA) [> 4.0952 = 6.8254 < 8.8730] w=0.3232 to align # Constraint # added constraint: constraint((T0317)N22.CB, (T0317)C95.CB) [> 4.2058 = 7.0097 < 9.1126] w=0.3232 to align # Constraint # added constraint: constraint((T0317)L110.CB, (T0317)V125.CB) [> 4.4513 = 7.4188 < 9.6444] w=0.3182 to align # Constraint # added constraint: constraint((T0317)M81.CB, (T0317)V105.CB) [> 4.3679 = 7.2798 < 9.4637] w=0.3181 to align # Constraint # added constraint: constraint((T0317)L74.CB, (T0317)A104.CB) [> 4.3840 = 7.3066 < 9.4986] w=0.3129 to align # Constraint # added constraint: constraint((T0317)A23.CB, (T0317)Y94.CB) [> 3.9039 = 6.5065 < 8.4584] w=0.3088 to align # Constraint # added constraint: constraint((T0317)T77.CB, (T0317)Y109.CB) [> 4.1964 = 6.9940 < 9.0922] w=0.2989 to align # Constraint # added constraint: constraint((T0317)L39.CB, (T0317)A80.CB) [> 4.2162 = 7.0271 < 9.1352] w=0.2989 to align # Constraint # added constraint: constraint((T0317)P61.CB, (T0317)H73.CB) [> 3.6680 = 6.1134 < 7.9474] w=0.2933 to align # Constraint # added constraint: constraint((T0317)F19.CB, (T0317)S102.CB) [> 3.8628 = 6.4381 < 8.3695] w=0.2910 to align # Constraint # added constraint: constraint((T0317)V43.CB, (T0317)P61.CB) [> 4.0288 = 6.7146 < 8.7290] w=0.2909 to align # Constraint # added constraint: constraint((T0317)F19.CB, (T0317)C91.CB) [> 4.0531 = 6.7551 < 8.7816] w=0.2753 to align # Constraint # added constraint: constraint((T0317)M111.CB, (T0317)L149.CB) [> 3.8018 = 6.3363 < 8.2371] w=0.2717 to align # Constraint # added constraint: constraint((T0317)R45.CB, (T0317)V62.CB) [> 3.9911 = 6.6519 < 8.6474] w=0.2617 to align # Constraint # added constraint: constraint((T0317)M111.CB, (T0317)Y145.CB) [> 3.7859 = 6.3099 < 8.2028] w=0.2600 to align # Constraint # added constraint: constraint((T0317)T38.CB, (T0317)G88.CA) [> 4.0243 = 6.7072 < 8.7194] w=0.2528 to align # Constraint # added constraint: constraint((T0317)A23.CB, (T0317)K96.CB) [> 3.0077 = 5.0129 < 6.5168] w=0.2523 to align # Constraint # added constraint: constraint((T0317)A23.CB, (T0317)C95.CB) [> 4.2370 = 7.0617 < 9.1802] w=0.2523 to align # Constraint # added constraint: constraint((T0317)G21.CA, (T0317)V93.CB) [> 4.2368 = 7.0614 < 9.1798] w=0.2523 to align # Constraint # added constraint: constraint((T0317)M81.CB, (T0317)V93.CB) [> 4.4616 = 7.4360 < 9.6668] w=0.2495 to align # Constraint # added constraint: constraint((T0317)V43.CB, (T0317)A104.CB) [> 4.5732 = 7.6219 < 9.9085] w=0.2482 to align # Constraint # added constraint: constraint((T0317)R59.CB, (T0317)T77.CB) [> 3.5691 = 5.9485 < 7.7330] w=0.2466 to align # Constraint # added constraint: constraint((T0317)I20.CB, (T0317)C106.CB) [> 3.6246 = 6.0410 < 7.8533] w=0.2429 to align # Constraint # added constraint: constraint((T0317)Q46.CB, (T0317)P61.CB) [> 4.2443 = 7.0738 < 9.1959] w=0.2424 to align # Constraint # added constraint: constraint((T0317)E57.CB, (T0317)A80.CB) [> 4.0085 = 6.6808 < 8.6850] w=0.2389 to align # Constraint # added constraint: constraint((T0317)S44.CB, (T0317)V60.CB) [> 4.4423 = 7.4038 < 9.6250] w=0.2359 to align # Constraint # added constraint: constraint((T0317)I37.CB, (T0317)G54.CA) [> 4.4633 = 7.4388 < 9.6704] w=0.2309 to align # Constraint # added constraint: constraint((T0317)A23.CB, (T0317)N97.CB) [> 4.5578 = 7.5964 < 9.8753] w=0.2280 to align # Constraint # added constraint: constraint((T0317)F19.CB, (T0317)I37.CB) [> 4.0768 = 6.7947 < 8.8331] w=0.2268 to align # Constraint # added constraint: constraint((T0317)L70.CB, (T0317)Q141.CB) [> 3.8850 = 6.4750 < 8.4176] w=0.2252 to align # Constraint # added constraint: constraint((T0317)I20.CB, (T0317)A103.CB) [> 3.9010 = 6.5016 < 8.4522] w=0.2187 to align # Constraint # added constraint: constraint((T0317)R45.CB, (T0317)K96.CB) [> 3.9986 = 6.6644 < 8.6636] w=0.2186 to align # Constraint # added constraint: constraint((T0317)N42.CB, (T0317)P61.CB) [> 4.3174 = 7.1957 < 9.3545] w=0.2181 to align # Constraint # added constraint: constraint((T0317)A108.CB, (T0317)L149.CB) [> 4.1656 = 6.9427 < 9.0255] w=0.2142 to align # Constraint # added constraint: constraint((T0317)L58.CB, (T0317)T77.CB) [> 4.1994 = 6.9991 < 9.0988] w=0.2109 to align # Constraint # added constraint: constraint((T0317)A12.CB, (T0317)A128.CB) [> 3.1061 = 5.1769 < 6.7300] w=0.2020 to align # Constraint # added constraint: constraint((T0317)T29.CB, (T0317)V55.CB) [> 4.2792 = 7.1321 < 9.2717] w=0.2020 to align # Constraint # added constraint: constraint((T0317)A56.CB, (T0317)A84.CB) [> 3.9166 = 6.5276 < 8.4859] w=0.2017 to align # Constraint # added constraint: constraint((T0317)F11.CB, (T0317)G21.CA) [> 2.8929 = 4.8216 < 6.2680] w=0.1939 to align # Constraint # added constraint: constraint((T0317)H73.CB, (T0317)V105.CB) [> 4.4809 = 7.4681 < 9.7086] w=0.1858 to align # Constraint # added constraint: constraint((T0317)F11.CB, (T0317)I20.CB) [> 3.8171 = 6.3618 < 8.2704] w=0.1858 to align # Constraint # added constraint: constraint((T0317)R45.CB, (T0317)F63.CB) [> 3.5687 = 5.9478 < 7.7321] w=0.1779 to align # Constraint # added constraint: constraint((T0317)V14.CB, (T0317)C106.CB) [> 3.5202 = 5.8669 < 7.6270] w=0.1777 to align # Constraint # added constraint: constraint((T0317)A108.CB, (T0317)A121.CB) [> 4.4296 = 7.3826 < 9.5974] w=0.1777 to align # Constraint # added constraint: constraint((T0317)V14.CB, (T0317)A128.CB) [> 3.0026 = 5.0043 < 6.5056] w=0.1777 to align # Constraint # added constraint: constraint((T0317)V14.CB, (T0317)V125.CB) [> 3.5331 = 5.8885 < 7.6551] w=0.1777 to align # Constraint # added constraint: constraint((T0317)A12.CB, (T0317)G21.CA) [> 3.9417 = 6.5695 < 8.5404] w=0.1777 to align # Constraint # added constraint: constraint((T0317)V14.CB, (T0317)M124.CB) [> 4.2060 = 7.0100 < 9.1130] w=0.1777 to align # Constraint # added constraint: constraint((T0317)V62.CB, (T0317)L74.CB) [> 4.4928 = 7.4879 < 9.7343] w=0.1773 to align # Constraint # added constraint: constraint((T0317)V62.CB, (T0317)C95.CB) [> 4.3954 = 7.3257 < 9.5234] w=0.1771 to align # Constraint # added constraint: constraint((T0317)E57.CB, (T0317)A84.CB) [> 3.9771 = 6.6286 < 8.6171] w=0.1739 to align # Constraint # added constraint: constraint((T0317)C106.CB, (T0317)A121.CB) [> 4.6609 = 7.7681 < 10.0985] w=0.1697 to align # Constraint # added constraint: constraint((T0317)A15.CB, (T0317)L110.CB) [> 4.2729 = 7.1215 < 9.2580] w=0.1697 to align # Constraint # added constraint: constraint((T0317)R13.CB, (T0317)A128.CB) [> 4.0429 = 6.7381 < 8.7595] w=0.1697 to align # Constraint # added constraint: constraint((T0317)D65.CB, (T0317)F138.CB) [> 4.6880 = 7.8134 < 10.1574] w=0.1673 to align # Constraint # added constraint: constraint((T0317)I20.CB, (T0317)V125.CB) [> 4.4581 = 7.4302 < 9.6592] w=0.1626 to align # Constraint # added constraint: constraint((T0317)A104.CB, (T0317)Y145.CB) [> 4.6178 = 7.6964 < 10.0053] w=0.1580 to align # Constraint # added constraint: constraint((T0317)A104.CB, (T0317)P134.CB) [> 3.7098 = 6.1830 < 8.0379] w=0.1535 to align # Constraint # added constraint: constraint((T0317)F19.CB, (T0317)C106.CB) [> 3.7861 = 6.3102 < 8.2032] w=0.1535 to align # Constraint # added constraint: constraint((T0317)D69.CB, (T0317)A104.CB) [> 3.7174 = 6.1956 < 8.0543] w=0.1532 to align # Constraint # added constraint: constraint((T0317)A104.CB, (T0317)W139.CB) [> 4.5738 = 7.6230 < 9.9098] w=0.1479 to align # Constraint # added constraint: constraint((T0317)N42.CB, (T0317)V55.CB) [> 4.0965 = 6.8275 < 8.8757] w=0.1470 to align # Constraint # added constraint: constraint((T0317)T29.CB, (T0317)P53.CB) [> 3.3816 = 5.6361 < 7.3269] w=0.1454 to align # Constraint # added constraint: constraint((T0317)N42.CB, (T0317)V93.CB) [> 4.6948 = 7.8247 < 10.1722] w=0.1454 to align # Constraint # added constraint: constraint((T0317)A103.CB, (T0317)K126.CB) [> 4.5414 = 7.5691 < 9.8398] w=0.1454 to align # Constraint # added constraint: constraint((T0317)M111.CB, (T0317)A153.CB) [> 3.6935 = 6.1558 < 8.0026] w=0.1393 to align # Constraint # added constraint: constraint((T0317)C91.CB, (T0317)Y109.CB) [> 4.3780 = 7.2966 < 9.4856] w=0.1388 to align # Constraint # added constraint: constraint((T0317)V14.CB, (T0317)R129.CB) [> 4.1359 = 6.8932 < 8.9611] w=0.1374 to align # Constraint # added constraint: constraint((T0317)F11.CB, (T0317)N22.CB) [> 4.3762 = 7.2937 < 9.4818] w=0.1374 to align # Constraint # added constraint: constraint((T0317)V14.CB, (T0317)L110.CB) [> 4.4039 = 7.3398 < 9.5417] w=0.1374 to align # Constraint # added constraint: constraint((T0317)P16.CB, (T0317)V85.CB) [> 4.3642 = 7.2736 < 9.4557] w=0.1374 to align # Constraint # added constraint: constraint((T0317)F11.CB, (T0317)L92.CB) [> 3.8780 = 6.4634 < 8.4024] w=0.1374 to align # Constraint # added constraint: constraint((T0317)F19.CB, (T0317)A103.CB) [> 3.9534 = 6.5890 < 8.5656] w=0.1374 to align # Constraint # added constraint: constraint((T0317)V85.CB, (T0317)Y109.CB) [> 4.3833 = 7.3054 < 9.4971] w=0.1352 to align # Constraint # added constraint: constraint((T0317)I20.CB, (T0317)A132.CB) [> 4.3720 = 7.2866 < 9.4726] w=0.1298 to align # Constraint # added constraint: constraint((T0317)V33.CB, (T0317)P53.CB) [> 3.6662 = 6.1104 < 7.9435] w=0.1289 to align # Constraint # added constraint: constraint((T0317)A79.CB, (T0317)R112.CB) [> 4.3859 = 7.3098 < 9.5027] w=0.1230 to align # Constraint # added constraint: constraint((T0317)L110.CB, (T0317)R120.CB) [> 4.5352 = 7.5587 < 9.8264] w=0.1212 to align # Constraint # added constraint: constraint((T0317)S102.CB, (T0317)R129.CB) [> 4.7073 = 7.8456 < 10.1992] w=0.1212 to align # Constraint # added constraint: constraint((T0317)G21.CA, (T0317)N42.CB) [> 4.6779 = 7.7965 < 10.1354] w=0.1209 to align # Constraint # added constraint: constraint((T0317)L18.CB, (T0317)I37.CB) [> 3.6676 = 6.1126 < 7.9464] w=0.1131 to align # Constraint # added constraint: constraint((T0317)A23.CB, (T0317)N42.CB) [> 4.6001 = 7.6669 < 9.9670] w=0.1125 to align # Constraint # added constraint: constraint((T0317)T38.CB, (T0317)D87.CB) [> 4.6007 = 7.6679 < 9.9682] w=0.1077 to align # Constraint # added constraint: constraint((T0317)F11.CB, (T0317)A25.CB) [> 2.8569 = 4.7615 < 6.1899] w=0.1050 to align # Constraint # added constraint: constraint((T0317)P10.CB, (T0317)A25.CB) [> 3.5402 = 5.9004 < 7.6705] w=0.1050 to align # Constraint # added constraint: constraint((T0317)S44.CB, (T0317)S102.CB) [> 4.5546 = 7.5910 < 9.8683] w=0.1050 to align # Constraint # added constraint: constraint((T0317)L32.CB, (T0317)S90.CB) [> 4.5351 = 7.5585 < 9.8261] w=0.1050 to align # Constraint # added constraint: constraint((T0317)V60.CB, (T0317)V105.CB) [> 4.5730 = 7.6216 < 9.9081] w=0.1047 to align # Constraint # added constraint: constraint((T0317)L70.CB, (T0317)R101.CB) [> 4.0297 = 6.7162 < 8.7311] w=0.0970 to align # Constraint # added constraint: constraint((T0317)M111.CB, (T0317)M124.CB) [> 4.1841 = 6.9735 < 9.0656] w=0.0970 to align # Constraint # added constraint: constraint((T0317)V43.CB, (T0317)L58.CB) [> 4.6782 = 7.7970 < 10.1361] w=0.0883 to align # Constraint # added constraint: constraint((T0317)P10.CB, (T0317)L31.CB) [> 3.6715 = 6.1192 < 7.9549] w=0.0808 to align # Constraint # added constraint: constraint((T0317)P9.CB, (T0317)N22.CB) [> 3.3585 = 5.5975 < 7.2768] w=0.0808 to align # Constraint # added constraint: constraint((T0317)N22.CB, (T0317)S102.CB) [> 4.6239 = 7.7066 < 10.0185] w=0.0808 to align # Constraint # added constraint: constraint((T0317)D119.CB, (T0317)Q143.CB) [> 4.5384 = 7.5641 < 9.8333] w=0.0727 to align # Constraint # added constraint: constraint((T0317)F11.CB, (T0317)I37.CB) [> 4.6754 = 7.7923 < 10.1300] w=0.0727 to align # Constraint # added constraint: constraint((T0317)A26.CB, (T0317)C40.CB) [> 3.8860 = 6.4766 < 8.4196] w=0.0727 to align # Constraint # added constraint: constraint((T0317)A26.CB, (T0317)N42.CB) [> 3.9355 = 6.5591 < 8.5268] w=0.0727 to align # Constraint # added constraint: constraint((T0317)A26.CB, (T0317)L92.CB) [> 3.9588 = 6.5979 < 8.5773] w=0.0727 to align # Constraint # added constraint: constraint((T0317)A26.CB, (T0317)Y94.CB) [> 2.7952 = 4.6588 < 6.0564] w=0.0727 to align # Constraint # added constraint: constraint((T0317)V62.CB, (T0317)V105.CB) [> 4.5965 = 7.6609 < 9.9592] w=0.0727 to align # Constraint # added constraint: constraint((T0317)L71.CB, (T0317)A108.CB) [> 4.6399 = 7.7332 < 10.0532] w=0.0727 to align # Constraint # added constraint: constraint((T0317)N22.CB, (T0317)R45.CB) [> 4.1943 = 6.9906 < 9.0877] w=0.0727 to align # Constraint # added constraint: constraint((T0317)A7.CB, (T0317)N97.CB) [> 3.5111 = 5.8518 < 7.6074] w=0.0646 to align # Constraint # added constraint: constraint((T0317)P9.CB, (T0317)G21.CA) [> 3.6924 = 6.1539 < 8.0001] w=0.0646 to align # Constraint # added constraint: constraint((T0317)A108.CB, (T0317)L118.CB) [> 4.6372 = 7.7286 < 10.0472] w=0.0566 to align # Constraint # added constraint: constraint((T0317)A7.CB, (T0317)G98.CA) [> 4.0573 = 6.7622 < 8.7908] w=0.0566 to align # Constraint # added constraint: constraint((T0317)S4.CB, (T0317)N97.CB) [> 4.4561 = 7.4268 < 9.6548] w=0.0566 to align # Constraint # added constraint: constraint((T0317)S4.CB, (T0317)K96.CB) [> 3.3574 = 5.5956 < 7.2743] w=0.0566 to align # Constraint # added constraint: constraint((T0317)P9.CB, (T0317)R24.CB) [> 4.1077 = 6.8461 < 8.9000] w=0.0566 to align # Constraint # added constraint: constraint((T0317)R45.CB, (T0317)C95.CB) [> 4.5535 = 7.5891 < 9.8658] w=0.0566 to align # Constraint # added constraint: constraint((T0317)A17.CB, (T0317)C106.CB) [> 2.8688 = 4.7814 < 6.2158] w=0.0566 to align # Constraint # added constraint: constraint((T0317)M111.CB, (T0317)L155.CB) [> 3.7793 = 6.2988 < 8.1884] w=0.0562 to align # Constraint # added constraint: constraint((T0317)C40.CB, (T0317)V60.CB) [> 3.5277 = 5.8794 < 7.6433] w=0.0486 to align # Constraint # added constraint: constraint((T0317)V33.CB, (T0317)L58.CB) [> 3.1935 = 5.3225 < 6.9193] w=0.0486 to align # Constraint # added constraint: constraint((T0317)A6.CB, (T0317)N97.CB) [> 4.1089 = 6.8481 < 8.9025] w=0.0485 to align # Constraint # added constraint: constraint((T0317)R45.CB, (T0317)R59.CB) [> 3.3810 = 5.6350 < 7.3255] w=0.0485 to align # Constraint # added constraint: constraint((T0317)V62.CB, (T0317)A104.CB) [> 4.7344 = 7.8907 < 10.2579] w=0.0485 to align # Constraint # added constraint: constraint((T0317)T29.CB, (T0317)Q47.CB) [> 4.5686 = 7.6143 < 9.8985] w=0.0432 to align # Constraint # added constraint: constraint((T0317)C40.CB, (T0317)P61.CB) [> 4.2269 = 7.0448 < 9.1582] w=0.0405 to align # Constraint # added constraint: constraint((T0317)L39.CB, (T0317)P61.CB) [> 3.0440 = 5.0733 < 6.5953] w=0.0405 to align # Constraint # added constraint: constraint((T0317)S4.CB, (T0317)G98.CA) [> 4.6432 = 7.7386 < 10.0602] w=0.0404 to align # Constraint # added constraint: constraint((T0317)W139.CB, (T0317)R157.CB) [> 4.3418 = 7.2364 < 9.4073] w=0.0404 to align # Constraint # added constraint: constraint((T0317)L136.CB, (T0317)R157.CB) [> 3.1720 = 5.2866 < 6.8726] w=0.0404 to align # Constraint # added constraint: constraint((T0317)E5.CB, (T0317)Y94.CB) [> 4.6589 = 7.7648 < 10.0943] w=0.0404 to align # Constraint # added constraint: constraint((T0317)A6.CB, (T0317)A23.CB) [> 3.6834 = 6.1391 < 7.9808] w=0.0404 to align # Constraint # added constraint: constraint((T0317)P8.CB, (T0317)Y94.CB) [> 4.1844 = 6.9739 < 9.0661] w=0.0404 to align # Constraint # added constraint: constraint((T0317)P8.CB, (T0317)A23.CB) [> 3.9183 = 6.5305 < 8.4896] w=0.0404 to align # Constraint # added constraint: constraint((T0317)A12.CB, (T0317)H113.CB) [> 3.7490 = 6.2483 < 8.1228] w=0.0404 to align # Constraint # added constraint: constraint((T0317)L32.CB, (T0317)L58.CB) [> 4.4759 = 7.4598 < 9.6977] w=0.0325 to align # Constraint # added constraint: constraint((T0317)A15.CB, (T0317)C106.CB) [> 4.5572 = 7.5953 < 9.8739] w=0.0323 to align # Constraint # added constraint: constraint((T0317)P8.CB, (T0317)P130.CB) [> 4.0964 = 6.8273 < 8.8754] w=0.0323 to align # Constraint # added constraint: constraint((T0317)T3.CB, (T0317)N97.CB) [> 3.5025 = 5.8375 < 7.5888] w=0.0323 to align # Constraint # added constraint: constraint((T0317)E5.CB, (T0317)A23.CB) [> 3.3747 = 5.6246 < 7.3119] w=0.0323 to align # Constraint # added constraint: constraint((T0317)A6.CB, (T0317)N22.CB) [> 4.4680 = 7.4467 < 9.6807] w=0.0323 to align # Constraint # added constraint: constraint((T0317)A6.CB, (T0317)R24.CB) [> 4.2966 = 7.1610 < 9.3093] w=0.0323 to align # Constraint # added constraint: constraint((T0317)L70.CB, (T0317)A108.CB) [> 4.5590 = 7.5983 < 9.8778] w=0.0323 to align # Constraint # added constraint: constraint((T0317)G98.CA, (T0317)P130.CB) [> 3.5570 = 5.9284 < 7.7069] w=0.0323 to align # Constraint # added constraint: constraint((T0317)S117.CB, (T0317)L155.CB) [> 3.1955 = 5.3258 < 6.9235] w=0.0320 to align # Constraint # added constraint: constraint((T0317)A7.CB, (T0317)K96.CB) [> 3.4558 = 5.7597 < 7.4876] w=0.0242 to align # Constraint # added constraint: constraint((T0317)Q141.CB, (T0317)I154.CB) [> 3.9100 = 6.5167 < 8.4717] w=0.0242 to align # Constraint # added constraint: constraint((T0317)L118.CB, (T0317)A153.CB) [> 3.7231 = 6.2051 < 8.0667] w=0.0242 to align # Constraint # added constraint: constraint((T0317)A108.CB, (T0317)I154.CB) [> 4.2315 = 7.0525 < 9.1683] w=0.0242 to align # Constraint # added constraint: constraint((T0317)G27.CA, (T0317)Y94.CB) [> 4.5304 = 7.5506 < 9.8158] w=0.0242 to align # Constraint # added constraint: constraint((T0317)K126.CB, (T0317)W139.CB) [> 4.7960 = 7.9934 < 10.3914] w=0.0242 to align # Constraint # added constraint: constraint((T0317)T107.CB, (T0317)F138.CB) [> 4.2444 = 7.0741 < 9.1963] w=0.0242 to align # Constraint # added constraint: constraint((T0317)S102.CB, (T0317)A128.CB) [> 4.6851 = 7.8086 < 10.1511] w=0.0242 to align # Constraint # added constraint: constraint((T0317)A17.CB, (T0317)L110.CB) [> 3.7825 = 6.3042 < 8.1954] w=0.0242 to align # Constraint # added constraint: constraint((T0317)I20.CB, (T0317)T107.CB) [> 4.7431 = 7.9052 < 10.2768] w=0.0242 to align # Constraint # added constraint: constraint((T0317)V14.CB, (T0317)T107.CB) [> 3.5290 = 5.8817 < 7.6462] w=0.0242 to align # Constraint # added constraint: constraint((T0317)C78.CB, (T0317)C106.CB) [> 4.7479 = 7.9132 < 10.2872] w=0.0242 to align # Constraint # added constraint: constraint((T0317)L18.CB, (T0317)C95.CB) [> 4.7515 = 7.9192 < 10.2950] w=0.0242 to align # Constraint # added constraint: constraint((T0317)L58.CB, (T0317)A83.CB) [> 3.9684 = 6.6140 < 8.5982] w=0.0236 to align # Constraint # added constraint: constraint((T0317)A6.CB, (T0317)K96.CB) [> 4.6502 = 7.7503 < 10.0754] w=0.0162 to align # Constraint # added constraint: constraint((T0317)A6.CB, (T0317)C95.CB) [> 4.7339 = 7.8898 < 10.2567] w=0.0162 to align # Constraint # added constraint: constraint((T0317)A6.CB, (T0317)Y94.CB) [> 3.9198 = 6.5330 < 8.4929] w=0.0162 to align # Constraint # added constraint: constraint((T0317)P10.CB, (T0317)C95.CB) [> 3.9369 = 6.5616 < 8.5300] w=0.0162 to align # Constraint # added constraint: constraint((T0317)T3.CB, (T0317)Y94.CB) [> 3.5439 = 5.9065 < 7.6785] w=0.0162 to align # Constraint # added constraint: constraint((T0317)R59.CB, (T0317)L70.CB) [> 4.1712 = 6.9520 < 9.0375] w=0.0162 to align # Constraint # added constraint: constraint((T0317)G21.CA, (T0317)R45.CB) [> 4.4432 = 7.4053 < 9.6268] w=0.0162 to align # Constraint # added constraint: constraint((T0317)P16.CB, (T0317)Y109.CB) [> 4.3590 = 7.2650 < 9.4445] w=0.0162 to align # Constraint # added constraint: constraint((T0317)C91.CB, (T0317)C106.CB) [> 4.7281 = 7.8802 < 10.2443] w=0.0162 to align # Constraint # added constraint: constraint((T0317)A108.CB, (T0317)N135.CB) [> 4.5265 = 7.5442 < 9.8074] w=0.0162 to align # Constraint # added constraint: constraint((T0317)P53.CB, (T0317)C95.CB) [> 4.7106 = 7.8510 < 10.2063] w=0.0162 to align # Constraint # added constraint: constraint((T0317)F63.CB, (T0317)Q141.CB) [> 4.7583 = 7.9306 < 10.3097] w=0.0162 to align # Constraint # added constraint: constraint((T0317)C106.CB, (T0317)P130.CB) [> 3.8527 = 6.4212 < 8.3475] w=0.0162 to align # Constraint # added constraint: constraint((T0317)S102.CB, (T0317)P130.CB) [> 4.5752 = 7.6253 < 9.9129] w=0.0162 to align # Constraint # added constraint: constraint((T0317)E57.CB, (T0317)V105.CB) [> 4.7241 = 7.8735 < 10.2355] w=0.0159 to align # Constraint # added constraint: constraint((T0317)F63.CB, (T0317)R101.CB) [> 3.7592 = 6.2654 < 8.1450] w=0.0159 to align # Constraint # added constraint: constraint((T0317)P134.CB, (T0317)L155.CB) [> 3.2224 = 5.3707 < 6.9819] w=0.0081 to align # Constraint # added constraint: constraint((T0317)R114.CB, (T0317)I154.CB) [> 3.4779 = 5.7965 < 7.5355] w=0.0081 to align # Constraint # added constraint: constraint((T0317)R59.CB, (T0317)V105.CB) [> 4.6768 = 7.7946 < 10.1330] w=0.0078 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0317/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0317/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 T0317 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 133 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 133 # 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 133 # 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 100 # 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 139 # 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 129 # 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 129 # 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 44 # 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 51 # 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 131 # 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 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 161 # 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 T0317 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 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 161 # 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 T0317 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 T0317 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 T0317 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 T0317 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 161 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 141 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 89 # 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 130 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 T0317 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 6, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 131, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 287, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 289, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 291, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 293, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 331, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 333, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 335, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 337, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 359, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 361, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 363, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 365, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 367, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 369, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 371, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 373, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 391, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 393, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 395, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 397, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 399, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 401, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 403, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 405, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 467, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 469, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 471, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 473, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 483, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 485, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 487, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 489, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 527, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 529, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 531, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 533, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz # WARNING: incomplete conformation T0317 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 T0317 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 # WARNING: incomplete conformation T0317 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 T0317 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 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 T0317 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 117 # 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 162 # 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 128 # 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 107 # 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 145 # 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 T0317 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 T0317 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 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 T0317 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 # WARNING: incomplete conformation T0317 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 T0317 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 Skipped atom 150, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 152, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 154, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 156, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 458, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 460, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 462, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz Skipped atom 464, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 T0317 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 161 # 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 161 # 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 161 # 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 158 # 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 161 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 # Found a chain break before 148 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 48 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 T0317 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 T0317 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 T0317 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 49 # copying to AlignedFragments data structure # 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 152 # 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 # 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 114 # 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 134 # 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 155 # 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 160 # 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 161 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 133 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 50 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 # Found a chain break before 55 # 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 T0317 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 T0317 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 # Found a chain break before 43 # 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 # Found a chain break before 43 # 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 # Found a chain break before 49 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 134 # copying to AlignedFragments data structure # 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 130 # 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 # Found a chain break before 148 # copying to AlignedFragments data structure # 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 130 # 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 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # 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 160 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 158 # 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 161 # 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 161 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 130 # 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 99 # 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 148 # 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 46 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 49 # 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 52 # 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 8 # 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 134 # 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 140 # 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 147 # 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 # Found a chain break before 145 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 152 # 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 # WARNING: incomplete conformation T0317 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 # WARNING: incomplete conformation T0317 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 # WARNING: incomplete conformation T0317 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 T0317 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 # WARNING: incomplete conformation T0317 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 # WARNING: incomplete conformation T0317 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 # WARNING: incomplete conformation T0317 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 # WARNING: incomplete conformation T0317 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 T0317 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 T0317 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 158 # 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 T0317 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 T0317 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 T0317 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 T0317 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 # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 65 # 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 95 # 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 152 # 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 158 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 11 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 145 # 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 131 # 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 T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 T0317 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 # WARNING: incomplete conformation T0317 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 T0317 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 # WARNING: incomplete conformation T0317 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 T0317 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 # WARNING: incomplete conformation T0317 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 158 # 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 158 # 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 158 # 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 158 # 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 159 # 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 # Found a chain break before 162 # 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 T0317 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 T0317 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 T0317 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 Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 146, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 148, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 438, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 440, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 442, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 444, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz # WARNING: incomplete conformation T0317 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 T0317 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 T0317 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 131 # 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 130 # 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 # 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 130 # 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.4_TS1.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 160 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 160 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 159 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 T0317 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # 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 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 T0317 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 T0317 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 T0317 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 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 T0317 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 T0317 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0317 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.4554 model score -0.4527 model score -0.1731 model score -0.1697 model score -0.1725 model score -0.4420 model score -0.4256 model score -0.3946 model score -0.2525 model score -0.4236 model score 0.0801 model score -0.3813 model score -0.4531 model score -0.3722 model score 0.1391 model score -0.5107 model score 0.4797 model score 0.4778 model score 0.6176 model score 1.7894 model score 1.0704 model score 1.3176 model score 1.5793 model score 1.3473 model score 1.1104 model score 0.1067 model score -0.4689 model score -0.4435 model score -0.4674 model score -0.4744 model score -0.4380 model score -0.4749 model score -0.5029 model score -0.5104 model score -0.5009 model score -0.5010 model score -0.4532 model score -0.1810 model score -0.3277 model score 0.0903 model score 0.3438 model score 0.1129 model score 1.2586 model score 1.2608 model score 1.2545 model score 1.2561 model score 1.2575 model score -0.2387 model score -0.4739 model score -0.2613 model score -0.4459 model score -0.3728 model score -0.4997 model score -0.4749 model score -0.5029 model score -0.5010 model score -0.4459 model score -0.5013 model score 0.8378 model score 1.4163 model score 0.5403 model score 1.5172 model score 1.2643 model score 1.2806 model score 1.2899 model score 1.2669 model score 1.2708 model score 1.2643 model score 1.2651 model score 1.2806 model score 1.2909 model score 1.2908 model score 2.2693 model score 2.0619 model score 2.0304 model score 2.1533 model score 2.1193 model score -0.4765 model score -0.0266 model score 0.3471 model score -0.2271 model score -0.0703 model score 1.2631 model score 1.2655 model score 1.2664 model score 1.2764 model score 1.2656 model score -0.5000 model score -0.4507 model score -0.4269 model score -0.1462 model score -0.4352 model score -0.4540 model score -0.4735 model score -0.5210 model score -0.4362 model score -0.3470 model score -0.5051 model score 0.0921 model score 0.0921 model score -0.3717 model score -0.3569 model score -0.4748 model score 0.1009 model score -0.3473 model score -0.4253 model score -0.3797 model score 0.2533 model score -0.2610 model score -0.3946 model score -0.5206 model score -0.4683 model score -0.3598 model score -0.1553 model score 0.0157 model score -0.4597 model score -0.4398 model score -0.4599 model score -0.3693 model score -0.4671 model score -0.5104 model score -0.5164 model score -0.5209 model score -0.5166 model score -0.5185 model score -0.5177 model score -0.3929 model score -0.4531 model score -0.4728 model score -0.4992 model score -0.5166 model score -0.4740 model score -0.4413 model score -0.4258 model score -0.5141 model score -0.5216 model score -0.3209 model score -0.4708 model score -0.4441 model score -0.4441 model score -0.4788 model score -0.4788 model score -0.4687 model score -0.4740 model score -0.2956 model score -0.3537 model score -0.2725 model score -0.4772 model score -0.5189 model score -0.4793 model score -0.4556 model score -0.4873 model score -0.2743 model score -0.4546 model score -0.4518 model score -0.5037 model score -0.5047 model score -0.4564 model score -0.4829 model score -0.4536 model score -0.5205 model score -0.5250 model score -0.4844 model score -0.4687 model score -0.5037 model score -0.5129 model score -0.2725 model score 0.0929 model score -0.4582 model score -0.3730 model score -0.4398 model score -0.3006 model score 1.2614 model score 1.2617 model score 1.2643 model score 1.2712 model score 1.2638 model score 1.2712 model score 1.2633 model score 1.2614 model score 1.2629 model score 1.2617 model score -0.3572 model score -0.5017 model score -0.4499 model score -0.3641 model score -0.1482 model score -0.4873 model score -0.5146 model score -0.3587 model score -0.2040 model score -0.0710 model score -0.4358 model score -0.5146 model score -0.3587 model score -0.3119 model score -0.3845 model score -0.3554 model score -0.4755 model score -0.5119 model score -0.0998 model score -0.0942 model score 1.2712 model score 1.2643 model score 1.2638 model score 1.2617 model score 1.2614 model score -0.4692 model score 1.2712 model score 1.2643 model score 1.2638 model score 1.2617 model score 1.2614 model score -0.5057 model score -0.5016 model score -0.4714 model score 0.0820 model score -0.5161 model score -0.4529 model score -0.4721 model score 1.2643 model score 1.2631 model score 1.2664 model score 1.2666 model score 1.2750 model score 1.2712 model score 1.2643 model score 1.2918 model score 1.2911 model score 1.2915 model score -0.4683 model score -0.4700 model score -0.4402 model score -0.4745 model score -0.4632 model score 2.3372 model score 2.1427 model score 1.5895 model score 1.9452 model score 2.0357 model score 0.0838 model score -0.3690 model score -0.4843 model score 0.1520 model score 0.0364 model score -0.4723 model score -0.4547 model score -0.3255 model score 0.1021 model score -0.4411 model score -0.5104 model score -0.4313 model score 0.2177 model score 0.0943 model score 0.0452 model score -0.4062 model score -0.4626 USE_META, weight: 0.9781 cost: -0.4554 min: -0.5250 max: 2.3372 USE_META, weight: 0.9773 cost: -0.4527 min: -0.5250 max: 2.3372 USE_META, weight: 0.8894 cost: -0.1731 min: -0.5250 max: 2.3372 USE_META, weight: 0.8883 cost: -0.1697 min: -0.5250 max: 2.3372 USE_META, weight: 0.8892 cost: -0.1725 min: -0.5250 max: 2.3372 USE_META, weight: 0.9739 cost: -0.4420 min: -0.5250 max: 2.3372 USE_META, weight: 0.9687 cost: -0.4256 min: -0.5250 max: 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0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9587 eval: 0.0010 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9587 eval: 0.0010 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9587 eval: 0.0010 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9626 eval: 0.0009 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9626 eval: 0.0009 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9626 eval: 0.0009 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9438 eval: 0.0013 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9438 eval: 0.0013 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9438 eval: 0.0013 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9589 eval: 0.0010 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9589 eval: 0.0010 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9589 eval: 0.0010 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.1000 eval: 0.0212 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.1000 eval: 0.0212 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.1000 eval: 0.0212 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.3876 eval: 0.0144 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.3876 eval: 0.0144 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.3876 eval: 0.0144 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9612 eval: 0.0009 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9612 eval: 0.0009 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9612 eval: 0.0009 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9843 eval: 0.0004 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9843 eval: 0.0004 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 0.9843 eval: 0.0004 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0212 Number of contacts in models: 257 Number of contacts in alignments: 129 NUMB_ALIGNS: 129 Adding 4807 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: -275.8566, CN propb: -275.8566 weights: 0.4522 constraints: 370 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 370 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 370 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 4437 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 4437 # 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 4807 # command: