# 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/T0291/ # command:# Making conformation for sequence T0291 numbered 1 through 310 Created new target T0291 from T0291.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0291/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0291//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0291/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0291//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0291/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0291/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0291/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u59A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u59A expands to /projects/compbio/data/pdb/1u59.pdb.gz 1u59A:Skipped atom 483, because occupancy 0.5 <= existing 0.500 in 1u59A Skipped atom 485, because occupancy 0.500 <= existing 0.500 in 1u59A Skipped atom 487, because occupancy 0.500 <= existing 0.500 in 1u59A Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 1u59A Skipped atom 491, because occupancy 0.500 <= existing 0.500 in 1u59A Skipped atom 1215, because occupancy 0.500 <= existing 0.500 in 1u59A # T0291 read from 1u59A/merged-good-all-a2m # 1u59A read from 1u59A/merged-good-all-a2m # adding 1u59A to template set # found chain 1u59A in template set Warning: unaligning (T0291)K47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u59A)K362 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u59A)K362 T0291 19 :AKELDATNISIDK 1u59A 329 :KLFLKRDNLLIAD # choosing archetypes in rotamer library T0291 32 :VVGAGEFGEVCSGRL 1u59A 343 :ELGCGNFGSVRQGVY T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1u59A 363 :QIDVAIKVLKQGTEKADTEEMMREAQIMHQLDNPYIVRLIGVCQA T0291 99 :KPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1u59A 408 :EALMLVMEMAGGGPLHKFLVGKREEIPVSNVAELLHQVSMGMKYLEEKNFVHRDLAARNVLLVNRHYAKISDFGLSKALGADDSYYTARSAGKWPLKWYAPECINFRKFSSRSDVWSYGVTMWEALSYGQKPYKKMKGPEVMAFIEQGKRMECPPECPPELYALMSDCWIYKWEDRPDFLTVEQRMRACYYS Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 Number of alignments=1 # 1u59A read from 1u59A/merged-good-all-a2m # found chain 1u59A in template set Warning: unaligning (T0291)K47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u59A)K362 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u59A)K362 T0291 19 :AKELDATNISIDK 1u59A 329 :KLFLKRDNLLIAD T0291 32 :VVGAGEFGEVCSGRL 1u59A 343 :ELGCGNFGSVRQGVY T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1u59A 363 :QIDVAIKVLKQGTEKADTEEMMREAQIMHQLDNPYIVRLIGVCQA T0291 99 :KPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1u59A 408 :EALMLVMEMAGGGPLHKFLVGKREEIPVSNVAELLHQVSMGMKYLEEKNFVHRDLAARNVLLVNRHYAKISDFGLSKALGADDSYYTARSAGKWPLKWYAPECINFRKFSSRSDVWSYGVTMWEALSYGQKPYKKMKGPEVMAFIEQGKRMECPPECPPELYALMSDCWIYKWEDRPDFLTVEQRMRACYY Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 Number of alignments=2 # 1u59A read from 1u59A/merged-good-all-a2m # found chain 1u59A in template set Warning: unaligning (T0291)K47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u59A)K362 Warning: unaligning (T0291)K51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u59A)K362 T0291 19 :AKELDATNISIDK 1u59A 329 :KLFLKRDNLLIAD T0291 32 :VVGAGEFGEVCSGRL 1u59A 343 :ELGCGNFGSVRQGVY T0291 52 :KEI 1u59A 363 :QID T0291 56 :VAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1u59A 366 :VAIKVLKQGTEKADTEEMMREAQIMHQLDNPYIVRLIGVCQA T0291 99 :KPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1u59A 408 :EALMLVMEMAGGGPLHKFLVGKREEIPVSNVAELLHQVSMGMKYLEEKNFVHRDLAARNVLLVNRHYAKISDFGLSKALGADDSYYTARSAGKWPLKWYAPECINFRKFSSRSDVWSYGVTMWEALSYGQKPYKKMKGPEVMAFIEQGKRMECPPECPPELYALMSDCWIYKWEDRPDFLTVEQRMRACYY Number of specific fragments extracted= 5 number of extra gaps= 0 total=13 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lufA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lufA expands to /projects/compbio/data/pdb/1luf.pdb.gz 1lufA:# T0291 read from 1lufA/merged-good-all-a2m # 1lufA read from 1lufA/merged-good-all-a2m # adding 1lufA to template set # found chain 1lufA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1lufA)L560 Warning: unaligning (T0291)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lufA)P694 Warning: unaligning (T0291)Y185 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lufA)D761 Warning: unaligning (T0291)G190 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lufA)D761 Warning: unaligning (T0291)R289 because last residue in template chain is (1lufA)E860 T0291 14 :AVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1lufA 561 :NPKLLSLEYPRNNIEYVRDIGEGAFGRVFQARAP T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1lufA 597 :LPYEPFTMVAVKMLKEEASADMQADFQREAALMAEFDNPNIVKLLGVCAVGKPMCLLFEYMAYGDLNEFLRSM T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1lufA 695 :PLSCAEQLCIARQVAAGMAYLSERKFVHRDLATRNCLVGENMVVKIADFGLSRNIYSA T0291 182 :EAA 1lufA 753 :DYY T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 1lufA 762 :AIPIRWMPPESIFYNRYTTESDVWAYGVVLWEIFSYGLQPYYGMAHEEVIYYVRDGNILACPENCPLELYNLMRLCWSKLPADRPSFCSIHRILQRMC Number of specific fragments extracted= 5 number of extra gaps= 0 total=18 Number of alignments=4 # 1lufA read from 1lufA/merged-good-all-a2m # found chain 1lufA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1lufA)L560 Warning: unaligning (T0291)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lufA)P694 Warning: unaligning (T0291)Y185 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lufA)D761 Warning: unaligning (T0291)G190 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lufA)D761 Warning: unaligning (T0291)R289 because last residue in template chain is (1lufA)E860 T0291 14 :AVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1lufA 561 :NPKLLSLEYPRNNIEYVRDIGEGAFGRVFQARAP T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1lufA 597 :LPYEPFTMVAVKMLKEEASADMQADFQREAALMAEFDNPNIVKLLGVCAVGKPMCLLFEYMAYGDLNEFLR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1lufA 695 :PLSCAEQLCIARQVAAGMAYLSERKFVHRDLATRNCLVGENMVVKIADFGLSRNIYSA T0291 182 :EAA 1lufA 753 :DYY T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 1lufA 762 :AIPIRWMPPESIFYNRYTTESDVWAYGVVLWEIFSYGLQPYYGMAHEEVIYYVRDGNILACPENCPLELYNLMRLCWSKLPADRPSFCSIHRILQRMC Number of specific fragments extracted= 5 number of extra gaps= 0 total=23 Number of alignments=5 # 1lufA read from 1lufA/merged-good-all-a2m # found chain 1lufA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1lufA)L560 Warning: unaligning (T0291)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lufA)P694 Warning: unaligning (T0291)Y185 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lufA)D761 Warning: unaligning (T0291)G190 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lufA)D761 Warning: unaligning (T0291)R289 because last residue in template chain is (1lufA)E860 T0291 14 :AVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1lufA 561 :NPKLLSLEYPRNNIEYVRDIGEGAFGRVFQARAPG T0291 49 :PSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1lufA 598 :PYEPFTMVAVKMLKEEASADMQADFQREAALMAEFDNPNIVKLLGVCAVGKPMCLLFEYMAYGDLNEFLR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1lufA 695 :PLSCAEQLCIARQVAAGMAYLSERKFVHRDLATRNCLVGENMVVKIADFGLSRNIYSADYY T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 1lufA 762 :AIPIRWMPPESIFYNRYTTESDVWAYGVVLWEIFSYGLQPYYGMAHEEVIYYVRDGNILACPENCPLELYNLMRLCWSKLPADRPSFCSIHRILQRMC Number of specific fragments extracted= 4 number of extra gaps= 0 total=27 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z57A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z57A expands to /projects/compbio/data/pdb/1z57.pdb.gz 1z57A:Skipped atom 406, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 408, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1026, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1028, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1181, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1184, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1255, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1257, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1259, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1261, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1263, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1499, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1501, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 2508, because occupancy 0.500 <= existing 0.500 in 1z57A Skipped atom 2512, because occupancy 0.500 <= existing 0.500 in 1z57A Skipped atom 2514, because occupancy 0.500 <= existing 0.500 in 1z57A Skipped atom 2516, because occupancy 0.500 <= existing 0.500 in 1z57A Skipped atom 2518, because occupancy 0.500 <= existing 0.500 in 1z57A # T0291 read from 1z57A/merged-good-all-a2m # 1z57A read from 1z57A/merged-good-all-a2m # adding 1z57A to template set # found chain 1z57A in template set Warning: unaligning (T0291)T105 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1z57A)E242 Warning: unaligning (T0291)E106 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1z57A)E242 T0291 12 :TQAVHEFAKEL 1z57A -1 :MHLICQSGDVL T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1z57A 158 :SARYEIVDTLGEGAFGKVVECID T0291 49 :PSKKEISVAIKTLKVG 1z57A 181 :HKAGGRHVAVKIVKNV T0291 67 :EKQRRDFLGEASIMGQF 1z57A 197 :DRYCEAARSEIQVLEHL T0291 85 :HPNIIRLEGVVTKSKPVMIV 1z57A 221 :TFRCVQMLEWFEHHGHICIV T0291 107 :YMEN 1z57A 243 :LLGL T0291 112 :SLDSFLRKHDAQ 1z57A 247 :STYDFIKENGFL T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1z57A 260 :FRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILF T0291 161 :NSNLVCKVSDFGLGRVLEDD 1z57A 316 :LINPDIKVVDFGSATYDDEH T0291 187 :TRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1z57A 336 :HSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYL T0291 227 :GERPYWEMSNQDVIKAVD 1z57A 375 :GFTVFPTHDSKEHLAMME T0291 246 :GYRLPPPMDC 1z57A 414 :HDRLDWDEHS T0291 257 :AALYQLMLDCWQKDRNNRPKFEQIVS 1z57A 448 :ERLFDLIQKMLEYDPAKRITLREALK Number of specific fragments extracted= 13 number of extra gaps= 1 total=40 Number of alignments=7 # 1z57A read from 1z57A/merged-good-all-a2m # found chain 1z57A in template set Warning: unaligning (T0291)T105 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1z57A)E242 Warning: unaligning (T0291)E106 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1z57A)E242 T0291 18 :FAKEL 1z57A 153 :SGDVL T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1z57A 158 :SARYEIVDTLGEGAFGKVVECID T0291 49 :PSKKEISVAIKTLKV 1z57A 181 :HKAGGRHVAVKIVKN T0291 66 :TEKQRRDFLGEASIMGQF 1z57A 196 :VDRYCEAARSEIQVLEHL T0291 84 :DHPN 1z57A 219 :NSTF T0291 88 :IIRLEGVVTKSKPVMIV 1z57A 224 :CVQMLEWFEHHGHICIV T0291 107 :YMEN 1z57A 243 :LLGL T0291 112 :SLDSFLRKHDA 1z57A 247 :STYDFIKENGF T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1z57A 259 :PFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILF T0291 161 :NSNLVCKVSDFGLGRVLED 1z57A 316 :LINPDIKVVDFGSATYDDE T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1z57A 335 :HHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYL T0291 227 :GERPYWEMS 1z57A 375 :GFTVFPTHD T0291 236 :NQDVIKAV 1z57A 399 :PKHMIQKT T0291 244 :DEGYRLPPPM 1z57A 412 :FHHDRLDWDE T0291 255 :CPAALYQLMLDCWQKDRNNRPKFEQIVSI 1z57A 446 :EHERLFDLIQKMLEYDPAKRITLREALKH Number of specific fragments extracted= 15 number of extra gaps= 1 total=55 Number of alignments=8 # 1z57A read from 1z57A/merged-good-all-a2m # found chain 1z57A in template set Warning: unaligning (T0291)T105 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1z57A)E242 Warning: unaligning (T0291)E106 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1z57A)E242 T0291 24 :ATNISIDKVVGAGEFGEVCSGRLKL 1z57A 158 :SARYEIVDTLGEGAFGKVVECIDHK T0291 49 :PSKKEISVAIK 1z57A 184 :GGRHVAVKIVK T0291 65 :YTEKQRRDFLGEASIMGQF 1z57A 195 :NVDRYCEAARSEIQVLEHL T0291 84 :DHPNIIRLEGVVTKSKPVMIV 1z57A 220 :STFRCVQMLEWFEHHGHICIV T0291 107 :YMEN 1z57A 243 :LLGL T0291 112 :SLDSFLRKHD 1z57A 247 :STYDFIKENG T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1z57A 258 :LPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILF T0291 161 :NSNLVCKVSDFGLGRVLEDD 1z57A 316 :LINPDIKVVDFGSATYDDEH T0291 187 :TRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1z57A 336 :HSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMM T0291 249 :LPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1z57A 440 :MLSQDVEHERLFDLIQKMLEYDPAKRITLREALKH Number of specific fragments extracted= 10 number of extra gaps= 1 total=65 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uu3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0291 read from 1uu3A/merged-good-all-a2m # 1uu3A read from 1uu3A/merged-good-all-a2m # found chain 1uu3A in training set Warning: unaligning (T0291)F18 because first residue in template chain is (1uu3A)Q73 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uu3A)F242 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uu3A)F242 Warning: unaligning (T0291)K276 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uu3A)G332 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLK 1uu3A 74 :PRKKRPEDFKFGKILGEGSFSTVVLAREL T0291 51 :KKEISVAIKTLK 1uu3A 103 :ATSREYAIKILE T0291 68 :KQRRD 1uu3A 116 :RHIIK T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1uu3A 127 :VTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGS T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1uu3A 177 :FDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKV T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1uu3A 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVA T0291 227 :GERPYWEMSNQDVIKAVDEG 1uu3A 278 :GLPPFRAGNEYLIFQKIIKL T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1uu3A 298 :EYDFPEKFFPKARDLVEKLLVLDATKRL T0291 277 :FEQIVS 1uu3A 333 :YGPLKA Number of specific fragments extracted= 9 number of extra gaps= 1 total=74 Number of alignments=10 # 1uu3A read from 1uu3A/merged-good-all-a2m # found chain 1uu3A in training set Warning: unaligning (T0291)F18 because first residue in template chain is (1uu3A)Q73 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uu3A)F242 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uu3A)F242 Warning: unaligning (T0291)K276 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uu3A)G332 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLK 1uu3A 74 :PRKKRPEDFKFGKILGEGSFSTVVLAREL T0291 51 :KKEISVAIKTLKVGYT 1uu3A 103 :ATSREYAIKILEKRHI T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1uu3A 121 :ENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGS T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1uu3A 177 :FDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKV T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1uu3A 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVA T0291 227 :GERPYWEMSNQDVIKAVDEG 1uu3A 278 :GLPPFRAGNEYLIFQKIIKL T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1uu3A 298 :EYDFPEKFFPKARDLVEKLLVLDATKRL T0291 277 :FEQIVSILDKLIRNPGSLKIIT 1uu3A 333 :YGPLKAHPFFESVTWENLHQQT Number of specific fragments extracted= 8 number of extra gaps= 1 total=82 Number of alignments=11 # 1uu3A read from 1uu3A/merged-good-all-a2m # found chain 1uu3A in training set Warning: unaligning (T0291)F18 because first residue in template chain is (1uu3A)Q73 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uu3A)F242 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uu3A)F242 Warning: unaligning (T0291)K276 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uu3A)G332 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1uu3A 74 :PRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHI T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1uu3A 119 :IKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1uu3A 176 :SFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKV T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDE 1uu3A 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKL T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1uu3A 298 :EYDFPEKFFPKARDLVEKLLVLDATKRL T0291 277 :FEQIVSIL 1uu3A 333 :YGPLKAHP T0291 290 :NPGSLKIITSAAA 1uu3A 341 :FFESVTWENLHQQ Number of specific fragments extracted= 7 number of extra gaps= 1 total=89 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1opjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1opjA expands to /projects/compbio/data/pdb/1opj.pdb.gz 1opjA:# T0291 read from 1opjA/merged-good-all-a2m # 1opjA read from 1opjA/merged-good-all-a2m # adding 1opjA to template set # found chain 1opjA in template set T0291 12 :TQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRL 1opjA 246 :PSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVW T0291 50 :SKKEISVAIKTLKVGYTE 1opjA 281 :KKYSLTVAVKTLKEDTME T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1opjA 299 :VEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLREC T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1opjA 351 :RQEVSAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDT T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNP 1opjA 412 :YTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQES Number of specific fragments extracted= 5 number of extra gaps= 0 total=94 Number of alignments=13 # 1opjA read from 1opjA/merged-good-all-a2m # found chain 1opjA in template set T0291 3 :VDPHT 1opjA 244 :MDPSS T0291 15 :VHEFAKELDATNISIDKVVGAGEFGEVCSGRL 1opjA 249 :PNYDKWEMERTDITMKHKLGGGQYGEVYEGVW T0291 50 :SKKEISVAIKTLKVGYTE 1opjA 281 :KKYSLTVAVKTLKEDTME T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1opjA 299 :VEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1opjA 353 :EVSAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDT T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1opjA 412 :YTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESS Number of specific fragments extracted= 6 number of extra gaps= 0 total=100 Number of alignments=14 # 1opjA read from 1opjA/merged-good-all-a2m # found chain 1opjA in template set T0291 10 :DPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKLPSK 1opjA 244 :MDPSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSL T0291 55 :SVAIKTLKVGYTE 1opjA 286 :TVAVKTLKEDTME T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1opjA 299 :VEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLR T0291 119 :KHD 1opjA 350 :NRQ T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1opjA 353 :EVSAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTY T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNP 1opjA 413 :TAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQES Number of specific fragments extracted= 6 number of extra gaps= 0 total=106 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u46A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u46A expands to /projects/compbio/data/pdb/1u46.pdb.gz 1u46A:# T0291 read from 1u46A/merged-good-all-a2m # 1u46A read from 1u46A/merged-good-all-a2m # adding 1u46A to template set # found chain 1u46A in template set Warning: unaligning (T0291)F18 because first residue in template chain is (1u46A)L117 Warning: unaligning (T0291)K20 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1u46A)L120 Warning: unaligning (T0291)E21 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1u46A)L120 Warning: unaligning (T0291)G34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)G138 Warning: unaligning (T0291)G39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)G138 Warning: unaligning (T0291)T60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)P168 Warning: unaligning (T0291)E67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)P168 Warning: unaligning (T0291)Q82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u46A)L184 Warning: unaligning (T0291)F83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)L184 Warning: unaligning (T0291)R175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u46A)A276 Warning: unaligning (T0291)V176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)A276 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)D281 Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)D281 Warning: unaligning (T0291)E182 because of BadResidue code BAD_PEPTIDE at template residue (1u46A)D282 Warning: unaligning (T0291)T186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)V292 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)V292 Warning: unaligning (T0291)P193 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)P293 Warning: unaligning (T0291)I288 because last residue in template chain is (1u46A)Q389 T0291 19 :A 1u46A 118 :T T0291 22 :LDATNISIDKVV 1u46A 121 :IGEKDLRLLEKL T0291 40 :EVCSGRLKLPSKKEISVAIK 1u46A 139 :VVRRGEWDAPSGKTVSVAVK T0291 68 :KQRRDFLGEASIMG 1u46A 169 :EAMDDFIREVNAMH T0291 84 :DHPNIIRLEGVVTK 1u46A 185 :DHRNLIRLYGVVLT T0291 99 :KPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLG 1u46A 199 :PPMKMVTELAPLGSLLDRLRKHQGHFLLGTLSRYAVQVAEGMGYLESKRFIHRDLAARNLLLATRDLVKIGDFGLM T0291 177 :LE 1u46A 277 :LP T0291 183 :AAY 1u46A 283 :HYV T0291 194 :IRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 1u46A 294 :FAWCAPESLKTRTFSHASDTWMFGVTLWEMFTYGQEPWIGLNGSQILHKIDKE T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKL 1u46A 348 :ERLPRPEDCPQDIYNVMVQCWAHKPEDRPTFVALRDFLLEA Number of specific fragments extracted= 10 number of extra gaps= 3 total=116 Number of alignments=16 # 1u46A read from 1u46A/merged-good-all-a2m # found chain 1u46A in template set Warning: unaligning (T0291)K20 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1u46A)L120 Warning: unaligning (T0291)E21 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1u46A)L120 Warning: unaligning (T0291)G34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)G138 Warning: unaligning (T0291)G39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)G138 Warning: unaligning (T0291)T60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)P168 Warning: unaligning (T0291)E67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)P168 Warning: unaligning (T0291)Q82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u46A)L184 Warning: unaligning (T0291)F83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)L184 Warning: unaligning (T0291)R175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u46A)A276 Warning: unaligning (T0291)V176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)A276 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)D281 Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)D281 Warning: unaligning (T0291)E182 because of BadResidue code BAD_PEPTIDE at template residue (1u46A)D282 Warning: unaligning (T0291)T186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)V292 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)V292 Warning: unaligning (T0291)P193 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)P293 Warning: unaligning (T0291)I288 because last residue in template chain is (1u46A)Q389 T0291 22 :LDATNISIDKVV 1u46A 121 :IGEKDLRLLEKL T0291 40 :EVCSGRLKLPSKKEISVAIK 1u46A 139 :VVRRGEWDAPSGKTVSVAVK T0291 68 :KQRRDFLGEASIMG 1u46A 169 :EAMDDFIREVNAMH T0291 84 :DHPNIIRLEGVVTKSKP 1u46A 185 :DHRNLIRLYGVVLTPPM T0291 102 :MIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLG 1u46A 202 :KMVTELAPLGSLLDRLRKHQGHFLLGTLSRYAVQVAEGMGYLESKRFIHRDLAARNLLLATRDLVKIGDFGLM T0291 177 :LE 1u46A 277 :LP T0291 183 :AAY 1u46A 283 :HYV T0291 194 :IRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 1u46A 294 :FAWCAPESLKTRTFSHASDTWMFGVTLWEMFTYGQEPWIGLNGSQILHKIDKE T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKL 1u46A 348 :ERLPRPEDCPQDIYNVMVQCWAHKPEDRPTFVALRDFLLEA Number of specific fragments extracted= 9 number of extra gaps= 3 total=125 Number of alignments=17 # 1u46A read from 1u46A/merged-good-all-a2m # found chain 1u46A in template set Warning: unaligning (T0291)K20 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1u46A)L120 Warning: unaligning (T0291)E21 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1u46A)L120 Warning: unaligning (T0291)G34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)G138 Warning: unaligning (T0291)G39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)G138 Warning: unaligning (T0291)T60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)P168 Warning: unaligning (T0291)E67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)P168 Warning: unaligning (T0291)Q82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u46A)L184 Warning: unaligning (T0291)F83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)L184 Warning: unaligning (T0291)R175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u46A)A276 Warning: unaligning (T0291)V176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)A276 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)D281 Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)D281 Warning: unaligning (T0291)E182 because of BadResidue code BAD_PEPTIDE at template residue (1u46A)D282 Warning: unaligning (T0291)T186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)V292 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)V292 Warning: unaligning (T0291)P193 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)P293 Warning: unaligning (T0291)I288 because last residue in template chain is (1u46A)Q389 T0291 22 :LDATNISIDKVV 1u46A 121 :IGEKDLRLLEKL T0291 40 :EVCSGRLKLPSKKEISVAIK 1u46A 139 :VVRRGEWDAPSGKTVSVAVK T0291 68 :KQRRDFLGEASIMG 1u46A 169 :EAMDDFIREVNAMH T0291 84 :DHPNIIRLEGVVTKSK 1u46A 185 :DHRNLIRLYGVVLTPP T0291 101 :VMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLG 1u46A 201 :MKMVTELAPLGSLLDRLRKHQGHFLLGTLSRYAVQVAEGMGYLESKRFIHRDLAARNLLLATRDLVKIGDFGLM T0291 177 :LE 1u46A 277 :LP T0291 183 :AAY 1u46A 283 :HYV T0291 194 :IRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1u46A 294 :FAWCAPESLKTRTFSHASDTWMFGVTLWEMFTYGQEPWIGLNGSQILHK T0291 243 :VDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKL 1u46A 344 :DKEGERLPRPEDCPQDIYNVMVQCWAHKPEDRPTFVALRDFLLEA Number of specific fragments extracted= 9 number of extra gaps= 3 total=134 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p4oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0291 read from 1p4oA/merged-good-all-a2m # 1p4oA read from 1p4oA/merged-good-all-a2m # found chain 1p4oA in training set T0291 7 :TYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1p4oA 949 :EYFSAADVYVPDEWEVAREKITMSRELGQGSFGMVYEGVAK T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1p4oA 992 :VKDEPETRVAIKTVNEAASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQGQPTLVIMELMTRGDLKSYLRSL T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1p4oA 1077 :PSLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGMTRDIYET T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 1p4oA 1134 :DYYRKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSIKEEM Number of specific fragments extracted= 4 number of extra gaps= 0 total=138 Number of alignments=19 # 1p4oA read from 1p4oA/merged-good-all-a2m # found chain 1p4oA in training set Warning: unaligning (T0291)H6 because first residue in template chain is (1p4oA)P948 T0291 7 :TYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1p4oA 949 :EYFSAADVYVPDEWEVAREKITMSRELGQGSFGMVYEGVAK T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1p4oA 992 :VKDEPETRVAIKTVNEAASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQGQPTLVIMELMTRGDLKSYLR T0291 119 :KHDA 1p4oA 1070 :NNPV T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1p4oA 1076 :PPSLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGMTRDIYET T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNP 1p4oA 1134 :DYYRKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSIKEEMEPG Number of specific fragments extracted= 5 number of extra gaps= 0 total=143 Number of alignments=20 # 1p4oA read from 1p4oA/merged-good-all-a2m # found chain 1p4oA in training set Warning: unaligning (T0291)H6 because first residue in template chain is (1p4oA)P948 T0291 7 :TYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1p4oA 949 :EYFSAADVYVPDEWEVAREKITMSRELGQGSFGMVYEGVAKG T0291 49 :PSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1p4oA 993 :KDEPETRVAIKTVNEAASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQGQPTLVIMELMTRGDLKSYLR T0291 119 :KHD 1p4oA 1070 :NNP T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1p4oA 1075 :APPSLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGMTRDIYETDYY T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1p4oA 1137 :RKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSIKEEMEP Number of specific fragments extracted= 5 number of extra gaps= 0 total=148 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fmk/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fmk expands to /projects/compbio/data/pdb/1fmk.pdb.gz 1fmk:Warning: there is no chain 1fmk will retry with 1fmkA 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 # T0291 read from 1fmk/merged-good-all-a2m # 1fmk read from 1fmk/merged-good-all-a2m # adding 1fmk to template set # found chain 1fmk in template set Warning: unaligning (T0291)V94 because of BadResidue code BAD_PEPTIDE in next template residue (1fmk)V329 Warning: unaligning (T0291)V95 because of BadResidue code BAD_PEPTIDE at template residue (1fmk)V329 Warning: unaligning (T0291)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fmk)P333 Warning: unaligning (T0291)P100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fmk)P333 Warning: unaligning (T0291)R175 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmk)F424 Warning: unaligning (T0291)I192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmk)F424 Warning: unaligning (T0291)N290 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fmk)T523 Warning: unaligning (T0291)P291 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fmk)T523 Warning: unaligning (T0291)G292 because of BadResidue code BAD_PEPTIDE at template residue (1fmk)E524 Warning: unaligning (T0291)L294 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmk)Q528 Warning: unaligning (T0291)I296 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmk)Q528 T0291 3 :VDPHT 1fmk 247 :TSKPQ T0291 12 :TQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRL 1fmk 252 :TQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTW T0291 51 :KKEISVAIKTLKVGY 1fmk 287 :NGTTRVAIKTLKPGT T0291 66 :TEKQ 1fmk 303 :SPEA T0291 73 :FLGEASIMGQFDHPNIIRLEG 1fmk 307 :FLQEAQVMKKLRHEKLVQLYA T0291 97 :KS 1fmk 330 :SE T0291 101 :VMIVTEYMENGSLDSFLRKH 1fmk 334 :IYIVTEYMSKGSLLDFLKGE T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLG 1fmk 356 :KYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLA T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1fmk 425 :PIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFT T0291 293 :S 1fmk 525 :P T0291 297 :IT 1fmk 529 :PG Number of specific fragments extracted= 11 number of extra gaps= 3 total=159 Number of alignments=22 # 1fmk read from 1fmk/merged-good-all-a2m # found chain 1fmk in template set Warning: unaligning (T0291)V94 because of BadResidue code BAD_PEPTIDE in next template residue (1fmk)V329 Warning: unaligning (T0291)V95 because of BadResidue code BAD_PEPTIDE at template residue (1fmk)V329 Warning: unaligning (T0291)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fmk)P333 Warning: unaligning (T0291)P100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fmk)P333 Warning: unaligning (T0291)R175 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmk)F424 Warning: unaligning (T0291)I192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmk)F424 Warning: unaligning (T0291)N290 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fmk)T523 Warning: unaligning (T0291)P291 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fmk)T523 Warning: unaligning (T0291)G292 because of BadResidue code BAD_PEPTIDE at template residue (1fmk)E524 Warning: unaligning (T0291)L294 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmk)Q528 Warning: unaligning (T0291)I296 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmk)Q528 T0291 3 :VDPHTYEDP 1fmk 247 :TSKPQTQGL T0291 16 :HEFAKELDATNISIDKVVGAGEFGEVCSGRL 1fmk 256 :AKDAWEIPRESLRLEVKLGQGCFGEVWMGTW T0291 51 :KKEISVAIKTLKVGYTEK 1fmk 287 :NGTTRVAIKTLKPGTMSP T0291 71 :RDFLGEASIMGQFDHPNIIRLEG 1fmk 305 :EAFLQEAQVMKKLRHEKLVQLYA T0291 96 :T 1fmk 330 :S T0291 98 :S 1fmk 331 :E T0291 101 :VMIVTEYMENGSLDSFLRKH 1fmk 334 :IYIVTEYMSKGSLLDFLKGE T0291 121 :D 1fmk 356 :K T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLG 1fmk 357 :YLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLA T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1fmk 425 :PIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFT T0291 293 :S 1fmk 525 :P T0291 297 :ITS 1fmk 529 :PGE Number of specific fragments extracted= 12 number of extra gaps= 3 total=171 Number of alignments=23 # 1fmk read from 1fmk/merged-good-all-a2m # found chain 1fmk in template set Warning: unaligning (T0291)V94 because of BadResidue code BAD_PEPTIDE in next template residue (1fmk)V329 Warning: unaligning (T0291)V95 because of BadResidue code BAD_PEPTIDE at template residue (1fmk)V329 Warning: unaligning (T0291)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fmk)P333 Warning: unaligning (T0291)P100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fmk)P333 Warning: unaligning (T0291)R175 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmk)F424 Warning: unaligning (T0291)I192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmk)F424 Warning: unaligning (T0291)N290 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fmk)T523 Warning: unaligning (T0291)P291 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fmk)T523 Warning: unaligning (T0291)G292 because of BadResidue code BAD_PEPTIDE at template residue (1fmk)E524 Warning: unaligning (T0291)L294 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmk)Q528 Warning: unaligning (T0291)I296 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmk)Q528 T0291 5 :PHTYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKLPS 1fmk 245 :CPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTT T0291 55 :SVAIKTLKVG 1fmk 291 :RVAIKTLKPG T0291 65 :YTEK 1fmk 302 :MSPE T0291 72 :DFLGEASIMGQFDHPNIIRLEG 1fmk 306 :AFLQEAQVMKKLRHEKLVQLYA T0291 96 :T 1fmk 330 :S T0291 98 :S 1fmk 331 :E T0291 101 :VMIVTEYMENGSLDSFLRK 1fmk 334 :IYIVTEYMSKGSLLDFLKG T0291 120 :H 1fmk 355 :G T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLG 1fmk 356 :KYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLA T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1fmk 425 :PIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFT T0291 293 :S 1fmk 525 :P T0291 297 :IT 1fmk 529 :PG Number of specific fragments extracted= 12 number of extra gaps= 3 total=183 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ia8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0291 read from 1ia8A/merged-good-all-a2m # 1ia8A read from 1ia8A/merged-good-all-a2m # found chain 1ia8A in training set Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ia8A)C48 Warning: unaligning (T0291)Q69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ia8A)C48 Warning: unaligning (T0291)P304 because last residue in template chain is (1ia8A)P276 T0291 23 :DATNISIDKVVGAGEFGEVCSGRL 1ia8A 5 :FVEDWDLVQTLGEGAYGEVQLAVN T0291 50 :SKKEISVAIKTLKVG 1ia8A 29 :RVTEEAVAVKIVDMK T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1ia8A 49 :PENIKKEICINKMLNHENVVKFYGHRREGNIQYLFLEYCSGGELFDRIE T0291 121 :DAQ 1ia8A 98 :PDI T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1ia8A 102 :MPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPENLLLDERDNLKISDFGLATVFRYN T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFT 1ia8A 159 :NRERLLNKMCGTLPYVAPELLKRREFH T0291 210 :ASDVWSYGIVLWEVMS 1ia8A 188 :PVDVWSCGIVLTAMLA T0291 227 :GERPYWEMS 1ia8A 204 :GELPWDQPS T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIV 1ia8A 215 :CQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIK T0291 289 :RNPGSLKIITSAAAR 1ia8A 261 :KDRWYNKPLKKGAKR Number of specific fragments extracted= 10 number of extra gaps= 0 total=193 Number of alignments=25 # 1ia8A read from 1ia8A/merged-good-all-a2m # found chain 1ia8A in training set Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ia8A)C48 Warning: unaligning (T0291)Q69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ia8A)C48 Warning: unaligning (T0291)R303 because last residue in template chain is (1ia8A)P276 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGR 1ia8A 3 :VPFVEDWDLVQTLGEGAYGEVQLAV T0291 49 :PSKKEISVAIKTLKVG 1ia8A 28 :NRVTEEAVAVKIVDMK T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFL 1ia8A 49 :PENIKKEICINKMLNHENVVKFYGHRREGNIQYLFLEYCSGGELFDRI T0291 119 :KHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1ia8A 97 :EPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPENLLLDERDNLKISDFGLATVFRYNNRE T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFT 1ia8A 162 :RLLNKMCGTLPYVAPELLKRREFH T0291 209 :SASDVWSYGIVLWEVMS 1ia8A 187 :EPVDVWSCGIVLTAMLA T0291 227 :GERPYWEMSNQ 1ia8A 204 :GELPWDQPSDS T0291 238 :DVIKAVDEG 1ia8A 216 :QEYSDWKEK T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1ia8A 226 :TYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKD T0291 290 :NPGSLKIITSAAA 1ia8A 263 :RWYNKPLKKGAKR Number of specific fragments extracted= 10 number of extra gaps= 0 total=203 Number of alignments=26 # 1ia8A read from 1ia8A/merged-good-all-a2m # found chain 1ia8A in training set Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ia8A)C48 Warning: unaligning (T0291)Q69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ia8A)C48 T0291 22 :LDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKT 1ia8A 4 :PFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDM T0291 64 :G 1ia8A 43 :K T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1ia8A 49 :PENIKKEICINKMLNHENVVKFYGHRREGNIQYLFLEYCSGGELFDRIEPDI T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1ia8A 101 :GMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPENLLLDERDNLKISDFGLATVFRYNNRE T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFT 1ia8A 162 :RLLNKMCGTLPYVAPELLKRREFH T0291 209 :SASDVWSYGIVLWEVMSYGERPYW 1ia8A 187 :EPVDVWSCGIVLTAMLAGELPWDQ T0291 233 :EMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1ia8A 212 :SDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKD T0291 289 :RNPGSLKII 1ia8A 263 :RWYNKPLKK Number of specific fragments extracted= 8 number of extra gaps= 0 total=211 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bdwA expands to /projects/compbio/data/pdb/2bdw.pdb.gz 2bdwA:# T0291 read from 2bdwA/merged-good-all-a2m # 2bdwA read from 2bdwA/merged-good-all-a2m # adding 2bdwA to template set # found chain 2bdwA in template set T0291 26 :NISIDKVVGAGEFGEVCSGRL 2bdwA 12 :NYDVKEELGKGAFSVVRRCVH T0291 50 :SKKEISVAIKTLK 2bdwA 33 :KTTGLEFAAKIIN T0291 63 :VGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 2bdwA 47 :KKLSARDFQKLEREARICRKLQHPNIVRLHDSIQEESFHYLVFDLVTGGELFEDIVARE T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 2bdwA 106 :FYSEADASHCIQQILESIAYCHSNGIVHRNLKPENLLL T0291 161 :NSNLVCKVSDFGLGRVLEDDPEAA 2bdwA 147 :AKGAAVKLADFGLAIEVNDSEAWH T0291 189 :GGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2bdwA 172 :GFAGTPGYLSPEVLKKDPYSKPVDIWACGVILYILLV T0291 227 :GERPYWEMSNQDVIKAVDEG 2bdwA 209 :GYPPFWDEDQHRLYAQIKAG T0291 247 :YRLPPP 2bdwA 230 :YDYPSP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKF 2bdwA 238 :DTVTPEAKSLIDSMLTVNPKKRITA T0291 278 :EQIVSILDKLI 2bdwA 284 :QDTVDCLKKFN Number of specific fragments extracted= 10 number of extra gaps= 0 total=221 Number of alignments=28 # 2bdwA read from 2bdwA/merged-good-all-a2m # found chain 2bdwA in template set Warning: unaligning (T0291)T12 because first residue in template chain is (2bdwA)S5 T0291 13 :QAVH 2bdwA 6 :TKFS T0291 25 :TNISIDKVVGAGEFGEVCSGRL 2bdwA 11 :DNYDVKEELGKGAFSVVRRCVH T0291 50 :SKKEISVAIKTLKV 2bdwA 33 :KTTGLEFAAKIINT T0291 64 :GYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 2bdwA 48 :KLSARDFQKLEREARICRKLQHPNIVRLHDSIQEESFHYLVFDLVTGGELFEDIVAREF T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 2bdwA 107 :YSEADASHCIQQILESIAYCHSNGIVHRNLKPENLLL T0291 161 :NSNLVCKVSDFGLGRVLEDDP 2bdwA 147 :AKGAAVKLADFGLAIEVNDSE T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2bdwA 169 :AWHGFAGTPGYLSPEVLKKDPYSKPVDIWACGVILYILLV T0291 227 :GERPYWEMSNQDVIKAVDEG 2bdwA 209 :GYPPFWDEDQHRLYAQIKAG T0291 249 :LPPPM 2bdwA 230 :YDYPS T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILD 2bdwA 239 :TVTPEAKSLIDSMLTVNPKKRITADQALKVPW Number of specific fragments extracted= 10 number of extra gaps= 0 total=231 Number of alignments=29 # 2bdwA read from 2bdwA/merged-good-all-a2m # found chain 2bdwA in template set Warning: unaligning (T0291)K20 because first residue in template chain is (2bdwA)S5 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIK 2bdwA 6 :TKFSDNYDVKEELGKGAFSVVRRCVHKTTGLEFAAKIIN T0291 62 :KVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 2bdwA 46 :TKKLSARDFQKLEREARICRKLQHPNIVRLHDSIQEESFHYLVFDLVTGGELFEDIVARE T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 2bdwA 106 :FYSEADASHCIQQILESIAYCHSNGIVHRNLKPENLLL T0291 161 :NSNLVCKVSDFGLGRVLEDDPE 2bdwA 147 :AKGAAVKLADFGLAIEVNDSEA T0291 187 :TRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLP 2bdwA 170 :WHGFAGTPGYLSPEVLKKDPYSKPVDIWACGVILYILLVGYPPFWDEDQHRLYAQIKAGAYDYP T0291 251 :PPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSIL 2bdwA 236 :EWDTVTPEAKSLIDSMLTVNPKKRITADQALKVP Number of specific fragments extracted= 6 number of extra gaps= 0 total=237 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jpaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jpaA expands to /projects/compbio/data/pdb/1jpa.pdb.gz 1jpaA:# T0291 read from 1jpaA/merged-good-all-a2m # 1jpaA read from 1jpaA/merged-good-all-a2m # adding 1jpaA to template set # found chain 1jpaA in template set Warning: unaligning (T0291)L48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jpaA)R654 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jpaA)R654 Warning: unaligning (T0291)F171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jpaA)P797 Warning: unaligning (T0291)P193 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jpaA)P797 Warning: unaligning (T0291)I296 because last residue in template chain is (1jpaA)A900 T0291 1 :TYVDPHTYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1jpaA 603 :IFIDPFTFEDPNEAVREFAKEIDISCVKIEQVIGAGEFGEVCSGHLK T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSD 1jpaA 655 :EIFVAIKTLKSGYTEKQRRDFLSEASIMGQFDHPNVIHLEGVVTKSTPVMIITEFMENGSLDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLADMNYVHRDLAARNILVNSNLVCKVSD T0291 194 :IRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLK 1jpaA 798 :IRWTAPEAIQYRKFTSASDVWSYGIVMWEVMSYGERPYWDMTNQDVINAIEQDYRLPPPMDCPSALHQLMLDCWQKDRNHRPKFGQIVNTLDKMIRNPNSLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=240 Number of alignments=31 # 1jpaA read from 1jpaA/merged-good-all-a2m # found chain 1jpaA in template set Warning: unaligning (T0291)L48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jpaA)R654 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jpaA)R654 Warning: unaligning (T0291)F171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jpaA)P797 Warning: unaligning (T0291)P193 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jpaA)P797 Warning: unaligning (T0291)I296 because last residue in template chain is (1jpaA)A900 T0291 1 :TYVDPHTYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1jpaA 603 :IFIDPFTFEDPNEAVREFAKEIDISCVKIEQVIGAGEFGEVCSGHLK T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSD 1jpaA 655 :EIFVAIKTLKSGYTEKQRRDFLSEASIMGQFDHPNVIHLEGVVTKSTPVMIITEFMENGSLDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLADMNYVHRDLAARNILVNSNLVCKVSD T0291 194 :IRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLK 1jpaA 798 :IRWTAPEAIQYRKFTSASDVWSYGIVMWEVMSYGERPYWDMTNQDVINAIEQDYRLPPPMDCPSALHQLMLDCWQKDRNHRPKFGQIVNTLDKMIRNPNSLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=243 Number of alignments=32 # 1jpaA read from 1jpaA/merged-good-all-a2m # found chain 1jpaA in template set Warning: unaligning (T0291)L48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jpaA)R654 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jpaA)R654 Warning: unaligning (T0291)F171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jpaA)P797 Warning: unaligning (T0291)P193 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jpaA)P797 T0291 8 :YEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1jpaA 610 :FEDPNEAVREFAKEIDISCVKIEQVIGAGEFGEVCSGHLK T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSD 1jpaA 655 :EIFVAIKTLKSGYTEKQRRDFLSEASIMGQFDHPNVIHLEGVVTKSTPVMIITEFMENGSLDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLADMNYVHRDLAARNILVNSNLVCKVSD T0291 194 :IRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLK 1jpaA 798 :IRWTAPEAIQYRKFTSASDVWSYGIVMWEVMSYGERPYWDMTNQDVINAIEQDYRLPPPMDCPSALHQLMLDCWQKDRNHRPKFGQIVNTLDKMIRNPNSLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=246 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mp8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mp8A expands to /projects/compbio/data/pdb/1mp8.pdb.gz 1mp8A:# T0291 read from 1mp8A/merged-good-all-a2m # 1mp8A read from 1mp8A/merged-good-all-a2m # adding 1mp8A to template set # found chain 1mp8A in template set Warning: unaligning (T0291)A19 because first residue in template chain is (1mp8A)D414 Warning: unaligning (T0291)P49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mp8A)P447 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mp8A)P447 Warning: unaligning (T0291)D170 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mp8A)L584 Warning: unaligning (T0291)I192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mp8A)L584 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKL 1mp8A 415 :YEIQRERIELGRCIGEGQFGDVHQGIYMS T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVV 1mp8A 448 :ALAVAIKTCKNCTSDSVREKFLQEALTMRQFDHPHIVKLIGVI T0291 97 :KSKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVS 1mp8A 491 :TENPVWIIMELCTLGELRSFLQVRKYSLDLASLILYAYQLSTALAYLESKRFVHRDIAARNVLVSSNDCVKLG T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1mp8A 585 :PIKWMAPESINFRRFTSASDVWMFGVCMWEILMHGVKPFQGVKNNDVIGRIENGERLPMPPNCPPTLYSLMTKCWAYDPSRRPRFTELKAQLSTILE Number of specific fragments extracted= 4 number of extra gaps= 0 total=250 Number of alignments=34 # 1mp8A read from 1mp8A/merged-good-all-a2m # found chain 1mp8A in template set Warning: unaligning (T0291)A19 because first residue in template chain is (1mp8A)D414 Warning: unaligning (T0291)P49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mp8A)P447 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mp8A)P447 Warning: unaligning (T0291)D170 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mp8A)L584 Warning: unaligning (T0291)I192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mp8A)L584 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKL 1mp8A 415 :YEIQRERIELGRCIGEGQFGDVHQGIYMS T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVT 1mp8A 448 :ALAVAIKTCKNCTSDSVREKFLQEALTMRQFDHPHIVKLIGVIT T0291 98 :SKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVS 1mp8A 492 :ENPVWIIMELCTLGELRSFLQVRKYSLDLASLILYAYQLSTALAYLESKRFVHRDIAARNVLVSSNDCVKLG T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1mp8A 585 :PIKWMAPESINFRRFTSASDVWMFGVCMWEILMHGVKPFQGVKNNDVIGRIENGERLPMPPNCPPTLYSLMTKCWAYDPSRRPRFTELKAQLSTILE Number of specific fragments extracted= 4 number of extra gaps= 0 total=254 Number of alignments=35 # 1mp8A read from 1mp8A/merged-good-all-a2m # found chain 1mp8A in template set Warning: unaligning (T0291)A19 because first residue in template chain is (1mp8A)D414 Warning: unaligning (T0291)P49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mp8A)P447 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mp8A)P447 Warning: unaligning (T0291)D170 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mp8A)L584 Warning: unaligning (T0291)I192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mp8A)L584 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKL 1mp8A 415 :YEIQRERIELGRCIGEGQFGDVHQGIYMS T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVT 1mp8A 448 :ALAVAIKTCKNCTSDSVREKFLQEALTMRQFDHPHIVKLIGVIT T0291 98 :SKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVS 1mp8A 492 :ENPVWIIMELCTLGELRSFLQVRKYSLDLASLILYAYQLSTALAYLESKRFVHRDIAARNVLVSSNDCVKLG T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1mp8A 585 :PIKWMAPESINFRRFTSASDVWMFGVCMWEILMHGVKPFQGVKNNDVIGRIENGERLPMPPNCPPTLYSLMTKCWAYDPSRRPRFTELKAQLSTILE Number of specific fragments extracted= 4 number of extra gaps= 0 total=258 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rdqE/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0291 read from 1rdqE/merged-good-all-a2m # 1rdqE read from 1rdqE/merged-good-all-a2m # found chain 1rdqE in training set Warning: unaligning (T0291)M108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)A124 Warning: unaligning (T0291)E109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)A124 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rdqE)L198 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rdqE)L198 Warning: unaligning (T0291)R205 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)G214 Warning: unaligning (T0291)K206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)G214 T0291 18 :FAKELDATNISIDKVVGAGEFGEVCSGRL 1rdqE 34 :SQNTAQLDQFDRIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLK 1rdqE 63 :KESGNHYAMKILD T0291 63 :VG 1rdqE 82 :LK T0291 66 :T 1rdqE 84 :Q T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEY 1rdqE 85 :IEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEY T0291 110 :NGSLDSFLRKHDA 1rdqE 125 :GGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1rdqE 138 :FSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGR T0291 186 :T 1rdqE 195 :T T0291 190 :GKIP 1rdqE 199 :CGTP T0291 195 :RWTSPEAIAY 1rdqE 203 :EALAPEIILS T0291 207 :FTSASDVWSYGIVLWEVMS 1rdqE 215 :YNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDE 1rdqE 234 :GYPPFFADQPIQIYEKIVS T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRP 1rdqE 253 :GKVRFPSHFSSDLKDLLRNLLQVDLTKRF Number of specific fragments extracted= 13 number of extra gaps= 2 total=271 Number of alignments=37 # 1rdqE read from 1rdqE/merged-good-all-a2m # found chain 1rdqE in training set Warning: unaligning (T0291)M108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)A124 Warning: unaligning (T0291)E109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)A124 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rdqE)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rdqE)L198 Warning: unaligning (T0291)R205 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)G214 Warning: unaligning (T0291)K206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)G214 T0291 18 :FAKELDATNISIDKVVGAGEFGEVCSGRL 1rdqE 34 :SQNTAQLDQFDRIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLKVGYT 1rdqE 63 :KESGNHYAMKILDKQKV T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEY 1rdqE 82 :LKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEY T0291 110 :NGSLDSFLRKHDA 1rdqE 125 :GGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1rdqE 138 :FSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKG T0291 186 :TT 1rdqE 194 :RT T0291 191 :KIPIRWTSPEAIAY 1rdqE 199 :CGTPEALAPEIILS T0291 207 :FTSASDVWSYGIVLWEVMS 1rdqE 215 :YNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDEG 1rdqE 234 :GYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNR 1rdqE 254 :KVRFPSHFSSDLKDLLRNLLQVDLTKR T0291 275 :PKFEQIV 1rdqE 300 :TDWIAIY T0291 288 :IRNPGSLKII 1rdqE 307 :QRKVEAPFIP Number of specific fragments extracted= 12 number of extra gaps= 2 total=283 Number of alignments=38 # 1rdqE read from 1rdqE/merged-good-all-a2m # found chain 1rdqE in training set Warning: unaligning (T0291)M108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)A124 Warning: unaligning (T0291)E109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)A124 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rdqE)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rdqE)L198 Warning: unaligning (T0291)R205 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)G214 Warning: unaligning (T0291)K206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)G214 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1rdqE 36 :NTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKV T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEY 1rdqE 80 :VKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEY T0291 110 :NGSLDSFLRKHD 1rdqE 125 :GGEMFSHLRRIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1rdqE 137 :RFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKG T0291 186 :TT 1rdqE 194 :RT T0291 191 :KIPIRWTSPEAIAY 1rdqE 199 :CGTPEALAPEIILS T0291 207 :FTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 1rdqE 215 :YNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK T0291 249 :LPPPMDCPAALYQLMLDCWQKDRNNRP 1rdqE 255 :VRFPSHFSSDLKDLLRNLLQVDLTKRF Number of specific fragments extracted= 8 number of extra gaps= 2 total=291 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t4hA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0291 read from 1t4hA/merged-good-all-a2m # 1t4hA read from 1t4hA/merged-good-all-a2m # found chain 1t4hA in training set Warning: unaligning (T0291)F18 because first residue in template chain is (1t4hA)A211 Warning: unaligning (T0291)P181 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)A380 Warning: unaligning (T0291)A184 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)A380 Warning: unaligning (T0291)F207 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)D400 Warning: unaligning (T0291)T208 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)D400 T0291 19 :AKELDATNISIDK 1t4hA 212 :VGMSNDGRFLKFD T0291 32 :VVGAGEFGEVCSGRL 1t4hA 226 :EIGRGSFKTVYKGLD T0291 50 :SKKEISVAIKTLK 1t4hA 241 :TETTVEVAWCELQ T0291 63 :VGYTEKQRRDFLGEASIMGQFDHPNIIRLEGV 1t4hA 255 :RKLTKSERQRFKEEAEMLKGLQHPNIVRFYDS T0291 95 :VTKSKP 1t4hA 289 :STVKGK T0291 101 :VMIVTEYMENGSLDSFLRKHD 1t4hA 297 :IVLVTELMTSGTLKTYLKRFK T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMG 1t4hA 318 :VMKIKVLRSWCRQILKGLQFLHTRT T0291 148 :YVHRDLAARNILI 1t4hA 345 :IIHRDLKCDNIFI T0291 161 :NSNLVCKVSDFGLGRVLEDD 1t4hA 359 :GPTGSVKIGDLGLATLKRAS T0291 185 :YTTR 1t4hA 381 :KAVI T0291 190 :GK 1t4hA 385 :GT T0291 194 :IRWTSPEAIA 1t4hA 387 :PEFMAPEMYE T0291 205 :RK 1t4hA 397 :EK T0291 209 :SASDVWSYGIVLWEVMS 1t4hA 401 :ESVDVYAFGMCMLEMAT T0291 227 :GERPYWEM 1t4hA 418 :SEYPYSEC T0291 235 :SNQDVIKAVDEGYRLPPPMDCP 1t4hA 427 :NAAQIYRRVTSGVKPASFDKVA T0291 257 :AALYQLMLDCWQKDRNNRPKFEQIVS 1t4hA 450 :PEVKEIIEGCIRQNKDERYSIKDLLN Number of specific fragments extracted= 17 number of extra gaps= 2 total=308 Number of alignments=40 # 1t4hA read from 1t4hA/merged-good-all-a2m # found chain 1t4hA in training set Warning: unaligning (T0291)F18 because first residue in template chain is (1t4hA)A211 Warning: unaligning (T0291)T186 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)A380 Warning: unaligning (T0291)T187 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)A380 Warning: unaligning (T0291)F207 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)D400 Warning: unaligning (T0291)T208 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)D400 T0291 19 :AKELDATNISIDK 1t4hA 212 :VGMSNDGRFLKFD T0291 32 :VVGAGEFGEVCSGRL 1t4hA 226 :EIGRGSFKTVYKGLD T0291 50 :SKKEISVAIKTLKV 1t4hA 241 :TETTVEVAWCELQD T0291 64 :GYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVT 1t4hA 256 :KLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWE T0291 97 :KSKP 1t4hA 291 :VKGK T0291 101 :VMIVTEYMENGSLDSFLRKHDA 1t4hA 297 :IVLVTELMTSGTLKTYLKRFKV T0291 124 :FTVIQLVGMLRGIASGMKYLSD 1t4hA 319 :MKIKVLRSWCRQILKGLQFLHT T0291 146 :MGYVHRDLAARNILIN 1t4hA 343 :PPIIHRDLKCDNIFIT T0291 162 :SNLVCKVSDFGLGRVLEDD 1t4hA 360 :PTGSVKIGDLGLATLKRAS T0291 188 :RGGKIPIRWTSPEAIAY 1t4hA 381 :KAVIGTPEFMAPEMYEE T0291 206 :K 1t4hA 398 :K T0291 209 :SASDVWSYGIVLWEVMS 1t4hA 401 :ESVDVYAFGMCMLEMAT T0291 227 :GERPYWEM 1t4hA 418 :SEYPYSEC T0291 235 :SNQDVIKAVDEGYRLPPPMDC 1t4hA 427 :NAAQIYRRVTSGVKPASFDKV T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVSI 1t4hA 449 :IPEVKEIIEGCIRQNKDERYSIKDLLNH Number of specific fragments extracted= 15 number of extra gaps= 2 total=323 Number of alignments=41 # 1t4hA read from 1t4hA/merged-good-all-a2m # found chain 1t4hA in training set Warning: unaligning (T0291)T186 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)A380 Warning: unaligning (T0291)T187 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)A380 Warning: unaligning (T0291)F207 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)D400 Warning: unaligning (T0291)T208 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)D400 T0291 20 :KELDATNIS 1t4hA 213 :GMSNDGRFL T0291 29 :IDKVVGAGEFGEVCSGRLKLPSKKEISVAIK 1t4hA 223 :FDIEIGRGSFKTVYKGLDTETTVEVAWCELQ T0291 62 :KVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1t4hA 254 :DRKLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWES T0291 98 :S 1t4hA 292 :K T0291 99 :KPVMIVTEYMENGSLDSFLRKHD 1t4hA 295 :KCIVLVTELMTSGTLKTYLKRFK T0291 123 :QFTVIQLVGMLRGIASGMKYLSD 1t4hA 318 :VMKIKVLRSWCRQILKGLQFLHT T0291 146 :MGYVHRDLAARNILI 1t4hA 343 :PPIIHRDLKCDNIFI T0291 161 :NSNLVCKVSDFGLGRVLEDD 1t4hA 359 :GPTGSVKIGDLGLATLKRAS T0291 188 :RGGKIPIRWTSPEAIAY 1t4hA 381 :KAVIGTPEFMAPEMYEE T0291 206 :K 1t4hA 398 :K T0291 209 :SASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDC 1t4hA 401 :ESVDVYAFGMCMLEMATSEYPYSECQNAAQIYRRVTSGVKPASFDKV T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVSI 1t4hA 449 :IPEVKEIIEGCIRQNKDERYSIKDLLNH Number of specific fragments extracted= 12 number of extra gaps= 2 total=335 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1csn/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1csn expands to /projects/compbio/data/pdb/1csn.pdb.gz 1csn:Warning: there is no chain 1csn will retry with 1csnA # T0291 read from 1csn/merged-good-all-a2m # 1csn read from 1csn/merged-good-all-a2m # adding 1csn to template set # found chain 1csn in template set T0291 25 :TNISIDKVVGAGEFGEVCSGRLK 1csn 10 :VHYKVGRRIGEGSFGVIFEGTNL T0291 49 :PS 1csn 33 :LN T0291 53 :EISVAIKTLK 1csn 35 :NQQVAIKFEP T0291 63 :VGYTE 1csn 47 :SDAPQ T0291 70 :RRDFLGEASIMGQFD 1csn 52 :LRDEYRTYKLLAGCT T0291 87 :NIIRLEGVVTKSKPVMIVTEYMEN 1csn 67 :GIPNVYYFGQEGLHNVLVIDLLGP T0291 112 :SLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1csn 91 :SLEDLLDLCGRKFSVKTVAMAAKQMLARVQSIHEKSLVYRDIKPDNFLI T0291 161 :NSNLVCKVSDFGLGRVLEDDPEAAYTTRGGK 1csn 145 :KNANMIYVVDFGMVKFYRDPVTKQHIPYREK T0291 192 :IPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1csn 180 :GTARYMSINTHLGREQSRRDDLEALGHVFMYFLR T0291 227 :GERPYWEMS 1csn 214 :GSLPWQGLK T0291 236 :NQDVIKAVDEG 1csn 230 :YERIGEKKQST T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSL 1csn 247 :AGFPEEFYKYMHYARNLAFDATPDYDYLQGLFSKVLERLNTT T0291 300 :AAARP 1csn 289 :EDENF Number of specific fragments extracted= 13 number of extra gaps= 0 total=348 Number of alignments=43 # 1csn read from 1csn/merged-good-all-a2m # found chain 1csn in template set T0291 24 :ATNISIDKVVGAGEFGEVCSGRLK 1csn 9 :GVHYKVGRRIGEGSFGVIFEGTNL T0291 51 :KKEISVAIKTLKV 1csn 33 :LNNQQVAIKFEPR T0291 66 :TEK 1csn 46 :RSD T0291 73 :FLGEASIMGQF 1csn 52 :LRDEYRTYKLL T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMEN 1csn 64 :GCTGIPNVYYFGQEGLHNVLVIDLLGP T0291 112 :SLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILIN 1csn 91 :SLEDLLDLCGRKFSVKTVAMAAKQMLARVQSIHEKSLVYRDIKPDNFLIG T0291 162 :SNLVCKVSDFGLGRVLEDDPEA 1csn 146 :NANMIYVVDFGMVKFYRDPVTK T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1csn 172 :YREKKNLSGTARYMSINTHLGREQSRRDDLEALGHVFMYFLR T0291 227 :GERPYWEMS 1csn 214 :GSLPWQGLK T0291 236 :NQDVIKAVDEG 1csn 230 :YERIGEKKQST T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKI 1csn 248 :GFPEEFYKYMHYARNLAFDATPDYDYLQGLFSKVLERLNTTED T0291 302 :ARPS 1csn 291 :ENFD Number of specific fragments extracted= 12 number of extra gaps= 0 total=360 Number of alignments=44 # 1csn read from 1csn/merged-good-all-a2m # found chain 1csn in template set T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKT 1csn 10 :VHYKVGRRIGEGSFGVIFEGTNLLNNQQVAIKFEPR T0291 62 :KVGYTE 1csn 46 :RSDAPQ T0291 73 :FLGEASIMGQF 1csn 52 :LRDEYRTYKLL T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMEN 1csn 64 :GCTGIPNVYYFGQEGLHNVLVIDLLGP T0291 112 :SLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1csn 91 :SLEDLLDLCGRKFSVKTVAMAAKQMLARVQSIHEKSLVYRDIKPDNFLI T0291 161 :NSNLVCKVSDFGLGRVLEDDPEA 1csn 145 :KNANMIYVVDFGMVKFYRDPVTK T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYW 1csn 172 :YREKKNLSGTARYMSINTHLGREQSRRDDLEALGHVFMYFLRGSLPWQG T0291 233 :EMSNQDVIKA 1csn 223 :AATNKQKYER T0291 243 :VDEG 1csn 245 :LCAG T0291 255 :CPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIITSAAAR 1csn 249 :FPEEFYKYMHYARNLAFDATPDYDYLQGLFSKVLERLNTTEDENFDWNL Number of specific fragments extracted= 10 number of extra gaps= 0 total=370 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jqhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jqhA expands to /projects/compbio/data/pdb/1jqh.pdb.gz 1jqhA:# T0291 read from 1jqhA/merged-good-all-a2m # 1jqhA read from 1jqhA/merged-good-all-a2m # adding 1jqhA to template set # found chain 1jqhA in template set Warning: unaligning (T0291)K99 because of BadResidue code BAD_PEPTIDE in next template residue (1jqhA)P1074 Warning: unaligning (T0291)P100 because of BadResidue code BAD_PEPTIDE at template residue (1jqhA)P1074 Warning: unaligning (T0291)Q123 because of BadResidue code BAD_PEPTIDE in next template residue (1jqhA)P1107 Warning: unaligning (T0291)F124 because of BadResidue code BAD_PEPTIDE at template residue (1jqhA)P1107 Warning: unaligning (T0291)G174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jqhA)Y1165 Warning: unaligning (T0291)A183 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jqhA)Y1165 T0291 16 :HEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1jqhA 988 :VPDEWEVAREKITMSRELGQGSFGMVYEGVAK T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1jqhA 1022 :VKDEPETRVAIKTVNEAASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQG T0291 101 :VMIVTEYMENGSLDSFLRKH 1jqhA 1075 :TLVIMELMTRGDLKSYLRSL T0291 121 :DA 1jqhA 1104 :LA T0291 125 :TVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGL 1jqhA 1108 :SLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGM T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSIL 1jqhA 1166 :YRKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSI Number of specific fragments extracted= 6 number of extra gaps= 2 total=376 Number of alignments=46 # 1jqhA read from 1jqhA/merged-good-all-a2m # found chain 1jqhA in template set Warning: unaligning (T0291)T12 because first residue in template chain is (1jqhA)A984 Warning: unaligning (T0291)K99 because of BadResidue code BAD_PEPTIDE in next template residue (1jqhA)P1074 Warning: unaligning (T0291)P100 because of BadResidue code BAD_PEPTIDE at template residue (1jqhA)P1074 Warning: unaligning (T0291)Q123 because of BadResidue code BAD_PEPTIDE in next template residue (1jqhA)P1107 Warning: unaligning (T0291)F124 because of BadResidue code BAD_PEPTIDE at template residue (1jqhA)P1107 Warning: unaligning (T0291)G174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jqhA)Y1165 Warning: unaligning (T0291)A183 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jqhA)Y1165 T0291 13 :QAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1jqhA 985 :DVYVPDEWEVAREKITMSRELGQGSFGMVYEGVAK T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1jqhA 1022 :VKDEPETRVAIKTVNEAASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQG T0291 101 :VMIVTEYMENGSLDSFLRKHDA 1jqhA 1075 :TLVIMELMTRGDLKSYLRSLRP T0291 125 :TVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGL 1jqhA 1108 :SLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGM T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1jqhA 1166 :YRKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSIKEEMEP Number of specific fragments extracted= 5 number of extra gaps= 2 total=381 Number of alignments=47 # 1jqhA read from 1jqhA/merged-good-all-a2m # found chain 1jqhA in template set Warning: unaligning (T0291)K99 because of BadResidue code BAD_PEPTIDE in next template residue (1jqhA)P1074 Warning: unaligning (T0291)P100 because of BadResidue code BAD_PEPTIDE at template residue (1jqhA)P1074 Warning: unaligning (T0291)H120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jqhA)V1103 Warning: unaligning (T0291)Q123 because of BadResidue code BAD_PEPTIDE in next template residue (1jqhA)P1107 Warning: unaligning (T0291)F124 because of BadResidue code BAD_PEPTIDE at template residue (1jqhA)P1107 Warning: unaligning (T0291)G174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jqhA)Y1165 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jqhA)Y1165 T0291 13 :QAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1jqhA 985 :DVYVPDEWEVAREKITMSRELGQGSFGMVYEGVAKG T0291 49 :PSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1jqhA 1023 :KDEPETRVAIKTVNEAASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQG T0291 101 :VMIVTEYMENGSLDSFLR 1jqhA 1075 :TLVIMELMTRGDLKSYLR T0291 121 :DA 1jqhA 1104 :LA T0291 125 :TVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGL 1jqhA 1108 :SLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGM T0291 183 :A 1jqhA 1166 :Y T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1jqhA 1167 :RKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSIKEEME Number of specific fragments extracted= 7 number of extra gaps= 2 total=388 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xh9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xh9A expands to /projects/compbio/data/pdb/1xh9.pdb.gz 1xh9A: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 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 # T0291 read from 1xh9A/merged-good-all-a2m # 1xh9A read from 1xh9A/merged-good-all-a2m # adding 1xh9A to template set # found chain 1xh9A in template set Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xh9A)L198 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xh9A)L198 Warning: unaligning (T0291)R205 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xh9A)G214 Warning: unaligning (T0291)K206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xh9A)G214 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRL 1xh9A 35 :QNTAHLDQFERIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLK 1xh9A 63 :METGNHYAMKILD T0291 63 :VG 1xh9A 82 :LK T0291 66 :T 1xh9A 84 :E T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1xh9A 85 :IEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYAPGGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1xh9A 138 :FSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLMIDQQGYIKVTDFGLAKRVKGR T0291 186 :T 1xh9A 195 :T T0291 190 :GKIP 1xh9A 199 :CGTP T0291 195 :RWTSPEAIAY 1xh9A 203 :EYLAPEIILS T0291 207 :FTSASDVWSYGIVLWEVMS 1xh9A 215 :YNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDE 1xh9A 234 :GYPPFFADQPIQIYEKIVS T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNR 1xh9A 253 :GKVRFPSHFSSDLKDLLRNLLQVDLTKR Number of specific fragments extracted= 12 number of extra gaps= 1 total=400 Number of alignments=49 # 1xh9A read from 1xh9A/merged-good-all-a2m # found chain 1xh9A in template set Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xh9A)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xh9A)L198 Warning: unaligning (T0291)R205 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xh9A)G214 Warning: unaligning (T0291)K206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xh9A)G214 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRL 1xh9A 35 :QNTAHLDQFERIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLKVGYT 1xh9A 63 :METGNHYAMKILDKQKV T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1xh9A 82 :LKEIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYAPGGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1xh9A 138 :FSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLMIDQQGYIKVTDFGLAKRVKG T0291 186 :TT 1xh9A 194 :RT T0291 191 :KIPIRWTSPEAIAY 1xh9A 199 :CGTPEYLAPEIILS T0291 207 :FTSASDVWSYGIVLWEVMS 1xh9A 215 :YNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDEG 1xh9A 234 :GYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1xh9A 254 :KVRFPSHFSSDLKDLLRNLLQVDLTKRF T0291 276 :KFEQIVSI 1xh9A 287 :GVNDIKNH T0291 284 :LDKLIRNPGSLKII 1xh9A 302 :WIAIYQRKVEAPFI Number of specific fragments extracted= 11 number of extra gaps= 1 total=411 Number of alignments=50 # 1xh9A read from 1xh9A/merged-good-all-a2m # found chain 1xh9A in template set Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xh9A)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xh9A)L198 Warning: unaligning (T0291)R205 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xh9A)G214 Warning: unaligning (T0291)K206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xh9A)G214 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1xh9A 36 :NTAHLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKV T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1xh9A 80 :VKLKEIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYAPGGEMFSHLRRIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1xh9A 137 :RFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLMIDQQGYIKVTDFGLAKRVKG T0291 186 :TT 1xh9A 194 :RT T0291 191 :KIPIRWTSPEAIAY 1xh9A 199 :CGTPEYLAPEIILS T0291 207 :FTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDE 1xh9A 215 :YNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1xh9A 254 :KVRFPSHFSSDLKDLLRNLLQVDLTKRF Number of specific fragments extracted= 7 number of extra gaps= 1 total=418 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jvpP/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jvpP expands to /projects/compbio/data/pdb/1jvp.pdb.gz 1jvpP:Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 175, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 177, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 643, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 645, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 679, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1015, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1182, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1184, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1186, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1188, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1190, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1192, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1194, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1196, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1200, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1202, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1204, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1212, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1214, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1220, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1222, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1224, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1226, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1230, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1232, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1234, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1288, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1290, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1292, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1336, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2006, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2008, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2010, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2012, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2014, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2016, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2018, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2020, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2022, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2024, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2026, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2028, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2030, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2032, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2034, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2036, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2038, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2040, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2042, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2046, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2048, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2050, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2052, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2054, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2056, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2058, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2062, because occupancy 0.500 <= existing 0.500 in 1jvpP # T0291 read from 1jvpP/merged-good-all-a2m # 1jvpP read from 1jvpP/merged-good-all-a2m # adding 1jvpP to template set # found chain 1jvpP in template set Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V44 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V163 Warning: unaligning (T0291)K191 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V163 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1jvpP 2 :ENFQKVEKIGEGTYGVVYKARN T0291 50 :SKKEISVAIKTL 1jvpP 24 :KLTGEVVALKKI T0291 66 :TEKQ 1jvpP 45 :PSTA T0291 74 :LGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1jvpP 49 :IREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLRKH 1jvpP 86 :DLKKFMDAS T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1jvpP 96 :LTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARA T0291 192 :IPIRWTSPEAIAY 1jvpP 164 :VTLWYRAPEILLG T0291 205 :RKFTSASDVWSYGIVLWEVMSY 1jvpP 178 :KYYSTAVDIWSLGCIFAEMVTR T0291 228 :ERPYWEMSNQDVIKAVD 1jvpP 200 :RALFPGDSEIDQLFRIF T0291 245 :EGYRLPPP 1jvpP 234 :PDYKPSFP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIV 1jvpP 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAAL T0291 290 :NPGSLKIITSAAARPS 1jvpP 282 :AHPFFQDVTKPVPHLR Number of specific fragments extracted= 12 number of extra gaps= 0 total=430 Number of alignments=52 # 1jvpP read from 1jvpP/merged-good-all-a2m # found chain 1jvpP in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1jvpP)M1 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V44 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V163 Warning: unaligning (T0291)K191 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V163 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1jvpP 2 :ENFQKVEKIGEGTYGVVYKARN T0291 50 :SKKEISVAIKTL 1jvpP 24 :KLTGEVVALKKI T0291 66 :TEK 1jvpP 45 :PST T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1jvpP 48 :AIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLRKHDA 1jvpP 86 :DLKKFMDASAL T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1jvpP 98 :GIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARA T0291 192 :IPIRWTSPEAIAY 1jvpP 164 :VTLWYRAPEILLG T0291 205 :RKFTSASDVWSYGIVLWEVMS 1jvpP 178 :KYYSTAVDIWSLGCIFAEMVT T0291 227 :GERPYWEMSNQDVIKAVDEGYRLPPPM 1jvpP 199 :RRALFPGDSEIDQLFRIFRTLGTPDEV T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1jvpP 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKP Number of specific fragments extracted= 10 number of extra gaps= 0 total=440 Number of alignments=53 # 1jvpP read from 1jvpP/merged-good-all-a2m # found chain 1jvpP in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1jvpP)M1 Warning: unaligning (T0291)K59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V44 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V163 Warning: unaligning (T0291)K191 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V163 T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAI 1jvpP 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKI T0291 66 :TEKQR 1jvpP 45 :PSTAI T0291 75 :GEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1jvpP 50 :REISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLR 1jvpP 86 :DLKKFMD T0291 120 :HDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1jvpP 95 :ALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARA T0291 192 :IPIRWTSPEAIAY 1jvpP 164 :VTLWYRAPEILLG T0291 205 :RKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1jvpP 178 :KYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRI T0291 243 :VDEGYRLPPP 1jvpP 236 :YKPSFPKWAR T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVSILD 1jvpP 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAALAHPF T0291 288 :IRNPG 1jvpP 286 :FQDVT Number of specific fragments extracted= 10 number of extra gaps= 0 total=450 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lck/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3lck expands to /projects/compbio/data/pdb/3lck.pdb.gz 3lck:Warning: there is no chain 3lck will retry with 3lckA Skipped atom 153, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 155, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 157, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 159, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 161, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 163, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 165, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 167, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 250, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 252, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 254, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 256, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 258, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 260, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 262, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 390, because occupancy 0.350 <= existing 0.650 in 3lck Skipped atom 392, because occupancy 0.350 <= existing 0.650 in 3lck Skipped atom 394, because occupancy 0.350 <= existing 0.650 in 3lck Skipped atom 396, because occupancy 0.350 <= existing 0.650 in 3lck Skipped atom 398, because occupancy 0.350 <= existing 0.650 in 3lck Skipped atom 400, because occupancy 0.350 <= existing 0.650 in 3lck Skipped atom 419, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 421, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 423, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 425, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 427, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 429, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 431, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 433, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 435, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 461, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 463, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 465, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 467, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 469, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 471, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 473, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 666, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 668, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 670, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 672, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 674, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 676, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 678, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 739, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 741, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 743, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 745, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 747, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 749, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 751, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 753, because occupancy 0.180 <= existing 0.820 in 3lck 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 Skipped atom 1618, because occupancy 0.160 <= existing 0.840 in 3lck Skipped atom 1620, because occupancy 0.160 <= existing 0.840 in 3lck Skipped atom 1622, because occupancy 0.160 <= existing 0.840 in 3lck Skipped atom 1624, because occupancy 0.160 <= existing 0.840 in 3lck Skipped atom 1626, because occupancy 0.160 <= existing 0.840 in 3lck Skipped atom 1628, because occupancy 0.160 <= existing 0.840 in 3lck Skipped atom 1659, because occupancy 0.260 <= existing 0.740 in 3lck Skipped atom 1661, because occupancy 0.260 <= existing 0.740 in 3lck Skipped atom 1663, because occupancy 0.260 <= existing 0.740 in 3lck Skipped atom 1665, because occupancy 0.260 <= existing 0.740 in 3lck Skipped atom 1667, because occupancy 0.260 <= existing 0.740 in 3lck Skipped atom 1669, because occupancy 0.260 <= existing 0.740 in 3lck Skipped atom 1762, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1764, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1766, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1768, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1770, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1772, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1774, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1776, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1778, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1780, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1782, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1875, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1877, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1879, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1881, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1883, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1885, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1887, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1889, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 2034, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2036, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2038, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2040, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2042, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2044, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2046, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2048, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2050, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2264, because occupancy 0.290 <= existing 0.710 in 3lck Skipped atom 2266, because occupancy 0.290 <= existing 0.710 in 3lck Skipped atom 2268, because occupancy 0.290 <= existing 0.710 in 3lck Skipped atom 2270, because occupancy 0.290 <= existing 0.710 in 3lck Skipped atom 2272, because occupancy 0.290 <= existing 0.710 in 3lck Skipped atom 2274, because occupancy 0.290 <= existing 0.710 in 3lck # T0291 read from 3lck/merged-good-all-a2m # 3lck read from 3lck/merged-good-all-a2m # adding 3lck to template set # found chain 3lck in template set Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3lck)T395 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3lck)T395 T0291 15 :VHEFAKELDATNISIDKVVGAGEFGEVCSGRL 3lck 233 :WWEDEWEVPRETLKLVERLGAGQFGEVWMGYY T0291 51 :KKEISVAIKTLKVGY 3lck 265 :NGHTKVAVKSLKQGS T0291 66 :TEK 3lck 281 :SPD T0291 72 :DFLGEASIMGQFDHPNIIRLEGVVT 3lck 284 :AFLAEANLMKQLQHQRLVRLYAVVT T0291 98 :SKPVMIVTEYMENGSLDSFLRKH 3lck 309 :QEPIYIITEYMENGSLVDFLKTP T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 3lck 335 :KLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 3lck 396 :AREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFT Number of specific fragments extracted= 7 number of extra gaps= 0 total=457 Number of alignments=55 # 3lck read from 3lck/merged-good-all-a2m # found chain 3lck in template set Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3lck)T395 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3lck)T395 T0291 16 :HEFAKELDATNISIDKVVGAGEFGEVCSGRL 3lck 234 :WEDEWEVPRETLKLVERLGAGQFGEVWMGYY T0291 51 :KKEISVAIKTLKVGYTEK 3lck 265 :NGHTKVAVKSLKQGSMSP T0291 71 :RDFLGEASIMGQFDHPNIIRLEGVVT 3lck 283 :DAFLAEANLMKQLQHQRLVRLYAVVT T0291 98 :SKPVMIVTEYMENGSLDSFLRKH 3lck 309 :QEPIYIITEYMENGSLVDFLKTP T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 3lck 335 :KLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 3lck 396 :AREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFT Number of specific fragments extracted= 6 number of extra gaps= 0 total=463 Number of alignments=56 # 3lck read from 3lck/merged-good-all-a2m # found chain 3lck in template set Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3lck)T395 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3lck)T395 T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRLKLPS 3lck 235 :EDEWEVPRETLKLVERLGAGQFGEVWMGYYNGHT T0291 52 :KEISV 3lck 269 :KVAVK T0291 60 :TLKVG 3lck 274 :SLKQG T0291 65 :YTE 3lck 280 :MSP T0291 71 :RDFLGEASIMGQFDHPNIIRLEGVVTK 3lck 283 :DAFLAEANLMKQLQHQRLVRLYAVVTQ T0291 99 :KPVMIVTEYMENGSLDSFLRKHD 3lck 310 :EPIYIITEYMENGSLVDFLKTPS T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 3lck 334 :IKLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 3lck 396 :AREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFT Number of specific fragments extracted= 8 number of extra gaps= 0 total=471 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vjyA expands to /projects/compbio/data/pdb/1vjy.pdb.gz 1vjyA:# T0291 read from 1vjyA/merged-good-all-a2m # 1vjyA read from 1vjyA/merged-good-all-a2m # adding 1vjyA to template set # found chain 1vjyA in template set Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vjyA)R372 T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1vjyA 202 :ARTIVLQESIGKGRFGEVWRGKW T0291 52 :KEISVAIKTLKVG 1vjyA 225 :RGEEVAVKIFSSR T0291 69 :QRRDFLGEASIM 1vjyA 238 :EERSWFREAEIY T0291 81 :GQFDHPNIIRLEGVVTKSKP 1vjyA 252 :VMLRHENILGFIAADNKDNG T0291 101 :VMIVTEYMENGSLDSFLRK 1vjyA 276 :LWLVSDYHEHGSLFDYLNR T0291 122 :AQFTVIQLVGMLRGIASGMKYLS 1vjyA 295 :YTVTVEGMIKLALSTASGLAHLH T0291 147 :G 1vjyA 324 :Q T0291 148 :YVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAY 1vjyA 329 :IAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTID T0291 191 :KIPIRWTSPEAIAY 1vjyA 373 :VGTKRYMAPEVLDD T0291 206 :KFTSA 1vjyA 387 :SINMK T0291 211 :SDVWSYGIVLWEVMSYG 1vjyA 399 :ADIYAMGLVFWEIARRC T0291 228 :ERPYWE 1vjyA 425 :QLPYYD T0291 234 :MSNQDVIKAVDEG 1vjyA 436 :PSVEEMRKVVCEQ T0291 247 :YRLPPPM 1vjyA 450 :LRPNIPN T0291 254 :DCP 1vjyA 460 :SCE T0291 257 :AALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1vjyA 465 :RVMAKIMRECWYANGAARLTALRIKKTLSQLSQQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=487 Number of alignments=58 # 1vjyA read from 1vjyA/merged-good-all-a2m # found chain 1vjyA in template set Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vjyA)R372 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vjyA)R372 T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1vjyA 202 :ARTIVLQESIGKGRFGEVWRGKW T0291 52 :KEISVAIKTL 1vjyA 225 :RGEEVAVKIF T0291 66 :TEKQRRDFLGEASIMG 1vjyA 235 :SSREERSWFREAEIYQ T0291 82 :QFDHPNIIRLEGVVT 1vjyA 253 :MLRHENILGFIAADN T0291 97 :KSKP 1vjyA 270 :NGTW T0291 101 :VMIVTEYMENGSLDSFLRKH 1vjyA 276 :LWLVSDYHEHGSLFDYLNRY T0291 123 :QFTVIQLVGMLRGIASGMKYLSD 1vjyA 296 :TVTVEGMIKLALSTASGLAHLHM T0291 146 :MGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1vjyA 327 :PAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDT T0291 184 :A 1vjyA 366 :D T0291 191 :KIPIRWTSPEAIAY 1vjyA 373 :VGTKRYMAPEVLDD T0291 206 :KFTSA 1vjyA 387 :SINMK T0291 211 :SDVWSYGIVLWEVMSY 1vjyA 399 :ADIYAMGLVFWEIARR T0291 228 :ERPYW 1vjyA 425 :QLPYY T0291 233 :EMSNQDVIKAVDEG 1vjyA 435 :DPSVEEMRKVVCEQ T0291 247 :YRLPPPM 1vjyA 450 :LRPNIPN T0291 254 :DC 1vjyA 460 :SC T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1vjyA 464 :LRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQEG Number of specific fragments extracted= 17 number of extra gaps= 0 total=504 Number of alignments=59 # 1vjyA read from 1vjyA/merged-good-all-a2m # found chain 1vjyA in template set Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vjyA)R372 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vjyA)R372 T0291 24 :ATNISIDKVVGAGEFGEVCSGRLK 1vjyA 202 :ARTIVLQESIGKGRFGEVWRGKWR T0291 50 :SKKEISVAI 1vjyA 226 :GEEVAVKIF T0291 66 :TEKQRRDFLGEASIMG 1vjyA 235 :SSREERSWFREAEIYQ T0291 82 :QFDHPNIIRLEGVVTKS 1vjyA 253 :MLRHENILGFIAADNKD T0291 99 :KPVMIVTEYMENGSLDSFLRKH 1vjyA 274 :TQLWLVSDYHEHGSLFDYLNRY T0291 123 :QFTVIQLVGMLRGIASGMKYLSD 1vjyA 296 :TVTVEGMIKLALSTASGLAHLHM T0291 146 :MGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1vjyA 327 :PAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDT T0291 184 :A 1vjyA 366 :D T0291 191 :KIPIRWTSPEAIAY 1vjyA 373 :VGTKRYMAPEVLDD T0291 206 :KFTSA 1vjyA 387 :SINMK T0291 211 :SDVWSYGIVLWEVMSYGER 1vjyA 399 :ADIYAMGLVFWEIARRCSI T0291 230 :PYWEMSNQDVIKA 1vjyA 432 :VPSDPSVEEMRKV T0291 243 :VDEGYRLPPPMD 1vjyA 446 :CEQKLRPNIPNR T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1vjyA 464 :LRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQ Number of specific fragments extracted= 14 number of extra gaps= 0 total=518 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1py5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1py5A expands to /projects/compbio/data/pdb/1py5.pdb.gz 1py5A:# T0291 read from 1py5A/merged-good-all-a2m # 1py5A read from 1py5A/merged-good-all-a2m # adding 1py5A to template set # found chain 1py5A in template set Warning: unaligning (T0291)L22 because first residue in template chain is (1py5A)T200 T0291 23 :DATNISIDKVVGAGEFGEVCSGRL 1py5A 201 :IARTIVLQESIGKGRFGEVWRGKW T0291 52 :KEISVAIKTLKVGY 1py5A 225 :RGEEVAVKIFSSRE T0291 70 :RRDFLGEASIMGQ 1py5A 239 :ERSWFREAEIYQT T0291 83 :FDHPNIIRLEGVVTK 1py5A 254 :LRHENILGFIAADNK T0291 98 :SKPVMIVTEYMENGSLDSFLRK 1py5A 273 :WTQLWLVSDYHEHGSLFDYLNR T0291 122 :AQFTVIQLVGMLRGIASGMKYLS 1py5A 295 :YTVTVEGMIKLALSTASGLAHLH T0291 146 :MG 1py5A 323 :TQ T0291 148 :YVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAYTTR 1py5A 329 :IAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDIAP T0291 189 :GGKIPIRWTSPEAI 1py5A 371 :HRVGTKRYMAPEVL T0291 204 :YRKFTSA 1py5A 385 :DDSINMK T0291 211 :SDVWSYGIVLWEVMSYG 1py5A 399 :ADIYAMGLVFWEIARRC T0291 228 :ERPYWE 1py5A 425 :QLPYYD T0291 234 :MSNQDVIKAVDEG 1py5A 436 :PSVEEMRKVVCEQ T0291 247 :YRLPPPMD 1py5A 450 :LRPNIPNR T0291 255 :CP 1py5A 461 :CE T0291 257 :AALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1py5A 465 :RVMAKIMRECWYANGAARLTALRIKKTLSQLSQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=534 Number of alignments=61 # 1py5A read from 1py5A/merged-good-all-a2m # found chain 1py5A in template set Warning: unaligning (T0291)L22 because first residue in template chain is (1py5A)T200 T0291 23 :DATNISIDKVVGAGEFGEVCSGRL 1py5A 201 :IARTIVLQESIGKGRFGEVWRGKW T0291 52 :KEISVAIKTLKV 1py5A 225 :RGEEVAVKIFSS T0291 68 :KQRRDFLGEASIMGQF 1py5A 237 :REERSWFREAEIYQTV T0291 84 :DHPNIIRLEGVVTK 1py5A 255 :RHENILGFIAADNK T0291 98 :SK 1py5A 271 :GT T0291 101 :VMIVTEYMENGSLDSFLRKH 1py5A 276 :LWLVSDYHEHGSLFDYLNRY T0291 123 :QFTVIQLVGMLRGIASGMKYLSD 1py5A 296 :TVTVEGMIKLALSTASGLAHLHM T0291 146 :MGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1py5A 327 :PAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDT T0291 184 :AYTTRGGKIPIRWTSPEAIA 1py5A 366 :DIAPNHRVGTKRYMAPEVLD T0291 205 :RKFTSA 1py5A 386 :DSINMK T0291 211 :SDVWSYGIVLWEVMSY 1py5A 399 :ADIYAMGLVFWEIARR T0291 228 :ERPYW 1py5A 425 :QLPYY T0291 233 :EMSNQDVIKAVDEG 1py5A 435 :DPSVEEMRKVVCEQ T0291 247 :YRLPPPM 1py5A 450 :LRPNIPN T0291 255 :C 1py5A 461 :C T0291 257 :AALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1py5A 465 :RVMAKIMRECWYANGAARLTALRIKKTLSQLSQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=550 Number of alignments=62 # 1py5A read from 1py5A/merged-good-all-a2m # found chain 1py5A in template set Warning: unaligning (T0291)L22 because first residue in template chain is (1py5A)T200 T0291 23 :DATNISIDKVVGAGEFGEVCSGRLK 1py5A 201 :IARTIVLQESIGKGRFGEVWRGKWR T0291 50 :SKKEISVAI 1py5A 226 :GEEVAVKIF T0291 66 :TEKQRRDFLGEASIMGQF 1py5A 235 :SSREERSWFREAEIYQTV T0291 84 :DHPNIIRLEGVVTKS 1py5A 255 :RHENILGFIAADNKD T0291 99 :KPVMIVTEYMENGSLDSFLRKH 1py5A 274 :TQLWLVSDYHEHGSLFDYLNRY T0291 123 :QFTVIQLVGMLRGIASGMKYLSD 1py5A 296 :TVTVEGMIKLALSTASGLAHLHM T0291 146 :MGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1py5A 327 :PAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDT T0291 184 :AYTTRGGKIPIRWTSPEAIAY 1py5A 366 :DIAPNHRVGTKRYMAPEVLDD T0291 206 :KFTSA 1py5A 387 :SINMK T0291 211 :SDVWSYGIVLWEVMSYGER 1py5A 399 :ADIYAMGLVFWEIARRCSI T0291 230 :PYWEMSNQDVIKA 1py5A 432 :VPSDPSVEEMRKV T0291 243 :VDEGYRLPPPMD 1py5A 446 :CEQKLRPNIPNR T0291 257 :AALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1py5A 465 :RVMAKIMRECWYANGAARLTALRIKKTLSQLSQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=563 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bfxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bfxA expands to /projects/compbio/data/pdb/2bfx.pdb.gz 2bfxA: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 # T0291 read from 2bfxA/merged-good-all-a2m # 2bfxA read from 2bfxA/merged-good-all-a2m # adding 2bfxA to template set # found chain 2bfxA in template set Warning: unaligning (T0291)K20 because first residue in template chain is (2bfxA)R86 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bfxA)M249 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bfxA)M249 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRL 2bfxA 87 :KFTIDDFDIGRPLGKGKFGNVYLARE T0291 50 :SKKEISVAIKTLK 2bfxA 113 :KQNKFIMALKVLF T0291 67 :EKQRRD 2bfxA 126 :KSQLEK T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 2bfxA 138 :LRREIEIQSHLRHPNILRMYNYFHDRKRIYLMLEFAPRGELYKELQKHGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 2bfxA 188 :FDEQRSATFMEELADALHYCHERKVIHRDIKPENLLMGYKGELKIADFGWSVHAPSL T0291 186 :TT 2bfxA 245 :RR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2bfxA 250 :CGTLDYLPPEMIEGKTHDEKVDLWCAGVLCYEFLV T0291 227 :GERPYWEMSNQDVIKAVDE 2bfxA 285 :GMPPFDSPSHTETHRRIVN T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 2bfxA 304 :VDLKFPPFLSDGSKDLISKLLRYHPPQRLPLKGVME T0291 283 :ILDKLIRNPG 2bfxA 342 :WVKANSRRVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=573 Number of alignments=64 # 2bfxA read from 2bfxA/merged-good-all-a2m # found chain 2bfxA in template set Warning: unaligning (T0291)K20 because first residue in template chain is (2bfxA)R86 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bfxA)M249 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bfxA)M249 Warning: unaligning (T0291)I296 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bfxA)Q356 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRL 2bfxA 87 :KFTIDDFDIGRPLGKGKFGNVYLARE T0291 50 :SKKEISVAIKTLKVGYT 2bfxA 113 :KQNKFIMALKVLFKSQL T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 2bfxA 132 :EGVEHQLRREIEIQSHLRHPNILRMYNYFHDRKRIYLMLEFAPRGELYKELQKHGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 2bfxA 188 :FDEQRSATFMEELADALHYCHERKVIHRDIKPENLLMGYKGELKIADFGWSVHAPSL T0291 186 :TT 2bfxA 245 :RR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2bfxA 250 :CGTLDYLPPEMIEGKTHDEKVDLWCAGVLCYEFLV T0291 227 :GERPYWEMSNQDVIKAVDEG 2bfxA 285 :GMPPFDSPSHTETHRRIVNV T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 2bfxA 305 :DLKFPPFLSDGSKDLISKLLRYHPPQRLPLKGVME T0291 283 :ILDKLIRNPGSLK 2bfxA 342 :WVKANSRRVLPPV Number of specific fragments extracted= 9 number of extra gaps= 1 total=582 Number of alignments=65 # 2bfxA read from 2bfxA/merged-good-all-a2m # found chain 2bfxA in template set Warning: unaligning (T0291)K20 because first residue in template chain is (2bfxA)R86 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bfxA)M249 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bfxA)M249 Warning: unaligning (T0291)I296 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bfxA)Q356 Warning: unaligning (T0291)I297 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bfxA)Q356 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKT 2bfxA 87 :KFTIDDFDIGRPLGKGKFGNVYLAREKQNKFIMALKVLFK T0291 67 :EKQRR 2bfxA 127 :SQLEK T0291 72 :DFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 2bfxA 137 :QLRREIEIQSHLRHPNILRMYNYFHDRKRIYLMLEFAPRGELYKELQKHG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 2bfxA 187 :RFDEQRSATFMEELADALHYCHERKVIHRDIKPENLLMGYKGELKIADFGWSVHAPSL T0291 186 :TT 2bfxA 245 :RR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAV 2bfxA 250 :CGTLDYLPPEMIEGKTHDEKVDLWCAGVLCYEFLVGMPPFDSPSHTETHRRIV T0291 246 :GYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 2bfxA 303 :NVDLKFPPFLSDGSKDLISKLLRYHPPQRLPLKGVME T0291 283 :ILDKLIRNPGSLK 2bfxA 342 :WVKANSRRVLPPV Number of specific fragments extracted= 8 number of extra gaps= 1 total=590 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fvrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fvrA expands to /projects/compbio/data/pdb/1fvr.pdb.gz 1fvrA:# T0291 read from 1fvrA/merged-good-all-a2m # 1fvrA read from 1fvrA/merged-good-all-a2m # adding 1fvrA to template set # found chain 1fvrA in template set Warning: unaligning (T0291)H16 because first residue in template chain is (1fvrA)P813 Warning: unaligning (T0291)G64 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fvrA)R867 Warning: unaligning (T0291)R71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fvrA)R867 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fvrA)L1000 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fvrA)L1000 T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRLKLPS 1fvrA 814 :TIYPVLDWNDIKFQDVIGEGNFGQVLKARIKKDG T0291 52 :KEISVAIKTLKV 1fvrA 848 :LRMDAAIKRMKE T0291 72 :DFLGEASIMGQFD 1fvrA 868 :DFAGELEVLCKLG T0291 85 :HPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1fvrA 882 :HPNIINLLGACEHRGYLYLAIEYAPHGNLLDFLRKS T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGR 1fvrA 935 :TLSSQQLLHFAADVARGMDYLSQKQFIHRDLAARNILVGENYVAKIADFGLSR T0291 180 :DPEAAYT 1fvrA 988 :GQEVYVK T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIITSAAARPSNL 1fvrA 1001 :PVRWMAIESLNYSVYTTNSDVWSYGVLLWEIVSLGGTPYCGMTCAELYEKLPQGYRLEKPLNCDDEVYDLMRQCWREKPYERPSFAQILVSLNRMLEERKTYVNTTLYEKFTYAG Number of specific fragments extracted= 7 number of extra gaps= 0 total=597 Number of alignments=67 # 1fvrA read from 1fvrA/merged-good-all-a2m # found chain 1fvrA in template set Warning: unaligning (T0291)H16 because first residue in template chain is (1fvrA)P813 Warning: unaligning (T0291)G64 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fvrA)R867 Warning: unaligning (T0291)R71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fvrA)R867 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fvrA)L1000 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fvrA)L1000 Warning: unaligning (T0291)L308 because last residue in template chain is (1fvrA)E1121 T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1fvrA 814 :TIYPVLDWNDIKFQDVIGEGNFGQVLKARIKK T0291 50 :SKKEISVAIKTLKV 1fvrA 846 :DGLRMDAAIKRMKE T0291 72 :DFLGEASIMGQF 1fvrA 868 :DFAGELEVLCKL T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1fvrA 881 :HHPNIINLLGACEHRGYLYLAIEYAPHGNLLDFLR T0291 119 :KHDA 1fvrA 929 :ANST T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGR 1fvrA 935 :TLSSQQLLHFAADVARGMDYLSQKQFIHRDLAARNILVGENYVAKIADFGLSR T0291 180 :DPEAAYT 1fvrA 988 :GQEVYVK T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKII 1fvrA 1001 :PVRWMAIESLNYSVYTTNSDVWSYGVLLWEIVSLGGTPYCGMTCAELYEKLPQGYRLEKPLNCDDEVYDLMRQCWREKPYERPSFAQILVSLNRMLEERKTYVNT T0291 298 :TSAAARPSNL 1fvrA 1111 :FTYAGIDCSA Number of specific fragments extracted= 9 number of extra gaps= 0 total=606 Number of alignments=68 # 1fvrA read from 1fvrA/merged-good-all-a2m # found chain 1fvrA in template set Warning: unaligning (T0291)H16 because first residue in template chain is (1fvrA)P813 Warning: unaligning (T0291)G64 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fvrA)R867 Warning: unaligning (T0291)R71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fvrA)R867 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fvrA)L1000 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fvrA)L1000 T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEI 1fvrA 814 :TIYPVLDWNDIKFQDVIGEGNFGQVLKARIKKDGLRMD T0291 56 :VAIKTLKV 1fvrA 852 :AAIKRMKE T0291 72 :DFLGEASIMGQF 1fvrA 868 :DFAGELEVLCKL T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1fvrA 881 :HHPNIINLLGACEHRGYLYLAIEYAPHGNLLDFLR T0291 119 :KHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGR 1fvrA 931 :STASTLSSQQLLHFAADVARGMDYLSQKQFIHRDLAARNILVGENYVAKIADFGLSR T0291 180 :DPEAAYT 1fvrA 988 :GQEVYVK T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIITSAAARPSN 1fvrA 1001 :PVRWMAIESLNYSVYTTNSDVWSYGVLLWEIVSLGGTPYCGMTCAELYEKLPQGYRLEKPLNCDDEVYDLMRQCWREKPYERPSFAQILVSLNRMLEERKTYVNTTLYEKFTYA Number of specific fragments extracted= 7 number of extra gaps= 0 total=613 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gz8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0291 read from 1gz8A/merged-good-all-a2m # 1gz8A read from 1gz8A/merged-good-all-a2m # found chain 1gz8A in training set Warning: unaligning (T0291)C42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gz8A)K20 Warning: unaligning (T0291)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gz8A)K20 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)V44 Warning: unaligning (T0291)Y204 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)K178 Warning: unaligning (T0291)R205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)K178 Warning: unaligning (T0291)F207 because of BadResidue code BAD_PEPTIDE in next template residue (1gz8A)S181 Warning: unaligning (T0291)T208 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)S181 Warning: unaligning (T0291)M253 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)P253 T0291 25 :TNISIDKVVGAGEFGEV 1gz8A 2 :ENFQKVEKIGEGTYGVV T0291 44 :GRL 1gz8A 21 :ARN T0291 50 :SKKEISVAIKTL 1gz8A 24 :KLTGEVVALKKI T0291 66 :TEKQ 1gz8A 45 :PSTA T0291 74 :LGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1gz8A 49 :IREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLRKH 1gz8A 86 :DLKKFMDAS T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1gz8A 96 :LTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPV T0291 185 :YTTRGGKIPIRWTSPEAIA 1gz8A 157 :RTYTHEVVTLWYRAPEILL T0291 206 :K 1gz8A 179 :Y T0291 209 :SASDVWSYGIVLWEVMSY 1gz8A 182 :TAVDIWSLGCIFAEMVTR T0291 228 :ERPYWEMSNQDVIKAVD 1gz8A 200 :RALFPGDSEIDQLFRIF T0291 245 :EGYRLPPP 1gz8A 234 :PDYKPSFP T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1gz8A 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAH T0291 292 :GSL 1gz8A 284 :PFF Number of specific fragments extracted= 14 number of extra gaps= 3 total=627 Number of alignments=70 # 1gz8A read from 1gz8A/merged-good-all-a2m # found chain 1gz8A in training set Warning: unaligning (T0291)A24 because first residue in template chain is (1gz8A)M1 Warning: unaligning (T0291)C42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gz8A)K20 Warning: unaligning (T0291)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gz8A)K20 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)V44 Warning: unaligning (T0291)Y204 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)K178 Warning: unaligning (T0291)R205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)K178 Warning: unaligning (T0291)F207 because of BadResidue code BAD_PEPTIDE in next template residue (1gz8A)S181 Warning: unaligning (T0291)T208 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)S181 T0291 25 :TNISIDKVVGAGEFGEV 1gz8A 2 :ENFQKVEKIGEGTYGVV T0291 44 :GRL 1gz8A 21 :ARN T0291 50 :SKKEISVAIKTL 1gz8A 24 :KLTGEVVALKKI T0291 66 :TEK 1gz8A 45 :PST T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1gz8A 48 :AIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLRKHDA 1gz8A 86 :DLKKFMDASAL T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1gz8A 98 :GIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVR T0291 186 :TTRGGKIPIRWTSPEAIA 1gz8A 158 :TYTHEVVTLWYRAPEILL T0291 206 :K 1gz8A 179 :Y T0291 209 :SASDVWSYGIVLWEVMS 1gz8A 182 :TAVDIWSLGCIFAEMVT T0291 227 :GERPYWEMSNQDVIKAVDEGYRLPPPM 1gz8A 199 :RRALFPGDSEIDQLFRIFRTLGTPDEV T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKL 1gz8A 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQ T0291 292 :G 1gz8A 288 :D Number of specific fragments extracted= 13 number of extra gaps= 2 total=640 Number of alignments=71 # 1gz8A read from 1gz8A/merged-good-all-a2m # found chain 1gz8A in training set Warning: unaligning (T0291)A24 because first residue in template chain is (1gz8A)M1 Warning: unaligning (T0291)C42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gz8A)K20 Warning: unaligning (T0291)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gz8A)K20 Warning: unaligning (T0291)K59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)V44 Warning: unaligning (T0291)Y204 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)K178 Warning: unaligning (T0291)R205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)K178 Warning: unaligning (T0291)F207 because of BadResidue code BAD_PEPTIDE in next template residue (1gz8A)S181 Warning: unaligning (T0291)T208 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)S181 Warning: unaligning (T0291)M253 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)P253 T0291 25 :TNISIDKVVGAGEFGEV 1gz8A 2 :ENFQKVEKIGEGTYGVV T0291 44 :GRLKLPSKKEISVAI 1gz8A 21 :ARNKLTGEVVALKKI T0291 66 :TEKQ 1gz8A 45 :PSTA T0291 74 :LGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1gz8A 49 :IREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLR 1gz8A 86 :DLKKFMD T0291 120 :HDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1gz8A 95 :ALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVR T0291 186 :TTRGGKIPIRWTSPEAIA 1gz8A 158 :TYTHEVVTLWYRAPEILL T0291 206 :K 1gz8A 179 :Y T0291 209 :SASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1gz8A 182 :TAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRI T0291 243 :VDEGYRLPPP 1gz8A 236 :YKPSFPKWAR T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILD 1gz8A 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAHPF T0291 291 :PGSLKIIT 1gz8A 286 :FQDVTKPV Number of specific fragments extracted= 12 number of extra gaps= 3 total=652 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ir3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ir3A expands to /projects/compbio/data/pdb/1ir3.pdb.gz 1ir3A: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 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 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 # T0291 read from 1ir3A/merged-good-all-a2m # 1ir3A read from 1ir3A/merged-good-all-a2m # adding 1ir3A to template set # found chain 1ir3A in template set Warning: unaligning (T0291)T12 because first residue in template chain is (1ir3A)S981 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ir3A)E1159 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ir3A)E1159 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ir3A)R1164 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ir3A)R1164 T0291 13 :QAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1ir3A 982 :SVFVPDEWEVSREKITLLRELGQGSFGMVYEGNAR T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1ir3A 1019 :IKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSL T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1ir3A 1101 :RPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRD T0291 180 :D 1ir3A 1160 :T T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDK 1ir3A 1165 :KGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKD Number of specific fragments extracted= 5 number of extra gaps= 0 total=657 Number of alignments=73 # 1ir3A read from 1ir3A/merged-good-all-a2m # found chain 1ir3A in template set Warning: unaligning (T0291)T12 because first residue in template chain is (1ir3A)S981 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ir3A)E1159 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ir3A)E1159 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ir3A)R1164 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ir3A)R1164 T0291 13 :QAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1ir3A 982 :SVFVPDEWEVSREKITLLRELGQGSFGMVYEGNAR T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1ir3A 1019 :IKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLR T0291 119 :KHDAQ 1ir3A 1098 :NPGRP T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1ir3A 1104 :PTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRD T0291 180 :D 1ir3A 1160 :T T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1ir3A 1165 :KGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHP Number of specific fragments extracted= 6 number of extra gaps= 0 total=663 Number of alignments=74 # 1ir3A read from 1ir3A/merged-good-all-a2m # found chain 1ir3A in template set Warning: unaligning (T0291)T12 because first residue in template chain is (1ir3A)S981 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ir3A)E1159 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ir3A)E1159 Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ir3A)R1164 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ir3A)R1164 T0291 13 :QAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1ir3A 982 :SVFVPDEWEVSREKITLLRELGQGSFGMVYEGNARD T0291 49 :PSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1ir3A 1020 :KGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLR T0291 119 :KHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1ir3A 1099 :PGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRD T0291 180 :D 1ir3A 1160 :T T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 1ir3A 1165 :KGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDL Number of specific fragments extracted= 5 number of extra gaps= 0 total=668 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2evaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2evaA expands to /projects/compbio/data/pdb/2eva.pdb.gz 2evaA:Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 2evaA Skipped atom 696, because occupancy 0.500 <= existing 0.500 in 2evaA Skipped atom 698, because occupancy 0.500 <= existing 0.500 in 2evaA Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2evaA # T0291 read from 2evaA/merged-good-all-a2m # 2evaA read from 2evaA/merged-good-all-a2m # adding 2evaA to template set # found chain 2evaA in template set Warning: unaligning (T0291)L173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2evaA)G191 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2evaA)G191 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRL 2evaA 28 :LHMIDYKEIEVEEVVGRGAFGVVCKAKW T0291 52 :KEISVAIKTLKVG 2evaA 56 :RAKDVAIKQIESE T0291 68 :KQRRDFLGEASIMGQFDHPNIIRLEGVVTK 2evaA 69 :SERKAFIVELRQLSRVNHPNIVKLYGACLN T0291 100 :PVMIVTEYMENGSLDSFLRKHDA 2evaA 99 :PVCLVMEYAEGGSLYNVLHGAEP T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMG 2evaA 124 :YYTAAHAMSWCLQCSQGVAYLHSMQ T0291 148 :YVHRDLAARNILI 2evaA 152 :LIHRDLKPPNLLL T0291 161 :NSNLVCKVSDFG 2evaA 166 :AGGTVLKICDFG T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2evaA 192 :SAAWMAPEVFEGSNYSEKCDVFSWGIILWEVIT T0291 227 :GERPYWEMS 2evaA 225 :RRKPFDEIG T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 2evaA 236 :AFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMR T0291 290 :NPGSLKIITSAAARPSN 2evaA 293 :GADEPLQYPCQHSLPPG Number of specific fragments extracted= 11 number of extra gaps= 0 total=679 Number of alignments=76 # 2evaA read from 2evaA/merged-good-all-a2m # found chain 2evaA in template set Warning: unaligning (T0291)L173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2evaA)G191 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2evaA)G191 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRL 2evaA 29 :HMIDYKEIEVEEVVGRGAFGVVCKAKW T0291 52 :KEISVAIKTLK 2evaA 56 :RAKDVAIKQIE T0291 66 :TEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 2evaA 67 :SESERKAFIVELRQLSRVNHPNIVKLYGACLNP T0291 101 :VMIVTEYMENGSLDSFLRKHDA 2evaA 100 :VCLVMEYAEGGSLYNVLHGAEP T0291 123 :QFTVIQLVGMLRGIASGMKYLSD 2evaA 124 :YYTAAHAMSWCLQCSQGVAYLHS T0291 146 :MGYVHRDLAARNILINSNL 2evaA 150 :KALIHRDLKPPNLLLVAGG T0291 165 :VCKVSDFG 2evaA 170 :VLKICDFG T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2evaA 192 :SAAWMAPEVFEGSNYSEKCDVFSWGIILWEVIT T0291 227 :GERPYW 2evaA 225 :RRKPFD T0291 233 :EMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKII 2evaA 233 :GGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMRYFPGADEP T0291 298 :TSAAARPSNL 2evaA 302 :CQHSLPPGED Number of specific fragments extracted= 11 number of extra gaps= 0 total=690 Number of alignments=77 # 2evaA read from 2evaA/merged-good-all-a2m # found chain 2evaA in template set Warning: unaligning (T0291)L173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2evaA)G191 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2evaA)G191 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKL 2evaA 29 :HMIDYKEIEVEEVVGRGAFGVVCKAKWRA T0291 51 :KKEISVAI 2evaA 58 :KDVAIKQI T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 2evaA 66 :ESESERKAFIVELRQLSRVNHPNIVKLYGACLNP T0291 101 :VMIVTEYMENGSLDSFLRKHD 2evaA 100 :VCLVMEYAEGGSLYNVLHGAE T0291 122 :AQFTVIQLVGMLRGIASGMKYLSD 2evaA 123 :PYYTAAHAMSWCLQCSQGVAYLHS T0291 146 :MGYVHRDLAARNILI 2evaA 150 :KALIHRDLKPPNLLL T0291 161 :NSNLVCKVSDFG 2evaA 166 :AGGTVLKICDFG T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYW 2evaA 192 :SAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFDE T0291 233 :EMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 2evaA 233 :GGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMRY T0291 291 :PGSLKIITSAAARPSNLLL 2evaA 294 :ADEPLQYPCQHSLPPGEDG Number of specific fragments extracted= 10 number of extra gaps= 0 total=700 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mq4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mq4A expands to /projects/compbio/data/pdb/1mq4.pdb.gz 1mq4A:# T0291 read from 1mq4A/merged-good-all-a2m # 1mq4A read from 1mq4A/merged-good-all-a2m # adding 1mq4A to template set # found chain 1mq4A in template set Warning: unaligning (T0291)K20 because first residue in template chain is (1mq4A)R126 Warning: unaligning (T0291)L177 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1mq4A)P282 Warning: unaligning (T0291)E178 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1mq4A)P282 Warning: unaligning (T0291)A184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mq4A)T288 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mq4A)T288 Warning: unaligning (T0291)R289 because last residue in template chain is (1mq4A)S388 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRL 1mq4A 127 :QWALEDFEIGRPLGKGKFGNVYLARE T0291 50 :SKKEISVAIKTLK 1mq4A 153 :KQSKFILALKVLF T0291 67 :EKQRRD 1mq4A 166 :KAQLEK T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1mq4A 178 :LRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSK T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1mq4A 228 :FDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVH T0291 179 :DD 1mq4A 283 :SS T0291 188 :RGGKI 1mq4A 289 :LCGTL T0291 195 :RWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1mq4A 294 :DYLPPEMIEGRMHDEKVDLWSLGVLCYEFLV T0291 227 :GERPYWEMSNQDVIKAVDE 1mq4A 325 :GKPPFEANTYQETYKRISR T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIV 1mq4A 344 :VEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVL T0291 282 :SILDKLI 1mq4A 381 :PWITANS Number of specific fragments extracted= 11 number of extra gaps= 1 total=711 Number of alignments=79 # 1mq4A read from 1mq4A/merged-good-all-a2m # found chain 1mq4A in template set Warning: unaligning (T0291)K20 because first residue in template chain is (1mq4A)R126 Warning: unaligning (T0291)L177 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1mq4A)P282 Warning: unaligning (T0291)E178 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1mq4A)P282 Warning: unaligning (T0291)T186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mq4A)T288 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mq4A)T288 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRL 1mq4A 127 :QWALEDFEIGRPLGKGKFGNVYLARE T0291 50 :SKKEISVAIKTLKVGYTEK 1mq4A 153 :KQSKFILALKVLFKAQLEK T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1mq4A 174 :VEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSK T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1mq4A 228 :FDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVH T0291 179 :DD 1mq4A 283 :SS T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1mq4A 289 :LCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLV T0291 227 :GERPYWEMSNQDVIKAVDEG 1mq4A 325 :GKPPFEANTYQETYKRISRV T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILD 1mq4A 345 :EFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPW Number of specific fragments extracted= 8 number of extra gaps= 1 total=719 Number of alignments=80 # 1mq4A read from 1mq4A/merged-good-all-a2m # found chain 1mq4A in template set Warning: unaligning (T0291)K20 because first residue in template chain is (1mq4A)R126 Warning: unaligning (T0291)L177 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1mq4A)P282 Warning: unaligning (T0291)E178 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1mq4A)P282 Warning: unaligning (T0291)T186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mq4A)T288 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mq4A)T288 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKT 1mq4A 127 :QWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFK T0291 67 :EKQRR 1mq4A 167 :AQLEK T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1mq4A 178 :LRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLS T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1mq4A 227 :KFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVH T0291 179 :DD 1mq4A 283 :SS T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 1mq4A 289 :LCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVE T0291 249 :LPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1mq4A 346 :FTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEH Number of specific fragments extracted= 7 number of extra gaps= 1 total=726 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e1xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1e1xA expands to /projects/compbio/data/pdb/1e1x.pdb.gz 1e1xA:# T0291 read from 1e1xA/merged-good-all-a2m # 1e1xA read from 1e1xA/merged-good-all-a2m # adding 1e1xA to template set # found chain 1e1xA in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1e1xA)M1 Warning: unaligning (T0291)L61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1e1xA)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1e1xA)V44 Warning: unaligning (T0291)M108 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)H84 Warning: unaligning (T0291)E109 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)H84 Warning: unaligning (T0291)F207 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)S181 Warning: unaligning (T0291)T208 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)S181 Warning: unaligning (T0291)E233 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)D206 Warning: unaligning (T0291)M234 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)D206 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1e1xA 2 :ENFQKVEKIGEGTYGVVYKARN T0291 50 :SKKEISVAIKT 1e1xA 24 :KLTGEVVALKK T0291 66 :TEKQ 1e1xA 45 :PSTA T0291 74 :LGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEY 1e1xA 49 :IREISLLKELNHPNIVKLLDVIHTENKLYLVFEF T0291 110 :N 1e1xA 85 :Q T0291 112 :SLDSFLRKH 1e1xA 86 :DLKKFMDAS T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1e1xA 96 :LTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPV T0291 185 :YTTRGGKIPIRWTSPEAIAY 1e1xA 157 :RTYTHEVVTLWYRAPEILLG T0291 205 :RK 1e1xA 178 :KY T0291 209 :SASDVWSYGIVLWEVMSY 1e1xA 182 :TAVDIWSLGCIFAEMVTR T0291 228 :ERPYW 1e1xA 200 :RALFP T0291 235 :SNQDVIKAVD 1e1xA 207 :SEIDQLFRIF T0291 245 :EGYRLPPP 1e1xA 234 :PDYKPSFP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIV 1e1xA 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAAL T0291 290 :NPGSLKIITSAAARPS 1e1xA 282 :AHPFFQDVTKPVPHLR Number of specific fragments extracted= 15 number of extra gaps= 3 total=741 Number of alignments=82 # 1e1xA read from 1e1xA/merged-good-all-a2m # found chain 1e1xA in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1e1xA)M1 Warning: unaligning (T0291)L61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1e1xA)V44 Warning: unaligning (T0291)M108 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)H84 Warning: unaligning (T0291)E109 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)H84 Warning: unaligning (T0291)F207 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)S181 Warning: unaligning (T0291)T208 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)S181 Warning: unaligning (T0291)E233 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)D206 Warning: unaligning (T0291)M234 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)D206 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1e1xA 2 :ENFQKVEKIGEGTYGVVYKARN T0291 50 :SKKEISVAIKT 1e1xA 24 :KLTGEVVALKK T0291 67 :EK 1e1xA 46 :ST T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEY 1e1xA 48 :AIREISLLKELNHPNIVKLLDVIHTENKLYLVFEF T0291 110 :N 1e1xA 85 :Q T0291 112 :SLDSFLRKHDA 1e1xA 86 :DLKKFMDASAL T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1e1xA 98 :GIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVR T0291 186 :TTRGGKIPIRWTSPEAIAY 1e1xA 158 :TYTHEVVTLWYRAPEILLG T0291 205 :RK 1e1xA 178 :KY T0291 209 :SASDVWSYGIVLWEVMS 1e1xA 182 :TAVDIWSLGCIFAEMVT T0291 227 :GERPYW 1e1xA 199 :RRALFP T0291 235 :SNQDVIKAVDEGYRLPPPM 1e1xA 207 :SEIDQLFRIFRTLGTPDEV T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSIL 1e1xA 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAHP T0291 293 :SLKI 1e1xA 285 :FFQD Number of specific fragments extracted= 14 number of extra gaps= 3 total=755 Number of alignments=83 # 1e1xA read from 1e1xA/merged-good-all-a2m # found chain 1e1xA in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1e1xA)M1 Warning: unaligning (T0291)I58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1e1xA)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1e1xA)V44 Warning: unaligning (T0291)M108 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)H84 Warning: unaligning (T0291)E109 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)H84 Warning: unaligning (T0291)F207 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)S181 Warning: unaligning (T0291)T208 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)S181 Warning: unaligning (T0291)W232 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)D206 Warning: unaligning (T0291)E233 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)D206 T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISVA 1e1xA 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKK T0291 66 :TEKQR 1e1xA 45 :PSTAI T0291 75 :GEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEY 1e1xA 50 :REISLLKELNHPNIVKLLDVIHTENKLYLVFEF T0291 110 :N 1e1xA 85 :Q T0291 112 :SLDSFLR 1e1xA 86 :DLKKFMD T0291 120 :HDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1e1xA 95 :ALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVR T0291 186 :TTRGGKIPIRWTSPEAIAY 1e1xA 158 :TYTHEVVTLWYRAPEILLG T0291 205 :RK 1e1xA 178 :KY T0291 209 :SASDVWSYGIVLWEVMSYGERPY 1e1xA 182 :TAVDIWSLGCIFAEMVTRRALFP T0291 234 :MSNQDVIKA 1e1xA 207 :SEIDQLFRI T0291 243 :VDEGYRLPPP 1e1xA 236 :YKPSFPKWAR T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1e1xA 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAALAH T0291 298 :TSAAARP 1e1xA 284 :PFFQDVT Number of specific fragments extracted= 13 number of extra gaps= 3 total=768 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ptk/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/T0291/2ptk/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0291/2ptk/merged-good-all-a2m.gz for input Trying 2ptk/merged-good-all-a2m Error: Couldn't open file 2ptk/merged-good-all-a2m or 2ptk/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fgkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fgkA expands to /projects/compbio/data/pdb/1fgk.pdb.gz 1fgkA:Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 1fgkA # T0291 read from 1fgkA/merged-good-all-a2m # 1fgkA read from 1fgkA/merged-good-all-a2m # adding 1fgkA to template set # found chain 1fgkA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1fgkA)E464 Warning: unaligning (T0291)G34 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fgkA)Q491 Warning: unaligning (T0291)E40 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)Q491 Warning: unaligning (T0291)S50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)P505 Warning: unaligning (T0291)D121 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)E592 T0291 14 :AVHEFAKELDATNISIDKVV 1fgkA 465 :LPEDPRWELPRDRLVLGKPL T0291 41 :VCSGRLKL 1fgkA 492 :VVLAEAIG T0291 51 :KKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFD 1fgkA 506 :NRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIG T0291 85 :HPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1fgkA 541 :HKNIINLLGACTQDGPLYVIVEYASKGNLREYLQAR T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1fgkA 593 :EQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHI T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNP 1fgkA 652 :DYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALT Number of specific fragments extracted= 6 number of extra gaps= 0 total=774 Number of alignments=85 # 1fgkA read from 1fgkA/merged-good-all-a2m # found chain 1fgkA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1fgkA)E464 Warning: unaligning (T0291)G34 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fgkA)Q491 Warning: unaligning (T0291)E40 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)Q491 Warning: unaligning (T0291)S50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)P505 Warning: unaligning (T0291)D121 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)E592 Warning: unaligning (T0291)G292 because last residue in template chain is (1fgkA)S762 T0291 14 :AVHEFAKELDATNISIDKVV 1fgkA 465 :LPEDPRWELPRDRLVLGKPL T0291 41 :VCSGRLK 1fgkA 492 :VVLAEAI T0291 51 :KKEISVAIKTLKVGYTEKQRRDFLGEASIMGQF 1fgkA 506 :NRVTKVAVKMLKSDATEKDLSDLISEMEMMKMI T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1fgkA 540 :KHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQ T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1fgkA 593 :EQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHH T0291 181 :PEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNP 1fgkA 651 :IDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALT Number of specific fragments extracted= 6 number of extra gaps= 0 total=780 Number of alignments=86 # 1fgkA read from 1fgkA/merged-good-all-a2m # found chain 1fgkA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1fgkA)E464 Warning: unaligning (T0291)G34 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fgkA)Q491 Warning: unaligning (T0291)E40 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)Q491 Warning: unaligning (T0291)S50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)P505 Warning: unaligning (T0291)D121 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)E592 Warning: unaligning (T0291)G292 because last residue in template chain is (1fgkA)S762 T0291 14 :AVHEFAKELDATNISIDKVV 1fgkA 465 :LPEDPRWELPRDRLVLGKPL T0291 41 :VCSGRLKL 1fgkA 492 :VVLAEAIG T0291 51 :KKEISVAIKTLKVGYTEKQRRDFLGEASIMGQF 1fgkA 506 :NRVTKVAVKMLKSDATEKDLSDLISEMEMMKMI T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1fgkA 540 :KHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQ T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1fgkA 593 :EQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYY T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNP 1fgkA 655 :KKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALT Number of specific fragments extracted= 6 number of extra gaps= 0 total=786 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hcl/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hcl expands to /projects/compbio/data/pdb/1hcl.pdb.gz 1hcl:Warning: there is no chain 1hcl will retry with 1hclA Skipped atom 1022, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 1024, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 1026, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 1028, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 1030, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 2093, because occupancy 0.370 <= existing 0.660 in 1hcl # T0291 read from 1hcl/merged-good-all-a2m # 1hcl read from 1hcl/merged-good-all-a2m # adding 1hcl to template set # found chain 1hcl in template set Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hcl)T41 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1hcl 2 :ENFQKVEKIGEGTYGVVYKARN T0291 50 :SKKEISVAIKTL 1hcl 24 :KLTGEVVALKKI T0291 63 :VGYTEKQ 1hcl 42 :EGVPSTA T0291 74 :LGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1hcl 49 :IREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLRKH 1hcl 86 :DLKKFMDAS T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1hcl 96 :LTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPV T0291 185 :YTTRGGKIPIRWTSPEAIAY 1hcl 157 :RTYTHEVVTLWYRAPEILLG T0291 205 :RKFTSASDVWSYGIVLWEVMSY 1hcl 178 :KYYSTAVDIWSLGCIFAEMVTR T0291 228 :ERPYWEMSNQDVIKAVD 1hcl 200 :RALFPGDSEIDQLFRIF T0291 245 :EGYRLPPP 1hcl 234 :PDYKPSFP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIV 1hcl 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAAL T0291 290 :NPGSL 1hcl 282 :AHPFF Number of specific fragments extracted= 12 number of extra gaps= 0 total=798 Number of alignments=88 # 1hcl read from 1hcl/merged-good-all-a2m # found chain 1hcl in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1hcl)M1 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hcl)T41 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1hcl 2 :ENFQKVEKIGEGTYGVVYKARN T0291 50 :SKKEISVAIKTL 1hcl 24 :KLTGEVVALKKI T0291 64 :GYTEK 1hcl 43 :GVPST T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1hcl 48 :AIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLRKHDAQ 1hcl 86 :DLKKFMDASALT T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1hcl 99 :IPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVR T0291 186 :TTRGGKIPIRWTSPEAIAY 1hcl 158 :TYTHEVVTLWYRAPEILLG T0291 205 :RKFTSASDVWSYGIVLWEVMS 1hcl 178 :KYYSTAVDIWSLGCIFAEMVT T0291 227 :GERPYWEMSNQDVIKAVDEGYRLPPPM 1hcl 199 :RRALFPGDSEIDQLFRIFRTLGTPDEV T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILD 1hcl 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAHPF Number of specific fragments extracted= 10 number of extra gaps= 0 total=808 Number of alignments=89 # 1hcl read from 1hcl/merged-good-all-a2m # found chain 1hcl in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1hcl)M1 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hcl)T41 T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAI 1hcl 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKI T0291 63 :VGYTEKQR 1hcl 42 :EGVPSTAI T0291 75 :GEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1hcl 50 :REISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLR 1hcl 86 :DLKKFMD T0291 119 :KHD 1hcl 95 :ALT T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1hcl 98 :GIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVR T0291 186 :TTRGGKIPIRWTSPEAIAY 1hcl 158 :TYTHEVVTLWYRAPEILLG T0291 205 :RKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1hcl 178 :KYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRI T0291 243 :VDEGYRLPPP 1hcl 236 :YKPSFPKWAR T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVSIL 1hcl 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAALAHP T0291 287 :LIRNPGS 1hcl 285 :FFQDVTK Number of specific fragments extracted= 11 number of extra gaps= 0 total=819 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h1wA expands to /projects/compbio/data/pdb/1h1w.pdb.gz 1h1wA:Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1026, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1028, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1h1wA 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 Skipped atom 1432, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1436, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1986, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1988, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2280, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2282, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2284, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2286, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2288, because occupancy 0.500 <= existing 0.500 in 1h1wA # T0291 read from 1h1wA/merged-good-all-a2m # 1h1wA read from 1h1wA/merged-good-all-a2m # adding 1h1wA to template set # found chain 1h1wA in template set Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)A237 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)A237 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)F242 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)F242 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLK 1h1wA 74 :PRKKRPEDFKFGKILGEGSFSTVVLAREL T0291 51 :KKEISVAIKTLK 1h1wA 103 :ATSREYAIKILE T0291 63 :VGYTEKQR 1h1wA 120 :KENKVPYV T0291 74 :LGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1h1wA 128 :TRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGS T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLE 1h1wA 177 :FDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLS T0291 186 :TT 1h1wA 238 :RA T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1h1wA 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVA T0291 227 :GERPYWEMSNQDVIKAVDEG 1h1wA 278 :GLPPFRAGNEYLIFQKIIKL T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1h1wA 298 :EYDFPEKFFPKARDLVEKLLVLDATKRL T0291 276 :KFEQIVS 1h1wA 332 :GYGPLKA Number of specific fragments extracted= 10 number of extra gaps= 0 total=829 Number of alignments=91 # 1h1wA read from 1h1wA/merged-good-all-a2m # found chain 1h1wA in template set Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)A237 Warning: unaligning (T0291)A184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)A237 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)F242 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)F242 T0291 18 :FAKELDATNISIDKVVGAGEFGEVCSGRL 1h1wA 73 :QPRKKRPEDFKFGKILGEGSFSTVVLARE T0291 50 :SKKEISVAIKTLKVGYT 1h1wA 102 :LATSREYAIKILEKRHI T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1h1wA 121 :ENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGS T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLE 1h1wA 177 :FDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLS T0291 186 :TT 1h1wA 238 :RA T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1h1wA 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVA T0291 227 :GERPYWEMSNQDVIKAVDEG 1h1wA 278 :GLPPFRAGNEYLIFQKIIKL T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1h1wA 298 :EYDFPEKFFPKARDLVEKLLVLDATKRL T0291 276 :KFEQIVSILDK 1h1wA 332 :GYGPLKAHPFF T0291 299 :SAAARPSNLLLD 1h1wA 343 :ESVTWENLHQQT Number of specific fragments extracted= 10 number of extra gaps= 0 total=839 Number of alignments=92 # 1h1wA read from 1h1wA/merged-good-all-a2m # found chain 1h1wA in template set Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)A237 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)A237 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)F242 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)F242 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1h1wA 74 :PRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHI T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1h1wA 119 :IKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLE 1h1wA 176 :SFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLS T0291 186 :TT 1h1wA 238 :RA T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDE 1h1wA 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKL T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1h1wA 298 :EYDFPEKFFPKARDLVEKLLVLDATKRL T0291 276 :KFEQIVSI 1h1wA 332 :GYGPLKAH T0291 289 :RNPGSLKIITSAAARPS 1h1wA 340 :PFFESVTWENLHQQTPP Number of specific fragments extracted= 8 number of extra gaps= 0 total=847 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f3mC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f3mC expands to /projects/compbio/data/pdb/1f3m.pdb.gz 1f3mC:# T0291 read from 1f3mC/merged-good-all-a2m # 1f3mC read from 1f3mC/merged-good-all-a2m # adding 1f3mC to template set # found chain 1f3mC in template set Warning: unaligning (T0291)D10 because first residue in template chain is (1f3mC)S249 Warning: unaligning (T0291)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f3mC)T423 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f3mC)T423 T0291 11 :PTQAVHEFAKELDATN 1f3mC 250 :DEEILEKLRSIVSVGD T0291 27 :ISIDKVVGAGEFGEVCSGRL 1f3mC 270 :YTRFEKIGQGASGTVYTAMD T0291 50 :SKKEISVAIKTLKVGYTEK 1f3mC 290 :VATGQEVAIRQMNLQQQPK T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1f3mC 309 :KELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETC T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVL 1f3mC 361 :MDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQI T0291 189 :GGKIP 1f3mC 424 :MVGTP T0291 195 :RWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1f3mC 429 :YWMAPEVVTRKAYGPKVDIWSLGIMAIEMIE T0291 227 :GERPYWEMSNQDVIKAVDEG 1f3mC 460 :GEPPYLNENPLRALYLIATN T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIV 1f3mC 482 :PELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELL T0291 290 :NPGSLKIITSA 1f3mC 517 :QHQFLKIAKPL Number of specific fragments extracted= 10 number of extra gaps= 0 total=857 Number of alignments=94 # 1f3mC read from 1f3mC/merged-good-all-a2m # found chain 1f3mC in template set Warning: unaligning (T0291)D10 because first residue in template chain is (1f3mC)S249 Warning: unaligning (T0291)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f3mC)T423 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f3mC)T423 T0291 11 :PTQAVHEFAKELDATN 1f3mC 250 :DEEILEKLRSIVSVGD T0291 27 :ISIDKVVGAGEFGEVCSGRL 1f3mC 270 :YTRFEKIGQGASGTVYTAMD T0291 50 :SKKEISVAIKTLKVGYTEK 1f3mC 290 :VATGQEVAIRQMNLQQQPK T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1f3mC 309 :KELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETC T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVL 1f3mC 361 :MDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQI T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1f3mC 424 :MVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIE T0291 227 :GERPYWEMSNQDVIKAVDEG 1f3mC 460 :GEPPYLNENPLRALYLIATN T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 1f3mC 482 :PELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELLQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=865 Number of alignments=95 # 1f3mC read from 1f3mC/merged-good-all-a2m # found chain 1f3mC in template set Warning: unaligning (T0291)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f3mC)T423 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f3mC)T423 T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISV 1f3mC 268 :KKYTRFEKIGQGASGTVYTAMDVATGQEVAIR T0291 60 :TLKVGYTE 1f3mC 300 :QMNLQQQP T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1f3mC 308 :KKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETC T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVL 1f3mC 361 :MDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQI T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 1f3mC 424 :MVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNG T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 1f3mC 482 :PELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELLQ T0291 297 :ITSAAARPSNLL 1f3mC 518 :HQFLKIAKPLSS Number of specific fragments extracted= 7 number of extra gaps= 0 total=872 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bikB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0291 read from 2bikB/merged-good-all-a2m # 2bikB read from 2bikB/merged-good-all-a2m # found chain 2bikB in training set Warning: unaligning (T0291)P256 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bikB)E262 Warning: unaligning (T0291)A258 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bikB)E262 T0291 26 :NISIDKVVGAGEFGEVCSGRL 2bikB 37 :QYQVGPLLGSGGFGSVYSGIR T0291 50 :SKKEISVAIKTLKVGY 2bikB 58 :VSDNLPVAIKHVEKDR T0291 75 :GEASIMGQFDHP 2bikB 88 :MEVVLLKKVSSG T0291 87 :NIIRLEGVVTKSKPVMIVTEYMEN 2bikB 102 :GVIRLLDWFERPDSFVLILERPEP T0291 112 :SLDSFLRKHDA 2bikB 128 :DLFDFITERGA T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 2bikB 139 :LQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILI T0291 161 :NSNLVCKVSDFGLGRVLEDDP 2bikB 177 :LNRGELKLIDFGSGALLKDTV T0291 184 :AYTTRGGK 2bikB 198 :YTDFDGTR T0291 195 :RWTSPEAIAYRKFT 2bikB 206 :VYSPPEWIRYHRYH T0291 210 :ASDVWSYGIVLWEVMS 2bikB 222 :SAAVWSLGILLYDMVC T0291 227 :GERPYW 2bikB 238 :GDIPFE T0291 235 :SNQDVIK 2bikB 244 :HDEEIIG T0291 247 :YRLPPPMDC 2bikB 251 :GQVFFRQRV T0291 259 :LYQLMLDCWQKDRNNRPKFEQIVS 2bikB 263 :CQHLIRWCLALRPSDRPTFEEIQN Number of specific fragments extracted= 14 number of extra gaps= 0 total=886 Number of alignments=97 # 2bikB read from 2bikB/merged-good-all-a2m # found chain 2bikB in training set Warning: unaligning (T0291)P256 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bikB)E262 Warning: unaligning (T0291)A258 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bikB)E262 T0291 23 :DATNISIDKVVGAGEFGEVCSGRLK 2bikB 34 :LESQYQVGPLLGSGGFGSVYSGIRV T0291 51 :KKEISVAIKTLKVGYT 2bikB 59 :SDNLPVAIKHVEKDRI T0291 67 :EK 2bikB 81 :PN T0291 75 :GEASIMGQFDHP 2bikB 88 :MEVVLLKKVSSG T0291 87 :NIIRLEGVVTKSKPVMIVTEYMEN 2bikB 102 :GVIRLLDWFERPDSFVLILERPEP T0291 111 :GSLDSFLRKHDA 2bikB 127 :QDLFDFITERGA T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILIN 2bikB 139 :LQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILID T0291 162 :SNLVCKVSDFGLGRVLEDD 2bikB 178 :NRGELKLIDFGSGALLKDT T0291 186 :TTRGGKIPIRWTSPEAIAYRKFT 2bikB 197 :VYTDFDGTRVYSPPEWIRYHRYH T0291 209 :SASDVWSYGIVLWEVMS 2bikB 221 :RSAAVWSLGILLYDMVC T0291 227 :GERPY 2bikB 238 :GDIPF T0291 234 :MSNQDVIK 2bikB 243 :EHDEEIIG T0291 247 :YRLPPPMDC 2bikB 251 :GQVFFRQRV T0291 259 :LYQLMLDCWQKDRNNRPKFEQIVSILD 2bikB 263 :CQHLIRWCLALRPSDRPTFEEIQNHPW Number of specific fragments extracted= 14 number of extra gaps= 0 total=900 Number of alignments=98 # 2bikB read from 2bikB/merged-good-all-a2m # found chain 2bikB in training set Warning: unaligning (T0291)L22 because first residue in template chain is (2bikB)P33 Warning: unaligning (T0291)P256 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bikB)E262 Warning: unaligning (T0291)A258 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bikB)E262 T0291 23 :DATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIK 2bikB 34 :LESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVE T0291 60 :TLKVGYTE 2bikB 77 :WGELPNGT T0291 75 :GEASIMGQF 2bikB 88 :MEVVLLKKV T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMEN 2bikB 99 :GFSGVIRLLDWFERPDSFVLILERPEP T0291 111 :GSLDSFLRKHD 2bikB 127 :QDLFDFITERG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 2bikB 138 :ALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILI T0291 161 :NSNLVCKVSDFGLGRVLEDD 2bikB 177 :LNRGELKLIDFGSGALLKDT T0291 186 :TTRGGKIPIRWTSPEAIAYRKFT 2bikB 197 :VYTDFDGTRVYSPPEWIRYHRYH T0291 210 :ASDVWSYGIVLWEVMSYGERPY 2bikB 222 :SAAVWSLGILLYDMVCGDIPFE T0291 235 :SNQDVIK 2bikB 244 :HDEEIIG T0291 247 :YRLPPPMDC 2bikB 251 :GQVFFRQRV T0291 259 :LYQLMLDCWQKDRNNRPKFEQIVSIL 2bikB 263 :CQHLIRWCLALRPSDRPTFEEIQNHP Number of specific fragments extracted= 12 number of extra gaps= 0 total=912 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a19B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a19B expands to /projects/compbio/data/pdb/2a19.pdb.gz 2a19B:# T0291 read from 2a19B/merged-good-all-a2m # 2a19B read from 2a19B/merged-good-all-a2m # adding 2a19B to template set # found chain 2a19B in template set Warning: unaligning (T0291)Y65 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E303 Warning: unaligning (T0291)E67 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E303 Warning: unaligning (T0291)D121 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E384 Warning: unaligning (T0291)A122 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E384 Warning: unaligning (T0291)A183 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a19B)R447 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a19B)R447 Warning: unaligning (T0291)R289 because last residue in template chain is (2a19B)K541 T0291 27 :ISIDKVVGAGEFGEVCSGRL 2a19B 267 :FKEIELIGSGGFGQVFKAKH T0291 50 :SKKEISVAIKTLKVG 2a19B 287 :RIDGKTYVIKRVKYN T0291 68 :KQ 2a19B 304 :KA T0291 74 :LGEASIMGQFDHPNIIRLEGVVTK 2a19B 306 :EREVKALAKLDHVNIVHYNGCWDG T0291 99 :K 2a19B 357 :S T0291 101 :VMIVTEYMENGSLDSFLRKH 2a19B 362 :LFIQMEFCDKGTLEQWIEKR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 2a19B 385 :KLDKVLALELFEQITKGVDYIHSKKLINRDLKPSNIFLVDTKQVKIGDFGLVTSLKNDGK T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGER 2a19B 448 :SKGTLRYMSPEQISSQDYGKEVDLYALGLILAELLHVCDT T0291 235 :SNQDVIKAVDEG 2a19B 490 :ETSKFFTDLRDG T0291 250 :PPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 2a19B 502 :IISDIFDKKEKTLLQKLLSKKPEDRPNTSEILRTLTVWK Number of specific fragments extracted= 10 number of extra gaps= 2 total=922 Number of alignments=100 # 2a19B read from 2a19B/merged-good-all-a2m # found chain 2a19B in template set Warning: unaligning (T0291)Y65 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E303 Warning: unaligning (T0291)T66 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E303 Warning: unaligning (T0291)D121 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E384 Warning: unaligning (T0291)A122 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E384 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a19B)R447 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a19B)R447 Warning: unaligning (T0291)R289 because last residue in template chain is (2a19B)K541 T0291 27 :ISIDKVVGAGEFGEVCSGRL 2a19B 267 :FKEIELIGSGGFGQVFKAKH T0291 50 :SKKEISVAIKTLKVG 2a19B 287 :RIDGKTYVIKRVKYN T0291 67 :E 2a19B 304 :K T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTK 2a19B 305 :AEREVKALAKLDHVNIVHYNGCWDG T0291 101 :VMIVTEYMENGSLDSFLRKH 2a19B 362 :LFIQMEFCDKGTLEQWIEKR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 2a19B 385 :KLDKVLALELFEQITKGVDYIHSKKLINRDLKPSNIFLVDTKQVKIGDFGLVTSLKNDG T0291 186 :T 2a19B 444 :K T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSY 2a19B 448 :SKGTLRYMSPEQISSQDYGKEVDLYALGLILAELLHV T0291 233 :EMSNQDV 2a19B 485 :CDTAFET T0291 240 :IKAVDEG 2a19B 495 :FTDLRDG T0291 250 :PPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 2a19B 502 :IISDIFDKKEKTLLQKLLSKKPEDRPNTSEILRTLTVWK Number of specific fragments extracted= 11 number of extra gaps= 2 total=933 Number of alignments=101 # 2a19B read from 2a19B/merged-good-all-a2m # found chain 2a19B in template set Warning: unaligning (T0291)K62 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E303 Warning: unaligning (T0291)V63 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E303 Warning: unaligning (T0291)D121 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E384 Warning: unaligning (T0291)A122 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E384 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a19B)R447 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a19B)R447 Warning: unaligning (T0291)R289 because last residue in template chain is (2a19B)K541 T0291 26 :NISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTL 2a19B 266 :DFKEIELIGSGGFGQVFKAKHRIDGKTYVIKRVKYN T0291 64 :G 2a19B 304 :K T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKS 2a19B 305 :AEREVKALAKLDHVNIVHYNGCWDGF T0291 99 :KPVMIVTEYMENGSLDSFLRK 2a19B 360 :KCLFIQMEFCDKGTLEQWIEK T0291 120 :H 2a19B 382 :R T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 2a19B 385 :KLDKVLALELFEQITKGVDYIHSKKLINRDLKPSNIFLVDTKQVKIGDFGLVTSLKNDG T0291 186 :T 2a19B 444 :K T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYG 2a19B 448 :SKGTLRYMSPEQISSQDYGKEVDLYALGLILAELLHVC T0291 234 :MSNQDVIKA 2a19B 486 :DTAFETSKF T0291 243 :VDEG 2a19B 498 :LRDG T0291 250 :PPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 2a19B 502 :IISDIFDKKEKTLLQKLLSKKPEDRPNTSEILRTLTVWK Number of specific fragments extracted= 11 number of extra gaps= 2 total=944 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r0pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0291 read from 1r0pA/merged-good-all-a2m # 1r0pA read from 1r0pA/merged-good-all-a2m # found chain 1r0pA in training set Warning: unaligning (T0291)K47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1r0pA)D1099 Warning: unaligning (T0291)L48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1r0pA)D1099 Warning: unaligning (T0291)E53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0pA)K1104 Warning: unaligning (T0291)W232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1r0pA)I1292 Warning: unaligning (T0291)V239 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0pA)I1292 T0291 2 :YVDPHTYE 1r0pA 1052 :HIDLSALN T0291 12 :TQAVHEFA 1r0pA 1060 :PELVQAVQ T0291 20 :KELDATNISI 1r0pA 1069 :VVIGPSSLIV T0291 30 :DKVVGAGEFGEVCSGRL 1r0pA 1081 :NEVIGRGHFGCVYHGTL T0291 54 :ISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSK 1r0pA 1105 :IHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSE T0291 100 :PVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1r0pA 1152 :SPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKFLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKE T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPY 1r0pA 1235 :DSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPY T0291 240 :IKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIITSA 1r0pA 1293 :TVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYVHVN Number of specific fragments extracted= 8 number of extra gaps= 1 total=952 Number of alignments=103 # 1r0pA read from 1r0pA/merged-good-all-a2m # found chain 1r0pA in training set Warning: unaligning (T0291)K47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1r0pA)D1099 Warning: unaligning (T0291)L48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1r0pA)D1099 Warning: unaligning (T0291)E53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0pA)K1104 Warning: unaligning (T0291)W232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1r0pA)I1292 Warning: unaligning (T0291)V239 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0pA)I1292 T0291 2 :YVDPHTYE 1r0pA 1052 :HIDLSALN T0291 12 :TQAVHEFAK 1r0pA 1060 :PELVQAVQH T0291 21 :ELDATNISI 1r0pA 1070 :VIGPSSLIV T0291 30 :DKVVGAGEFGEVCSGRL 1r0pA 1081 :NEVIGRGHFGCVYHGTL T0291 54 :ISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1r0pA 1105 :IHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRS T0291 99 :KPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1r0pA 1151 :GSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKFLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKE T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPY 1r0pA 1235 :DSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPY T0291 240 :IKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKII 1r0pA 1293 :TVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYV T0291 298 :TSAAA 1r0pA 1352 :VNATY Number of specific fragments extracted= 9 number of extra gaps= 1 total=961 Number of alignments=104 # 1r0pA read from 1r0pA/merged-good-all-a2m # found chain 1r0pA in training set Warning: unaligning (T0291)K47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1r0pA)D1099 Warning: unaligning (T0291)L48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1r0pA)D1099 Warning: unaligning (T0291)E53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0pA)K1104 Warning: unaligning (T0291)W232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1r0pA)I1292 Warning: unaligning (T0291)V239 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0pA)I1292 T0291 19 :AKELDATNIS 1r0pA 1068 :HVVIGPSSLI T0291 29 :IDKVVGAGEFGEVCSGRL 1r0pA 1080 :FNEVIGRGHFGCVYHGTL T0291 54 :ISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1r0pA 1105 :IHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRS T0291 99 :KPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1r0pA 1151 :GSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKFLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEFD T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPY 1r0pA 1237 :VHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPY T0291 240 :IKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIITSAAA 1r0pA 1293 :TVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYVHVNAT Number of specific fragments extracted= 6 number of extra gaps= 1 total=967 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1apmE/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1apmE expands to /projects/compbio/data/pdb/1apm.pdb.gz 1apmE:Skipped atom 336, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 338, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 340, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 342, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 344, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 346, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 348, because occupancy 0.460 <= existing 0.540 in 1apmE # T0291 read from 1apmE/merged-good-all-a2m # 1apmE read from 1apmE/merged-good-all-a2m # adding 1apmE to template set # found chain 1apmE in template set T0291 18 :FAKELDATNISIDKVVGAGEFGEVCSGRL 1apmE 34 :SQNTAQLDQFDRIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLK 1apmE 63 :KESGNHYAMKILD T0291 63 :VG 1apmE 82 :LK T0291 66 :T 1apmE 84 :Q T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1apmE 85 :IEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1apmE 138 :FAEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGR T0291 186 :TTRGGKIP 1apmE 195 :TWTLCGTP T0291 195 :RWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1apmE 203 :EYLAPEIILSKGYNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDEG 1apmE 234 :GYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNR 1apmE 254 :KVRFPSHFSSDLKDLLRNLLQVDLTKR Number of specific fragments extracted= 10 number of extra gaps= 0 total=977 Number of alignments=106 # 1apmE read from 1apmE/merged-good-all-a2m # found chain 1apmE in template set T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRL 1apmE 33 :PSQNTAQLDQFDRIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLKVGYT 1apmE 63 :KESGNHYAMKILDKQKV T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1apmE 82 :LKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1apmE 138 :FAEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKG T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1apmE 194 :RTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDEG 1apmE 234 :GYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1apmE 254 :KVRFPSHFSSDLKDLLRNLLQVDLTKRF T0291 276 :KFEQIVSI 1apmE 287 :GVNDIKNH T0291 284 :LDKLIRNPGSLKII 1apmE 302 :WIAIYQRKVEAPFI T0291 298 :T 1apmE 337 :V Number of specific fragments extracted= 10 number of extra gaps= 0 total=987 Number of alignments=107 # 1apmE read from 1apmE/merged-good-all-a2m # found chain 1apmE in template set T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1apmE 35 :QNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKV T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1apmE 80 :VKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1apmE 137 :RFAEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKG T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGY 1apmE 194 :RTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKV T0291 250 :PPPMDCPAALYQLMLDCWQKDRNNR 1apmE 256 :RFPSHFSSDLKDLLRNLLQVDLTKR T0291 275 :PKFEQIVS 1apmE 300 :TDWIAIYQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=993 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ywnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ywnA expands to /projects/compbio/data/pdb/1ywn.pdb.gz 1ywnA: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 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 # T0291 read from 1ywnA/merged-good-all-a2m # 1ywnA read from 1ywnA/merged-good-all-a2m # adding 1ywnA to template set # found chain 1ywnA in template set Warning: unaligning (T0291)L61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)T873 Warning: unaligning (T0291)T66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)T873 Warning: unaligning (T0291)Q123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)F997 Warning: unaligning (T0291)D170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)I1051 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)I1051 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)K1053 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)V1058 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)V1058 T0291 16 :HEFAKELDATNISIDKVVGAGEFGEVCSGRLKLPSKK 1ywnA 821 :DASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKT T0291 53 :EISVAIKT 1ywnA 860 :CRTVAVKM T0291 67 :EKQRRDFLGEASIMGQFD 1ywnA 874 :HSEHRALMSELKILIHIG T0291 85 :HPNIIRLEGVVTK 1ywnA 893 :HLNVVNLLGACTK T0291 98 :SKPVMIVTEYMENGSLDSFLRKH 1ywnA 907 :GGPLMVIVEFCKFGNLSTYLRSK T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVS 1ywnA 998 :LTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKIC T0291 180 :DP 1ywnA 1054 :DP T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMS 1ywnA 1059 :RKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVK T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1ywnA 1110 :DEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQA Number of specific fragments extracted= 9 number of extra gaps= 0 total=1002 Number of alignments=109 # 1ywnA read from 1ywnA/merged-good-all-a2m # found chain 1ywnA in template set Warning: unaligning (T0291)L61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)T873 Warning: unaligning (T0291)T66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)T873 Warning: unaligning (T0291)Q123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)F997 Warning: unaligning (T0291)D170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)I1051 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)I1051 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)K1053 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)V1058 Warning: unaligning (T0291)A184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)V1058 T0291 14 :AVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1ywnA 819 :PYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAF T0291 49 :PSKKEISVAIKT 1ywnA 856 :KTATCRTVAVKM T0291 67 :EKQRRDFLGEASIMGQF 1ywnA 874 :HSEHRALMSELKILIHI T0291 84 :DHPNIIRLEGVVTKS 1ywnA 892 :HHLNVVNLLGACTKP T0291 99 :KPVMIVTEYMENGSLDSFLR 1ywnA 908 :GPLMVIVEFCKFGNLSTYLR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVS 1ywnA 998 :LTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKIC T0291 180 :DP 1ywnA 1054 :DP T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMS 1ywnA 1059 :RKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVK T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1ywnA 1110 :DEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANA Number of specific fragments extracted= 9 number of extra gaps= 0 total=1011 Number of alignments=110 # 1ywnA read from 1ywnA/merged-good-all-a2m # found chain 1ywnA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1ywnA)L818 Warning: unaligning (T0291)L61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)T873 Warning: unaligning (T0291)T66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)T873 Warning: unaligning (T0291)Q123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)F997 Warning: unaligning (T0291)D170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)I1051 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)I1051 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)K1053 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)V1058 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)V1058 T0291 14 :AVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1ywnA 819 :PYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFG T0291 49 :PSKKEISVAIKT 1ywnA 856 :KTATCRTVAVKM T0291 67 :EKQRRDFLGEASIMGQF 1ywnA 874 :HSEHRALMSELKILIHI T0291 84 :DHPNIIRLEGVVTKS 1ywnA 892 :HHLNVVNLLGACTKP T0291 99 :KPVMIVTEYMENGSLDSFLR 1ywnA 908 :GPLMVIVEFCKFGNLSTYLR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVS 1ywnA 998 :LTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKIC T0291 180 :DP 1ywnA 1054 :DP T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMS 1ywnA 1059 :RKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVK T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1ywnA 1110 :DEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQA Number of specific fragments extracted= 9 number of extra gaps= 0 total=1020 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xjdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xjdA expands to /projects/compbio/data/pdb/1xjd.pdb.gz 1xjdA: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 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 # T0291 read from 1xjdA/merged-good-all-a2m # 1xjdA read from 1xjdA/merged-good-all-a2m # adding 1xjdA to template set # found chain 1xjdA in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1xjdA)I377 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjdA)F539 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjdA)F539 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1xjdA 378 :EDFILHKMLGKGSFGKVFLAEF T0291 50 :SKKEISVAIKTLK 1xjdA 400 :KKTNQFFAIKALK T0291 63 :VGYTEKQRRDFLGEASIMGQ 1xjdA 418 :MDDDVECTMVEKRVLSLAWE T0291 85 :HPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1xjdA 438 :HPFLTHMFCTFQTKENLFFVMEYLNGGDLMYHIQSCHK T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1xjdA 476 :FDLSRATFYAAEIILGLQFLHSKGIVYRDLKLDNILLDKDGHIKIADFGMCKENMLG T0291 182 :EAAY 1xjdA 533 :DAKT T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1xjdA 540 :CGTPDYIAPEILLGQKYNHSVDWWSFGVLLYEMLI T0291 227 :GERPYWEMSNQDVIKAVDE 1xjdA 575 :GQSPFHGQDEEELFHSIRM T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRP 1xjdA 594 :DNPFYPRWLEKEAKDLLVKLFVREPEKRL T0291 276 :KFEQIV 1xjdA 638 :NWEELE Number of specific fragments extracted= 10 number of extra gaps= 0 total=1030 Number of alignments=112 # 1xjdA read from 1xjdA/merged-good-all-a2m # found chain 1xjdA in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1xjdA)I377 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjdA)F539 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjdA)F539 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1xjdA 378 :EDFILHKMLGKGSFGKVFLAEF T0291 50 :SKKEISVAIKTLKVGYT 1xjdA 400 :KKTNQFFAIKALKKDVV T0291 67 :EKQRRDFLGEASIMGQF 1xjdA 419 :DDDVECTMVEKRVLSLA T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1xjdA 437 :EHPFLTHMFCTFQTKENLFFVMEYLNGGDLMYHIQSCHK T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1xjdA 476 :FDLSRATFYAAEIILGLQFLHSKGIVYRDLKLDNILLDKDGHIKIADFGMCKENMLGDA T0291 186 :TT 1xjdA 535 :KT T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1xjdA 540 :CGTPDYIAPEILLGQKYNHSVDWWSFGVLLYEMLI T0291 227 :GERPYWEMSNQDVIKAVDEG 1xjdA 575 :GQSPFHGQDEEELFHSIRMD T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNR 1xjdA 595 :NPFYPRWLEKEAKDLLVKLFVREPEKR T0291 275 :PKFEQIVS 1xjdA 637 :INWEELER Number of specific fragments extracted= 10 number of extra gaps= 0 total=1040 Number of alignments=113 # 1xjdA read from 1xjdA/merged-good-all-a2m # found chain 1xjdA in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1xjdA)I377 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjdA)F539 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjdA)F539 T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKT 1xjdA 378 :EDFILHKMLGKGSFGKVFLAEFKKTNQFFAIKALKK T0291 66 :TE 1xjdA 414 :DV T0291 68 :KQRRDFLGEASIMGQF 1xjdA 420 :DDVECTMVEKRVLSLA T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1xjdA 437 :EHPFLTHMFCTFQTKENLFFVMEYLNGGDLMYHIQSCH T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1xjdA 475 :KFDLSRATFYAAEIILGLQFLHSKGIVYRDLKLDNILLDKDGHIKIADFGMCKENMLGDA T0291 186 :TT 1xjdA 535 :KT T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 1xjdA 540 :CGTPDYIAPEILLGQKYNHSVDWWSFGVLLYEMLIGQSPFHGQDEEELFHSIRMDN T0291 249 :LPPPMDCPAALYQLMLDCWQKDRNNRP 1xjdA 596 :PFYPRWLEKEAKDLLVKLFVREPEKRL T0291 276 :KFEQIV 1xjdA 638 :NWEELE Number of specific fragments extracted= 9 number of extra gaps= 0 total=1049 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yhvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yhvA expands to /projects/compbio/data/pdb/1yhv.pdb.gz 1yhvA:# T0291 read from 1yhvA/merged-good-all-a2m # 1yhvA read from 1yhvA/merged-good-all-a2m # adding 1yhvA to template set # found chain 1yhvA in template set Warning: unaligning (T0291)D180 because of BadResidue code BAD_PEPTIDE in next template residue (1yhvA)Q418 Warning: unaligning (T0291)P181 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)Q418 Warning: unaligning (T0291)E182 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)S419 T0291 22 :LDATNISIDKVVGAGEFGEVCSGRLK 1yhvA 265 :DPKKKYTRFEKIGQGASGTVYTAMDV T0291 51 :KKEISVAIKTLK 1yhvA 291 :ATGQEVAIRQMN T0291 64 :GYT 1yhvA 306 :QPK T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1yhvA 309 :KELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETC T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1yhvA 361 :MDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITP T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1yhvA 420 :KRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIE T0291 227 :GERPYWEMSNQDVIKAVDEG 1yhvA 460 :GEPPYLNENPLRALYLIATN T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIV 1yhvA 482 :PELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELL T0291 290 :NPGSLKIITS 1yhvA 517 :QHQFLKIAKP Number of specific fragments extracted= 9 number of extra gaps= 1 total=1058 Number of alignments=115 # 1yhvA read from 1yhvA/merged-good-all-a2m # found chain 1yhvA in template set Warning: unaligning (T0291)D180 because of BadResidue code BAD_PEPTIDE in next template residue (1yhvA)Q418 Warning: unaligning (T0291)P181 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)Q418 Warning: unaligning (T0291)E182 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)S419 T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRLK 1yhvA 260 :IVSVGDPKKKYTRFEKIGQGASGTVYTAMDV T0291 51 :KKEISVAIKTLKVGYTEK 1yhvA 291 :ATGQEVAIRQMNLQQQPK T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1yhvA 309 :KELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETC T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1yhvA 361 :MDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITP T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1yhvA 420 :KRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIE T0291 227 :GERPYWEMSNQDVIKAVDEG 1yhvA 460 :GEPPYLNENPLRALYLIATN T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 1yhvA 482 :PELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELLQ Number of specific fragments extracted= 7 number of extra gaps= 1 total=1065 Number of alignments=116 # 1yhvA read from 1yhvA/merged-good-all-a2m # found chain 1yhvA in template set Warning: unaligning (T0291)D180 because of BadResidue code BAD_PEPTIDE in next template residue (1yhvA)Q418 Warning: unaligning (T0291)P181 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)Q418 Warning: unaligning (T0291)E182 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)S419 T0291 22 :LDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKVG 1yhvA 265 :DPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIRQMNLQQQP T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1yhvA 308 :KKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETC T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1yhvA 361 :MDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITP T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1yhvA 420 :KRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLI T0291 243 :VDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 1yhvA 478 :TNGTPELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELLQ T0291 297 :ITSAAARPSNLL 1yhvA 518 :HQFLKIAKPLSS Number of specific fragments extracted= 6 number of extra gaps= 1 total=1071 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mqbA/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/T0291/1mqbA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0291/1mqbA/merged-good-all-a2m.gz for input Trying 1mqbA/merged-good-all-a2m Error: Couldn't open file 1mqbA/merged-good-all-a2m or 1mqbA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qpcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0291 read from 1qpcA/merged-good-all-a2m # 1qpcA read from 1qpcA/merged-good-all-a2m # found chain 1qpcA in training set Warning: unaligning (T0291)K62 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qpcA)Q277 Warning: unaligning (T0291)V63 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qpcA)Q277 Warning: unaligning (T0291)G64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qpcA)G278 Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qpcA)T395 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qpcA)T395 Warning: unaligning (T0291)P291 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qpcA)E502 Warning: unaligning (T0291)G292 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qpcA)E502 T0291 15 :VHEFAKELDATNISIDKVVGAGEFGEVCSGRL 1qpcA 233 :WWEDEWEVPRETLKLVERLGAGQFGEVWMGYY T0291 51 :KKEISVAIKTL 1qpcA 265 :NGHTKVAVKSL T0291 65 :Y 1qpcA 279 :S T0291 66 :TEK 1qpcA 281 :SPD T0291 72 :DFLGEASIMGQFDHPNIIRLEGVVT 1qpcA 284 :AFLAEANLMKQLQHQRLVRLYAVVT T0291 98 :SKPVMIVTEYMENGSLDSFLRKH 1qpcA 309 :QEPIYIITEYMENGSLVDFLKTP T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1qpcA 335 :KLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1qpcA 396 :AREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFTA Number of specific fragments extracted= 8 number of extra gaps= 2 total=1079 Number of alignments=118 # 1qpcA read from 1qpcA/merged-good-all-a2m # found chain 1qpcA in training set Warning: unaligning (T0291)K62 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qpcA)Q277 Warning: unaligning (T0291)V63 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qpcA)Q277 Warning: unaligning (T0291)G64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qpcA)G278 Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qpcA)T395 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qpcA)T395 T0291 16 :HEFAKELDATNISIDKVVGAGEFGEVCSGRL 1qpcA 234 :WEDEWEVPRETLKLVERLGAGQFGEVWMGYY T0291 51 :KKEISVAIKTL 1qpcA 265 :NGHTKVAVKSL T0291 65 :YTEK 1qpcA 279 :SMSP T0291 71 :RDFLGEASIMGQFDHPNIIRLEGVVT 1qpcA 283 :DAFLAEANLMKQLQHQRLVRLYAVVT T0291 98 :SKPVMIVTEYMENGSLDSFLRKH 1qpcA 309 :QEPIYIITEYMENGSLVDFLKTP T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1qpcA 335 :KLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1qpcA 396 :AREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFTA Number of specific fragments extracted= 7 number of extra gaps= 1 total=1086 Number of alignments=119 # 1qpcA read from 1qpcA/merged-good-all-a2m # found chain 1qpcA in training set Warning: unaligning (T0291)K59 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qpcA)Q277 Warning: unaligning (T0291)T60 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qpcA)Q277 Warning: unaligning (T0291)L61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qpcA)G278 Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qpcA)T395 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qpcA)T395 T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRLKLP 1qpcA 235 :EDEWEVPRETLKLVERLGAGQFGEVWMGYYNGH T0291 51 :KKEISVAI 1qpcA 268 :TKVAVKSL T0291 62 :KV 1qpcA 279 :SM T0291 66 :T 1qpcA 281 :S T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVT 1qpcA 282 :PDAFLAEANLMKQLQHQRLVRLYAVVT T0291 98 :SKPVMIVTEYMENGSLDSFLRKHD 1qpcA 309 :QEPIYIITEYMENGSLVDFLKTPS T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1qpcA 334 :IKLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1qpcA 396 :AREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFTA Number of specific fragments extracted= 8 number of extra gaps= 1 total=1094 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1irk/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1irk expands to /projects/compbio/data/pdb/1irk.pdb.gz 1irk:Warning: there is no chain 1irk will retry with 1irkA Skipped atom 548, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 550, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 1165, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 1167, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 1169, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 1173, because occupancy 0.500 <= existing 0.500 in 1irk # T0291 read from 1irk/merged-good-all-a2m # 1irk read from 1irk/merged-good-all-a2m # adding 1irk to template set # found chain 1irk in template set Warning: unaligning (T0291)D4 because first residue in template chain is (1irk)S981 T0291 5 :PHTYED 1irk 982 :SVFVPD T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLK 1irk 988 :EWEVSREKITLLRELGQGSFGMVYEGNAR T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1irk 1019 :IKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSL T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1irk 1101 :RPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYET T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILD 1irk 1161 :DYYRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLK Number of specific fragments extracted= 5 number of extra gaps= 0 total=1099 Number of alignments=121 # 1irk read from 1irk/merged-good-all-a2m # found chain 1irk in template set Warning: unaligning (T0291)D4 because first residue in template chain is (1irk)S981 T0291 5 :PHTYEDPT 1irk 982 :SVFVPDEW T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRLK 1irk 990 :EVSREKITLLRELGQGSFGMVYEGNAR T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1irk 1019 :IKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLR T0291 119 :KHDAQ 1irk 1098 :NPGRP T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGR 1irk 1104 :PTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTR T0291 177 :LEDDPEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1irk 1156 :DIYETDYYRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLH Number of specific fragments extracted= 6 number of extra gaps= 0 total=1105 Number of alignments=122 # 1irk read from 1irk/merged-good-all-a2m # found chain 1irk in template set Warning: unaligning (T0291)T12 because first residue in template chain is (1irk)S981 T0291 13 :QAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1irk 982 :SVFVPDEWEVSREKITLLRELGQGSFGMVYEGNARD T0291 49 :PSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1irk 1020 :KGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLR T0291 120 :HDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1irk 1100 :GRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDY T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKL 1irk 1163 :YRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDD Number of specific fragments extracted= 4 number of extra gaps= 0 total=1109 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y57A/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/T0291/1y57A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0291/1y57A/merged-good-all-a2m.gz for input Trying 1y57A/merged-good-all-a2m Error: Couldn't open file 1y57A/merged-good-all-a2m or 1y57A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qcfA/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/T0291/1qcfA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0291/1qcfA/merged-good-all-a2m.gz for input Trying 1qcfA/merged-good-all-a2m Error: Couldn't open file 1qcfA/merged-good-all-a2m or 1qcfA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o6yA expands to /projects/compbio/data/pdb/1o6y.pdb.gz 1o6yA:# T0291 read from 1o6yA/merged-good-all-a2m # 1o6yA read from 1o6yA/merged-good-all-a2m # adding 1o6yA to template set # found chain 1o6yA in template set Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)A180 Warning: unaligning (T0291)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6yA)A180 Warning: unaligning (T0291)K241 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6yA)Q227 Warning: unaligning (T0291)A242 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6yA)Q227 Warning: unaligning (T0291)R289 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)G279 T0291 24 :ATNISIDKVVGAGEFGEVCSGRLK 1o6yA 8 :SDRYELGEILGFGGMSEVHLARDL T0291 51 :KKEISVAIKTLKVGY 1o6yA 32 :RLHRDVAVKVLRADL T0291 66 :TEKQRRDFLGEASIMGQFDHPNIIRLE 1o6yA 49 :DPSFYLRFRREAQNAAALNHPAIVAVY T0291 93 :GVVTKSKP 1o6yA 78 :GEAETPAG T0291 101 :VMIVTEYMENGSLDSFLRKHDA 1o6yA 88 :PYIVMEYVDGVTLRDIVHTEGP T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1o6yA 110 :MTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATNAVKVMDFGIARA T0291 195 :RWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1o6yA 181 :QYLSPEQARGDSVDARSDVYSLGCVLYEVLT T0291 227 :GERPYWEMSNQDVI 1o6yA 212 :GEPPFTGDSPVSVA T0291 243 :VDEG 1o6yA 228 :HVRE T0291 248 :RLPPP 1o6yA 232 :DPIPP T0291 253 :MDCPAALYQLMLDCWQKDRNNRP 1o6yA 241 :EGLSADLDAVVLKALAKNPENRY T0291 276 :KFEQIVSILDKLI 1o6yA 265 :TAAEMRADLVRVH Number of specific fragments extracted= 12 number of extra gaps= 3 total=1121 Number of alignments=124 # 1o6yA read from 1o6yA/merged-good-all-a2m # found chain 1o6yA in template set Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)A180 Warning: unaligning (T0291)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6yA)A180 Warning: unaligning (T0291)K241 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6yA)Q227 Warning: unaligning (T0291)A242 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6yA)Q227 Warning: unaligning (T0291)R289 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)G279 T0291 24 :ATNISIDKVVGAGEFGEVCSGRLK 1o6yA 8 :SDRYELGEILGFGGMSEVHLARDL T0291 51 :KKEISVAIKTLKVG 1o6yA 32 :RLHRDVAVKVLRAD T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1o6yA 48 :RDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAE T0291 99 :K 1o6yA 85 :G T0291 101 :VMIVTEYMENGSLDSFLRKHDA 1o6yA 88 :PYIVMEYVDGVTLRDIVHTEGP T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1o6yA 110 :MTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATNAVKVMDFGIARA T0291 195 :RWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1o6yA 181 :QYLSPEQARGDSVDARSDVYSLGCVLYEVLT T0291 227 :GERPYWEMSNQDVI 1o6yA 212 :GEPPFTGDSPVSVA T0291 243 :VDEG 1o6yA 228 :HVRE T0291 248 :RLPPPM 1o6yA 232 :DPIPPS T0291 254 :DCPAALYQLMLDCWQKDRNNRP 1o6yA 242 :GLSADLDAVVLKALAKNPENRY T0291 276 :KFEQIVSILDKLI 1o6yA 265 :TAAEMRADLVRVH Number of specific fragments extracted= 12 number of extra gaps= 3 total=1133 Number of alignments=125 # 1o6yA read from 1o6yA/merged-good-all-a2m # found chain 1o6yA in template set Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)A180 Warning: unaligning (T0291)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6yA)A180 Warning: unaligning (T0291)I240 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6yA)Q227 Warning: unaligning (T0291)K241 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6yA)Q227 Warning: unaligning (T0291)R289 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)G279 T0291 24 :ATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIK 1o6yA 8 :SDRYELGEILGFGGMSEVHLARDLRLHRDVAVKVLR T0291 61 :LKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1o6yA 44 :ADLARDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAE T0291 99 :KPVMIVTEYMENGSLDSFLRKHD 1o6yA 86 :PLPYIVMEYVDGVTLRDIVHTEG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1o6yA 109 :PMTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATNAVKVMDFGIARA T0291 195 :RWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDV 1o6yA 181 :QYLSPEQARGDSVDARSDVYSLGCVLYEVLTGEPPFTGDSPVSVA T0291 242 :AVDEGYRLP 1o6yA 228 :HVREDPIPP T0291 251 :PPMDCPAALYQLMLDCWQKDRNNRP 1o6yA 239 :RHEGLSADLDAVVLKALAKNPENRY T0291 276 :KFEQIVSILDKLI 1o6yA 265 :TAAEMRADLVRVH Number of specific fragments extracted= 8 number of extra gaps= 3 total=1141 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cdkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cdkA expands to /projects/compbio/data/pdb/1cdk.pdb.gz 1cdkA:# T0291 read from 1cdkA/merged-good-all-a2m # 1cdkA read from 1cdkA/merged-good-all-a2m # adding 1cdkA to template set # found chain 1cdkA in template set Warning: unaligning (T0291)D114 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)S130 Warning: unaligning (T0291)S115 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)S130 Warning: unaligning (T0291)F116 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)H131 Warning: unaligning (T0291)R151 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)D166 Warning: unaligning (T0291)D152 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)D166 Warning: unaligning (T0291)L177 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K192 Warning: unaligning (T0291)E178 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)K192 Warning: unaligning (T0291)P193 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)E203 Warning: unaligning (T0291)R195 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)E203 Warning: unaligning (T0291)N236 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)I244 Warning: unaligning (T0291)Q237 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)I244 Warning: unaligning (T0291)W267 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)Q274 Warning: unaligning (T0291)Q268 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)Q274 Warning: unaligning (T0291)R271 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)T278 Warning: unaligning (T0291)N272 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)T278 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRL 1cdkA 35 :QNTAHLDQFERIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLK 1cdkA 63 :KETGNHFAMKILD T0291 63 :V 1cdkA 82 :L T0291 65 :YTEK 1cdkA 83 :KQIE T0291 72 :DFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSL 1cdkA 87 :HTLNEKRILQAVNFPFLVKLEYSFKDNSNLYMVMEYVPGGEM T0291 117 :LRKHDA 1cdkA 132 :LRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVH 1cdkA 138 :FSEPHARFYAAQIVLTFEYLHSLDLIY T0291 153 :LAARNILINSNLVCKVSDFGLGRV 1cdkA 167 :LKPENLLIDQQGYIQVTDFGFAKR T0291 179 :DD 1cdkA 193 :GR T0291 186 :TTRGGKI 1cdkA 195 :TWTLCGT T0291 196 :WTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1cdkA 204 :YLAPEIILSKGYNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMS 1cdkA 234 :GYPPFFADQ T0291 238 :DVIKAVDEG 1cdkA 245 :QIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDC 1cdkA 254 :KVRFPSHFSSDLKDLLRNL T0291 269 :KD 1cdkA 275 :VD T0291 273 :NR 1cdkA 279 :KR Number of specific fragments extracted= 16 number of extra gaps= 7 total=1157 Number of alignments=127 # 1cdkA read from 1cdkA/merged-good-all-a2m # found chain 1cdkA in template set Warning: unaligning (T0291)D114 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)S130 Warning: unaligning (T0291)S115 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)S130 Warning: unaligning (T0291)F116 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)H131 Warning: unaligning (T0291)R151 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)D166 Warning: unaligning (T0291)D152 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)D166 Warning: unaligning (T0291)L177 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K192 Warning: unaligning (T0291)E178 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)K192 Warning: unaligning (T0291)I194 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)E203 Warning: unaligning (T0291)R195 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)E203 Warning: unaligning (T0291)N236 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)I244 Warning: unaligning (T0291)Q237 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)I244 Warning: unaligning (T0291)W267 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)Q274 Warning: unaligning (T0291)Q268 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)Q274 Warning: unaligning (T0291)R271 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)T278 Warning: unaligning (T0291)N272 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)T278 Warning: unaligning (T0291)K276 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)V288 Warning: unaligning (T0291)F277 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)V288 Warning: unaligning (T0291)I283 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K295 T0291 18 :FAKELDATNISIDKVVGAGEFGEVCSGRL 1cdkA 34 :AQNTAHLDQFERIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLKVGYT 1cdkA 63 :KETGNHFAMKILDKQKV T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSL 1cdkA 82 :LKQIEHTLNEKRILQAVNFPFLVKLEYSFKDNSNLYMVMEYVPGGEM T0291 117 :LRKHDA 1cdkA 132 :LRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVH 1cdkA 138 :FSEPHARFYAAQIVLTFEYLHSLDLIY T0291 153 :LAARNILINSNLVCKVSDFGLGRV 1cdkA 167 :LKPENLLIDQQGYIQVTDFGFAKR T0291 179 :D 1cdkA 193 :G T0291 186 :TTRGGKIP 1cdkA 194 :RTWTLCGT T0291 196 :WTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1cdkA 204 :YLAPEIILSKGYNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMS 1cdkA 234 :GYPPFFADQ T0291 238 :DVIKAVDEG 1cdkA 245 :QIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDC 1cdkA 254 :KVRFPSHFSSDLKDLLRNL T0291 269 :KD 1cdkA 275 :VD T0291 273 :NRP 1cdkA 279 :KRF T0291 278 :EQIVS 1cdkA 289 :NDIKN T0291 284 :LDKLIRNPGSLKII 1cdkA 302 :WIAIYQRKVEAPFI T0291 298 :TSAAARPSNL 1cdkA 337 :VSINEKCGKE Number of specific fragments extracted= 17 number of extra gaps= 9 total=1174 Number of alignments=128 # 1cdkA read from 1cdkA/merged-good-all-a2m # found chain 1cdkA in template set Warning: unaligning (T0291)D114 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)S130 Warning: unaligning (T0291)S115 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)S130 Warning: unaligning (T0291)F116 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)H131 Warning: unaligning (T0291)R151 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)D166 Warning: unaligning (T0291)D152 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)D166 Warning: unaligning (T0291)L177 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K192 Warning: unaligning (T0291)E178 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)K192 Warning: unaligning (T0291)I194 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)E203 Warning: unaligning (T0291)R195 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)E203 Warning: unaligning (T0291)S235 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)I244 Warning: unaligning (T0291)N236 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)I244 Warning: unaligning (T0291)W267 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)Q274 Warning: unaligning (T0291)Q268 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)Q274 Warning: unaligning (T0291)R271 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)T278 Warning: unaligning (T0291)N272 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)T278 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1cdkA 36 :NTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHFAMKILDKQKV T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSL 1cdkA 80 :VKLKQIEHTLNEKRILQAVNFPFLVKLEYSFKDNSNLYMVMEYVPGGEM T0291 117 :LRKHD 1cdkA 132 :LRRIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVH 1cdkA 137 :RFSEPHARFYAAQIVLTFEYLHSLDLIY T0291 153 :LAARNILINSNLVCKVSDFGLGRV 1cdkA 167 :LKPENLLIDQQGYIQVTDFGFAKR T0291 179 :D 1cdkA 193 :G T0291 186 :TTRGGKIP 1cdkA 194 :RTWTLCGT T0291 196 :WTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEM 1cdkA 204 :YLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQ T0291 237 :QDVIKAVDEGY 1cdkA 245 :QIYEKIVSGKV T0291 250 :PPPMDCPAALYQLMLDC 1cdkA 256 :RFPSHFSSDLKDLLRNL T0291 269 :KD 1cdkA 275 :VD T0291 273 :NRP 1cdkA 279 :KRF Number of specific fragments extracted= 12 number of extra gaps= 7 total=1186 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xbbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0291 read from 1xbbA/merged-good-all-a2m # 1xbbA read from 1xbbA/merged-good-all-a2m # found chain 1xbbA in training set Warning: unaligning (T0291)K20 because first residue in template chain is (1xbbA)V363 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xbbA)P411 Warning: unaligning (T0291)E67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xbbA)P411 Warning: unaligning (T0291)T186 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xbbA)K533 Warning: unaligning (T0291)K191 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xbbA)K533 T0291 21 :ELDATNISID 1xbbA 364 :YLDRKLLTLE T0291 31 :KVVGAGEFGEVCSGRLKLP 1xbbA 375 :KELGSGNFGTVKKGYYQMK T0291 51 :KKEISVAIKTL 1xbbA 394 :KVVKTVAVKIL T0291 68 :KQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1xbbA 412 :ALKDELLAEANVMQQLDNPYIVRMIGICEA T0291 99 :KPVMIVTEYMENGSLDSFLRKHDA 1xbbA 442 :ESWMLVMEMAELGPLNKYLQQNRH T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAY 1xbbA 466 :VKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYK T0291 192 :IPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1xbbA 534 :WPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYD Number of specific fragments extracted= 7 number of extra gaps= 0 total=1193 Number of alignments=130 # 1xbbA read from 1xbbA/merged-good-all-a2m # found chain 1xbbA in training set Warning: unaligning (T0291)K20 because first residue in template chain is (1xbbA)V363 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xbbA)P411 Warning: unaligning (T0291)E67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xbbA)P411 Warning: unaligning (T0291)T186 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xbbA)K533 Warning: unaligning (T0291)K191 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xbbA)K533 T0291 21 :ELDATNISID 1xbbA 364 :YLDRKLLTLE T0291 31 :KVVGAGEFGEVCSGRLKL 1xbbA 375 :KELGSGNFGTVKKGYYQM T0291 50 :SKKEISVAIKTL 1xbbA 393 :KKVVKTVAVKIL T0291 68 :KQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1xbbA 412 :ALKDELLAEANVMQQLDNPYIVRMIGICEA T0291 99 :KPVMIVTEYMENGSLDSFLRKHDA 1xbbA 442 :ESWMLVMEMAELGPLNKYLQQNRH T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAY 1xbbA 466 :VKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYK T0291 192 :IPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1xbbA 534 :WPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYY Number of specific fragments extracted= 7 number of extra gaps= 0 total=1200 Number of alignments=131 # 1xbbA read from 1xbbA/merged-good-all-a2m # found chain 1xbbA in training set Warning: unaligning (T0291)K20 because first residue in template chain is (1xbbA)V363 Warning: unaligning (T0291)L61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xbbA)P411 Warning: unaligning (T0291)E67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xbbA)P411 Warning: unaligning (T0291)T186 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xbbA)K533 Warning: unaligning (T0291)K191 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xbbA)K533 T0291 21 :ELDATNISID 1xbbA 364 :YLDRKLLTLE T0291 31 :KVVGAGEFGEVCSGRLKLPSKKEISVAIKT 1xbbA 375 :KELGSGNFGTVKKGYYQMKKVVKTVAVKIL T0291 68 :KQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1xbbA 412 :ALKDELLAEANVMQQLDNPYIVRMIGICEA T0291 99 :KPVMIVTEYMENGSLDSFLRKHD 1xbbA 442 :ESWMLVMEMAELGPLNKYLQQNR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAY 1xbbA 465 :HVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYK T0291 192 :IPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1xbbA 534 :WPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYY Number of specific fragments extracted= 6 number of extra gaps= 0 total=1206 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t46A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0291 read from 1t46A/merged-good-all-a2m # 1t46A read from 1t46A/merged-good-all-a2m # found chain 1t46A in training set Warning: unaligning (T0291)V3 because first residue in template chain is (1t46A)G565 Warning: unaligning (T0291)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t46A)L762 T0291 4 :DPHTYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1t46A 566 :NNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAY T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFD 1t46A 612 :IKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLG T0291 85 :HPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1t46A 650 :HMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRK T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1t46A 763 :ALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKND T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMS 1t46A 821 :SNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMP T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1t46A 876 :DSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISEST Number of specific fragments extracted= 6 number of extra gaps= 0 total=1212 Number of alignments=133 # 1t46A read from 1t46A/merged-good-all-a2m # found chain 1t46A in training set Warning: unaligning (T0291)V3 because first residue in template chain is (1t46A)G565 Warning: unaligning (T0291)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t46A)L762 T0291 4 :DPHTYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1t46A 566 :NNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAY T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQF 1t46A 612 :IKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYL T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1t46A 649 :NHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1t46A 763 :ALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKND T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMS 1t46A 821 :SNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMP T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1t46A 876 :DSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISEST Number of specific fragments extracted= 6 number of extra gaps= 0 total=1218 Number of alignments=134 # 1t46A read from 1t46A/merged-good-all-a2m # found chain 1t46A in training set Warning: unaligning (T0291)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t46A)L762 Warning: unaligning (T0291)S293 because last residue in template chain is (1t46A)N933 T0291 4 :DPHTYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1t46A 566 :NNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYG T0291 49 :PSK 1t46A 614 :SDA T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQF 1t46A 617 :AMTVAVKMLKPSAHLTEREALMSELKVLSYL T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1t46A 649 :NHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1t46A 763 :ALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNY T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMS 1t46A 824 :VVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMP T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1t46A 876 :DSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISEST Number of specific fragments extracted= 7 number of extra gaps= 0 total=1225 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j1bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0291 read from 1j1bA/merged-good-all-a2m # 1j1bA read from 1j1bA/merged-good-all-a2m # found chain 1j1bA in training set T0291 23 :DATNISI 1j1bA 50 :RPQEVSY T0291 30 :DKVVGAGEFGEVCSGRL 1j1bA 59 :TKVIGNGSFGVVYQAKL T0291 50 :SKKEISVAIK 1j1bA 76 :CDSGELVAIK T0291 60 :TLKVGYT 1j1bA 88 :LQDKRFK T0291 75 :GEASIMGQFDHPNIIRLEGVVTK 1j1bA 96 :RELQIMRKLDHCNIVRLRYFFYS T0291 98 :SKP 1j1bA 123 :KDE T0291 101 :VMIVTEYMEN 1j1bA 128 :LNLVLDYVPE T0291 112 :SLDSFLRKH 1j1bA 138 :TVYRVARHY T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSN 1j1bA 150 :KQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPD T0291 164 :LVCKVSDFGLGRVLEDDP 1j1bA 194 :AVLKLCDFGSAKQLVRGE T0291 186 :TTRGGKIPIRWTSPEAIAY 1j1bA 212 :PNVSYICSRYYRAPELIFG T0291 205 :RKFTSASDVWSYGIVLWEVMS 1j1bA 232 :TDYTSSIDVWSAGCVLAELLL T0291 227 :GERPYWEMSNQDVIKAVDE 1j1bA 253 :GQPIFPGDSGVDQLVEIIK T0291 247 :YRLPPP 1j1bA 289 :TEFKFP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIV 1j1bA 307 :PRTPPEAIALCSRLLEYTPTARLTPLEAC T0291 283 :ILDKLIRNPGSLKI 1j1bA 339 :FFDELRDPNVKLPN T0291 299 :SAAA 1j1bA 353 :GRDT Number of specific fragments extracted= 17 number of extra gaps= 0 total=1242 Number of alignments=136 # 1j1bA read from 1j1bA/merged-good-all-a2m # found chain 1j1bA in training set T0291 22 :LDATN 1j1bA 46 :QGPDR T0291 27 :ISIDKVVGAGEFGEVCSGRL 1j1bA 56 :YTDTKVIGNGSFGVVYQAKL T0291 50 :SKKEISVAIKTLKVGYTEK 1j1bA 76 :CDSGELVAIKKVLQDKRFK T0291 75 :GEASIMGQFDHPNIIRLEGVVTK 1j1bA 96 :RELQIMRKLDHCNIVRLRYFFYS T0291 98 :SKP 1j1bA 123 :KDE T0291 101 :VMIVTEYMEN 1j1bA 128 :LNLVLDYVPE T0291 112 :SLDSFLR 1j1bA 138 :TVYRVAR T0291 119 :KHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSN 1j1bA 148 :RAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPD T0291 164 :LVCKVSDFGLGRVLEDDP 1j1bA 194 :AVLKLCDFGSAKQLVRGE T0291 186 :TTRGGKIPIRWTSPEAIAY 1j1bA 212 :PNVSYICSRYYRAPELIFG T0291 205 :RKFTSASDVWSYGIVLWEVMS 1j1bA 232 :TDYTSSIDVWSAGCVLAELLL T0291 227 :GERPYWEMS 1j1bA 253 :GQPIFPGDS T0291 236 :NQDVIKAVDEG 1j1bA 277 :TREQIREMNPN T0291 247 :YRLPPPM 1j1bA 289 :TEFKFPQ T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1j1bA 308 :RTPPEAIALCSRLLEYTPTARLTPLEACAH T0291 284 :LDKLIRNPGSLKIITSAAAR 1j1bA 340 :FDELRDPNVKLPNGRDTPAL Number of specific fragments extracted= 16 number of extra gaps= 0 total=1258 Number of alignments=137 # 1j1bA read from 1j1bA/merged-good-all-a2m # found chain 1j1bA in training set T0291 3 :VDPHTYEDPTQAVH 1j1bA 42 :ATPGQGPDRPQEVS T0291 27 :ISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKVGYT 1j1bA 56 :YTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKN T0291 75 :GEASIMGQFDHPNIIRLEGVVTK 1j1bA 96 :RELQIMRKLDHCNIVRLRYFFYS T0291 99 :K 1j1bA 124 :D T0291 100 :PVMIVTEYMEN 1j1bA 127 :YLNLVLDYVPE T0291 112 :SLDSFLR 1j1bA 138 :TVYRVAR T0291 119 :KHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSN 1j1bA 148 :RAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPD T0291 164 :LVCKVSDFGLGRVLEDDP 1j1bA 194 :AVLKLCDFGSAKQLVRGE T0291 186 :TTRGGKIPIRWTSPEAIAY 1j1bA 212 :PNVSYICSRYYRAPELIFG T0291 205 :RKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1j1bA 232 :TDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEI T0291 243 :VDEGYRLP 1j1bA 293 :FPQIKAHP T0291 251 :PPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1j1bA 305 :FRPRTPPEAIALCSRLLEYTPTARLTPLEACAH T0291 284 :LDKLIRNPGSL 1j1bA 340 :FDELRDPNVKL Number of specific fragments extracted= 13 number of extra gaps= 0 total=1271 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1phk/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1phk expands to /projects/compbio/data/pdb/1phk.pdb.gz 1phk:Warning: there is no chain 1phk will retry with 1phkA # T0291 read from 1phk/merged-good-all-a2m # 1phk read from 1phk/merged-good-all-a2m # adding 1phk to template set # found chain 1phk in template set T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1phk 16 :YENYEPKEILGRGVSSVVRRCIH T0291 50 :SKKEISVAIKTLK 1phk 39 :KPTCKEYAVKIID T0291 63 :VGYTEKQRRDFLG 1phk 56 :GSFSAEEVQELRE T0291 76 :EASIMGQFD 1phk 73 :EVDILRKVS T0291 85 :HPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1phk 83 :HPNIIQLKDTYETNTFFFLVFDLMKKGELFDYLTEKVT T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1phk 121 :LSEKETRKIMRALLEVICALHKLNIVHRDLKPENILLDDDMNIKLTDFGFSCQLDPGE T0291 186 :TTRGGKIPIRWTSPEAIAY 1phk 179 :KLREVCGTPSYLAPEIIEC T0291 205 :RKFTSASDVWSYGIVLWEVMS 1phk 204 :PGYGKEVDMWSTGVIMYTLLA T0291 227 :GERPYWEMSNQDVIKAVDEG 1phk 225 :GSPPFWHRKQMLMLRMIMSG T0291 247 :YRLPPP 1phk 246 :YQFGSP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVS 1phk 254 :DDYSDTVKDLVSRFLVVQPQKRYTAEEALA Number of specific fragments extracted= 11 number of extra gaps= 0 total=1282 Number of alignments=139 # 1phk read from 1phk/merged-good-all-a2m # found chain 1phk in template set Warning: unaligning (T0291)D23 because first residue in template chain is (1phk)F15 T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1phk 16 :YENYEPKEILGRGVSSVVRRCIH T0291 50 :SKKEISVAIKTLKV 1phk 39 :KPTCKEYAVKIIDV T0291 64 :GYTEK 1phk 57 :SFSAE T0291 69 :QRRDFLGEASIMGQF 1phk 66 :LREATLKEVDILRKV T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1phk 82 :GHPNIIQLKDTYETNTFFFLVFDLMKKGELFDYLTEKVT T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1phk 121 :LSEKETRKIMRALLEVICALHKLNIVHRDLKPENILLDDDMNIKLTDFGFSCQLDPGE T0291 186 :TTRGGKIPIRWTSPEAIA 1phk 179 :KLREVCGTPSYLAPEIIE T0291 204 :YRKFTSASDVWSYGIVLWEVMS 1phk 203 :HPGYGKEVDMWSTGVIMYTLLA T0291 227 :GERPYWEMSNQDVIKAVDEG 1phk 225 :GSPPFWHRKQMLMLRMIMSG T0291 248 :RLPPPM 1phk 245 :NYQFGS T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILDK 1phk 255 :DYSDTVKDLVSRFLVVQPQKRYTAEEALAHPFF Number of specific fragments extracted= 11 number of extra gaps= 0 total=1293 Number of alignments=140 # 1phk read from 1phk/merged-good-all-a2m # found chain 1phk in template set Warning: unaligning (T0291)D23 because first residue in template chain is (1phk)F15 T0291 24 :ATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIK 1phk 16 :YENYEPKEILGRGVSSVVRRCIHKPTCKEYAVKIID T0291 60 :TLKVGYTEKQRRDFLG 1phk 53 :TGGGSFSAEEVQELRE T0291 76 :EASIMGQF 1phk 73 :EVDILRKV T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1phk 82 :GHPNIIQLKDTYETNTFFFLVFDLMKKGELFDYLTEKV T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1phk 120 :TLSEKETRKIMRALLEVICALHKLNIVHRDLKPENILLDDDMNIKLTDFGFSCQLDPGE T0291 186 :TTRGGKIPIRWTSPEAIAY 1phk 179 :KLREVCGTPSYLAPEIIEC T0291 205 :RKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPP 1phk 204 :PGYGKEVDMWSTGVIMYTLLAGSPPFWHRKQMLMLRMIMSGNYQFGSP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1phk 254 :DDYSDTVKDLVSRFLVVQPQKRYTAEEALAH Number of specific fragments extracted= 8 number of extra gaps= 0 total=1301 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c30A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c30A expands to /projects/compbio/data/pdb/2c30.pdb.gz 2c30A:Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 699, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 701, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 904, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 906, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 908, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1238, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1240, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1242, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1244, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1246, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1248, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1278, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1280, because occupancy 0.350 <= existing 0.650 in 2c30A 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 Skipped atom 1523, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1525, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1533, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1535, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1537, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1539, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1541, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1762, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1764, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1820, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1822, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1824, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1826, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1828, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1955, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1957, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1959, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 2309, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 2311, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 2313, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 2315, because occupancy 0.500 <= existing 0.500 in 2c30A # T0291 read from 2c30A/merged-good-all-a2m # 2c30A read from 2c30A/merged-good-all-a2m # adding 2c30A to template set # found chain 2c30A in template set Warning: unaligning (T0291)E9 because first residue in template chain is (2c30A)V385 Warning: unaligning (T0291)C42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)L423 Warning: unaligning (T0291)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)L423 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c30A)L561 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c30A)L561 Warning: unaligning (T0291)E245 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)S616 Warning: unaligning (T0291)G246 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)S616 Warning: unaligning (T0291)D254 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2c30A)V627 Warning: unaligning (T0291)C255 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2c30A)V627 T0291 10 :DPTQAVHEFAKELDATN 2c30A 386 :THEQFKAALRMVVDQGD T0291 27 :ISIDKVVGAGEFGEV 2c30A 407 :LDSYVKIGEGSTGIV T0291 44 :GRL 2c30A 424 :ARE T0291 50 :SKKEISVAIKTLK 2c30A 427 :KHSGRQVAVKMMD T0291 63 :VGYTE 2c30A 441 :RKQQR T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRK 2c30A 446 :RELLFNEVVIMRDYQHFNVVEMYKSYLVGEELWVLMEFLQGGALTDIVSQ T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 2c30A 496 :VRLNEEQIATVCEAVLQALAYLHAQGVIHRDIKSDSILLTLDGRVKLSDFGFCAQISKD T0291 184 :AYTT 2c30A 555 :VPKR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2c30A 562 :VGTPYWMAPEVISRSLYATEVDIWSLGIMVIEMVD T0291 227 :GERPYWEMSNQDVIKAVD 2c30A 597 :GEPPYFSDSPVQAMKRLR T0291 247 :YRLPP 2c30A 617 :PPPKL T0291 252 :PM 2c30A 624 :SH T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVS 2c30A 628 :SPVLRDFLERMLVRDPQERATAQELLD T0291 291 :PGSLKIITS 2c30A 655 :HPFLLQTGL Number of specific fragments extracted= 14 number of extra gaps= 3 total=1315 Number of alignments=142 # 2c30A read from 2c30A/merged-good-all-a2m # found chain 2c30A in template set Warning: unaligning (T0291)E9 because first residue in template chain is (2c30A)V385 Warning: unaligning (T0291)C42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)L423 Warning: unaligning (T0291)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)L423 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c30A)L561 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c30A)L561 Warning: unaligning (T0291)E245 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)S616 Warning: unaligning (T0291)G246 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)S616 Warning: unaligning (T0291)D254 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2c30A)V627 Warning: unaligning (T0291)C255 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2c30A)V627 T0291 10 :DPTQAVHEFAKELDATN 2c30A 386 :THEQFKAALRMVVDQGD T0291 27 :ISIDKVVGAGEFGEV 2c30A 407 :LDSYVKIGEGSTGIV T0291 44 :GRL 2c30A 424 :ARE T0291 50 :SKKEISVAIKTLKVGYTEK 2c30A 427 :KHSGRQVAVKMMDLRKQQR T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 2c30A 446 :RELLFNEVVIMRDYQHFNVVEMYKSYLVGEELWVLMEFLQGGALTDIVSQV T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 2c30A 497 :RLNEEQIATVCEAVLQALAYLHAQGVIHRDIKSDSILLTLDGRVKLSDFGFCAQISKDVP T0291 186 :TT 2c30A 557 :KR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2c30A 562 :VGTPYWMAPEVISRSLYATEVDIWSLGIMVIEMVD T0291 227 :GERPYWEMSNQDVIKAVD 2c30A 597 :GEPPYFSDSPVQAMKRLR T0291 247 :YRLPP 2c30A 617 :PPPKL T0291 252 :PM 2c30A 624 :SH T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGS 2c30A 628 :SPVLRDFLERMLVRDPQERATAQELLDHPFLLQTGLPE Number of specific fragments extracted= 12 number of extra gaps= 3 total=1327 Number of alignments=143 # 2c30A read from 2c30A/merged-good-all-a2m # found chain 2c30A in template set Warning: unaligning (T0291)C42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)L423 Warning: unaligning (T0291)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)L423 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c30A)L561 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c30A)L561 Warning: unaligning (T0291)D244 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)S616 Warning: unaligning (T0291)E245 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)S616 Warning: unaligning (T0291)D254 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2c30A)V627 Warning: unaligning (T0291)C255 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2c30A)V627 T0291 27 :ISIDKVVGAGEFGEV 2c30A 407 :LDSYVKIGEGSTGIV T0291 44 :GRLKLPSKKEISVAIKTLKVG 2c30A 424 :AREKHSGRQVAVKMMDLRKQQ T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 2c30A 445 :RRELLFNEVVIMRDYQHFNVVEMYKSYLVGEELWVLMEFLQGGALTDIVSQV T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 2c30A 497 :RLNEEQIATVCEAVLQALAYLHAQGVIHRDIKSDSILLTLDGRVKLSDFGFCAQISKDVP T0291 186 :TT 2c30A 557 :KR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAV 2c30A 562 :VGTPYWMAPEVISRSLYATEVDIWSLGIMVIEMVDGEPPYFSDSPVQAMKRLR T0291 246 :GY 2c30A 617 :PP T0291 249 :LP 2c30A 619 :PK T0291 251 :PPM 2c30A 623 :NSH T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVSI 2c30A 628 :SPVLRDFLERMLVRDPQERATAQELLDH T0291 298 :TSAAARPSNLL 2c30A 656 :PFLLQTGLPEC Number of specific fragments extracted= 11 number of extra gaps= 3 total=1338 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jksA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0291 read from 1jksA/merged-good-all-a2m # 1jksA read from 1jksA/merged-good-all-a2m # found chain 1jksA in training set Warning: unaligning (T0291)N161 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jksA)V152 T0291 7 :TYEDP 1jksA 5 :RQENV T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1jksA 10 :DDYYDTGEELGSGQFAVVKKCRE T0291 50 :SKKEISVAIKTLK 1jksA 33 :KSTGLQYAAKFIK T0291 63 :VGYTEK 1jksA 54 :RGVSRE T0291 72 :DFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1jksA 60 :DIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKES T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1jksA 111 :LTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIML T0291 162 :SNLVCKVSDFGLGRVLEDDP 1jksA 153 :PKPRIKIIDFGLAHKIDFGN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1jksA 173 :EFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLS T0291 227 :GERPYWEMSNQDVIKAVDEG 1jksA 213 :GASPFLGDTKQETLANVSAV T0291 247 :YRLP 1jksA 234 :YEFE T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVS 1jksA 242 :SNTSALAKDFIRRLLVKDPKKRMTIQDSLQ Number of specific fragments extracted= 11 number of extra gaps= 1 total=1349 Number of alignments=145 # 1jksA read from 1jksA/merged-good-all-a2m # found chain 1jksA in training set Warning: unaligning (T0291)N161 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jksA)V152 T0291 8 :YEDPT 1jksA 5 :RQENV T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1jksA 10 :DDYYDTGEELGSGQFAVVKKCRE T0291 50 :SKKEISVAIKTLKVGYTEK 1jksA 33 :KSTGLQYAAKFIKKRRTKS T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1jksA 57 :SREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKES T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1jksA 111 :LTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIML T0291 162 :SNLVCKVSDFGLGRVLEDDP 1jksA 153 :PKPRIKIIDFGLAHKIDFGN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1jksA 173 :EFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLS T0291 227 :GERPYWEMSNQDVIKAVDEG 1jksA 213 :GASPFLGDTKQETLANVSAV T0291 248 :RLPPPM 1jksA 233 :NYEFED T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1jksA 243 :NTSALAKDFIRRLLVKDPKKRMTIQDSLQH Number of specific fragments extracted= 10 number of extra gaps= 1 total=1359 Number of alignments=146 # 1jksA read from 1jksA/merged-good-all-a2m # found chain 1jksA in training set Warning: unaligning (T0291)N161 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jksA)V152 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKVGYTEK 1jksA 7 :ENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRR T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1jksA 57 :SREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKE T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1jksA 110 :SLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIML T0291 162 :SNLVCKVSDFGLGRVLEDDP 1jksA 153 :PKPRIKIIDFGLAHKIDFGN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLP 1jksA 173 :EFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFE T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1jksA 242 :SNTSALAKDFIRRLLVKDPKKRMTIQDSLQH Number of specific fragments extracted= 6 number of extra gaps= 1 total=1365 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o6lA expands to /projects/compbio/data/pdb/1o6l.pdb.gz 1o6lA: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 # T0291 read from 1o6lA/merged-good-all-a2m # 1o6lA read from 1o6lA/merged-good-all-a2m # adding 1o6lA to template set # found chain 1o6lA in template set Warning: unaligning (T0291)I27 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6lA)D153 Warning: unaligning (T0291)S28 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6lA)D153 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6lA)F310 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6lA)F310 T0291 22 :LDATN 1o6lA 147 :VTMND T0291 29 :IDKVVGAGEFGEVCSGRL 1o6lA 154 :YLKLLGKGTFGKVILVRE T0291 50 :SKKEISVAIKTLK 1o6lA 172 :KATGRYYAMKILR T0291 63 :VGY 1o6lA 191 :KDE T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1o6lA 194 :VAHTVTESRVLQNTRHPFLTALKYAFQTHDRLCFVMEYANGGELFFHLSRER T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1o6lA 246 :VFTEERARFYGAEIVSALEYLHSRDVVYRDIKLENLMLDKDGHIKITDFGLCKEGISD T0291 184 :AYTT 1o6lA 304 :GATM T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1o6lA 311 :CGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMC T0291 227 :GERPYWEMSNQDVIKAVDE 1o6lA 346 :GRLPFYNQDHERLFELILM T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNR 1o6lA 365 :EEIRFPRTLSPEAKSLLAGLLKKDPKQR T0291 275 :PKFEQIVSI 1o6lA 412 :INWQDVVQK Number of specific fragments extracted= 11 number of extra gaps= 1 total=1376 Number of alignments=148 # 1o6lA read from 1o6lA/merged-good-all-a2m # found chain 1o6lA in template set Warning: unaligning (T0291)E21 because first residue in template chain is (1o6lA)K146 Warning: unaligning (T0291)I27 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6lA)D153 Warning: unaligning (T0291)S28 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6lA)D153 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6lA)F310 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6lA)F310 T0291 22 :LDATN 1o6lA 147 :VTMND T0291 29 :IDKVVGAGEFGEVCSGRL 1o6lA 154 :YLKLLGKGTFGKVILVRE T0291 50 :SKKEISVAIKTLKVGYT 1o6lA 172 :KATGRYYAMKILRKEVI T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1o6lA 191 :KDEVAHTVTESRVLQNTRHPFLTALKYAFQTHDRLCFVMEYANGGELFFHLSRERV T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1o6lA 247 :FTEERARFYGAEIVSALEYLHSRDVVYRDIKLENLMLDKDGHIKITDFGLCKEGIS T0291 181 :PEA 1o6lA 303 :DGA T0291 186 :TT 1o6lA 306 :TM T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1o6lA 311 :CGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMC T0291 227 :GERPYWEMSNQDVIKAVDEG 1o6lA 346 :GRLPFYNQDHERLFELILME T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNR 1o6lA 366 :EIRFPRTLSPEAKSLLAGLLKKDPKQR T0291 275 :PKFEQIVS 1o6lA 412 :INWQDVVQ T0291 290 :NPGSLKII 1o6lA 420 :KKLLPPFK Number of specific fragments extracted= 12 number of extra gaps= 1 total=1388 Number of alignments=149 # 1o6lA read from 1o6lA/merged-good-all-a2m # found chain 1o6lA in template set Warning: unaligning (T0291)I27 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6lA)D153 Warning: unaligning (T0291)S28 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6lA)D153 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6lA)F310 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6lA)F310 T0291 22 :LDATN 1o6lA 147 :VTMND T0291 29 :IDKVVGAGEFGEVCSGRLKLPSKKEISVAIKT 1o6lA 154 :YLKLLGKGTFGKVILVREKATGRYYAMKILRK T0291 67 :E 1o6lA 186 :E T0291 68 :KQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1o6lA 192 :DEVAHTVTESRVLQNTRHPFLTALKYAFQTHDRLCFVMEYANGGELFFHLSRER T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1o6lA 246 :VFTEERARFYGAEIVSALEYLHSRDVVYRDIKLENLMLDKDGHIKITDFGLCKEGISDGA T0291 186 :TT 1o6lA 306 :TM T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGY 1o6lA 311 :CGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHERLFELILMEEI T0291 250 :PPPMDCPAALYQLMLDCWQKDRNNR 1o6lA 368 :RFPRTLSPEAKSLLAGLLKKDPKQR T0291 275 :PKFEQIVSI 1o6lA 412 :INWQDVVQK T0291 289 :RNPGSLKIITSAA 1o6lA 421 :KLLPPFKPQVTSE Number of specific fragments extracted= 10 number of extra gaps= 1 total=1398 Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f57A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f57A expands to /projects/compbio/data/pdb/2f57.pdb.gz 2f57A:Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 2f57A Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2f57A Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2f57A 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 Skipped atom 1969, because occupancy 0.500 <= existing 0.500 in 2f57A Skipped atom 1973, because occupancy 0.500 <= existing 0.500 in 2f57A Skipped atom 1975, because occupancy 0.500 <= existing 0.500 in 2f57A # T0291 read from 2f57A/merged-good-all-a2m # 2f57A read from 2f57A/merged-good-all-a2m # adding 2f57A to template set # found chain 2f57A in template set Warning: unaligning (T0291)G36 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2f57A)S459 Warning: unaligning (T0291)E37 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2f57A)S459 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f57A)L603 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f57A)L603 T0291 1 :TYVDPHTYEDPTQAVHEFAKELD 2f57A -5 :LYFQSMSRVSHEQFRAALQLVVS T0291 24 :ATNISIDKVVGA 2f57A 446 :REYLANFIKIGE T0291 38 :FGEVCSGRL 2f57A 460 :TGIVCIATE T0291 50 :SKKEISVAIKTLK 2f57A 469 :KHTGKQVAVKKMD T0291 63 :VGY 2f57A 485 :QQR T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRK 2f57A 488 :RELLFNEVVIMRDYHHDNVVDMYSSYLVGDELWVVMEFLEGGALTDIVTH T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 2f57A 538 :TRMNEEQIATVCLSVLRALSYLHNQGVIHRDIKSDSILLTSDGRIKLSDFGFCAQVSKEV T0291 185 :YTT 2f57A 598 :PKR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2f57A 604 :VGTPYWMAPEVISRLPYGTEVDIWSLGIMVIEMID T0291 227 :GERPYWEMSNQDVIKAVDEG 2f57A 639 :GEPPYFNEPPLQAMRRIRDS T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIV 2f57A 661 :PRVKDLHKVSSVLRGFLDLMLVREPSQRATAQELL T0291 290 :NP 2f57A 696 :GH T0291 293 :SLKIITSAAARPSNLLLD 2f57A 698 :PFLKLAGPPSCIVPLMRQ Number of specific fragments extracted= 13 number of extra gaps= 1 total=1411 Number of alignments=151 # 2f57A read from 2f57A/merged-good-all-a2m # found chain 2f57A in template set Warning: unaligning (T0291)G36 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2f57A)S459 Warning: unaligning (T0291)E37 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2f57A)S459 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f57A)L603 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f57A)L603 Warning: unaligning (T0291)L309 because last residue in template chain is (2f57A)Q715 T0291 1 :TYVDPHTYEDPTQAVHEFAKELDATN 2f57A -5 :LYFQSMSRVSHEQFRAALQLVVSPGD T0291 27 :ISIDKVVGA 2f57A 449 :LANFIKIGE T0291 38 :FGEVCSGRL 2f57A 460 :TGIVCIATE T0291 50 :SKKEISVAIKTLKVGYTEK 2f57A 469 :KHTGKQVAVKKMDLRKQQR T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 2f57A 488 :RELLFNEVVIMRDYHHDNVVDMYSSYLVGDELWVVMEFLEGGALTDIVTHT T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 2f57A 539 :RMNEEQIATVCLSVLRALSYLHNQGVIHRDIKSDSILLTSDGRIKLSDFGFCAQVSKEVP T0291 186 :TT 2f57A 599 :KR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2f57A 604 :VGTPYWMAPEVISRLPYGTEVDIWSLGIMVIEMID T0291 227 :GERPYWEMSNQDVIKAVDEG 2f57A 639 :GEPPYFNEPPLQAMRRIRDS T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 2f57A 661 :PRVKDLHKVSSVLRGFLDLMLVREPSQRATAQELLG T0291 291 :PGSLKIITSAAARPSNLL 2f57A 697 :HPFLKLAGPPSCIVPLMR Number of specific fragments extracted= 11 number of extra gaps= 1 total=1422 Number of alignments=152 # 2f57A read from 2f57A/merged-good-all-a2m # found chain 2f57A in template set Warning: unaligning (T0291)G36 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2f57A)S459 Warning: unaligning (T0291)E37 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2f57A)S459 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f57A)L603 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f57A)L603 T0291 22 :LDATNISIDKVVGA 2f57A 444 :DPREYLANFIKIGE T0291 38 :FGEVCSGRLKLPSKKEISVAIKTLKVG 2f57A 460 :TGIVCIATEKHTGKQVAVKKMDLRKQQ T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 2f57A 487 :RRELLFNEVVIMRDYHHDNVVDMYSSYLVGDELWVVMEFLEGGALTDIVTHTR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 2f57A 540 :MNEEQIATVCLSVLRALSYLHNQGVIHRDIKSDSILLTSDGRIKLSDFGFCAQVSKEVP T0291 186 :TT 2f57A 599 :KR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 2f57A 604 :VGTPYWMAPEVISRLPYGTEVDIWSLGIMVIEMIDGEPPYFNEPPLQAMRRIRDSL T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 2f57A 661 :PRVKDLHKVSSVLRGFLDLMLVREPSQRATAQELLGH T0291 298 :TSAAARPSNLL 2f57A 698 :PFLKLAGPPSC Number of specific fragments extracted= 8 number of extra gaps= 1 total=1430 Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b7aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b7aA expands to /projects/compbio/data/pdb/2b7a.pdb.gz 2b7aA: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 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 # T0291 read from 2b7aA/merged-good-all-a2m # 2b7aA read from 2b7aA/merged-good-all-a2m # adding 2b7aA to template set # found chain 2b7aA in template set Warning: unaligning (T0291)E21 because first residue in template chain is (2b7aA)Q843 Warning: unaligning (T0291)K97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7aA)N924 Warning: unaligning (T0291)P100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b7aA)N924 Warning: unaligning (T0291)M108 because of BadResidue code BAD_PEPTIDE in next template residue (2b7aA)P933 Warning: unaligning (T0291)E109 because of BadResidue code BAD_PEPTIDE at template residue (2b7aA)P933 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7aA)K1009 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b7aA)K1009 T0291 22 :LDATNISIDKVVGAGEFGEVCSGRLKLPSKK 2b7aA 844 :FEERHLKFLQQLGKGNFGSVEMCRYDPLQDN T0291 53 :EISVAIKTL 2b7aA 876 :GEVVAVKKL T0291 63 :VGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVT 2b7aA 885 :QHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCY T0291 101 :VMIVTEY 2b7aA 925 :LKLIMEY T0291 110 :NGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 2b7aA 934 :YGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDK T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSY 2b7aA 1010 :VKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTY T0291 227 :GERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 2b7aA 1066 :GNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRD Number of specific fragments extracted= 7 number of extra gaps= 1 total=1437 Number of alignments=154 # 2b7aA read from 2b7aA/merged-good-all-a2m # found chain 2b7aA in template set Warning: unaligning (T0291)E21 because first residue in template chain is (2b7aA)Q843 Warning: unaligning (T0291)K97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7aA)N924 Warning: unaligning (T0291)M108 because of BadResidue code BAD_PEPTIDE in next template residue (2b7aA)P933 Warning: unaligning (T0291)E109 because of BadResidue code BAD_PEPTIDE at template residue (2b7aA)P933 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7aA)K1009 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b7aA)K1009 T0291 22 :LDATNISIDKVVGAGEFGEVCSGRLK 2b7aA 844 :FEERHLKFLQQLGKGNFGSVEMCRYD T0291 48 :LPSKKEISVAIKTL 2b7aA 871 :LQDNTGEVVAVKKL T0291 63 :VGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVT 2b7aA 885 :QHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCY T0291 101 :VMIVTEY 2b7aA 925 :LKLIMEY T0291 110 :NGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 2b7aA 934 :YGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDK T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSY 2b7aA 1010 :VKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTY T0291 230 :PYWEM 2b7aA 1051 :IEKSK T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 2b7aA 1075 :VFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRD Number of specific fragments extracted= 8 number of extra gaps= 1 total=1445 Number of alignments=155 # 2b7aA read from 2b7aA/merged-good-all-a2m # found chain 2b7aA in template set Warning: unaligning (T0291)E21 because first residue in template chain is (2b7aA)Q843 Warning: unaligning (T0291)K97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7aA)N924 Warning: unaligning (T0291)P100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b7aA)N924 Warning: unaligning (T0291)M108 because of BadResidue code BAD_PEPTIDE in next template residue (2b7aA)P933 Warning: unaligning (T0291)E109 because of BadResidue code BAD_PEPTIDE at template residue (2b7aA)P933 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7aA)K1009 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b7aA)K1009 T0291 22 :LDATNISIDKVVGAGEFGEVCSGRLKL 2b7aA 844 :FEERHLKFLQQLGKGNFGSVEMCRYDP T0291 49 :PSKKEISVAI 2b7aA 875 :TGEVVAVKKL T0291 63 :VGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVT 2b7aA 885 :QHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCY T0291 101 :VMIVTEY 2b7aA 925 :LKLIMEY T0291 110 :NGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 2b7aA 934 :YGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDK T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGE 2b7aA 1010 :VKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIE T0291 231 :YWEMSNQDVIKA 2b7aA 1053 :KSKSPPAEFMRM T0291 243 :VDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 2b7aA 1082 :LKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRD Number of specific fragments extracted= 8 number of extra gaps= 1 total=1453 Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cmkE/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cmkE expands to /projects/compbio/data/pdb/1cmk.pdb.gz 1cmkE: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 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 # T0291 read from 1cmkE/merged-good-all-a2m # 1cmkE read from 1cmkE/merged-good-all-a2m # adding 1cmkE to template set # found chain 1cmkE in template set Warning: unaligning (T0291)A19 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)Q35 Warning: unaligning (T0291)D23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L40 Warning: unaligning (T0291)A24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L40 Warning: unaligning (T0291)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)K111 Warning: unaligning (T0291)T96 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)K111 Warning: unaligning (T0291)K97 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)N113 Warning: unaligning (T0291)S98 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)N113 Warning: unaligning (T0291)L164 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cmkE)Y179 Warning: unaligning (T0291)V165 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cmkE)Y179 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L198 Warning: unaligning (T0291)K191 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)G200 Warning: unaligning (T0291)I192 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)G200 Warning: unaligning (T0291)A257 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)D264 Warning: unaligning (T0291)A258 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)D264 T0291 20 :KEL 1cmkE 36 :NTA T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1cmkE 41 :DQFERIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLK 1cmkE 63 :KETGNHFAMKILD T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGV 1cmkE 85 :IEHTLNEKRILQAVNFPFLVKLEYS T0291 99 :KPVMIVTEYMENGSLDSFLRKHDA 1cmkE 114 :SNLYMVMEYVPGGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSN 1cmkE 138 :FSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQ T0291 166 :CKVSDFGLGRVLEDD 1cmkE 180 :IQVTDFGFAKRVKGR T0291 187 :T 1cmkE 195 :T T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1cmkE 201 :TPEYLAPEIILSKGYNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDEG 1cmkE 234 :GYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCP 1cmkE 254 :KVRFPSHFS T0291 259 :LYQLMLDCWQKDRNNR 1cmkE 265 :LKDLLRNLLQVDLTKR Number of specific fragments extracted= 12 number of extra gaps= 5 total=1465 Number of alignments=157 # 1cmkE read from 1cmkE/merged-good-all-a2m # found chain 1cmkE in template set Warning: unaligning (T0291)F18 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)Q35 Warning: unaligning (T0291)A19 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)Q35 Warning: unaligning (T0291)D23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L40 Warning: unaligning (T0291)A24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L40 Warning: unaligning (T0291)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)K111 Warning: unaligning (T0291)T96 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)K111 Warning: unaligning (T0291)K97 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)N113 Warning: unaligning (T0291)S98 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)N113 Warning: unaligning (T0291)L164 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cmkE)Y179 Warning: unaligning (T0291)V165 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cmkE)Y179 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L198 Warning: unaligning (T0291)K191 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)G200 Warning: unaligning (T0291)I192 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)G200 Warning: unaligning (T0291)A257 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)D264 Warning: unaligning (T0291)A258 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)D264 Warning: unaligning (T0291)V281 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)N293 Warning: unaligning (T0291)S282 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)N293 Warning: unaligning (T0291)K295 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)F314 Warning: unaligning (T0291)I296 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)F314 Warning: unaligning (T0291)T298 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)I339 Warning: unaligning (T0291)A300 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)I339 Warning: unaligning (T0291)A301 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)E341 Warning: unaligning (T0291)A302 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)E341 T0291 20 :KEL 1cmkE 36 :NTA T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1cmkE 41 :DQFERIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLKVGYT 1cmkE 63 :KETGNHFAMKILDKQKV T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGV 1cmkE 82 :LKQIEHTLNEKRILQAVNFPFLVKLEYS T0291 99 :KPVMIVTEYMENGSLDSFLRKHDA 1cmkE 114 :SNLYMVMEYVPGGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSN 1cmkE 138 :FSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQ T0291 166 :CKVSDFGLGRVLED 1cmkE 180 :IQVTDFGFAKRVKG T0291 186 :TT 1cmkE 194 :RT T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1cmkE 201 :TPEYLAPEIILSKGYNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDEG 1cmkE 234 :GYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCP 1cmkE 254 :KVRFPSHFS T0291 259 :LYQLMLDCWQKDRNNRP 1cmkE 265 :LKDLLRNLLQVDLTKRF T0291 276 :KFEQI 1cmkE 287 :GVNDI T0291 284 :LDKLIRNPGSL 1cmkE 302 :WIAIYQRKVEA T0291 297 :I 1cmkE 315 :I T0291 303 :RPSN 1cmkE 342 :KCGK Number of specific fragments extracted= 16 number of extra gaps= 7 total=1481 Number of alignments=158 # 1cmkE read from 1cmkE/merged-good-all-a2m # found chain 1cmkE in template set Warning: unaligning (T0291)D23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L40 Warning: unaligning (T0291)A24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L40 Warning: unaligning (T0291)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)K111 Warning: unaligning (T0291)T96 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)K111 Warning: unaligning (T0291)K97 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)N113 Warning: unaligning (T0291)S98 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)N113 Warning: unaligning (T0291)L164 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cmkE)Y179 Warning: unaligning (T0291)V165 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cmkE)Y179 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L198 Warning: unaligning (T0291)K191 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)G200 Warning: unaligning (T0291)I192 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)G200 Warning: unaligning (T0291)A257 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)D264 Warning: unaligning (T0291)A258 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)D264 T0291 20 :KEL 1cmkE 36 :NTA T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1cmkE 41 :DQFERIKTLGTGSFGRVMLVKHKETGNHFAMKILDKQKV T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGV 1cmkE 80 :VKLKQIEHTLNEKRILQAVNFPFLVKLEYS T0291 99 :KPVMIVTEYMENGSLDSFLRKHD 1cmkE 114 :SNLYMVMEYVPGGEMFSHLRRIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSN 1cmkE 137 :RFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQ T0291 166 :CKVSDFGLGRVLED 1cmkE 180 :IQVTDFGFAKRVKG T0291 186 :TT 1cmkE 194 :RT T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGY 1cmkE 201 :TPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKV T0291 250 :PPPMDCP 1cmkE 256 :RFPSHFS T0291 259 :LYQLMLDCWQKDRNNRP 1cmkE 265 :LKDLLRNLLQVDLTKRF Number of specific fragments extracted= 10 number of extra gaps= 4 total=1491 Number of alignments=159 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0291//projects/compbio/experiments/protein-predict/casp7/T0291/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0291//projects/compbio/experiments/protein-predict/casp7/T0291/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0291/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0291/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((T0291)M140.CB, (T0291)D212.CB) [> 3.4503 = 5.7505 < 7.4756] w=1.0000 to align # Constraint # added constraint: constraint((T0291)M140.CB, (T0291)H150.CB) [> 4.1571 = 6.9285 < 9.0070] w=1.0000 to align # Constraint # added constraint: constraint((T0291)G139.CA, (T0291)V168.CB) [> 3.5685 = 5.9474 < 7.7316] w=1.0000 to align # Constraint # added constraint: constraint((T0291)A137.CB, (T0291)Y216.CB) [> 4.1592 = 6.9320 < 9.0116] w=1.0000 to align # Constraint # added constraint: constraint((T0291)I136.CB, (T0291)Y216.CB) [> 3.9077 = 6.5129 < 8.4667] w=1.0000 to align # Constraint # added constraint: constraint((T0291)I136.CB, (T0291)C166.CB) [> 3.6085 = 6.0142 < 7.8185] w=1.0000 to align # Constraint # added constraint: constraint((T0291)G135.CA, (T0291)C166.CB) [> 3.3197 = 5.5328 < 7.1926] w=1.0000 to align # Constraint # added constraint: constraint((T0291)L133.CB, (T0291)L220.CB) [> 3.3605 = 5.6007 < 7.2810] w=1.0000 to align # Constraint # added constraint: constraint((T0291)M132.CB, (T0291)V223.CB) [> 3.8225 = 6.3709 < 8.2822] w=1.0000 to align # Constraint # added constraint: constraint((T0291)M132.CB, (T0291)C166.CB) [> 3.2056 = 5.3427 < 6.9455] w=1.0000 to align # Constraint # added constraint: constraint((T0291)L129.CB, (T0291)M224.CB) [> 3.5847 = 5.9745 < 7.7668] w=1.0000 to align # Constraint # added constraint: constraint((T0291)L129.CB, (T0291)V223.CB) [> 2.8788 = 4.7979 < 6.2373] w=1.0000 to align # Constraint # added constraint: constraint((T0291)L113.CB, (T0291)I160.CB) [> 3.6574 = 6.0957 < 7.9244] w=1.0000 to align # Constraint # added constraint: constraint((T0291)L113.CB, (T0291)I158.CB) [> 2.4309 = 4.0515 < 5.2670] w=1.0000 to align # Constraint # added constraint: constraint((T0291)L113.CB, (T0291)A155.CB) [> 2.6789 = 4.4649 < 5.8044] w=1.0000 to align # Constraint # added constraint: constraint((T0291)S112.CB, (T0291)L159.CB) [> 3.5203 = 5.8672 < 7.6273] w=1.0000 to align # Constraint # added constraint: constraint((T0291)G93.CA, (T0291)I103.CB) [> 4.2070 = 7.0117 < 9.1152] w=1.0000 to align # Constraint # added constraint: constraint((T0291)E92.CB, (T0291)V104.CB) [> 2.7406 = 4.5677 < 5.9380] w=1.0000 to align # Constraint # added constraint: constraint((T0291)L91.CB, (T0291)V104.CB) [> 4.4143 = 7.3572 < 9.5644] w=1.0000 to align # Constraint # added constraint: constraint((T0291)I89.CB, (T0291)S169.CB) [> 2.8183 = 4.6972 < 6.1063] w=1.0000 to align # Constraint # added constraint: constraint((T0291)I89.CB, (T0291)K167.CB) [> 2.8672 = 4.7786 < 6.2122] w=1.0000 to align # Constraint # added constraint: constraint((T0291)I88.CB, (T0291)V168.CB) [> 3.0476 = 5.0793 < 6.6031] w=1.0000 to align # Constraint # added constraint: constraint((T0291)I88.CB, (T0291)K167.CB) [> 3.6474 = 6.0791 < 7.9028] w=1.0000 to align # Constraint # added constraint: constraint((T0291)I88.CB, (T0291)G139.CA) [> 3.6330 = 6.0550 < 7.8714] w=1.0000 to align # Constraint # added constraint: constraint((T0291)N87.CB, (T0291)G139.CA) [> 2.5619 = 4.2699 < 5.5509] w=1.0000 to align # Constraint # added constraint: constraint((T0291)N87.CB, (T0291)S138.CB) [> 3.2454 = 5.4090 < 7.0317] w=1.0000 to align # Constraint # added constraint: constraint((T0291)W221.CB, (T0291)M263.CB) [> 3.5481 = 5.9135 < 7.6875] w=1.0000 to align # Constraint # added constraint: constraint((T0291)G217.CA, (T0291)C266.CB) [> 2.3531 = 3.9218 < 5.0983] w=1.0000 to align # Constraint # added constraint: constraint((T0291)G217.CA, (T0291)M263.CB) [> 3.2629 = 5.4381 < 7.0695] w=1.0000 to align # Constraint # added constraint: constraint((T0291)Y216.CB, (T0291)C266.CB) [> 3.5364 = 5.8941 < 7.6623] w=1.0000 to align # Constraint # added constraint: constraint((T0291)W214.CB, (T0291)C266.CB) [> 3.6226 = 6.0377 < 7.8489] w=1.0000 to align # Constraint # added constraint: constraint((T0291)V213.CB, (T0291)C266.CB) [> 3.1346 = 5.2243 < 6.7915] w=1.0000 to align # Constraint # added constraint: constraint((T0291)A201.CB, (T0291)S211.CB) [> 3.3100 = 5.5166 < 7.1716] w=1.0000 to align # Constraint # added constraint: constraint((T0291)E200.CB, (T0291)S211.CB) [> 4.0226 = 6.7043 < 8.7156] w=1.0000 to align # Constraint # added constraint: constraint((T0291)S198.CB, (T0291)S215.CB) [> 4.1737 = 6.9562 < 9.0430] w=1.0000 to align # Constraint # added constraint: constraint((T0291)S198.CB, (T0291)W214.CB) [> 2.2402 = 3.7337 < 4.8538] w=1.0000 to align # Constraint # added constraint: constraint((T0291)S198.CB, (T0291)S211.CB) [> 2.5449 = 4.2416 < 5.5141] w=1.0000 to align # Constraint # added constraint: constraint((T0291)W196.CB, (T0291)I218.CB) [> 3.0106 = 5.0176 < 6.5229] w=1.0000 to align # Constraint # added constraint: constraint((T0291)L159.CB, (T0291)S169.CB) [> 3.2081 = 5.3468 < 6.9508] w=1.0000 to align # Constraint # added constraint: constraint((T0291)I158.CB, (T0291)V168.CB) [> 3.6974 = 6.1624 < 8.0112] w=1.0000 to align # Constraint # added constraint: constraint((T0291)M140.CB, (T0291)Y216.CB) [> 3.9502 = 6.5836 < 8.5587] w=1.0000 to align # Constraint # added constraint: constraint((T0291)V149.CB, (T0291)D212.CB) [> 3.5744 = 5.9574 < 7.7446] w=1.0000 to align # Constraint # added constraint: constraint((T0291)H150.CB, (T0291)V168.CB) [> 4.2081 = 7.0135 < 9.1175] w=1.0000 to align # Constraint # added constraint: constraint((T0291)H150.CB, (T0291)D212.CB) [> 3.1644 = 5.2741 < 6.8563] w=1.0000 to align # Constraint # added constraint: constraint((T0291)L153.CB, (T0291)D212.CB) [> 3.3787 = 5.6311 < 7.3204] w=1.0000 to align # Constraint # added constraint: constraint((T0291)L153.CB, (T0291)S215.CB) [> 2.3360 = 3.8934 < 5.0614] w=1.0000 to align # Constraint # added constraint: constraint((T0291)L153.CB, (T0291)Y216.CB) [> 3.6040 = 6.0067 < 7.8087] w=1.0000 to align # Constraint # added constraint: constraint((T0291)L153.CB, (T0291)V219.CB) [> 3.7168 = 6.1947 < 8.0530] w=1.0000 to align # Constraint # added constraint: constraint((T0291)A154.CB, (T0291)S215.CB) [> 4.0722 = 6.7870 < 8.8231] w=1.0000 to align # Constraint # added constraint: constraint((T0291)A154.CB, (T0291)V219.CB) [> 3.8350 = 6.3917 < 8.3092] w=1.0000 to align # Constraint # added constraint: constraint((T0291)A155.CB, (T0291)V219.CB) [> 3.5440 = 5.9066 < 7.6786] w=1.0000 to align # Constraint # added constraint: constraint((T0291)A155.CB, (T0291)E222.CB) [> 3.2994 = 5.4991 < 7.1488] w=1.0000 to align # Constraint # added constraint: constraint((T0291)N157.CB, (T0291)V168.CB) [> 4.0755 = 6.7925 < 8.8302] w=1.0000 to align # Constraint # added constraint: constraint((T0291)N157.CB, (T0291)S169.CB) [> 3.1400 = 5.2333 < 6.8033] w=1.0000 to align # Constraint # added constraint: constraint((T0291)I158.CB, (T0291)K167.CB) [> 4.2985 = 7.1642 < 9.3134] w=1.0000 to align # Constraint # added constraint: constraint((T0291)G81.CA, (T0291)L91.CB) [> 3.1194 = 5.1990 < 6.7587] w=0.9936 to align # Constraint # added constraint: constraint((T0291)I29.CB, (T0291)G44.CA) [> 3.3113 = 5.5188 < 7.1745] w=0.9936 to align # Constraint # added constraint: constraint((T0291)N87.CB, (T0291)G135.CA) [> 3.0793 = 5.1322 < 6.6719] w=0.9936 to align # Constraint # added constraint: constraint((T0291)N87.CB, (T0291)C166.CB) [> 3.6444 = 6.0740 < 7.8962] w=0.9936 to align # Constraint # added constraint: constraint((T0291)N87.CB, (T0291)K167.CB) [> 3.4149 = 5.6915 < 7.3990] w=0.9936 to align # Constraint # added constraint: constraint((T0291)N87.CB, (T0291)V168.CB) [> 3.7505 = 6.2508 < 8.1260] w=0.9936 to align # Constraint # added constraint: constraint((T0291)M80.CB, (T0291)L91.CB) [> 2.5993 = 4.3322 < 5.6318] w=0.9936 to align # Constraint # added constraint: constraint((T0291)G93.CA, (T0291)V104.CB) [> 2.7018 = 4.5029 < 5.8538] w=0.9936 to align # Constraint # added constraint: constraint((T0291)G44.CA, (T0291)S55.CB) [> 3.6814 = 6.1356 < 7.9763] w=0.9872 to align # Constraint # added constraint: constraint((T0291)D114.CB, (T0291)A155.CB) [> 2.3907 = 3.9846 < 5.1800] w=0.9809 to align # Constraint # added constraint: constraint((T0291)R151.CB, (T0291)S211.CB) [> 4.1296 = 6.8827 < 8.9475] w=0.9809 to align # Constraint # added constraint: constraint((T0291)W214.CB, (T0291)W267.CB) [> 3.8466 = 6.4111 < 8.3344] w=0.9809 to align # Constraint # added constraint: constraint((T0291)V32.CB, (T0291)V41.CB) [> 4.3320 = 7.2201 < 9.3861] w=0.9808 to align # Constraint # added constraint: constraint((T0291)L91.CB, (T0291)I103.CB) [> 4.0258 = 6.7097 < 8.7226] w=0.9808 to align # Constraint # added constraint: constraint((T0291)R90.CB, (T0291)E106.CB) [> 2.7266 = 4.5444 < 5.9077] w=0.9808 to align # Constraint # added constraint: constraint((T0291)R90.CB, (T0291)T105.CB) [> 3.8484 = 6.4139 < 8.3381] w=0.9808 to align # Constraint # added constraint: constraint((T0291)I89.CB, (T0291)E106.CB) [> 3.2793 = 5.4654 < 7.1051] w=0.9808 to align # Constraint # added constraint: constraint((T0291)I89.CB, (T0291)T105.CB) [> 3.2539 = 5.4231 < 7.0501] w=0.9808 to align # Constraint # added constraint: constraint((T0291)V56.CB, (T0291)T105.CB) [> 4.0303 = 6.7172 < 8.7324] w=0.9808 to align # Constraint # added constraint: constraint((T0291)V149.CB, (T0291)S211.CB) [> 4.1532 = 6.9219 < 8.9985] w=0.9808 to align # Constraint # added constraint: constraint((T0291)N110.CB, (T0291)I160.CB) [> 2.3027 = 3.8379 < 4.9892] w=0.9808 to align # Constraint # added constraint: constraint((T0291)N110.CB, (T0291)L159.CB) [> 4.3180 = 7.1967 < 9.3557] w=0.9808 to align # Constraint # added constraint: constraint((T0291)W196.CB, (T0291)S215.CB) [> 2.7613 = 4.6022 < 5.9829] w=0.9808 to align # Constraint # added constraint: constraint((T0291)A154.CB, (T0291)W196.CB) [> 2.9772 = 4.9620 < 6.4506] w=0.9808 to align # Constraint # added constraint: constraint((T0291)L153.CB, (T0291)W196.CB) [> 3.9214 = 6.5356 < 8.4963] w=0.9808 to align # Constraint # added constraint: constraint((T0291)I136.CB, (T0291)I158.CB) [> 3.8814 = 6.4689 < 8.4096] w=0.9808 to align # Constraint # added constraint: constraint((T0291)A77.CB, (T0291)I103.CB) [> 3.7301 = 6.2169 < 8.0820] w=0.9808 to align # Constraint # added constraint: constraint((T0291)L117.CB, (T0291)V223.CB) [> 3.9306 = 6.5511 < 8.5164] w=0.9808 to align # Constraint # added constraint: constraint((T0291)D265.CB, (T0291)R274.CB) [> 4.1386 = 6.8977 < 8.9670] w=0.9808 to align # Constraint # added constraint: constraint((T0291)L220.CB, (T0291)C266.CB) [> 4.3237 = 7.2062 < 9.3680] w=0.9808 to align # Constraint # added constraint: constraint((T0291)L220.CB, (T0291)M263.CB) [> 3.3357 = 5.5595 < 7.2273] w=0.9808 to align # Constraint # added constraint: constraint((T0291)W214.CB, (T0291)R274.CB) [> 4.0150 = 6.6917 < 8.6992] w=0.9808 to align # Constraint # added constraint: constraint((T0291)V213.CB, (T0291)R274.CB) [> 3.0384 = 5.0640 < 6.5832] w=0.9808 to align # Constraint # added constraint: constraint((T0291)I89.CB, (T0291)V168.CB) [> 4.0482 = 6.7470 < 8.7711] w=0.9808 to align # Constraint # added constraint: constraint((T0291)I89.CB, (T0291)L159.CB) [> 3.7578 = 6.2630 < 8.1419] w=0.9808 to align # Constraint # added constraint: constraint((T0291)L117.CB, (T0291)A155.CB) [> 3.7557 = 6.2595 < 8.1373] w=0.9808 to align # Constraint # added constraint: constraint((T0291)S144.CB, (T0291)D212.CB) [> 4.3469 = 7.2448 < 9.4182] w=0.9808 to align # Constraint # added constraint: constraint((T0291)E92.CB, (T0291)T105.CB) [> 3.7110 = 6.1849 < 8.0404] w=0.9808 to align # Constraint # added constraint: constraint((T0291)L91.CB, (T0291)T105.CB) [> 3.2229 = 5.3716 < 6.9831] w=0.9808 to align # Constraint # added constraint: constraint((T0291)L220.CB, (T0291)L262.CB) [> 4.1690 = 6.9484 < 9.0329] w=0.9789 to align # Constraint # added constraint: constraint((T0291)D30.CB, (T0291)G44.CA) [> 2.9293 = 4.8822 < 6.3468] w=0.9744 to align # Constraint # added constraint: constraint((T0291)I27.CB, (T0291)L46.CB) [> 3.4684 = 5.7807 < 7.5149] w=0.9744 to align # Constraint # added constraint: constraint((T0291)I27.CB, (T0291)G44.CA) [> 3.6534 = 6.0890 < 7.9157] w=0.9744 to align # Constraint # added constraint: constraint((T0291)I27.CB, (T0291)R45.CB) [> 4.1919 = 6.9865 < 9.0825] w=0.9744 to align # Constraint # added constraint: constraint((T0291)S28.CB, (T0291)G44.CA) [> 3.7036 = 6.1727 < 8.0245] w=0.9744 to align # Constraint # added constraint: constraint((T0291)S28.CB, (T0291)R45.CB) [> 2.9174 = 4.8624 < 6.3211] w=0.9744 to align # Constraint # added constraint: constraint((T0291)V94.CB, (T0291)I103.CB) [> 3.2854 = 5.4757 < 7.1184] w=0.9744 to align # Constraint # added constraint: constraint((T0291)V94.CB, (T0291)V104.CB) [> 4.1285 = 6.8808 < 8.9450] w=0.9744 to align # Constraint # added constraint: constraint((T0291)G217.CA, (T0291)W267.CB) [> 3.6547 = 6.0912 < 7.9185] w=0.9617 to align # Constraint # added constraint: constraint((T0291)D114.CB, (T0291)R156.CB) [> 2.8103 = 4.6839 < 6.0890] w=0.9617 to align # Constraint # added constraint: constraint((T0291)I136.CB, (T0291)V219.CB) [> 4.1267 = 6.8779 < 8.9412] w=0.9616 to align # Constraint # added constraint: constraint((T0291)V41.CB, (T0291)A57.CB) [> 3.6831 = 6.1385 < 7.9801] w=0.9616 to align # Constraint # added constraint: constraint((T0291)S198.CB, (T0291)A210.CB) [> 4.3175 = 7.1958 < 9.3546] w=0.9616 to align # Constraint # added constraint: constraint((T0291)L113.CB, (T0291)C166.CB) [> 4.0744 = 6.7907 < 8.8279] w=0.9616 to align # Constraint # added constraint: constraint((T0291)L113.CB, (T0291)L159.CB) [> 4.2708 = 7.1179 < 9.2533] w=0.9616 to align # Constraint # added constraint: constraint((T0291)K31.CB, (T0291)C42.CB) [> 3.9998 = 6.6663 < 8.6662] w=0.9616 to align # Constraint # added constraint: constraint((T0291)V32.CB, (T0291)C42.CB) [> 3.3389 = 5.5649 < 7.2344] w=0.9616 to align # Constraint # added constraint: constraint((T0291)V33.CB, (T0291)C42.CB) [> 3.8133 = 6.3555 < 8.2621] w=0.9616 to align # Constraint # added constraint: constraint((T0291)V33.CB, (T0291)S43.CB) [> 3.3053 = 5.5089 < 7.1616] w=0.9616 to align # Constraint # added constraint: constraint((T0291)S43.CB, (T0291)Y107.CB) [> 3.9924 = 6.6540 < 8.6502] w=0.9616 to align # Constraint # added constraint: constraint((T0291)E92.CB, (T0291)E106.CB) [> 3.9899 = 6.6499 < 8.6448] w=0.9616 to align # Constraint # added constraint: constraint((T0291)M108.CB, (T0291)L159.CB) [> 2.4486 = 4.0810 < 5.3054] w=0.9597 to align # Constraint # added constraint: constraint((T0291)H85.CB, (T0291)Y142.CB) [> 2.7436 = 4.5726 < 5.9444] w=0.9552 to align # Constraint # added constraint: constraint((T0291)H85.CB, (T0291)G139.CA) [> 3.4517 = 5.7528 < 7.4787] w=0.9552 to align # Constraint # added constraint: constraint((T0291)C42.CB, (T0291)A57.CB) [> 4.3115 = 7.1858 < 9.3415] w=0.9488 to align # Constraint # added constraint: constraint((T0291)F116.CB, (T0291)I160.CB) [> 3.5235 = 5.8724 < 7.6342] w=0.9425 to align # Constraint # added constraint: constraint((T0291)A210.CB, (T0291)R274.CB) [> 3.0383 = 5.0639 < 6.5830] w=0.9424 to align # Constraint # added constraint: constraint((T0291)S144.CB, (T0291)S209.CB) [> 2.8333 = 4.7221 < 6.1387] w=0.9424 to align # Constraint # added constraint: constraint((T0291)P199.CB, (T0291)W214.CB) [> 4.5526 = 7.5877 < 9.8641] w=0.9424 to align # Constraint # added constraint: constraint((T0291)D30.CB, (T0291)C42.CB) [> 3.9042 = 6.5070 < 8.4590] w=0.9424 to align # Constraint # added constraint: constraint((T0291)M224.CB, (T0291)L259.CB) [> 3.7852 = 6.3086 < 8.2012] w=0.9424 to align # Constraint # added constraint: constraint((T0291)L113.CB, (T0291)R156.CB) [> 4.5616 = 7.6027 < 9.8835] w=0.9424 to align # Constraint # added constraint: constraint((T0291)A77.CB, (T0291)V94.CB) [> 3.2981 = 5.4969 < 7.1460] w=0.9424 to align # Constraint # added constraint: constraint((T0291)N110.CB, (T0291)N161.CB) [> 3.8123 = 6.3538 < 8.2600] w=0.9424 to align # Constraint # added constraint: constraint((T0291)I58.CB, (T0291)I103.CB) [> 4.2227 = 7.0379 < 9.1492] w=0.9418 to align # Constraint # added constraint: constraint((T0291)I58.CB, (T0291)M102.CB) [> 3.5497 = 5.9161 < 7.6910] w=0.9418 to align # Constraint # added constraint: constraint((T0291)I89.CB, (T0291)M108.CB) [> 4.0126 = 6.6876 < 8.6939] w=0.9405 to align # Constraint # added constraint: constraint((T0291)M108.CB, (T0291)I160.CB) [> 3.8591 = 6.4319 < 8.3615] w=0.9405 to align # Constraint # added constraint: constraint((T0291)V213.CB, (T0291)P275.CB) [> 3.7317 = 6.2194 < 8.0852] w=0.9361 to align # Constraint # added constraint: constraint((T0291)V149.CB, (T0291)S209.CB) [> 3.3903 = 5.6505 < 7.3456] w=0.9360 to align # Constraint # added constraint: constraint((T0291)D30.CB, (T0291)S43.CB) [> 2.8186 = 4.6976 < 6.1069] w=0.9360 to align # Constraint # added constraint: constraint((T0291)K31.CB, (T0291)S43.CB) [> 2.9683 = 4.9472 < 6.4313] w=0.9296 to align # Constraint # added constraint: constraint((T0291)I88.CB, (T0291)Y142.CB) [> 4.1399 = 6.8998 < 8.9698] w=0.9233 to align # Constraint # added constraint: constraint((T0291)R195.CB, (T0291)I218.CB) [> 4.0994 = 6.8323 < 8.8820] w=0.9233 to align # Constraint # added constraint: constraint((T0291)M224.CB, (T0291)C255.CB) [> 3.1792 = 5.2986 < 6.8882] w=0.9232 to align # Constraint # added constraint: constraint((T0291)N26.CB, (T0291)L46.CB) [> 3.6618 = 6.1030 < 7.9339] w=0.9232 to align # Constraint # added constraint: constraint((T0291)S43.CB, (T0291)S55.CB) [> 4.1759 = 6.9599 < 9.0479] w=0.9168 to align # Constraint # added constraint: constraint((T0291)I158.CB, (T0291)S169.CB) [> 4.0997 = 6.8328 < 8.8827] w=0.9040 to align # Constraint # added constraint: constraint((T0291)G44.CA, (T0291)Y107.CB) [> 4.5860 = 7.6433 < 9.9363] w=0.9040 to align # Constraint # added constraint: constraint((T0291)N157.CB, (T0291)D170.CB) [> 2.6664 = 4.4440 < 5.7772] w=0.9040 to align # Constraint # added constraint: constraint((T0291)L117.CB, (T0291)E222.CB) [> 4.0817 = 6.8029 < 8.8437] w=0.9040 to align # Constraint # added constraint: constraint((T0291)L133.CB, (T0291)V223.CB) [> 3.9834 = 6.6389 < 8.6306] w=0.9021 to align # Constraint # added constraint: constraint((T0291)A137.CB, (T0291)F277.CB) [> 3.2837 = 5.4729 < 7.1147] w=0.8913 to align # Constraint # added constraint: constraint((T0291)R195.CB, (T0291)Y231.CB) [> 3.5650 = 5.9416 < 7.7241] w=0.8913 to align # Constraint # added constraint: constraint((T0291)P199.CB, (T0291)V243.CB) [> 3.3107 = 5.5178 < 7.1732] w=0.8906 to align # Constraint # added constraint: constraint((T0291)V56.CB, (T0291)V104.CB) [> 3.2678 = 5.4464 < 7.0803] w=0.8906 to align # Constraint # added constraint: constraint((T0291)K141.CB, (T0291)F277.CB) [> 2.4866 = 4.1444 < 5.3877] w=0.8849 to align # Constraint # added constraint: constraint((T0291)A137.CB, (T0291)I280.CB) [> 2.9697 = 4.9496 < 6.4345] w=0.8849 to align # Constraint # added constraint: constraint((T0291)D152.CB, (T0291)D170.CB) [> 3.7760 = 6.2933 < 8.1813] w=0.8849 to align # Constraint # added constraint: constraint((T0291)F83.CB, (T0291)L143.CB) [> 4.2595 = 7.0991 < 9.2289] w=0.8848 to align # Constraint # added constraint: constraint((T0291)F83.CB, (T0291)M146.CB) [> 3.9865 = 6.6442 < 8.6375] w=0.8848 to align # Constraint # added constraint: constraint((T0291)T208.CB, (T0291)R271.CB) [> 3.8617 = 6.4362 < 8.3670] w=0.8830 to align # Constraint # added constraint: constraint((T0291)I79.CB, (T0291)Y148.CB) [> 3.9614 = 6.6023 < 8.5830] w=0.8829 to align # Constraint # added constraint: constraint((T0291)A137.CB, (T0291)V281.CB) [> 3.0215 = 5.0358 < 6.5465] w=0.8785 to align # Constraint # added constraint: constraint((T0291)V95.CB, (T0291)V104.CB) [> 4.4106 = 7.3510 < 9.5563] w=0.8785 to align # Constraint # added constraint: constraint((T0291)G111.CA, (T0291)I160.CB) [> 3.3108 = 5.5180 < 7.1733] w=0.8765 to align # Constraint # added constraint: constraint((T0291)I218.CB, (T0291)P230.CB) [> 3.4850 = 5.8083 < 7.5508] w=0.8720 to align # Constraint # added constraint: constraint((T0291)T60.CB, (T0291)V101.CB) [> 4.1678 = 6.9463 < 9.0302] w=0.8714 to align # Constraint # added constraint: constraint((T0291)I158.CB, (T0291)V219.CB) [> 4.4019 = 7.3364 < 9.5374] w=0.8657 to align # Constraint # added constraint: constraint((T0291)M140.CB, (T0291)F277.CB) [> 2.9256 = 4.8759 < 6.3387] w=0.8657 to align # Constraint # added constraint: constraint((T0291)V213.CB, (T0291)I280.CB) [> 4.3125 = 7.1875 < 9.3438] w=0.8657 to align # Constraint # added constraint: constraint((T0291)A154.CB, (T0291)P193.CB) [> 3.5991 = 5.9985 < 7.7980] w=0.8656 to align # Constraint # added constraint: constraint((T0291)A77.CB, (T0291)L91.CB) [> 4.1507 = 6.9178 < 8.9931] w=0.8656 to align # Constraint # added constraint: constraint((T0291)I29.CB, (T0291)C42.CB) [> 3.0495 = 5.0825 < 6.6072] w=0.8656 to align # Constraint # added constraint: constraint((T0291)V149.CB, (T0291)T208.CB) [> 4.0185 = 6.6975 < 8.7067] w=0.8637 to align # Constraint # added constraint: constraint((T0291)L220.CB, (T0291)L259.CB) [> 4.1844 = 6.9741 < 9.0663] w=0.8637 to align # Constraint # added constraint: constraint((T0291)M108.CB, (T0291)N161.CB) [> 3.0693 = 5.1154 < 6.6501] w=0.8637 to align # Constraint # added constraint: constraint((T0291)S144.CB, (T0291)F277.CB) [> 3.3967 = 5.6612 < 7.3596] w=0.8593 to align # Constraint # added constraint: constraint((T0291)F73.CB, (T0291)V101.CB) [> 3.6843 = 6.1406 < 7.9827] w=0.8573 to align # Constraint # added constraint: constraint((T0291)I88.CB, (T0291)L143.CB) [> 4.3282 = 7.2136 < 9.3777] w=0.8465 to align # Constraint # added constraint: constraint((T0291)L262.CB, (T0291)I280.CB) [> 4.1580 = 6.9300 < 9.0091] w=0.8465 to align # Constraint # added constraint: constraint((T0291)H150.CB, (T0291)S215.CB) [> 4.5798 = 7.6330 < 9.9229] w=0.8464 to align # Constraint # added constraint: constraint((T0291)E76.CB, (T0291)G172.CA) [> 2.9369 = 4.8949 < 6.3634] w=0.8464 to align # Constraint # added constraint: constraint((T0291)D30.CB, (T0291)R45.CB) [> 3.9957 = 6.6596 < 8.6574] w=0.8400 to align # Constraint # added constraint: constraint((T0291)L153.CB, (T0291)V168.CB) [> 4.5036 = 7.5059 < 9.7577] w=0.8274 to align # Constraint # added constraint: constraint((T0291)D152.CB, (T0291)W196.CB) [> 4.4785 = 7.4641 < 9.7034] w=0.8273 to align # Constraint # added constraint: constraint((T0291)W196.CB, (T0291)V219.CB) [> 4.3715 = 7.2859 < 9.4716] w=0.8272 to align # Constraint # added constraint: constraint((T0291)H150.CB, (T0291)F171.CB) [> 3.9629 = 6.6048 < 8.5863] w=0.8272 to align # Constraint # added constraint: constraint((T0291)S138.CB, (T0291)V281.CB) [> 3.6046 = 6.0077 < 7.8100] w=0.8146 to align # Constraint # added constraint: constraint((T0291)T197.CB, (T0291)S215.CB) [> 4.4139 = 7.3564 < 9.5634] w=0.8082 to align # Constraint # added constraint: constraint((T0291)T197.CB, (T0291)S211.CB) [> 4.5222 = 7.5370 < 9.7981] w=0.8082 to align # Constraint # added constraint: constraint((T0291)V213.CB, (T0291)F277.CB) [> 3.9500 = 6.5833 < 8.5583] w=0.8082 to align # Constraint # added constraint: constraint((T0291)V213.CB, (T0291)K276.CB) [> 4.3013 = 7.1688 < 9.3195] w=0.8082 to align # Constraint # added constraint: constraint((T0291)V32.CB, (T0291)S43.CB) [> 4.6316 = 7.7193 < 10.0351] w=0.8080 to align # Constraint # added constraint: constraint((T0291)V126.CB, (T0291)P256.CB) [> 3.7276 = 6.2127 < 8.0765] w=0.8061 to align # Constraint # added constraint: constraint((T0291)N87.CB, (T0291)V165.CB) [> 4.2722 = 7.1203 < 9.2564] w=0.8017 to align # Constraint # added constraint: constraint((T0291)L117.CB, (T0291)G227.CA) [> 3.3281 = 5.5469 < 7.2110] w=0.7940 to align # Constraint # added constraint: constraint((T0291)I27.CB, (T0291)V104.CB) [> 4.2373 = 7.0621 < 9.1808] w=0.7933 to align # Constraint # added constraint: constraint((T0291)I202.CB, (T0291)I240.CB) [> 3.3155 = 5.5258 < 7.1836] w=0.7882 to align # Constraint # added constraint: constraint((T0291)R134.CB, (T0291)V281.CB) [> 4.0062 = 6.6771 < 8.6802] w=0.7826 to align # Constraint # added constraint: constraint((T0291)T60.CB, (T0291)P100.CB) [> 3.4446 = 5.7410 < 7.4633] w=0.7818 to align # Constraint # added constraint: constraint((T0291)E109.CB, (T0291)N161.CB) [> 3.9258 = 6.5430 < 8.5059] w=0.7805 to align # Constraint # added constraint: constraint((T0291)F83.CB, (T0291)Y142.CB) [> 4.4516 = 7.4194 < 9.6452] w=0.7762 to align # Constraint # added constraint: constraint((T0291)G147.CA, (T0291)S209.CB) [> 4.2706 = 7.1177 < 9.2530] w=0.7760 to align # Constraint # added constraint: constraint((T0291)V41.CB, (T0291)I58.CB) [> 4.1584 = 6.9307 < 9.0100] w=0.7754 to align # Constraint # added constraint: constraint((T0291)V41.CB, (T0291)K59.CB) [> 3.0621 = 5.1034 < 6.6345] w=0.7754 to align # Constraint # added constraint: constraint((T0291)G44.CA, (T0291)V56.CB) [> 3.2969 = 5.4948 < 7.1433] w=0.7754 to align # Constraint # added constraint: constraint((T0291)G44.CA, (T0291)A57.CB) [> 4.4188 = 7.3646 < 9.5740] w=0.7754 to align # Constraint # added constraint: constraint((T0291)A57.CB, (T0291)V104.CB) [> 4.4373 = 7.3955 < 9.6142] w=0.7754 to align # Constraint # added constraint: constraint((T0291)I58.CB, (T0291)V104.CB) [> 3.2312 = 5.3853 < 7.0009] w=0.7754 to align # Constraint # added constraint: constraint((T0291)K59.CB, (T0291)M102.CB) [> 4.1711 = 6.9517 < 9.0373] w=0.7754 to align # Constraint # added constraint: constraint((T0291)V33.CB, (T0291)A57.CB) [> 3.9436 = 6.5727 < 8.5445] w=0.7690 to align # Constraint # added constraint: constraint((T0291)G44.CA, (T0291)I58.CB) [> 3.5453 = 5.9089 < 7.6815] w=0.7690 to align # Constraint # added constraint: constraint((T0291)V56.CB, (T0291)E92.CB) [> 3.7244 = 6.2074 < 8.0696] w=0.7690 to align # Constraint # added constraint: constraint((T0291)K59.CB, (T0291)I103.CB) [> 2.6147 = 4.3578 < 5.6651] w=0.7690 to align # Constraint # added constraint: constraint((T0291)K141.CB, (T0291)E278.CB) [> 3.2466 = 5.4110 < 7.0343] w=0.7634 to align # Constraint # added constraint: constraint((T0291)I29.CB, (T0291)S43.CB) [> 4.5208 = 7.5346 < 9.7950] w=0.7632 to align # Constraint # added constraint: constraint((T0291)I194.CB, (T0291)V239.CB) [> 3.3720 = 5.6200 < 7.3060] w=0.7627 to align # Constraint # added constraint: constraint((T0291)L46.CB, (T0291)V56.CB) [> 3.2932 = 5.4886 < 7.1352] w=0.7626 to align # Constraint # added constraint: constraint((T0291)R45.CB, (T0291)S55.CB) [> 3.4896 = 5.8160 < 7.5608] w=0.7626 to align # Constraint # added constraint: constraint((T0291)S55.CB, (T0291)Y107.CB) [> 2.8104 = 4.6839 < 6.0891] w=0.7626 to align # Constraint # added constraint: constraint((T0291)V56.CB, (T0291)E106.CB) [> 4.1171 = 6.8619 < 8.9205] w=0.7626 to align # Constraint # added constraint: constraint((T0291)A57.CB, (T0291)T105.CB) [> 3.0712 = 5.1186 < 6.6542] w=0.7626 to align # Constraint # added constraint: constraint((T0291)R45.CB, (T0291)I54.CB) [> 4.1961 = 6.9936 < 9.0916] w=0.7626 to align # Constraint # added constraint: constraint((T0291)T60.CB, (T0291)M102.CB) [> 3.3762 = 5.6269 < 7.3150] w=0.7626 to align # Constraint # added constraint: constraint((T0291)R195.CB, (T0291)R229.CB) [> 3.6529 = 6.0882 < 7.9147] w=0.7569 to align # Constraint # added constraint: constraint((T0291)K59.CB, (T0291)T105.CB) [> 4.1127 = 6.8544 < 8.9108] w=0.7563 to align # Constraint # added constraint: constraint((T0291)A57.CB, (T0291)E106.CB) [> 4.1471 = 6.9118 < 8.9854] w=0.7563 to align # Constraint # added constraint: constraint((T0291)S225.CB, (T0291)P252.CB) [> 3.1964 = 5.3274 < 6.9256] w=0.7549 to align # Constraint # added constraint: constraint((T0291)D212.CB, (T0291)F277.CB) [> 4.5297 = 7.5494 < 9.8142] w=0.7506 to align # Constraint # added constraint: constraint((T0291)L113.CB, (T0291)V223.CB) [> 4.4929 = 7.4881 < 9.7346] w=0.7505 to align # Constraint # added constraint: constraint((T0291)S43.CB, (T0291)A57.CB) [> 3.8925 = 6.4875 < 8.4338] w=0.7499 to align # Constraint # added constraint: constraint((T0291)W221.CB, (T0291)P230.CB) [> 3.3341 = 5.5568 < 7.2238] w=0.7499 to align # Constraint # added constraint: constraint((T0291)E109.CB, (T0291)S162.CB) [> 3.2631 = 5.4386 < 7.0701] w=0.7485 to align # Constraint # added constraint: constraint((T0291)C42.CB, (T0291)I58.CB) [> 3.0107 = 5.0179 < 6.5233] w=0.7435 to align # Constraint # added constraint: constraint((T0291)W221.CB, (T0291)L249.CB) [> 3.6795 = 6.1325 < 7.9722] w=0.7422 to align # Constraint # added constraint: constraint((T0291)L61.CB, (T0291)V101.CB) [> 2.8068 = 4.6781 < 6.0815] w=0.7422 to align # Constraint # added constraint: constraint((T0291)L143.CB, (T0291)V168.CB) [> 4.3949 = 7.3249 < 9.5224] w=0.7314 to align # Constraint # added constraint: constraint((T0291)R151.CB, (T0291)G174.CA) [> 3.2002 = 5.3336 < 6.9337] w=0.7313 to align # Constraint # added constraint: constraint((T0291)L262.CB, (T0291)I283.CB) [> 3.4613 = 5.7689 < 7.4996] w=0.7307 to align # Constraint # added constraint: constraint((T0291)R45.CB, (T0291)V56.CB) [> 4.2862 = 7.1437 < 9.2869] w=0.7307 to align # Constraint # added constraint: constraint((T0291)C42.CB, (T0291)T60.CB) [> 4.1692 = 6.9486 < 9.0332] w=0.7307 to align # Constraint # added constraint: constraint((T0291)A155.CB, (T0291)V223.CB) [> 4.2183 = 7.0305 < 9.1397] w=0.7293 to align # Constraint # added constraint: constraint((T0291)L143.CB, (T0291)D212.CB) [> 4.6164 = 7.6940 < 10.0023] w=0.7293 to align # Constraint # added constraint: constraint((T0291)P251.CB, (T0291)Y260.CB) [> 2.9325 = 4.8875 < 6.3538] w=0.7229 to align # Constraint # added constraint: constraint((T0291)E40.CB, (T0291)T60.CB) [> 3.1685 = 5.2808 < 6.8651] w=0.7179 to align # Constraint # added constraint: constraint((T0291)P86.CB, (T0291)V165.CB) [> 4.3403 = 7.2339 < 9.4041] w=0.7121 to align # Constraint # added constraint: constraint((T0291)D152.CB, (T0291)G174.CA) [> 4.2434 = 7.0724 < 9.1941] w=0.7121 to align # Constraint # added constraint: constraint((T0291)H150.CB, (T0291)G174.CA) [> 3.5125 = 5.8541 < 7.6103] w=0.7121 to align # Constraint # added constraint: constraint((T0291)R195.CB, (T0291)V239.CB) [> 3.7441 = 6.2402 < 8.1123] w=0.7115 to align # Constraint # added constraint: constraint((T0291)G39.CA, (T0291)T60.CB) [> 3.5413 = 5.9021 < 7.6727] w=0.7115 to align # Constraint # added constraint: constraint((T0291)A154.CB, (T0291)I218.CB) [> 4.4017 = 7.3362 < 9.5370] w=0.7102 to align # Constraint # added constraint: constraint((T0291)I136.CB, (T0291)L153.CB) [> 4.5242 = 7.5403 < 9.8025] w=0.7102 to align # Constraint # added constraint: constraint((T0291)R195.CB, (T0291)P230.CB) [> 3.3114 = 5.5189 < 7.1746] w=0.7058 to align # Constraint # added constraint: constraint((T0291)Y216.CB, (T0291)I280.CB) [> 4.2582 = 7.0970 < 9.2261] w=0.7038 to align # Constraint # added constraint: constraint((T0291)D152.CB, (T0291)P193.CB) [> 3.7120 = 6.1867 < 8.0427] w=0.7038 to align # Constraint # added constraint: constraint((T0291)S43.CB, (T0291)V56.CB) [> 4.6222 = 7.7036 < 10.0147] w=0.6987 to align # Constraint # added constraint: constraint((T0291)I202.CB, (T0291)V243.CB) [> 3.7931 = 6.3218 < 8.2184] w=0.6986 to align # Constraint # added constraint: constraint((T0291)M80.CB, (T0291)T105.CB) [> 4.4478 = 7.4130 < 9.6369] w=0.6974 to align # Constraint # added constraint: constraint((T0291)T197.CB, (T0291)W214.CB) [> 4.5735 = 7.6226 < 9.9093] w=0.6930 to align # Constraint # added constraint: constraint((T0291)F83.CB, (T0291)Y148.CB) [> 4.2648 = 7.1080 < 9.2403] w=0.6930 to align # Constraint # added constraint: constraint((T0291)D152.CB, (T0291)S215.CB) [> 4.5984 = 7.6639 < 9.9631] w=0.6930 to align # Constraint # added constraint: constraint((T0291)D152.CB, (T0291)L173.CB) [> 2.8772 = 4.7954 < 6.2340] w=0.6929 to align # Constraint # added constraint: constraint((T0291)Y148.CB, (T0291)R175.CB) [> 4.1786 = 6.9643 < 9.0536] w=0.6929 to align # Constraint # added constraint: constraint((T0291)A57.CB, (T0291)M108.CB) [> 4.4207 = 7.3679 < 9.5783] w=0.6910 to align # Constraint # added constraint: constraint((T0291)I27.CB, (T0291)V56.CB) [> 4.4387 = 7.3979 < 9.6172] w=0.6859 to align # Constraint # added constraint: constraint((T0291)F38.CB, (T0291)L61.CB) [> 3.4316 = 5.7194 < 7.4352] w=0.6846 to align # Constraint # added constraint: constraint((T0291)G39.CA, (T0291)L61.CB) [> 3.3048 = 5.5080 < 7.1604] w=0.6782 to align # Constraint # added constraint: constraint((T0291)V41.CB, (T0291)T60.CB) [> 4.5157 = 7.5262 < 9.7841] w=0.6731 to align # Constraint # added constraint: constraint((T0291)G217.CA, (T0291)L262.CB) [> 4.5001 = 7.5002 < 9.7503] w=0.6719 to align # Constraint # added constraint: constraint((T0291)L46.CB, (T0291)V104.CB) [> 4.1218 = 6.8697 < 8.9306] w=0.6718 to align # Constraint # added constraint: constraint((T0291)E40.CB, (T0291)K59.CB) [> 4.4334 = 7.3889 < 9.6056] w=0.6603 to align # Constraint # added constraint: constraint((T0291)G39.CA, (T0291)K62.CB) [> 3.5705 = 5.9508 < 7.7361] w=0.6590 to align # Constraint # added constraint: constraint((T0291)I79.CB, (T0291)G174.CA) [> 3.7275 = 6.2125 < 8.0763] w=0.6590 to align # Constraint # added constraint: constraint((T0291)I79.CB, (T0291)F171.CB) [> 3.0661 = 5.1101 < 6.6432] w=0.6590 to align # Constraint # added constraint: constraint((T0291)M132.CB, (T0291)I158.CB) [> 4.5152 = 7.5254 < 9.7830] w=0.6545 to align # Constraint # added constraint: constraint((T0291)I194.CB, (T0291)N236.CB) [> 2.9152 = 4.8586 < 6.3162] w=0.6539 to align # Constraint # added constraint: constraint((T0291)L22.CB, (T0291)V95.CB) [> 3.1732 = 5.2886 < 6.8752] w=0.6526 to align # Constraint # added constraint: constraint((T0291)D152.CB, (T0291)G172.CA) [> 4.1067 = 6.8446 < 8.8979] w=0.6526 to align # Constraint # added constraint: constraint((T0291)R151.CB, (T0291)L173.CB) [> 2.7493 = 4.5821 < 5.9568] w=0.6526 to align # Constraint # added constraint: constraint((T0291)V149.CB, (T0291)G174.CA) [> 3.6201 = 6.0335 < 7.8435] w=0.6526 to align # Constraint # added constraint: constraint((T0291)Y148.CB, (T0291)G174.CA) [> 3.8216 = 6.3694 < 8.2802] w=0.6526 to align # Constraint # added constraint: constraint((T0291)S198.CB, (T0291)F207.CB) [> 4.2579 = 7.0965 < 9.2255] w=0.6525 to align # Constraint # added constraint: constraint((T0291)G93.CA, (T0291)T105.CB) [> 4.6683 = 7.7805 < 10.1146] w=0.6481 to align # Constraint # added constraint: constraint((T0291)Y231.CB, (T0291)A242.CB) [> 3.5488 = 5.9147 < 7.6891] w=0.6411 to align # Constraint # added constraint: constraint((T0291)E76.CB, (T0291)I103.CB) [> 4.2389 = 7.0648 < 9.1842] w=0.6398 to align # Constraint # added constraint: constraint((T0291)P199.CB, (T0291)D244.CB) [> 3.4381 = 5.7301 < 7.4491] w=0.6398 to align # Constraint # added constraint: constraint((T0291)G139.CA, (T0291)F277.CB) [> 4.5704 = 7.6174 < 9.9026] w=0.6354 to align # Constraint # added constraint: constraint((T0291)L159.CB, (T0291)V168.CB) [> 4.6480 = 7.7467 < 10.0708] w=0.6353 to align # Constraint # added constraint: constraint((T0291)L129.CB, (T0291)L220.CB) [> 4.0747 = 6.7912 < 8.8286] w=0.6353 to align # Constraint # added constraint: constraint((T0291)M140.CB, (T0291)V213.CB) [> 4.5222 = 7.5370 < 9.7980] w=0.6353 to align # Constraint # added constraint: constraint((T0291)I29.CB, (T0291)I58.CB) [> 3.9996 = 6.6659 < 8.6657] w=0.6347 to align # Constraint # added constraint: constraint((T0291)L249.CB, (T0291)M263.CB) [> 4.4163 = 7.3606 < 9.5687] w=0.6334 to align # Constraint # added constraint: constraint((T0291)I58.CB, (T0291)T105.CB) [> 4.6013 = 7.6689 < 9.9696] w=0.6334 to align # Constraint # added constraint: constraint((T0291)L262.CB, (T0291)P275.CB) [> 4.4544 = 7.4240 < 9.6513] w=0.6289 to align # Constraint # added constraint: constraint((T0291)S43.CB, (T0291)I58.CB) [> 4.6133 = 7.6889 < 9.9956] w=0.6283 to align # Constraint # added constraint: constraint((T0291)L61.CB, (T0291)F73.CB) [> 3.4882 = 5.8137 < 7.5578] w=0.6270 to align # Constraint # added constraint: constraint((T0291)M80.CB, (T0291)I103.CB) [> 4.4167 = 7.3612 < 9.5696] w=0.6206 to align # Constraint # added constraint: constraint((T0291)I218.CB, (T0291)W267.CB) [> 4.4961 = 7.4935 < 9.7415] w=0.6161 to align # Constraint # added constraint: constraint((T0291)E106.CB, (T0291)K167.CB) [> 4.4125 = 7.3541 < 9.5603] w=0.6161 to align # Constraint # added constraint: constraint((T0291)L22.CB, (T0291)V104.CB) [> 3.8235 = 6.3725 < 8.2842] w=0.6142 to align # Constraint # added constraint: constraint((T0291)Y148.CB, (T0291)V176.CB) [> 3.4304 = 5.7174 < 7.4326] w=0.6142 to align # Constraint # added constraint: constraint((T0291)L117.CB, (T0291)Y226.CB) [> 3.1659 = 5.2765 < 6.8594] w=0.6091 to align # Constraint # added constraint: constraint((T0291)Q82.CB, (T0291)M146.CB) [> 4.1513 = 6.9188 < 8.9944] w=0.6079 to align # Constraint # added constraint: constraint((T0291)L22.CB, (T0291)G93.CA) [> 3.3053 = 5.5088 < 7.1615] w=0.6078 to align # Constraint # added constraint: constraint((T0291)Y216.CB, (T0291)F277.CB) [> 4.4239 = 7.3732 < 9.5852] w=0.5951 to align # Constraint # added constraint: constraint((T0291)V149.CB, (T0291)F207.CB) [> 3.5240 = 5.8733 < 7.6352] w=0.5951 to align # Constraint # added constraint: constraint((T0291)H150.CB, (T0291)L173.CB) [> 4.3325 = 7.2209 < 9.3871] w=0.5950 to align # Constraint # added constraint: constraint((T0291)L61.CB, (T0291)P100.CB) [> 3.8763 = 6.4604 < 8.3985] w=0.5886 to align # Constraint # added constraint: constraint((T0291)V130.CB, (T0291)L259.CB) [> 4.4542 = 7.4236 < 9.6507] w=0.5778 to align # Constraint # added constraint: constraint((T0291)W196.CB, (T0291)W214.CB) [> 4.6149 = 7.6915 < 9.9989] w=0.5778 to align # Constraint # added constraint: constraint((T0291)P86.CB, (T0291)K167.CB) [> 4.6648 = 7.7746 < 10.1070] w=0.5778 to align # Constraint # added constraint: constraint((T0291)L133.CB, (T0291)Y216.CB) [> 4.3963 = 7.3272 < 9.5254] w=0.5777 to align # Constraint # added constraint: constraint((T0291)L46.CB, (T0291)S55.CB) [> 4.6413 = 7.7356 < 10.0562] w=0.5707 to align # Constraint # added constraint: constraint((T0291)R134.CB, (T0291)L284.CB) [> 2.7762 = 4.6270 < 6.0152] w=0.5695 to align # Constraint # added constraint: constraint((T0291)V126.CB, (T0291)M224.CB) [> 4.2193 = 7.0321 < 9.1418] w=0.5585 to align # Constraint # added constraint: constraint((T0291)M108.CB, (T0291)S169.CB) [> 4.5199 = 7.5331 < 9.7931] w=0.5566 to align # Constraint # added constraint: constraint((T0291)L133.CB, (T0291)V219.CB) [> 4.4994 = 7.4990 < 9.7487] w=0.5566 to align # Constraint # added constraint: constraint((T0291)V126.CB, (T0291)L259.CB) [> 3.8767 = 6.4611 < 8.3994] w=0.5566 to align # Constraint # added constraint: constraint((T0291)N26.CB, (T0291)K47.CB) [> 3.0864 = 5.1440 < 6.6872] w=0.5509 to align # Constraint # added constraint: constraint((T0291)L133.CB, (T0291)L284.CB) [> 3.5152 = 5.8587 < 7.6164] w=0.5439 to align # Constraint # added constraint: constraint((T0291)V130.CB, (T0291)L284.CB) [> 3.6247 = 6.0411 < 7.8535] w=0.5439 to align # Constraint # added constraint: constraint((T0291)A24.CB, (T0291)M102.CB) [> 4.1085 = 6.8476 < 8.9018] w=0.5438 to align # Constraint # added constraint: constraint((T0291)M224.CB, (T0291)P252.CB) [> 3.1378 = 5.2297 < 6.7986] w=0.5438 to align # Constraint # added constraint: constraint((T0291)A154.CB, (T0291)R195.CB) [> 4.4717 = 7.4528 < 9.6887] w=0.5393 to align # Constraint # added constraint: constraint((T0291)V130.CB, (T0291)L287.CB) [> 3.4555 = 5.7592 < 7.4870] w=0.5375 to align # Constraint # added constraint: constraint((T0291)R151.CB, (T0291)F207.CB) [> 3.2570 = 5.4284 < 7.0569] w=0.5375 to align # Constraint # added constraint: constraint((T0291)A137.CB, (T0291)L284.CB) [> 3.7300 = 6.2167 < 8.0817] w=0.5311 to align # Constraint # added constraint: constraint((T0291)I218.CB, (T0291)R229.CB) [> 3.7186 = 6.1976 < 8.0569] w=0.5265 to align # Constraint # added constraint: constraint((T0291)G147.CA, (T0291)L177.CB) [> 3.2867 = 5.4779 < 7.1212] w=0.5246 to align # Constraint # added constraint: constraint((T0291)F38.CB, (T0291)K62.CB) [> 3.7667 = 6.2779 < 8.1612] w=0.5182 to align # Constraint # added constraint: constraint((T0291)S225.CB, (T0291)C255.CB) [> 4.3878 = 7.3130 < 9.5068] w=0.5182 to align # Constraint # added constraint: constraint((T0291)I79.CB, (T0291)V176.CB) [> 4.1613 = 6.9354 < 9.0160] w=0.5182 to align # Constraint # added constraint: constraint((T0291)I194.CB, (T0291)I240.CB) [> 3.9141 = 6.5235 < 8.4805] w=0.5055 to align # Constraint # added constraint: constraint((T0291)A154.CB, (T0291)E222.CB) [> 4.3881 = 7.3135 < 9.5075] w=0.4991 to align # Constraint # added constraint: constraint((T0291)L46.CB, (T0291)E92.CB) [> 4.1854 = 6.9757 < 9.0684] w=0.4991 to align # Constraint # added constraint: constraint((T0291)I27.CB, (T0291)M102.CB) [> 4.3259 = 7.2098 < 9.3727] w=0.4991 to align # Constraint # added constraint: constraint((T0291)V149.CB, (T0291)L177.CB) [> 3.6574 = 6.0956 < 7.9243] w=0.4990 to align # Constraint # added constraint: constraint((T0291)L61.CB, (T0291)M102.CB) [> 4.5361 = 7.5601 < 9.8282] w=0.4990 to align # Constraint # added constraint: constraint((T0291)V130.CB, (T0291)I288.CB) [> 3.3114 = 5.5189 < 7.1746] w=0.4927 to align # Constraint # added constraint: constraint((T0291)F73.CB, (T0291)I103.CB) [> 4.2526 = 7.0877 < 9.2140] w=0.4863 to align # Constraint # added constraint: constraint((T0291)P251.CB, (T0291)M263.CB) [> 4.3138 = 7.1897 < 9.3466] w=0.4862 to align # Constraint # added constraint: constraint((T0291)Q128.CB, (T0291)L164.CB) [> 4.1230 = 6.8717 < 8.9332] w=0.4818 to align # Constraint # added constraint: constraint((T0291)E200.CB, (T0291)A210.CB) [> 4.5530 = 7.5883 < 9.8649] w=0.4817 to align # Constraint # added constraint: constraint((T0291)F38.CB, (T0291)F73.CB) [> 4.1143 = 6.8571 < 8.9142] w=0.4798 to align # Constraint # added constraint: constraint((T0291)H85.CB, (T0291)L143.CB) [> 4.6575 = 7.7625 < 10.0913] w=0.4753 to align # Constraint # added constraint: constraint((T0291)I54.CB, (T0291)Y107.CB) [> 3.6586 = 6.0977 < 7.9271] w=0.4741 to align # Constraint # added constraint: constraint((T0291)G131.CA, (T0291)L284.CB) [> 4.3901 = 7.3169 < 9.5119] w=0.4671 to align # Constraint # added constraint: constraint((T0291)A258.CB, (T0291)L287.CB) [> 3.5338 = 5.8898 < 7.6567] w=0.4671 to align # Constraint # added constraint: constraint((T0291)T105.CB, (T0291)S169.CB) [> 4.4287 = 7.3811 < 9.5955] w=0.4626 to align # Constraint # added constraint: constraint((T0291)Y148.CB, (T0291)L177.CB) [> 4.3143 = 7.1906 < 9.3477] w=0.4607 to align # Constraint # added constraint: constraint((T0291)A203.CB, (T0291)D244.CB) [> 3.7966 = 6.3277 < 8.2260] w=0.4606 to align # Constraint # added constraint: constraint((T0291)D152.CB, (T0291)I192.CB) [> 3.3176 = 5.5294 < 7.1882] w=0.4562 to align # Constraint # added constraint: constraint((T0291)M80.CB, (T0291)R90.CB) [> 4.5450 = 7.5749 < 9.8474] w=0.4543 to align # Constraint # added constraint: constraint((T0291)I192.CB, (T0291)A201.CB) [> 4.0143 = 6.6905 < 8.6976] w=0.4543 to align # Constraint # added constraint: constraint((T0291)M80.CB, (T0291)I89.CB) [> 4.4638 = 7.4397 < 9.6716] w=0.4543 to align # Constraint # added constraint: constraint((T0291)F83.CB, (T0291)F171.CB) [> 4.5705 = 7.6175 < 9.9028] w=0.4497 to align # Constraint # added constraint: constraint((T0291)S28.CB, (T0291)K47.CB) [> 3.9653 = 6.6089 < 8.5915] w=0.4421 to align # Constraint # added constraint: constraint((T0291)R156.CB, (T0291)D170.CB) [> 4.6779 = 7.7965 < 10.1355] w=0.4415 to align # Constraint # added constraint: constraint((T0291)L129.CB, (T0291)L259.CB) [> 4.2863 = 7.1439 < 9.2871] w=0.4415 to align # Constraint # added constraint: constraint((T0291)R118.CB, (T0291)Y226.CB) [> 3.8960 = 6.4934 < 8.4414] w=0.4415 to align # Constraint # added constraint: constraint((T0291)A24.CB, (T0291)K97.CB) [> 3.6269 = 6.0449 < 7.8583] w=0.4415 to align # Constraint # added constraint: constraint((T0291)W221.CB, (T0291)P252.CB) [> 3.7413 = 6.2355 < 8.1062] w=0.4351 to align # Constraint # added constraint: constraint((T0291)R151.CB, (T0291)I192.CB) [> 3.5808 = 5.9681 < 7.7585] w=0.4351 to align # Constraint # added constraint: constraint((T0291)G131.CA, (T0291)C166.CB) [> 4.6261 = 7.7101 < 10.0232] w=0.4242 to align # Constraint # added constraint: constraint((T0291)K59.CB, (T0291)V104.CB) [> 4.6888 = 7.8146 < 10.1590] w=0.4235 to align # Constraint # added constraint: constraint((T0291)W196.CB, (T0291)P230.CB) [> 4.1912 = 6.9854 < 9.0810] w=0.4223 to align # Constraint # added constraint: constraint((T0291)R248.CB, (T0291)L264.CB) [> 4.0732 = 6.7887 < 8.8254] w=0.4223 to align # Constraint # added constraint: constraint((T0291)G131.CA, (T0291)I288.CB) [> 3.5177 = 5.8629 < 7.6217] w=0.4223 to align # Constraint # added constraint: constraint((T0291)R70.CB, (T0291)V101.CB) [> 3.7520 = 6.2533 < 8.1292] w=0.4166 to align # Constraint # added constraint: constraint((T0291)L61.CB, (T0291)I103.CB) [> 4.3569 = 7.2615 < 9.4400] w=0.4095 to align # Constraint # added constraint: constraint((T0291)F38.CB, (T0291)K59.CB) [> 4.1092 = 6.8487 < 8.9033] w=0.4044 to align # Constraint # added constraint: constraint((T0291)T197.CB, (T0291)V243.CB) [> 3.9994 = 6.6657 < 8.6655] w=0.4030 to align # Constraint # added constraint: constraint((T0291)K62.CB, (T0291)P100.CB) [> 3.6534 = 6.0891 < 7.9158] w=0.3966 to align # Constraint # added constraint: constraint((T0291)M132.CB, (T0291)I160.CB) [> 4.5571 = 7.5951 < 9.8736] w=0.3858 to align # Constraint # added constraint: constraint((T0291)L113.CB, (T0291)V219.CB) [> 4.4616 = 7.4360 < 9.6668] w=0.3858 to align # Constraint # added constraint: constraint((T0291)I218.CB, (T0291)L249.CB) [> 4.3020 = 7.1700 < 9.3209] w=0.3839 to align # Constraint # added constraint: constraint((T0291)I88.CB, (T0291)S169.CB) [> 4.4039 = 7.3397 < 9.5417] w=0.3839 to align # Constraint # added constraint: constraint((T0291)F124.CB, (T0291)Y226.CB) [> 4.3234 = 7.2056 < 9.3673] w=0.3839 to align # Constraint # added constraint: constraint((T0291)Y231.CB, (T0291)V243.CB) [> 3.6248 = 6.0414 < 7.8538] w=0.3787 to align # Constraint # added constraint: constraint((T0291)V63.CB, (T0291)P100.CB) [> 3.8202 = 6.3670 < 8.2771] w=0.3775 to align # Constraint # added constraint: constraint((T0291)A155.CB, (T0291)G227.CA) [> 3.7238 = 6.2064 < 8.0683] w=0.3711 to align # Constraint # added constraint: constraint((T0291)L173.CB, (T0291)I192.CB) [> 4.0570 = 6.7617 < 8.7902] w=0.3711 to align # Constraint # added constraint: constraint((T0291)I79.CB, (T0291)G172.CA) [> 4.1841 = 6.9735 < 9.0655] w=0.3711 to align # Constraint # added constraint: constraint((T0291)L91.CB, (T0291)E106.CB) [> 4.6549 = 7.7582 < 10.0857] w=0.3666 to align # Constraint # added constraint: constraint((T0291)I202.CB, (T0291)V239.CB) [> 3.5697 = 5.9495 < 7.7344] w=0.3666 to align # Constraint # added constraint: constraint((T0291)G135.CA, (T0291)V165.CB) [> 4.4632 = 7.4387 < 9.6703] w=0.3647 to align # Constraint # added constraint: constraint((T0291)F38.CB, (T0291)Y65.CB) [> 3.5646 = 5.9409 < 7.7232] w=0.3647 to align # Constraint # added constraint: constraint((T0291)I27.CB, (T0291)V95.CB) [> 4.0911 = 6.8185 < 8.8640] w=0.3519 to align # Constraint # added constraint: constraint((T0291)L259.CB, (T0291)L287.CB) [> 3.9908 = 6.6513 < 8.6468] w=0.3519 to align # Constraint # added constraint: constraint((T0291)L61.CB, (T0291)R70.CB) [> 3.7544 = 6.2574 < 8.1346] w=0.3519 to align # Constraint # added constraint: constraint((T0291)V63.CB, (T0291)K99.CB) [> 3.5264 = 5.8774 < 7.6406] w=0.3519 to align # Constraint # added constraint: constraint((T0291)L173.CB, (T0291)K191.CB) [> 3.2334 = 5.3891 < 7.0058] w=0.3519 to align # Constraint # added constraint: constraint((T0291)Y148.CB, (T0291)F171.CB) [> 4.4084 = 7.3474 < 9.5516] w=0.3474 to align # Constraint # added constraint: constraint((T0291)V126.CB, (T0291)C255.CB) [> 4.2901 = 7.1501 < 9.2951] w=0.3474 to align # Constraint # added constraint: constraint((T0291)W221.CB, (T0291)W267.CB) [> 4.4488 = 7.4146 < 9.6390] w=0.3455 to align # Constraint # added constraint: constraint((T0291)I127.CB, (T0291)I288.CB) [> 4.1563 = 6.9272 < 9.0054] w=0.3391 to align # Constraint # added constraint: constraint((T0291)T187.CB, (T0291)F207.CB) [> 3.6420 = 6.0699 < 7.8909] w=0.3390 to align # Constraint # added constraint: constraint((T0291)R195.CB, (T0291)W232.CB) [> 3.8398 = 6.3997 < 8.3196] w=0.3340 to align # Constraint # added constraint: constraint((T0291)R151.CB, (T0291)A201.CB) [> 4.5111 = 7.5184 < 9.7740] w=0.3283 to align # Constraint # added constraint: constraint((T0291)L177.CB, (T0291)T208.CB) [> 4.1873 = 6.9788 < 9.0724] w=0.3263 to align # Constraint # added constraint: constraint((T0291)R151.CB, (T0291)K191.CB) [> 3.3221 = 5.5369 < 7.1980] w=0.3199 to align # Constraint # added constraint: constraint((T0291)I192.CB, (T0291)S215.CB) [> 4.3859 = 7.3098 < 9.5028] w=0.3199 to align # Constraint # added constraint: constraint((T0291)W221.CB, (T0291)P251.CB) [> 4.4789 = 7.4649 < 9.7044] w=0.3198 to align # Constraint # added constraint: constraint((T0291)R195.CB, (T0291)N236.CB) [> 4.1812 = 6.9686 < 9.0592] w=0.3135 to align # Constraint # added constraint: constraint((T0291)Q82.CB, (T0291)Y148.CB) [> 4.3946 = 7.3244 < 9.5217] w=0.3135 to align # Constraint # added constraint: constraint((T0291)M108.CB, (T0291)S162.CB) [> 4.5347 = 7.5578 < 9.8251] w=0.3071 to align # Constraint # added constraint: constraint((T0291)A258.CB, (T0291)I283.CB) [> 4.0188 = 6.6980 < 8.7074] w=0.3020 to align # Constraint # added constraint: constraint((T0291)I54.CB, (T0291)E106.CB) [> 4.2195 = 7.0325 < 9.1422] w=0.3013 to align # Constraint # added constraint: constraint((T0291)D152.CB, (T0291)K191.CB) [> 4.2954 = 7.1589 < 9.3066] w=0.3007 to align # Constraint # added constraint: constraint((T0291)R156.CB, (T0291)P193.CB) [> 4.6459 = 7.7432 < 10.0661] w=0.2961 to align # Constraint # added constraint: constraint((T0291)P199.CB, (T0291)I240.CB) [> 4.2034 = 7.0057 < 9.1073] w=0.2956 to align # Constraint # added constraint: constraint((T0291)G93.CA, (T0291)M102.CB) [> 4.6325 = 7.7208 < 10.0371] w=0.2942 to align # Constraint # added constraint: constraint((T0291)G131.CA, (T0291)L164.CB) [> 4.3800 = 7.3000 < 9.4900] w=0.2898 to align # Constraint # added constraint: constraint((T0291)M132.CB, (T0291)L164.CB) [> 4.3143 = 7.1905 < 9.3476] w=0.2879 to align # Constraint # added constraint: constraint((T0291)F38.CB, (T0291)D72.CB) [> 4.1827 = 6.9712 < 9.0626] w=0.2879 to align # Constraint # added constraint: constraint((T0291)I218.CB, (T0291)C266.CB) [> 4.7319 = 7.8866 < 10.2526] w=0.2879 to align # Constraint # added constraint: constraint((T0291)T60.CB, (T0291)I103.CB) [> 4.6671 = 7.7786 < 10.1121] w=0.2879 to align # Constraint # added constraint: constraint((T0291)Q261.CB, (T0291)I283.CB) [> 4.4539 = 7.4231 < 9.6501] w=0.2764 to align # Constraint # added constraint: constraint((T0291)A203.CB, (T0291)I240.CB) [> 4.0979 = 6.8298 < 8.8787] w=0.2764 to align # Constraint # added constraint: constraint((T0291)I194.CB, (T0291)S235.CB) [> 3.6336 = 6.0560 < 7.8728] w=0.2706 to align # Constraint # added constraint: constraint((T0291)T186.CB, (T0291)T208.CB) [> 3.7724 = 6.2873 < 8.1735] w=0.2687 to align # Constraint # added constraint: constraint((T0291)P86.CB, (T0291)G139.CA) [> 4.6014 = 7.6691 < 9.9698] w=0.2643 to align # Constraint # added constraint: constraint((T0291)H120.CB, (T0291)Y226.CB) [> 4.1044 = 6.8407 < 8.8929] w=0.2636 to align # Constraint # added constraint: constraint((T0291)A57.CB, (T0291)I89.CB) [> 4.6575 = 7.7625 < 10.0913] w=0.2623 to align # Constraint # added constraint: constraint((T0291)K191.CB, (T0291)A201.CB) [> 3.9708 = 6.6181 < 8.6035] w=0.2623 to align # Constraint # added constraint: constraint((T0291)P199.CB, (T0291)G246.CA) [> 4.1765 = 6.9609 < 9.0492] w=0.2623 to align # Constraint # added constraint: constraint((T0291)E106.CB, (T0291)N161.CB) [> 4.4970 = 7.4950 < 9.7435] w=0.2560 to align # Constraint # added constraint: constraint((T0291)D265.CB, (T0291)Q279.CB) [> 4.5574 = 7.5957 < 9.8743] w=0.2559 to align # Constraint # added constraint: constraint((T0291)V149.CB, (T0291)T187.CB) [> 4.1974 = 6.9957 < 9.0944] w=0.2559 to align # Constraint # added constraint: constraint((T0291)L133.CB, (T0291)L262.CB) [> 4.5281 = 7.5468 < 9.8108] w=0.2496 to align # Constraint # added constraint: constraint((T0291)G39.CA, (T0291)Y65.CB) [> 4.3326 = 7.2210 < 9.3873] w=0.2495 to align # Constraint # added constraint: constraint((T0291)L153.CB, (T0291)I218.CB) [> 4.6452 = 7.7420 < 10.0646] w=0.2494 to align # Constraint # added constraint: constraint((T0291)G44.CA, (T0291)I54.CB) [> 4.4049 = 7.3415 < 9.5440] w=0.2438 to align # Constraint # added constraint: constraint((T0291)A24.CB, (T0291)S98.CB) [> 3.8627 = 6.4379 < 8.3692] w=0.2368 to align # Constraint # added constraint: constraint((T0291)K62.CB, (T0291)V101.CB) [> 4.5765 = 7.6276 < 9.9158] w=0.2367 to align # Constraint # added constraint: constraint((T0291)T187.CB, (T0291)T208.CB) [> 4.4852 = 7.4753 < 9.7178] w=0.2367 to align # Constraint # added constraint: constraint((T0291)H150.CB, (T0291)D170.CB) [> 4.4402 = 7.4004 < 9.6205] w=0.2323 to align # Constraint # added constraint: constraint((T0291)C42.CB, (T0291)K59.CB) [> 4.6086 = 7.6810 < 9.9853] w=0.2316 to align # Constraint # added constraint: constraint((T0291)V41.CB, (T0291)V56.CB) [> 3.0341 = 5.0568 < 6.5738] w=0.2310 to align # Constraint # added constraint: constraint((T0291)R151.CB, (T0291)S215.CB) [> 4.7046 = 7.8410 < 10.1934] w=0.2304 to align # Constraint # added constraint: constraint((T0291)V149.CB, (T0291)V176.CB) [> 4.6227 = 7.7044 < 10.0158] w=0.2304 to align # Constraint # added constraint: constraint((T0291)N110.CB, (T0291)N163.CB) [> 4.3891 = 7.3151 < 9.5097] w=0.2304 to align # Constraint # added constraint: constraint((T0291)M224.CB, (T0291)Y260.CB) [> 4.5740 = 7.6234 < 9.9104] w=0.2304 to align # Constraint # added constraint: constraint((T0291)G190.CA, (T0291)A201.CB) [> 3.7518 = 6.2530 < 8.1289] w=0.2303 to align # Constraint # added constraint: constraint((T0291)V41.CB, (T0291)I54.CB) [> 3.4488 = 5.7480 < 7.4725] w=0.2246 to align # Constraint # added constraint: constraint((T0291)V41.CB, (T0291)S55.CB) [> 4.1812 = 6.9687 < 9.0594] w=0.2246 to align # Constraint # added constraint: constraint((T0291)G44.CA, (T0291)E53.CB) [> 3.3139 = 5.5232 < 7.1801] w=0.2246 to align # Constraint # added constraint: constraint((T0291)S55.CB, (T0291)M102.CB) [> 3.4411 = 5.7351 < 7.4556] w=0.2246 to align # Constraint # added constraint: constraint((T0291)S55.CB, (T0291)I103.CB) [> 4.1965 = 6.9941 < 9.0923] w=0.2246 to align # Constraint # added constraint: constraint((T0291)V56.CB, (T0291)M102.CB) [> 4.1884 = 6.9807 < 9.0750] w=0.2246 to align # Constraint # added constraint: constraint((T0291)M224.CB, (T0291)P256.CB) [> 4.2897 = 7.1495 < 9.2944] w=0.2240 to align # Constraint # added constraint: constraint((T0291)G39.CA, (T0291)V56.CB) [> 4.0656 = 6.7760 < 8.8088] w=0.2182 to align # Constraint # added constraint: constraint((T0291)A57.CB, (T0291)M102.CB) [> 3.3700 = 5.6166 < 7.3015] w=0.2182 to align # Constraint # added constraint: constraint((T0291)E40.CB, (T0291)V56.CB) [> 4.4519 = 7.4199 < 9.6459] w=0.2182 to align # Constraint # added constraint: constraint((T0291)V33.CB, (T0291)I54.CB) [> 3.9791 = 6.6318 < 8.6214] w=0.2182 to align # Constraint # added constraint: constraint((T0291)F38.CB, (T0291)I58.CB) [> 3.5684 = 5.9474 < 7.7316] w=0.2175 to align # Constraint # added constraint: constraint((T0291)I89.CB, (T0291)F171.CB) [> 4.6684 = 7.7807 < 10.1149] w=0.2131 to align # Constraint # added constraint: constraint((T0291)I89.CB, (T0291)D170.CB) [> 4.2909 = 7.1515 < 9.2970] w=0.2131 to align # Constraint # added constraint: constraint((T0291)G39.CA, (T0291)A57.CB) [> 3.5298 = 5.8830 < 7.6479] w=0.2118 to align # Constraint # added constraint: constraint((T0291)E40.CB, (T0291)A57.CB) [> 3.1149 = 5.1915 < 6.7489] w=0.2118 to align # Constraint # added constraint: constraint((T0291)A57.CB, (T0291)V101.CB) [> 4.3642 = 7.2737 < 9.4558] w=0.2118 to align # Constraint # added constraint: constraint((T0291)C42.CB, (T0291)S55.CB) [> 3.0254 = 5.0423 < 6.5550] w=0.2118 to align # Constraint # added constraint: constraint((T0291)C42.CB, (T0291)I54.CB) [> 4.3738 = 7.2897 < 9.4766] w=0.2118 to align # Constraint # added constraint: constraint((T0291)W221.CB, (T0291)C255.CB) [> 4.5657 = 7.6095 < 9.8924] w=0.2112 to align # Constraint # added constraint: constraint((T0291)F18.CB, (T0291)V94.CB) [> 4.1772 = 6.9619 < 9.0505] w=0.1983 to align # Constraint # added constraint: constraint((T0291)M146.CB, (T0291)V176.CB) [> 4.2570 = 7.0950 < 9.2235] w=0.1982 to align # Constraint # added constraint: constraint((T0291)S198.CB, (T0291)V213.CB) [> 4.7601 = 7.9335 < 10.3135] w=0.1920 to align # Constraint # added constraint: constraint((T0291)R90.CB, (T0291)K167.CB) [> 4.6621 = 7.7701 < 10.1012] w=0.1920 to align # Constraint # added constraint: constraint((T0291)L177.CB, (T0291)T187.CB) [> 3.7214 = 6.2024 < 8.0631] w=0.1919 to align # Constraint # added constraint: constraint((T0291)Y247.CB, (T0291)W267.CB) [> 3.7489 = 6.2482 < 8.1227] w=0.1798 to align # Constraint # added constraint: constraint((T0291)A203.CB, (T0291)V243.CB) [> 3.7185 = 6.1975 < 8.0567] w=0.1798 to align # Constraint # added constraint: constraint((T0291)R195.CB, (T0291)M234.CB) [> 4.3037 = 7.1729 < 9.3248] w=0.1792 to align # Constraint # added constraint: constraint((T0291)E76.CB, (T0291)D170.CB) [> 4.5749 = 7.6248 < 9.9123] w=0.1791 to align # Constraint # added constraint: constraint((T0291)G36.CA, (T0291)K59.CB) [> 4.4131 = 7.3552 < 9.5618] w=0.1740 to align # Constraint # added constraint: constraint((T0291)R195.CB, (T0291)E228.CB) [> 2.9450 = 4.9084 < 6.3809] w=0.1734 to align # Constraint # added constraint: constraint((T0291)I194.CB, (T0291)D238.CB) [> 3.4550 = 5.7583 < 7.4858] w=0.1734 to align # Constraint # added constraint: constraint((T0291)I218.CB, (T0291)E228.CB) [> 3.7417 = 6.2361 < 8.1070] w=0.1734 to align # Constraint # added constraint: constraint((T0291)G189.CA, (T0291)A201.CB) [> 4.3466 = 7.2444 < 9.4177] w=0.1727 to align # Constraint # added constraint: constraint((T0291)R151.CB, (T0291)T187.CB) [> 4.3833 = 7.3054 < 9.4971] w=0.1664 to align # Constraint # added constraint: constraint((T0291)A154.CB, (T0291)I192.CB) [> 4.2499 = 7.0831 < 9.2081] w=0.1600 to align # Constraint # added constraint: constraint((T0291)R188.CB, (T0291)R205.CB) [> 3.7438 = 6.2396 < 8.1115] w=0.1599 to align # Constraint # added constraint: constraint((T0291)I192.CB, (T0291)S211.CB) [> 4.4529 = 7.4216 < 9.6480] w=0.1599 to align # Constraint # added constraint: constraint((T0291)F38.CB, (T0291)V63.CB) [> 3.7864 = 6.3107 < 8.2039] w=0.1599 to align # Constraint # added constraint: constraint((T0291)I88.CB, (T0291)F171.CB) [> 4.1500 = 6.9166 < 8.9916] w=0.1555 to align # Constraint # added constraint: constraint((T0291)F38.CB, (T0291)T60.CB) [> 4.4019 = 7.3364 < 9.5373] w=0.1485 to align # Constraint # added constraint: constraint((T0291)I202.CB, (T0291)A242.CB) [> 3.7105 = 6.1842 < 8.0395] w=0.1414 to align # Constraint # added constraint: constraint((T0291)I192.CB, (T0291)I202.CB) [> 4.3175 = 7.1958 < 9.3545] w=0.1408 to align # Constraint # added constraint: constraint((T0291)G217.CA, (T0291)P230.CB) [> 4.6577 = 7.7628 < 10.0917] w=0.1407 to align # Constraint # added constraint: constraint((T0291)E37.CB, (T0291)G172.CA) [> 3.3721 = 5.6202 < 7.3063] w=0.1344 to align # Constraint # added constraint: constraint((T0291)Y107.CB, (T0291)N161.CB) [> 4.6542 = 7.7569 < 10.0840] w=0.1344 to align # Constraint # added constraint: constraint((T0291)V15.CB, (T0291)T96.CB) [> 3.7585 = 6.2642 < 8.1435] w=0.1280 to align # Constraint # added constraint: constraint((T0291)I127.CB, (T0291)P291.CB) [> 3.1147 = 5.1912 < 6.7485] w=0.1280 to align # Constraint # added constraint: constraint((T0291)F73.CB, (T0291)V94.CB) [> 4.5234 = 7.5390 < 9.8007] w=0.1280 to align # Constraint # added constraint: constraint((T0291)V130.CB, (T0291)L294.CB) [> 3.8341 = 6.3902 < 8.3072] w=0.1229 to align # Constraint # added constraint: constraint((T0291)E37.CB, (T0291)L173.CB) [> 4.3580 = 7.2633 < 9.4423] w=0.1171 to align # Constraint # added constraint: constraint((T0291)E37.CB, (T0291)D170.CB) [> 4.1497 = 6.9162 < 8.9911] w=0.1171 to align # Constraint # added constraint: constraint((T0291)P193.CB, (T0291)S215.CB) [> 4.7073 = 7.8455 < 10.1992] w=0.1152 to align # Constraint # added constraint: constraint((T0291)I218.CB, (T0291)M263.CB) [> 4.7648 = 7.9412 < 10.3236] w=0.1152 to align # Constraint # added constraint: constraint((T0291)V130.CB, (T0291)P256.CB) [> 4.5919 = 7.6532 < 9.9492] w=0.1152 to align # Constraint # added constraint: constraint((T0291)L48.CB, (T0291)E92.CB) [> 4.1534 = 6.9224 < 8.9991] w=0.1152 to align # Constraint # added constraint: constraint((T0291)L153.CB, (T0291)I192.CB) [> 4.5409 = 7.5682 < 9.8386] w=0.1152 to align # Constraint # added constraint: constraint((T0291)R195.CB, (T0291)E222.CB) [> 4.6470 = 7.7451 < 10.0686] w=0.1152 to align # Constraint # added constraint: constraint((T0291)F116.CB, (T0291)A155.CB) [> 4.7180 = 7.8633 < 10.2223] w=0.1152 to align # Constraint # added constraint: constraint((T0291)N157.CB, (T0291)F171.CB) [> 4.1976 = 6.9961 < 9.0949] w=0.1152 to align # Constraint # added constraint: constraint((T0291)G189.CA, (T0291)Y204.CB) [> 4.0358 = 6.7263 < 8.7441] w=0.1152 to align # Constraint # added constraint: constraint((T0291)R188.CB, (T0291)K206.CB) [> 3.2437 = 5.4062 < 7.0281] w=0.1151 to align # Constraint # added constraint: constraint((T0291)A183.CB, (T0291)T208.CB) [> 3.9592 = 6.5988 < 8.5784] w=0.1088 to align # Constraint # added constraint: constraint((T0291)I194.CB, (T0291)V243.CB) [> 4.5034 = 7.5057 < 9.7575] w=0.1087 to align # Constraint # added constraint: constraint((T0291)I194.CB, (T0291)M234.CB) [> 3.7991 = 6.3318 < 8.2313] w=0.1030 to align # Constraint # added constraint: constraint((T0291)C42.CB, (T0291)V56.CB) [> 4.6613 = 7.7688 < 10.0995] w=0.1030 to align # Constraint # added constraint: constraint((T0291)G131.CA, (T0291)L287.CB) [> 4.2441 = 7.0736 < 9.1956] w=0.1023 to align # Constraint # added constraint: constraint((T0291)D179.CB, (T0291)T208.CB) [> 4.2050 = 7.0083 < 9.1108] w=0.1023 to align # Constraint # added constraint: constraint((T0291)H150.CB, (T0291)G172.CA) [> 3.7479 = 6.2465 < 8.1204] w=0.0979 to align # Constraint # added constraint: constraint((T0291)G36.CA, (T0291)V176.CB) [> 3.8426 = 6.4043 < 8.3256] w=0.0960 to align # Constraint # added constraint: constraint((T0291)G174.CA, (T0291)K191.CB) [> 4.1803 = 6.9672 < 9.0574] w=0.0960 to align # Constraint # added constraint: constraint((T0291)V130.CB, (T0291)D285.CB) [> 4.2374 = 7.0623 < 9.1810] w=0.0960 to align # Constraint # added constraint: constraint((T0291)L249.CB, (T0291)Y260.CB) [> 3.8939 = 6.4899 < 8.4369] w=0.0896 to align # Constraint # added constraint: constraint((T0291)E40.CB, (T0291)L61.CB) [> 4.4420 = 7.4033 < 9.6243] w=0.0896 to align # Constraint # added constraint: constraint((T0291)I127.CB, (T0291)G292.CA) [> 3.8167 = 6.3611 < 8.2695] w=0.0896 to align # Constraint # added constraint: constraint((T0291)I29.CB, (T0291)T60.CB) [> 4.6062 = 7.6770 < 9.9801] w=0.0832 to align # Constraint # added constraint: constraint((T0291)V130.CB, (T0291)K295.CB) [> 4.2091 = 7.0151 < 9.1197] w=0.0832 to align # Constraint # added constraint: constraint((T0291)F18.CB, (T0291)T96.CB) [> 3.9293 = 6.5488 < 8.5135] w=0.0832 to align # Constraint # added constraint: constraint((T0291)A14.CB, (T0291)L74.CB) [> 4.3364 = 7.2274 < 9.3956] w=0.0832 to align # Constraint # added constraint: constraint((T0291)L173.CB, (T0291)G190.CA) [> 4.1422 = 6.9036 < 8.9747] w=0.0832 to align # Constraint # added constraint: constraint((T0291)G36.CA, (T0291)R156.CB) [> 4.4000 = 7.3333 < 9.5333] w=0.0787 to align # Constraint # added constraint: constraint((T0291)F18.CB, (T0291)A77.CB) [> 4.2007 = 7.0012 < 9.1016] w=0.0768 to align # Constraint # added constraint: constraint((T0291)V41.CB, (T0291)F171.CB) [> 3.6129 = 6.0216 < 7.8280] w=0.0768 to align # Constraint # added constraint: constraint((T0291)A183.CB, (T0291)P193.CB) [> 3.7276 = 6.2126 < 8.0764] w=0.0768 to align # Constraint # added constraint: constraint((T0291)R175.CB, (T0291)K191.CB) [> 4.0196 = 6.6994 < 8.7092] w=0.0768 to align # Constraint # added constraint: constraint((T0291)V15.CB, (T0291)S78.CB) [> 4.0405 = 6.7341 < 8.7543] w=0.0768 to align # Constraint # added constraint: constraint((T0291)L91.CB, (T0291)F171.CB) [> 4.6004 = 7.6674 < 9.9676] w=0.0768 to align # Constraint # added constraint: constraint((T0291)A184.CB, (T0291)T208.CB) [> 4.3570 = 7.2617 < 9.4402] w=0.0768 to align # Constraint # added constraint: constraint((T0291)G36.CA, (T0291)D170.CB) [> 3.8275 = 6.3793 < 8.2930] w=0.0768 to align # Constraint # added constraint: constraint((T0291)L129.CB, (T0291)Y226.CB) [> 4.4292 = 7.3821 < 9.5967] w=0.0768 to align # Constraint # added constraint: constraint((T0291)G131.CA, (T0291)P291.CB) [> 4.0762 = 6.7937 < 8.8318] w=0.0768 to align # Constraint # added constraint: constraint((T0291)R188.CB, (T0291)Y204.CB) [> 3.9349 = 6.5582 < 8.5257] w=0.0767 to align # Constraint # added constraint: constraint((T0291)P199.CB, (T0291)V239.CB) [> 3.9619 = 6.6032 < 8.5841] w=0.0710 to align # Constraint # added constraint: constraint((T0291)G34.CA, (T0291)V176.CB) [> 4.5375 = 7.5626 < 9.8313] w=0.0704 to align # Constraint # added constraint: constraint((T0291)A184.CB, (T0291)P193.CB) [> 3.9215 = 6.5359 < 8.4967] w=0.0704 to align # Constraint # added constraint: constraint((T0291)I127.CB, (T0291)L294.CB) [> 4.4807 = 7.4679 < 9.7082] w=0.0704 to align # Constraint # added constraint: constraint((T0291)I194.CB, (T0291)Y231.CB) [> 4.5182 = 7.5304 < 9.7895] w=0.0704 to align # Constraint # added constraint: constraint((T0291)V15.CB, (T0291)L74.CB) [> 3.2980 = 5.4966 < 7.1456] w=0.0704 to align # Constraint # added constraint: constraint((T0291)R151.CB, (T0291)G190.CA) [> 4.1848 = 6.9747 < 9.0671] w=0.0704 to align # Constraint # added constraint: constraint((T0291)G131.CA, (T0291)L294.CB) [> 4.1483 = 6.9138 < 8.9879] w=0.0704 to align # Constraint # added constraint: constraint((T0291)I127.CB, (T0291)K295.CB) [> 3.9003 = 6.5005 < 8.4506] w=0.0704 to align # Constraint # added constraint: constraint((T0291)I127.CB, (T0291)S293.CB) [> 3.4854 = 5.8090 < 7.5517] w=0.0640 to align # Constraint # added constraint: constraint((T0291)V149.CB, (T0291)G172.CA) [> 4.0543 = 6.7572 < 8.7843] w=0.0595 to align # Constraint # added constraint: constraint((T0291)I127.CB, (T0291)T298.CB) [> 3.2170 = 5.3616 < 6.9701] w=0.0582 to align # Constraint # added constraint: constraint((T0291)A184.CB, (T0291)I194.CB) [> 3.1154 = 5.1923 < 6.7500] w=0.0576 to align # Constraint # added constraint: constraint((T0291)L133.CB, (T0291)C166.CB) [> 4.6993 = 7.8322 < 10.1818] w=0.0576 to align # Constraint # added constraint: constraint((T0291)N157.CB, (T0291)L173.CB) [> 4.3420 = 7.2367 < 9.4077] w=0.0576 to align # Constraint # added constraint: constraint((T0291)V41.CB, (T0291)T105.CB) [> 4.4885 = 7.4808 < 9.7250] w=0.0576 to align # Constraint # added constraint: constraint((T0291)M80.CB, (T0291)S169.CB) [> 4.3257 = 7.2095 < 9.3723] w=0.0576 to align # Constraint # added constraint: constraint((T0291)L46.CB, (T0291)G93.CA) [> 4.6588 = 7.7647 < 10.0941] w=0.0576 to align # Constraint # added constraint: constraint((T0291)Y107.CB, (T0291)S162.CB) [> 4.6466 = 7.7444 < 10.0677] w=0.0576 to align # Constraint # added constraint: constraint((T0291)I127.CB, (T0291)I297.CB) [> 3.5631 = 5.9384 < 7.7200] w=0.0576 to align # Constraint # added constraint: constraint((T0291)F116.CB, (T0291)V223.CB) [> 4.6598 = 7.7663 < 10.0962] w=0.0576 to align # Constraint # added constraint: constraint((T0291)I218.CB, (T0291)Y247.CB) [> 4.5068 = 7.5114 < 9.7647] w=0.0576 to align # Constraint # added constraint: constraint((T0291)I136.CB, (T0291)L220.CB) [> 4.7333 = 7.8888 < 10.2554] w=0.0576 to align # Constraint # added constraint: constraint((T0291)G190.CA, (T0291)Y204.CB) [> 4.3343 = 7.2238 < 9.3909] w=0.0576 to align # Constraint # added constraint: constraint((T0291)G131.CA, (T0291)I297.CB) [> 3.1861 = 5.3102 < 6.9033] w=0.0518 to align # Constraint # added constraint: constraint((T0291)V130.CB, (T0291)I297.CB) [> 2.7890 = 4.6484 < 6.0429] w=0.0518 to align # Constraint # added constraint: constraint((T0291)G131.CA, (T0291)A300.CB) [> 4.2500 = 7.0834 < 9.2084] w=0.0518 to align # Constraint # added constraint: constraint((T0291)P199.CB, (T0291)Y247.CB) [> 3.8606 = 6.4343 < 8.3646] w=0.0512 to align # Constraint # added constraint: constraint((T0291)P193.CB, (T0291)V239.CB) [> 3.6598 = 6.0998 < 7.9297] w=0.0512 to align # Constraint # added constraint: constraint((T0291)V130.CB, (T0291)I296.CB) [> 3.4449 = 5.7415 < 7.4640] w=0.0512 to align # Constraint # added constraint: constraint((T0291)K59.CB, (T0291)D170.CB) [> 4.5201 = 7.5335 < 9.7935] w=0.0512 to align # Constraint # added constraint: constraint((T0291)G131.CA, (T0291)T298.CB) [> 3.6247 = 6.0411 < 7.8535] w=0.0454 to align # Constraint # added constraint: constraint((T0291)V130.CB, (T0291)T298.CB) [> 4.0238 = 6.7063 < 8.7182] w=0.0454 to align # Constraint # added constraint: constraint((T0291)H16.CB, (T0291)T96.CB) [> 4.2934 = 7.1557 < 9.3024] w=0.0448 to align # Constraint # added constraint: constraint((T0291)L129.CB, (T0291)I297.CB) [> 4.2083 = 7.0138 < 9.1180] w=0.0448 to align # Constraint # added constraint: constraint((T0291)I127.CB, (T0291)I296.CB) [> 3.3286 = 5.5476 < 7.2119] w=0.0448 to align # Constraint # added constraint: constraint((T0291)I127.CB, (T0291)R303.CB) [> 3.9444 = 6.5740 < 8.5462] w=0.0448 to align # Constraint # added constraint: constraint((T0291)F116.CB, (T0291)L164.CB) [> 4.3599 = 7.2664 < 9.4464] w=0.0448 to align # Constraint # added constraint: constraint((T0291)E40.CB, (T0291)I58.CB) [> 4.6832 = 7.8054 < 10.1470] w=0.0448 to align # Constraint # added constraint: constraint((T0291)A35.CB, (T0291)G190.CA) [> 4.6653 = 7.7756 < 10.1083] w=0.0403 to align # Constraint # added constraint: constraint((T0291)G34.CA, (T0291)F171.CB) [> 4.0096 = 6.6827 < 8.6875] w=0.0384 to align # Constraint # added constraint: constraint((T0291)T186.CB, (T0291)I202.CB) [> 4.4760 = 7.4600 < 9.6980] w=0.0384 to align # Constraint # added constraint: constraint((T0291)R156.CB, (T0291)L173.CB) [> 4.2837 = 7.1395 < 9.2813] w=0.0384 to align # Constraint # added constraint: constraint((T0291)N157.CB, (T0291)G174.CA) [> 4.0101 = 6.6835 < 8.6885] w=0.0384 to align # Constraint # added constraint: constraint((T0291)N157.CB, (T0291)G172.CA) [> 4.7356 = 7.8926 < 10.2604] w=0.0384 to align # Constraint # added constraint: constraint((T0291)V41.CB, (T0291)L173.CB) [> 3.8281 = 6.3801 < 8.2942] w=0.0384 to align # Constraint # added constraint: constraint((T0291)L173.CB, (T0291)P193.CB) [> 4.7431 = 7.9052 < 10.2768] w=0.0384 to align # Constraint # added constraint: constraint((T0291)R156.CB, (T0291)F171.CB) [> 4.5191 = 7.5319 < 9.7914] w=0.0384 to align # Constraint # added constraint: constraint((T0291)G39.CA, (T0291)F171.CB) [> 4.5844 = 7.6407 < 9.9329] w=0.0384 to align # Constraint # added constraint: constraint((T0291)F124.CB, (T0291)I297.CB) [> 3.8284 = 6.3807 < 8.2949] w=0.0384 to align # Constraint # added constraint: constraint((T0291)E76.CB, (T0291)L91.CB) [> 4.4385 = 7.3975 < 9.6167] w=0.0384 to align # Constraint # added constraint: constraint((T0291)V149.CB, (T0291)E178.CB) [> 3.0340 = 5.0567 < 6.5738] w=0.0384 to align # Constraint # added constraint: constraint((T0291)T186.CB, (T0291)A201.CB) [> 4.4367 = 7.3945 < 9.6129] w=0.0384 to align # Constraint # added constraint: constraint((T0291)V33.CB, (T0291)F171.CB) [> 4.3551 = 7.2584 < 9.4360] w=0.0384 to align # Constraint # added constraint: constraint((T0291)G34.CA, (T0291)L173.CB) [> 3.5451 = 5.9085 < 7.6811] w=0.0384 to align # Constraint # added constraint: constraint((T0291)A57.CB, (T0291)F171.CB) [> 4.1705 = 6.9509 < 9.0362] w=0.0384 to align # Constraint # added constraint: constraint((T0291)E200.CB, (T0291)W214.CB) [> 4.6839 = 7.8066 < 10.1485] w=0.0384 to align # Constraint # added constraint: constraint((T0291)E109.CB, (T0291)L159.CB) [> 3.1954 = 5.3257 < 6.9234] w=0.0384 to align # Constraint # added constraint: constraint((T0291)L91.CB, (T0291)D170.CB) [> 4.2866 = 7.1444 < 9.2877] w=0.0384 to align # Constraint # added constraint: constraint((T0291)A155.CB, (T0291)W196.CB) [> 4.7186 = 7.8644 < 10.2237] w=0.0384 to align # Constraint # added constraint: constraint((T0291)I89.CB, (T0291)Y107.CB) [> 4.7369 = 7.8948 < 10.2633] w=0.0384 to align # Constraint # added constraint: constraint((T0291)G131.CA, (T0291)V165.CB) [> 3.9631 = 6.6052 < 8.5868] w=0.0384 to align # Constraint # added constraint: constraint((T0291)Y185.CB, (T0291)T208.CB) [> 4.4819 = 7.4698 < 9.7107] w=0.0320 to align # Constraint # added constraint: constraint((T0291)K191.CB, (T0291)I202.CB) [> 4.5353 = 7.5588 < 9.8264] w=0.0320 to align # Constraint # added constraint: constraint((T0291)L164.CB, (T0291)L307.CB) [> 3.3844 = 5.6406 < 7.3327] w=0.0320 to align # Constraint # added constraint: constraint((T0291)I127.CB, (T0291)A302.CB) [> 3.3841 = 5.6402 < 7.3322] w=0.0320 to align # Constraint # added constraint: constraint((T0291)V130.CB, (T0291)A301.CB) [> 4.5215 = 7.5359 < 9.7967] w=0.0320 to align # Constraint # added constraint: constraint((T0291)I160.CB, (T0291)I296.CB) [> 4.3510 = 7.2517 < 9.4273] w=0.0320 to align # Constraint # added constraint: constraint((T0291)I127.CB, (T0291)P304.CB) [> 2.4168 = 4.0280 < 5.2364] w=0.0262 to align # Constraint # added constraint: constraint((T0291)V281.CB, (T0291)A300.CB) [> 4.1000 = 6.8333 < 8.8833] w=0.0262 to align # Constraint # added constraint: constraint((T0291)I127.CB, (T0291)L308.CB) [> 3.6788 = 6.1313 < 7.9706] w=0.0256 to align # Constraint # added constraint: constraint((T0291)V130.CB, (T0291)A302.CB) [> 2.8209 = 4.7014 < 6.1119] w=0.0256 to align # Constraint # added constraint: constraint((T0291)A137.CB, (T0291)L294.CB) [> 4.3928 = 7.3214 < 9.5178] w=0.0256 to align # Constraint # added constraint: constraint((T0291)E37.CB, (T0291)N157.CB) [> 3.2918 = 5.4863 < 7.1322] w=0.0211 to align # Constraint # added constraint: constraint((T0291)G36.CA, (T0291)N157.CB) [> 3.1175 = 5.1958 < 6.7545] w=0.0211 to align # Constraint # added constraint: constraint((T0291)P199.CB, (T0291)P250.CB) [> 4.2278 = 7.0464 < 9.1603] w=0.0198 to align # Constraint # added constraint: constraint((T0291)Y8.CB, (T0291)V149.CB) [> 4.5585 = 7.5975 < 9.8768] w=0.0192 to align # Constraint # added constraint: constraint((T0291)P5.CB, (T0291)T208.CB) [> 3.2805 = 5.4675 < 7.1077] w=0.0192 to align # Constraint # added constraint: constraint((T0291)G36.CA, (T0291)S169.CB) [> 2.3646 = 3.9409 < 5.1232] w=0.0192 to align # Constraint # added constraint: constraint((T0291)G36.CA, (T0291)L159.CB) [> 3.9442 = 6.5737 < 8.5458] w=0.0192 to align # Constraint # added constraint: constraint((T0291)G36.CA, (T0291)I158.CB) [> 4.7943 = 7.9905 < 10.3876] w=0.0192 to align # Constraint # added constraint: constraint((T0291)A35.CB, (T0291)L159.CB) [> 3.7875 = 6.3124 < 8.2062] w=0.0192 to align # Constraint # added constraint: constraint((T0291)M132.CB, (T0291)V219.CB) [> 4.5905 = 7.6508 < 9.9461] w=0.0192 to align # Constraint # added constraint: constraint((T0291)G131.CA, (T0291)I296.CB) [> 3.9831 = 6.6386 < 8.6301] w=0.0192 to align # Constraint # added constraint: constraint((T0291)E178.CB, (T0291)T208.CB) [> 4.2660 = 7.1100 < 9.2429] w=0.0192 to align # Constraint # added constraint: constraint((T0291)S198.CB, (T0291)T208.CB) [> 4.7313 = 7.8856 < 10.2512] w=0.0192 to align # Constraint # added constraint: constraint((T0291)G39.CA, (T0291)G172.CA) [> 4.5538 = 7.5897 < 9.8666] w=0.0192 to align # Constraint # added constraint: constraint((T0291)A184.CB, (T0291)T197.CB) [> 4.0141 = 6.6901 < 8.6971] w=0.0192 to align # Constraint # added constraint: constraint((T0291)L159.CB, (T0291)L173.CB) [> 4.4950 = 7.4916 < 9.7391] w=0.0192 to align # Constraint # added constraint: constraint((T0291)R156.CB, (T0291)G190.CA) [> 4.7300 = 7.8833 < 10.2483] w=0.0192 to align # Constraint # added constraint: constraint((T0291)E222.CB, (T0291)L249.CB) [> 4.6420 = 7.7367 < 10.0578] w=0.0192 to align # Constraint # added constraint: constraint((T0291)L220.CB, (T0291)C255.CB) [> 4.2673 = 7.1121 < 9.2458] w=0.0192 to align # Constraint # added constraint: constraint((T0291)Y185.CB, (T0291)R195.CB) [> 4.6863 = 7.8105 < 10.1536] w=0.0192 to align # Constraint # added constraint: constraint((T0291)L48.CB, (T0291)G93.CA) [> 4.5895 = 7.6492 < 9.9440] w=0.0192 to align # Constraint # added constraint: constraint((T0291)V41.CB, (T0291)G174.CA) [> 3.5802 = 5.9670 < 7.7571] w=0.0192 to align # Constraint # added constraint: constraint((T0291)E40.CB, (T0291)G174.CA) [> 3.3245 = 5.5408 < 7.2030] w=0.0192 to align # Constraint # added constraint: constraint((T0291)E37.CB, (T0291)S169.CB) [> 2.6073 = 4.3455 < 5.6492] w=0.0192 to align # Constraint # added constraint: constraint((T0291)F124.CB, (T0291)I296.CB) [> 4.7459 = 7.9098 < 10.2827] w=0.0192 to align # Constraint # added constraint: constraint((T0291)L159.CB, (T0291)D170.CB) [> 4.4896 = 7.4827 < 9.7275] w=0.0192 to align # Constraint # added constraint: constraint((T0291)I158.CB, (T0291)D170.CB) [> 4.6431 = 7.7384 < 10.0599] w=0.0192 to align # Constraint # added constraint: constraint((T0291)V56.CB, (T0291)G93.CA) [> 4.7394 = 7.8990 < 10.2687] w=0.0192 to align # Constraint # added constraint: constraint((T0291)V33.CB, (T0291)L173.CB) [> 4.2860 = 7.1433 < 9.2862] w=0.0192 to align # Constraint # added constraint: constraint((T0291)Y8.CB, (T0291)V94.CB) [> 3.3496 = 5.5826 < 7.2573] w=0.0192 to align # Constraint # added constraint: constraint((T0291)R156.CB, (T0291)S169.CB) [> 4.7782 = 7.9637 < 10.3528] w=0.0192 to align # Constraint # added constraint: constraint((T0291)G190.CA, (T0291)F207.CB) [> 4.0100 = 6.6833 < 8.6883] w=0.0192 to align # Constraint # added constraint: constraint((T0291)T208.CB, (T0291)K269.CB) [> 4.6477 = 7.7462 < 10.0701] w=0.0192 to align # Constraint # added constraint: constraint((T0291)T197.CB, (T0291)I218.CB) [> 4.5914 = 7.6523 < 9.9480] w=0.0192 to align # Constraint # added constraint: constraint((T0291)W196.CB, (T0291)E222.CB) [> 4.4732 = 7.4554 < 9.6920] w=0.0192 to align # Constraint # added constraint: constraint((T0291)L173.CB, (T0291)Y185.CB) [> 3.3966 = 5.6611 < 7.3594] w=0.0192 to align # Constraint # added constraint: constraint((T0291)G217.CA, (T0291)I280.CB) [> 4.7504 = 7.9173 < 10.2924] w=0.0192 to align # Constraint # added constraint: constraint((T0291)H85.CB, (T0291)V168.CB) [> 4.7574 = 7.9290 < 10.3077] w=0.0192 to align # Constraint # added constraint: constraint((T0291)F124.CB, (T0291)S225.CB) [> 4.3133 = 7.1888 < 9.3454] w=0.0192 to align # Constraint # added constraint: constraint((T0291)E222.CB, (T0291)V239.CB) [> 4.3590 = 7.2650 < 9.4445] w=0.0192 to align # Constraint # added constraint: constraint((T0291)T197.CB, (T0291)W232.CB) [> 4.5673 = 7.6122 < 9.8959] w=0.0192 to align # Constraint # added constraint: constraint((T0291)I88.CB, (T0291)R175.CB) [> 4.6140 = 7.6900 < 9.9970] w=0.0192 to align # Constraint # added constraint: constraint((T0291)I160.CB, (T0291)P304.CB) [> 4.3595 = 7.2659 < 9.4457] w=0.0134 to align # Constraint # added constraint: constraint((T0291)V3.CB, (T0291)G64.CA) [> 4.0604 = 6.7674 < 8.7976] w=0.0128 to align # Constraint # added constraint: constraint((T0291)S198.CB, (T0291)M234.CB) [> 4.2776 = 7.1293 < 9.2682] w=0.0128 to align # Constraint # added constraint: constraint((T0291)D84.CB, (T0291)M146.CB) [> 3.9018 = 6.5030 < 8.4539] w=0.0128 to align # Constraint # added constraint: constraint((T0291)I29.CB, (T0291)M102.CB) [> 4.3516 = 7.2527 < 9.4284] w=0.0128 to align # Constraint # added constraint: constraint((T0291)A24.CB, (T0291)L46.CB) [> 4.1854 = 6.9757 < 9.0684] w=0.0128 to align # Constraint # added constraint: constraint((T0291)G131.CA, (T0291)L308.CB) [> 4.3621 = 7.2702 < 9.4513] w=0.0128 to align # Constraint # added constraint: constraint((T0291)A14.CB, (T0291)R90.CB) [> 4.7322 = 7.8870 < 10.2531] w=0.0128 to align # Constraint # added constraint: constraint((T0291)T7.CB, (T0291)R90.CB) [> 3.4702 = 5.7837 < 7.5188] w=0.0128 to align # Constraint # added constraint: constraint((T0291)A77.CB, (T0291)R90.CB) [> 4.4809 = 7.4681 < 9.7085] w=0.0128 to align # Constraint # added constraint: constraint((T0291)Y8.CB, (T0291)V95.CB) [> 3.6131 = 6.0219 < 7.8285] w=0.0128 to align # Constraint # added constraint: constraint((T0291)R70.CB, (T0291)G172.CA) [> 4.4363 = 7.3939 < 9.6121] w=0.0128 to align # Constraint # added constraint: constraint((T0291)V56.CB, (T0291)D170.CB) [> 4.7619 = 7.9365 < 10.3175] w=0.0128 to align # Constraint # added constraint: constraint((T0291)V3.CB, (T0291)V15.CB) [> 2.8868 = 4.8113 < 6.2547] w=0.0064 to align # Constraint # added constraint: constraint((T0291)V3.CB, (T0291)V94.CB) [> 3.6625 = 6.1042 < 7.9355] w=0.0064 to align # Constraint # added constraint: constraint((T0291)I29.CB, (T0291)L46.CB) [> 3.1615 = 5.2691 < 6.8498] w=0.0064 to align # Constraint # added constraint: constraint((T0291)I160.CB, (T0291)L307.CB) [> 3.8131 = 6.3551 < 8.2617] w=0.0064 to align # Constraint # added constraint: constraint((T0291)H16.CB, (T0291)E40.CB) [> 3.5529 = 5.9215 < 7.6979] w=0.0064 to align # Constraint # added constraint: constraint((T0291)C166.CB, (T0291)R303.CB) [> 4.2298 = 7.0496 < 9.1645] w=0.0064 to align # Constraint # added constraint: constraint((T0291)R195.CB, (T0291)L307.CB) [> 4.4881 = 7.4802 < 9.7242] w=0.0064 to align # Constraint # added constraint: constraint((T0291)W232.CB, (T0291)A301.CB) [> 4.1619 = 6.9364 < 9.0174] w=0.0064 to align # Constraint # added constraint: constraint((T0291)V33.CB, (T0291)V56.CB) [> 4.1498 = 6.9163 < 8.9912] w=0.0064 to align # Constraint # added constraint: constraint((T0291)V56.CB, (T0291)M108.CB) [> 4.3975 = 7.3292 < 9.5279] w=0.0064 to align # Constraint # added constraint: constraint((T0291)L117.CB, (T0291)L284.CB) [> 3.6754 = 6.1256 < 7.9633] w=0.0064 to align # Constraint # added constraint: constraint((T0291)T7.CB, (T0291)V95.CB) [> 2.9141 = 4.8568 < 6.3139] w=0.0064 to align # Constraint # added constraint: constraint((T0291)L74.CB, (T0291)G93.CA) [> 4.5476 = 7.5793 < 9.8531] w=0.0064 to align # Constraint # added constraint: constraint((T0291)G190.CA, (T0291)I240.CB) [> 4.0048 = 6.6746 < 8.6770] w=0.0064 to align # Constraint # added constraint: constraint((T0291)C166.CB, (T0291)A300.CB) [> 4.1361 = 6.8934 < 8.9615] w=0.0064 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0291/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0291/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 291 # 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 307 # 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 232 # 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 172 # 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 221 # 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 295 # 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 270 # 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 303 # 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 306 # 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 308 # 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 304 # 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 291 # 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 235 # 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 230 # 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 235 # 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 303 # 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 305 # 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 T0291 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 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 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 T0291 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 309 # 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 T0291 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 T0291 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 T0291 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 T0291 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 308 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 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 T0291 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 # Found a chain break before 305 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 170 # 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 305 # 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 283 # 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 301 # 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 299 # 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 T0291 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 T0291 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 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 # WARNING: incomplete conformation T0291 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 T0291 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 T0291 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 T0291 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 T0291 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 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 T0291 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 308 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 286 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 271 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 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 T0291 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 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 T0291 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 308 # 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 306 # 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 303 # 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 309 # 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 309 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 288 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 225 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 225 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 160 # 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 122 # 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 122 # 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 291 # 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 191 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 287 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 290 # 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 230 # 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 309 # 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 309 # 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 308 # 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 309 # 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 309 # 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 T0291 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 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 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 T0291 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 T0291 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 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 291 # 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 291 # 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 177 # 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 170 # 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 # Found a chain break before 291 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 308 # 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 108 # 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 303 # 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 307 # 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 295 # 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 291 # 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 225 # 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 170 # 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 307 # 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 120 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 187 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 192 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 188 # 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 291 # 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 232 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 253 # 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 72 # 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 292 # 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 T0291 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 T0291 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 T0291 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 T0291 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 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 295 # 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 119 # 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 301 # 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 286 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 286 # 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 291 # 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 296 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 301 # 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 286 # 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 187 # 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 119 # 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 204 # 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 295 # 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 308 # 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 296 # 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 291 # 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 308 # 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 T0291 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 T0291 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 T0291 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 T0291 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 272 # 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 253 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 302 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 196 # 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 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0291)G139.O and (T0291)M140.N only 0.000 apart, marking (T0291)M140.N as missing WARNING: atoms too close: (T0291)Y142.O and (T0291)L143.N only 0.000 apart, marking (T0291)L143.N as missing WARNING: atoms too close: (T0291)V168.O and (T0291)S169.N only 0.000 apart, marking (T0291)S169.N as missing # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 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 T0291 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 T0291 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 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 T0291 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 300 # copying to AlignedFragments data structure # 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 300 # 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 201 # 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: atom 1146 has residue number 1 < previous residue 301 in servers/mGen-3D_TS1.pdb.gz # WARNING: incomplete conformation T0291 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 T0291 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 T0291 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 T0291 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 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 T0291 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0291 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.5272 model score -0.5317 model score -0.5910 model score -0.4717 model score -0.4312 model score -0.4889 model score -0.5455 model score -0.5760 model score -0.4647 model score -0.4851 model score -0.4872 model score -0.4874 model score -0.6083 model score -0.5104 model score -0.5173 model score -0.6069 model score -0.5427 model score 0.5743 model score -0.0741 model score 1.2571 model score 1.7987 model score 1.6145 model score 1.7146 model score 1.7333 model score 1.7686 model score -0.5510 model score -0.5585 model score -0.5957 model score -0.5160 model score -0.5962 model score -0.5663 model score -0.5656 model score -0.5647 model score -0.5783 model score -0.5570 model score -0.5599 model score -0.5591 model score -0.5829 model score -0.4340 model score -0.4312 model score -0.5080 model score 1.2770 model score 1.2770 model score 1.2770 model score 1.2770 model score 1.2770 model score -0.5626 model score -0.5547 model score -0.5635 model score -0.5599 model score -0.5783 model score -0.5519 model score -0.5783 model score -0.5783 model score -0.5647 model score -0.5656 model score -0.5994 model score -0.3141 model score -0.2330 model score -0.3838 model score -0.2364 model score 1.2771 model score 1.2770 model score 1.2770 model score 1.2771 model score 1.2770 model score 1.2770 model score 1.2771 model score 1.2770 model score 1.2770 model score 1.2770 model score 2.2375 model score 0.0236 model score -0.4536 model score -0.2932 model score -0.4745 model score 1.8542 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2770 model score 1.2771 model score -0.5649 model score -0.5607 model score -0.5658 model score -0.5682 model score -0.5892 model score -0.5894 model score -0.4848 model score -0.5156 model score -0.6056 model score -0.5471 model score -0.5410 model score -0.5410 model score -0.5589 model score -0.5572 model score -0.6270 model score -0.6131 model score -0.2387 model score -0.5517 model score -0.5782 model score -0.6131 model score -0.5808 model score -0.5319 model score -0.5397 model score -0.6164 model score -0.6429 model score -0.6190 model score -0.5964 model score -0.3329 model score -0.1720 model score -0.2480 model score -0.1012 model score -0.1953 model score -0.5556 model score 0.8445 model score -0.2042 model score 0.4227 model score 0.4927 model score -0.1834 model score 0.0295 model score 1.0200 model score 1.0187 model score -0.1670 model score -0.1817 model score -0.5598 model score -0.5598 model score -0.5598 model score -0.5519 model score -0.5598 model score -0.5075 model score -0.6001 model score -0.4959 model score -0.6042 model score -0.5628 model score -0.6033 model score -0.5345 model score -0.5061 model score -0.5414 model score -0.5414 model score -0.5414 model score -0.5505 model score -0.5441 model score -0.5193 model score -0.6207 model score -0.5505 model score -0.5342 model score -0.5742 model score -0.4873 model score -0.4755 model score -0.4746 model score -0.5384 model score -0.5995 model score -0.6186 model score -0.5246 model score -0.5287 model score -0.5517 model score -0.5301 model score -0.5300 model score -0.5922 model score -0.5171 model score -0.5459 model score -0.6514 model score -0.6132 model score -0.5455 model score -0.5165 model score 1.2770 model score 1.2770 model score 1.2770 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2770 model score 1.2770 model score -0.4819 model score -0.5230 model score -0.2957 model score -0.6183 model score -0.4688 model score 1.2771 model score -0.6160 model score -0.5675 model score -0.5448 model score -0.6341 model score 1.2771 model score -0.6222 model score -0.6198 model score -0.5575 model score -0.5409 model score 1.2771 model score -0.5493 model score -0.6445 model score -0.5307 model score -0.5593 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2770 model score -0.5526 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2770 model score -0.6475 model score -0.6008 model score -0.5355 model score -0.6332 model score -0.5762 model score -0.6041 model score -0.5436 model score 1.2771 model score 1.2770 model score 1.2770 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2770 model score 1.2770 model score 2.3824 model score 2.2447 model score 2.2309 model score 2.5230 model 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weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 Number of contacts in models: 247 Number of contacts in alignments: 159 NUMB_ALIGNS: 159 Adding 11883 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: -545.4099, CN propb: -545.4099 weights: 0.4056 constraints: 832 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 832 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 832 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 11051 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 11051 # 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 11883 # command: