# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.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 # command:# Making conformation for sequence T0329 numbered 1 through 239 Created new target T0329 from T0329.a2m # command:CPU_time= 6.165 sec, elapsed time= 6.239 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ah5A/T0329-2ah5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ah5A expands to /projects/compbio/data/pdb/2ah5.pdb.gz 2ah5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0329 read from 2ah5A/T0329-2ah5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ah5A read from 2ah5A/T0329-2ah5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ah5A to template set # found chain 2ah5A in template set Warning: unaligning (T0329)N133 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0329)K134 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0329 2 :KYKAAIFDMDGTILDTSADLTSALNYAFEQTGHR 2ah5A 3 :SITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVP # choosing archetypes in rotamer library T0329 37 :DFTVEDIKNFFGSGVVVAVTR 2ah5A 37 :SPDAKTIRGFMGPPLESSFAT T0329 83 :AVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQK 2ah5A 58 :CLSKDQISEAVQIYRSYYKAKGIYEAQLFPQIIDLLEELSSS T0329 126 :VKLAVVS 2ah5A 100 :YPLYITT T0329 135 :PNEAVQVLVEEL 2ah5A 109 :DTSTAQDMAKNL T0329 147 :FPGSFDFALGEKSGIRRK 2ah5A 122 :IHHFFDGIYGSSPEAPHK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRSVPFLQKHGATVIVDTAEKLEEA 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLNYQPDYIAHKPLEVLAY Number of specific fragments extracted= 7 number of extra gaps= 1 total=7 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ah5A/T0329-2ah5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2ah5A/T0329-2ah5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ah5A read from 2ah5A/T0329-2ah5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ah5A in template set Warning: unaligning (T0329)N133 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0329)K134 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0329 2 :KYKAAIFDMDGTILDTSADLTSALNYAFEQTGHRH 2ah5A 3 :SITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVPS T0329 38 :FTVEDIKNFFGSGVVVAVTRAL 2ah5A 38 :PDAKTIRGFMGPPLESSFATCL T0329 85 :TQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQK 2ah5A 60 :SKDQISEAVQIYRSYYKAKGIYEAQLFPQIIDLLEELSSS T0329 126 :VKLAVVS 2ah5A 100 :YPLYITT T0329 135 :PNEAVQVLVEEL 2ah5A 109 :DTSTAQDMAKNL T0329 147 :FPGSFDFALGEKSGIRRK 2ah5A 122 :IHHFFDGIYGSSPEAPHK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRSVPFLQKHGATVIVDTAEKLEEA 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLNYQPDYIAHKPLEVLAY Number of specific fragments extracted= 7 number of extra gaps= 1 total=14 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ah5A/T0329-2ah5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2ah5A/T0329-2ah5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ah5A read from 2ah5A/T0329-2ah5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ah5A in template set Warning: unaligning (T0329)N133 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0329)K134 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0329 3 :YKAAIFDMDGTILDTSADLTSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVA 2ah5A 4 :ITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVPSPDAKTIRGFMGPPLESSF T0329 81 :PEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQK 2ah5A 56 :ATCLSKDQISEAVQIYRSYYKAKGIYEAQLFPQIIDLLEELSSS T0329 126 :VKLAVVS 2ah5A 100 :YPLYITT T0329 135 :PNEAVQVLVE 2ah5A 109 :DTSTAQDMAK T0329 145 :ELFPGSFDFALGEKSGIRRK 2ah5A 120 :LEIHHFFDGIYGSSPEAPHK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRSVPFLQKHGATVIVDTAEKLEEA 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLNYQPDYIAHKPLEVLAY Number of specific fragments extracted= 6 number of extra gaps= 1 total=20 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gfhA/T0329-2gfhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gfhA expands to /projects/compbio/data/pdb/2gfh.pdb.gz 2gfhA:Skipped atom 62, because occupancy 0.5 <= existing 0.500 in 2gfhA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 2gfhA # T0329 read from 2gfhA/T0329-2gfhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gfhA read from 2gfhA/T0329-2gfhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gfhA to template set # found chain 2gfhA in template set Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0329)S65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0329 2 :KYKAAI 2gfhA 5 :RVRAVF T0329 10 :MDGTILDTSADLTSALNYAFEQTGHRHDFT 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLLQSKYHYK T0329 49 :SGVVVAVTRALA 2gfhA 43 :EEAEIICDKVQV T0329 66 :SRESLVAFGTKD 2gfhA 68 :ITDVRTSHWEEA T0329 78 :EQIPE 2gfhA 81 :QETKG T0329 83 :AVTQTEVNRVLEVFKPYYAD 2gfhA 87 :ADNRKLAEECYFLWKSTRLQ T0329 107 :KTGPFPGILDLMKNLRQK 2gfhA 107 :HMILADDVKAMLTELRKE T0329 126 :VKLAVVSNKPNEAVQVLVEEL 2gfhA 125 :VRLLLLTNGDRQTQREKIEAC T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSE 2gfhA 147 :CQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTL T0329 192 :IDIQTARNSEMDEIAVNWGFRS 2gfhA 193 :TDIQGGLNAGLKATVWINKSGR T0329 222 :ATVIVDTAEKLEEAILG 2gfhA 223 :PHYMVSSVLELPALLQS Number of specific fragments extracted= 11 number of extra gaps= 1 total=31 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gfhA/T0329-2gfhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2gfhA/T0329-2gfhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gfhA read from 2gfhA/T0329-2gfhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gfhA in template set Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0329)E62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gfhA)C67 Warning: unaligning (T0329)R67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0329 2 :KYKAAI 2gfhA 5 :RVRAVF T0329 10 :MDGTILDTSADLTSALNYAFEQT 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLL T0329 33 :GHRHDFTVEDIKNFF 2gfhA 38 :KYHYKEEAEIICDKV T0329 52 :VVAVTRAL 2gfhA 53 :QVKLSKEC T0329 61 :Y 2gfhA 61 :F T0329 68 :ESLVAFGTKDEQIPEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQK 2gfhA 68 :ITDVRTSHWEEAIQETKGGADNRKLAEECYFLWKSTRLQHMILADDVKAMLTELRKE T0329 126 :VKLAVVSNKPNEAVQVLVEEL 2gfhA 125 :VRLLLLTNGDRQTQREKIEAC T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSE 2gfhA 147 :CQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTL T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFLQKHGATVIVDTAEKLEEAI 2gfhA 193 :TDIQGGLNAGLKATVWINKSGRVPLTSSPMPHYMVSSVLELPALL Number of specific fragments extracted= 9 number of extra gaps= 1 total=40 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gfhA/T0329-2gfhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2gfhA/T0329-2gfhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gfhA read from 2gfhA/T0329-2gfhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gfhA in template set Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0329)E62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gfhA)C67 Warning: unaligning (T0329)R67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0329 2 :KYKAAI 2gfhA 5 :RVRAVF T0329 10 :MDGTILDTSADLTSALNYAFEQT 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLL T0329 33 :GHRHDFTVEDIKN 2gfhA 38 :KYHYKEEAEIICD T0329 51 :VVVAVTRALAY 2gfhA 51 :KVQVKLSKECF T0329 68 :ESLVAFGTKDEQIPEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQK 2gfhA 68 :ITDVRTSHWEEAIQETKGGADNRKLAEECYFLWKSTRLQHMILADDVKAMLTELRKE T0329 126 :VKLAVVSNKPNEAVQVLVE 2gfhA 125 :VRLLLLTNGDRQTQREKIE T0329 145 :ELFPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSE 2gfhA 145 :CACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTL T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPF 2gfhA 193 :TDIQGGLNAGLKATVWINKSGRVPL T0329 218 :QKHGATVIVDTAEKLEEAIL 2gfhA 219 :SSPMPHYMVSSVLELPALLQ Number of specific fragments extracted= 9 number of extra gaps= 1 total=49 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fdrA/T0329-2fdrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fdrA expands to /projects/compbio/data/pdb/2fdr.pdb.gz 2fdrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 614, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 616, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 2fdrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1330, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1336, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 2fdrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0329 read from 2fdrA/T0329-2fdrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fdrA read from 2fdrA/T0329-2fdrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fdrA to template set # found chain 2fdrA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0329 3 :YKAAI 2fdrA 4 :FDLII T0329 10 :MDGTILDTSADLTSALNYAFEQTGHR 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYP T0329 38 :FTVED 2fdrA 37 :ISVEE T0329 43 :IKNFFGSGVVVAVTRALAYE 2fdrA 43 :GERFAGMTWKNILLQVESEA T0329 64 :GS 2fdrA 63 :SI T0329 83 :AVTQTEVNRVLEVFKPY 2fdrA 65 :PLSASLLDKSEKLLDMR T0329 104 :CQIKTGPFPGILDLMKNL 2fdrA 82 :LERDVKIIDGVKFALSRL T0329 126 :VKLAVVSNKPNEAVQVLVEEL 2fdrA 101 :TPRCICSNSSSHRLDMMLTKV T0329 147 :FPGSF 2fdrA 123 :LKPYF T0329 152 :DFALG 2fdrA 129 :PHIYS T0329 157 :EKSGIRRK 2fdrA 138 :GADRVKPK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRS 2fdrA 146 :PDIFLHGAAQFGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHT T0329 214 :VPFLQKHGATVIVDTAEKLEEAILG 2fdrA 197 :ADRLTDAGAETVISRMQDLPAVIAA Number of specific fragments extracted= 13 number of extra gaps= 1 total=62 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fdrA/T0329-2fdrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2fdrA/T0329-2fdrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fdrA read from 2fdrA/T0329-2fdrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fdrA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0329 3 :YKAAI 2fdrA 4 :FDLII T0329 10 :MDGTILDTSADLTSALNYAFEQTGHR 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYP T0329 38 :FTVEDI 2fdrA 37 :ISVEEM T0329 44 :KNFFGSGVVVAVTRAL 2fdrA 44 :ERFAGMTWKNILLQVE T0329 78 :EQIPEAVTQTEVNRVLEVFKPYYADH 2fdrA 60 :SEASIPLSASLLDKSEKLLDMRLERD T0329 108 :TGPFPGILDLMKNL 2fdrA 86 :VKIIDGVKFALSRL T0329 125 :GVKLAVVSNKPNEAVQVLVEEL 2fdrA 100 :TTPRCICSNSSSHRLDMMLTKV T0329 147 :FPGSF 2fdrA 123 :LKPYF T0329 152 :DFALG 2fdrA 129 :PHIYS T0329 157 :EKSGIRRK 2fdrA 138 :GADRVKPK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNW 2fdrA 146 :PDIFLHGAAQFGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTG T0329 210 :GFRSVPFLQKHGATVIVDTAEKLEEAI 2fdrA 193 :YPSHADRLTDAGAETVISRMQDLPAVI Number of specific fragments extracted= 12 number of extra gaps= 1 total=74 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fdrA/T0329-2fdrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2fdrA/T0329-2fdrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fdrA read from 2fdrA/T0329-2fdrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fdrA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0329 3 :YKAAI 2fdrA 4 :FDLII T0329 10 :MDGTILDTSADLTSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRA 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYPISVEEMGERFAGMTWKNILLQVE T0329 78 :EQIPEAVTQTEVNRVLEVFKPYYAD 2fdrA 60 :SEASIPLSASLLDKSEKLLDMRLER T0329 107 :KTGPFPGILDLMKNL 2fdrA 85 :DVKIIDGVKFALSRL T0329 125 :GVKLAVVSNKPNEAVQVLVE 2fdrA 100 :TTPRCICSNSSSHRLDMMLT T0329 145 :ELFPGSF 2fdrA 121 :VGLKPYF T0329 152 :DFALGE 2fdrA 129 :PHIYSA T0329 160 :GIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRS 2fdrA 139 :ADRVKPKPDIFLHGAAQFGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHT T0329 214 :VPFLQKHGATVIVDTAEKLEEAI 2fdrA 197 :ADRLTDAGAETVISRMQDLPAVI Number of specific fragments extracted= 9 number of extra gaps= 1 total=83 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1te2A/T0329-1te2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1te2A expands to /projects/compbio/data/pdb/1te2.pdb.gz 1te2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 79, because occupancy 0.470 <= existing 0.530 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 83, because occupancy 0.490 <= existing 0.510 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 87, because occupancy 0.440 <= existing 0.560 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 89, because occupancy 0.420 <= existing 0.580 in 1te2A Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 207, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 209, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 213, because occupancy 0.450 <= existing 0.550 in 1te2A Skipped atom 215, because occupancy 0.480 <= existing 0.520 in 1te2A Skipped atom 217, because occupancy 0.480 <= existing 0.520 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 420, because occupancy 0.480 <= existing 0.520 in 1te2A Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 426, because occupancy 0.490 <= existing 0.510 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 542, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 544, because occupancy 0.490 <= existing 0.510 in 1te2A Skipped atom 546, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 552, because occupancy 0.480 <= existing 0.520 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 996, because occupancy 0.500 <= existing 0.500 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 998, because occupancy 0.490 <= existing 0.510 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1000, because occupancy 0.500 <= existing 0.500 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0329 read from 1te2A/T0329-1te2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1te2A read from 1te2A/T0329-1te2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1te2A to template set # found chain 1te2A in template set Warning: unaligning (T0329)E145 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0329)L146 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0329 2 :KYKAAIFDMDGTILDTSADLTSALNYAFEQTGHR 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVD T0329 40 :VEDIKNF 1te2A 40 :ISRRNEL T0329 47 :FGSGVVVAVTRALAYE 1te2A 50 :LGLRIDMVVDLWYARQ T0329 64 :GS 1te2A 66 :PW T0329 82 :EAVTQTE 1te2A 68 :NGPSRQE T0329 92 :VLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1te2A 75 :VVERVIARAISLVEETRPLLPGVREAVALCKEQGLLVGLASASPLHMLEKVLT T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWG 1te2A 131 :LRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVNGMIASKAARMRSIVVPAP T0329 211 :FRSVPFLQK 1te2A 196 :AQNDPRFVL T0329 222 :ATVIVDTAEKL 1te2A 205 :ANVKLSSLTEL T0329 233 :EEAIL 1te2A 217 :AKDLL Number of specific fragments extracted= 10 number of extra gaps= 1 total=93 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1te2A/T0329-1te2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1te2A/T0329-1te2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1te2A read from 1te2A/T0329-1te2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1te2A in template set Warning: unaligning (T0329)E145 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0329)L146 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0329 2 :KYKAAIFDMDGTILDTSADLTSALNYAFEQTGHRHD 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDIS T0329 38 :FT 1te2A 46 :LP T0329 47 :FGSGVVVAVTRAL 1te2A 50 :LGLRIDMVVDLWY T0329 80 :IPEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1te2A 63 :ARQPWNGPSRQEVVERVIARAISLVEETRPLLPGVREAVALCKEQGLLVGLASASPLHMLEKVLT T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGF 1te2A 131 :LRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVNGMIASKAARMRSIVVPAPE T0329 212 :RSVPFLQK 1te2A 197 :QNDPRFVL T0329 222 :ATVIVDTAEKL 1te2A 205 :ANVKLSSLTEL T0329 233 :EEAI 1te2A 217 :AKDL Number of specific fragments extracted= 8 number of extra gaps= 1 total=101 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1te2A/T0329-1te2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1te2A/T0329-1te2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1te2A read from 1te2A/T0329-1te2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1te2A in template set Warning: unaligning (T0329)E145 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0329 2 :KYKAAIFDMDGTILDTSADLTSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTR 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDISRRNELPDTLGLRIDMVVDLW T0329 79 :QIPEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1te2A 62 :YARQPWNGPSRQEVVERVIARAISLVEETRPLLPGVREAVALCKEQGLLVGLASASPLHMLEKVLT T0329 146 :LFPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFR 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVNGMIASKAARMRSIVVPAPEA T0329 213 :SVPFL 1te2A 198 :NDPRF T0329 220 :HGATVIVDTAEK 1te2A 203 :VLANVKLSSLTE Number of specific fragments extracted= 5 number of extra gaps= 1 total=106 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o08A/T0329-1o08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1o08A/T0329-1o08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o08A read from 1o08A/T0329-1o08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o08A in training set Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 Warning: unaligning (T0329)G238 because of BadResidue code BAD_PEPTIDE in next template residue (1o08A)K1219 T0329 1 :M 1o08A 1001 :M T0329 3 :YKAAI 1o08A 1002 :FKAVL T0329 10 :MDGTILDTSADLTSALNYAFEQTGHR 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGIN T0329 37 :DFTVEDIKNFFGSGVVVAVTRALAYE 1o08A 1035 :GVDRQFNEQLKGVSREDSLQKILDLA T0329 81 :PEAVTQTEVNRVLEVFKPYYADHC 1o08A 1061 :DKKVSAEEFKELAKRKNDNYVKMI T0329 105 :QIKTGPFPGILDLMKNLRQKGVKLAVVSNK 1o08A 1087 :VSPADVYPGILQLLKDLRSNKIKIALASAS T0329 137 :EAVQVLVEEL 1o08A 1117 :KNGPFLLERM T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 1o08A 1128 :LTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIG T0329 211 :FRSVPFLQK 1o08A 1188 :VGRPEDLGD T0329 222 :ATVIVDTAEK 1o08A 1197 :DIVIVPDTSH T0329 232 :LEEAIL 1o08A 1212 :LKEVWL Number of specific fragments extracted= 11 number of extra gaps= 2 total=117 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o08A/T0329-1o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1o08A/T0329-1o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o08A read from 1o08A/T0329-1o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o08A in training set Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 Warning: unaligning (T0329)G238 because of BadResidue code BAD_PEPTIDE in next template residue (1o08A)K1219 Warning: unaligning (T0329)E239 because of BadResidue code BAD_PEPTIDE at template residue (1o08A)K1219 T0329 1 :M 1o08A 1001 :M T0329 3 :YKAAI 1o08A 1002 :FKAVL T0329 10 :MDGTILDTSADLTSALNYAFEQTGHR 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGIN T0329 37 :DFTVEDIKNFFGSGVVVAVTRAL 1o08A 1035 :GVDRQFNEQLKGVSREDSLQKIL T0329 78 :EQIPEAVTQTEVNRVLEVFKPYYADHCQI 1o08A 1058 :DLADKKVSAEEFKELAKRKNDNYVKMIQD T0329 108 :TG 1o08A 1087 :VS T0329 110 :PFPGILDLMKNLRQKGVKLAVVSNK 1o08A 1092 :VYPGILQLLKDLRSNKIKIALASAS T0329 137 :EAVQVLVEEL 1o08A 1117 :KNGPFLLERM T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAV 1o08A 1128 :LTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGV T0329 212 :RSVPFLQK 1o08A 1189 :GRPEDLGD T0329 222 :ATVIVDTAEK 1o08A 1197 :DIVIVPDTSH T0329 232 :LEEAIL 1o08A 1212 :LKEVWL Number of specific fragments extracted= 12 number of extra gaps= 2 total=129 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o08A/T0329-1o08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1o08A/T0329-1o08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o08A read from 1o08A/T0329-1o08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o08A in training set Warning: unaligning (T0329)K2 because first residue in template chain is (1o08A)M1001 Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 Warning: unaligning (T0329)G238 because of BadResidue code BAD_PEPTIDE in next template residue (1o08A)K1219 T0329 3 :YKAAI 1o08A 1002 :FKAVL T0329 10 :MDGTILDTSADLTSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVT 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQK T0329 76 :KDEQIPEAVTQTEVNRVLEVFKPYYADHCQI 1o08A 1056 :ILDLADKKVSAEEFKELAKRKNDNYVKMIQD T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSNK 1o08A 1089 :PADVYPGILQLLKDLRSNKIKIALASAS T0329 137 :EAVQVLVE 1o08A 1117 :KNGPFLLE T0329 145 :ELFPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAV 1o08A 1126 :MNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGV T0329 212 :RSVPFL 1o08A 1189 :GRPEDL T0329 220 :HGATVIVDTA 1o08A 1195 :GDDIVIVPDT T0329 230 :EKLEEAIL 1o08A 1210 :EFLKEVWL Number of specific fragments extracted= 9 number of extra gaps= 2 total=138 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1swvA/T0329-1swvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1swvA expands to /projects/compbio/data/pdb/1swv.pdb.gz 1swvA:# T0329 read from 1swvA/T0329-1swvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1swvA read from 1swvA/T0329-1swvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1swvA to template set # found chain 1swvA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1swvA)K5 T0329 3 :YKAAIFDMDGTILD 1swvA 6 :IEAVIFAWAGTTVD T0329 17 :TSADLTSALNYAFEQTGHR 1swvA 21 :GCFAPLEVFMEIFHKRGVA T0329 38 :FTVEDIKNFFGSGVVVAVTRALAYE 1swvA 40 :ITAEEARKPMGLLKIDHVRALTEMP T0329 64 :GSSRESLVAFGT 1swvA 65 :RIASEWNRVFRQ T0329 83 :AVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1swvA 77 :LPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0329 147 :FPGS 1swvA 142 :LQGY T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGV 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0329 180 :PRDKCVYIGDSEIDIQTARNSEMDEIAVNWG 1swvA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0329 211 :FRSVPFLQKHG 1swvA 212 :GLTEEEVENMD T0329 222 :ATVIVDTAEKLEEAILG 1swvA 242 :AHFTIETMQELESVMEH Number of specific fragments extracted= 10 number of extra gaps= 0 total=148 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1swvA/T0329-1swvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1swvA/T0329-1swvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1swvA read from 1swvA/T0329-1swvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1swvA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1swvA)K5 T0329 3 :YKAAIFDMDGTILDTS 1swvA 6 :IEAVIFAWAGTTVDYG T0329 19 :ADLTSALNYAFEQTGHR 1swvA 23 :FAPLEVFMEIFHKRGVA T0329 38 :FTVEDIKNFFGSGVVVAVTRAL 1swvA 40 :ITAEEARKPMGLLKIDHVRALT T0329 68 :ESLVAFGTKDEQIPEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1swvA 62 :EMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0329 147 :FPGS 1swvA 142 :LQGY T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGVPR 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGVYP T0329 182 :DKCVYIGDSEIDIQTARNSEMDEIAVNWGFR 1swvA 179 :NHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0329 213 :SVPFLQKHGATVIVDTAEKLEEAI 1swvA 233 :VRNRFVENGAHFTIETMQELESVM Number of specific fragments extracted= 8 number of extra gaps= 0 total=156 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1swvA/T0329-1swvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1swvA/T0329-1swvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1swvA read from 1swvA/T0329-1swvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1swvA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1swvA)K5 T0329 3 :YKAAIFDMDGTILDTS 1swvA 6 :IEAVIFAWAGTTVDYG T0329 20 :DL 1swvA 23 :FA T0329 22 :TSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRALAY 1swvA 26 :LEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPR T0329 72 :AFGTKDEQIPEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1swvA 66 :IASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAK T0329 145 :ELFP 1swvA 143 :QGYK T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGV 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0329 180 :PRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFR 1swvA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0329 213 :SVPF 1swvA 214 :TEEE T0329 217 :LQKHGATVIVDTAEKLEEAIL 1swvA 237 :FVENGAHFTIETMQELESVME Number of specific fragments extracted= 9 number of extra gaps= 0 total=165 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x42A/T0329-1x42A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x42A expands to /projects/compbio/data/pdb/1x42.pdb.gz 1x42A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0329 read from 1x42A/T0329-1x42A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x42A read from 1x42A/T0329-1x42A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x42A to template set # found chain 1x42A in template set T0329 1 :M 1x42A 1 :M T0329 3 :YKAAIFDMDGTILDTSAD 1x42A 2 :IRAVFFDFVGTLLSVEGE T0329 22 :TSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRALAYEAGSSRESLVAFGTKDEQIPE 1x42A 20 :AKTHLKIMEEVLGDYPLNPKTLLDEYEKLTREAFSNYAGKPYRPIRDIEEEVMRKLAEKYG T0329 83 :AVTQTEVNRVLEVFKPY 1x42A 82 :KYPENFWEIHLRMHQRY T0329 108 :TGPFPGILDLMKNLRQK 1x42A 99 :GELYPEVVEVLKSLKGK T0329 126 :VKLAVVSNKPNEAVQVLVEEL 1x42A 116 :YHVGMITDSDTEYLMAHLDAL T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSE 1x42A 138 :IKDLFDSITTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNP T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFLQK 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFWDK T0329 222 :ATVIVDTAEKLEEAILG 1x42A 212 :CDFIVSDLREVIKIVDE Number of specific fragments extracted= 9 number of extra gaps= 0 total=174 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x42A/T0329-1x42A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1x42A/T0329-1x42A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x42A read from 1x42A/T0329-1x42A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x42A in template set T0329 1 :M 1x42A 1 :M T0329 3 :YKAAIFDMDGTIL 1x42A 2 :IRAVFFDFVGTLL T0329 17 :TSADLTSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRAL 1x42A 15 :SVEGEAKTHLKIMEEVLGDYPLNPKTLLDEYEKLTREAFSNYA T0329 63 :AGSSRES 1x42A 58 :GKPYRPI T0329 82 :EAVTQTEVNRVLEV 1x42A 65 :RDIEEEVMRKLAEK T0329 96 :FKPYYADHCQIKTGPFPGILDLMKNLRQK 1x42A 87 :FWEIHLRMHQRYGELYPEVVEVLKSLKGK T0329 126 :VKLAVVSNKPNEAVQVLVEEL 1x42A 116 :YHVGMITDSDTEYLMAHLDAL T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSE 1x42A 138 :IKDLFDSITTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNP T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFLQK 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFWDK T0329 222 :ATVIVDTAEKLEEAI 1x42A 212 :CDFIVSDLREVIKIV Number of specific fragments extracted= 10 number of extra gaps= 0 total=184 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x42A/T0329-1x42A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1x42A/T0329-1x42A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x42A read from 1x42A/T0329-1x42A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x42A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1x42A)M1 T0329 3 :YKAAIFDMDGTILD 1x42A 2 :IRAVFFDFVGTLLS T0329 18 :SADLTSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAV 1x42A 16 :VEGEAKTHLKIMEEVLGDYPLNPKTLLDEYEKLTREAF T0329 71 :VAFGTKDEQIPEAVTQTEVNRVLEV 1x42A 54 :SNYAGKPYRPIRDIEEEVMRKLAEK T0329 96 :FKPYYADHCQIKTGPFPGILDLMKNLRQK 1x42A 87 :FWEIHLRMHQRYGELYPEVVEVLKSLKGK T0329 126 :VKLAVVSNKPNEAVQVLVE 1x42A 116 :YHVGMITDSDTEYLMAHLD T0329 145 :ELFPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSE 1x42A 136 :LGIKDLFDSITTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNP T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFL 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFW T0329 220 :HGATVIVDTAEKLEEAIL 1x42A 210 :DKCDFIVSDLREVIKIVD Number of specific fragments extracted= 8 number of extra gaps= 0 total=192 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zrn/T0329-1zrn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zrn expands to /projects/compbio/data/pdb/1zrn.pdb.gz 1zrn:Warning: there is no chain 1zrn will retry with 1zrnA # T0329 read from 1zrn/T0329-1zrn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zrn read from 1zrn/T0329-1zrn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zrn to template set # found chain 1zrn in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1zrn)Y3 Warning: unaligning (T0329)I236 because last residue in template chain is (1zrn)F222 T0329 3 :YKAAIFDMDGTILDTSAD 1zrn 4 :IKGIAFDLYGTLFDVHSV T0329 26 :NYAFEQTGHR 1zrn 22 :VGRCDEAFPG T0329 38 :F 1zrn 32 :R T0329 40 :VEDIKNFF 1zrn 33 :GREISALW T0329 48 :GSGVVVAVTRALAYEAGSSRESLVAFGTKDEQIPE 1zrn 42 :QKQLEYTWLRSLMNRYVNFQQATEDALRFTCRHLG T0329 83 :AVTQTEVNRVLEVFKP 1zrn 78 :DLDARTRSTLCDAYLR T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1zrn 94 :LAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHA T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRS 1zrn 134 :LRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAWDATGARYFGFPTCWINRTGNV T0329 220 :HGATVIVDTAEKLEEA 1zrn 206 :QTPDWEVTSLRAVVEL Number of specific fragments extracted= 9 number of extra gaps= 0 total=201 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zrn/T0329-1zrn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1zrn/T0329-1zrn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zrn read from 1zrn/T0329-1zrn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zrn in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1zrn)Y3 Warning: unaligning (T0329)I236 because last residue in template chain is (1zrn)F222 T0329 3 :YKAAIFDMDGTILDTSADLTSALNY 1zrn 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0329 34 :HR 1zrn 29 :FP T0329 37 :D 1zrn 31 :G T0329 39 :TVEDIKNFFGSGVVVAVTRALAYEAGSSRE 1zrn 32 :RGREISALWRQKQLEYTWLRSLMNRYVNFQ T0329 69 :SLVAFGTKDEQIPEAVTQTEVNRVLE 1zrn 64 :TEDALRFTCRHLGLDLDARTRSTLCD T0329 103 :HCQI 1zrn 90 :AYLR T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1zrn 94 :LAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHA T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRSVPF 1zrn 134 :LRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAWDATGARYFGFPTCWINRTGNVFEE T0329 218 :QKHGATVIVDTAEKLEEA 1zrn 204 :MGQTPDWEVTSLRAVVEL Number of specific fragments extracted= 9 number of extra gaps= 0 total=210 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zrn/T0329-1zrn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1zrn/T0329-1zrn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zrn read from 1zrn/T0329-1zrn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zrn in template set T0329 3 :YKAAIFDMDGTILDTSADLTSALNY 1zrn 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0329 34 :HRHDFTVEDIKNFFGSGVVVAVTRALAYEAGSSRESLVAFGTKDEQIPEAVTQTEVNRVLE 1zrn 29 :FPGRGREISALWRQKQLEYTWLRSLMNRYVNFQQATEDALRFTCRHLGLDLDARTRSTLCD T0329 104 :CQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1zrn 90 :AYLRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVS T0329 145 :ELFPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRSVPFL 1zrn 132 :AGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAWDATGARYFGFPTCWINRTGNVFEEM T0329 219 :KHGATVIVDTAEKLEEA 1zrn 205 :GQTPDWEVTSLRAVVEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=215 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rdfA/T0329-1rdfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rdfA expands to /projects/compbio/data/pdb/1rdf.pdb.gz 1rdfA:# T0329 read from 1rdfA/T0329-1rdfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdfA read from 1rdfA/T0329-1rdfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rdfA to template set # found chain 1rdfA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0329)P180 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0329 3 :YKAAIFDMDGTILDTSADL 1rdfA 6 :IEAVIFDWAGTTVDYGCFA T0329 22 :TSALNYAFEQTGHR 1rdfA 26 :LEVFMEIFHKRGVA T0329 38 :FTVEDI 1rdfA 40 :ITAEEA T0329 44 :KNF 1rdfA 58 :RAL T0329 49 :SGVVVAVTRALAYE 1rdfA 61 :TEMPRIASEWNRVF T0329 64 :GS 1rdfA 75 :RQ T0329 83 :AVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1rdfA 77 :LPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0329 147 :FPGS 1rdfA 142 :LQGY T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGV 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0329 181 :RDKCVYIGDSEIDIQTARNSEMDEIAVNWG 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0329 211 :FR 1rdfA 212 :GL T0329 214 :VPFLQKHGATVIVDTAEKLEEAILG 1rdfA 234 :RNRFVENGAHFTIETMQELESVMEH Number of specific fragments extracted= 12 number of extra gaps= 1 total=227 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rdfA/T0329-1rdfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1rdfA/T0329-1rdfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdfA read from 1rdfA/T0329-1rdfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rdfA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0329)P180 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0329 3 :YKAAIFDMDGTILDTS 1rdfA 6 :IEAVIFDWAGTTVDYG T0329 19 :ADLTSALNYAFEQTGHR 1rdfA 23 :FAPLEVFMEIFHKRGVA T0329 38 :FTVEDI 1rdfA 40 :ITAEEA T0329 48 :GSGVVVAVT 1rdfA 63 :MPRIASEWN T0329 78 :EQIPEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1rdfA 72 :RVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0329 147 :FPGS 1rdfA 142 :LQGY T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGV 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0329 181 :RDKCVYIGDSEIDIQTARNSEMDEIAVNWGFR 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0329 213 :SVPFLQKHGATVIVDTAEKLEEAI 1rdfA 233 :VRNRFVENGAHFTIETMQELESVM Number of specific fragments extracted= 9 number of extra gaps= 1 total=236 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rdfA/T0329-1rdfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1rdfA/T0329-1rdfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdfA read from 1rdfA/T0329-1rdfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rdfA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0329)P180 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0329 3 :YKAAIFDMDGTILDTSADL 1rdfA 6 :IEAVIFDWAGTTVDYGCFA T0329 22 :TSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRA 1rdfA 26 :LEVFMEIFHKRGVAITAEEARKPMPLLKIDHVRALTE T0329 69 :SLVAFGTKDEQIPEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1rdfA 63 :MPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAK T0329 145 :ELFP 1rdfA 143 :QGYK T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGV 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0329 181 :RDKCVYIGDSEIDIQTARNSEMDEIAVNWGFR 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0329 214 :VPFLQKHGATVIVDTAEKLEEAIL 1rdfA 234 :RNRFVENGAHFTIETMQELESVME Number of specific fragments extracted= 7 number of extra gaps= 1 total=243 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2go7A/T0329-2go7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2go7A expands to /projects/compbio/data/pdb/2go7.pdb.gz 2go7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0329 read from 2go7A/T0329-2go7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2go7A read from 2go7A/T0329-2go7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2go7A to template set # found chain 2go7A in template set Warning: unaligning (T0329)Y3 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0329)V130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0329)V131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0329 4 :KAAI 2go7A 4 :TAFI T0329 10 :MDGTILDTSADLTSALNYAFEQTGHR 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIP T0329 38 :FTVEDIKNFF 2go7A 36 :YDKEKVREFI T0329 48 :GSGVVVAVTRALAYE 2go7A 47 :KYSVQDLLVRVAEDR T0329 83 :AVTQTEVNRVL 2go7A 62 :NLDVEVLNQVR T0329 97 :KPYYAD 2go7A 73 :AQSLAE T0329 104 :CQIKTGPFPGILDLMKNLRQKGVKLA 2go7A 79 :KNAQVVLMPGAREVLAWADESGIQQF T0329 132 :SNKPN 2go7A 107 :THKGN T0329 138 :AVQVLVEEL 2go7A 112 :NAFTILKDL T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 2go7A 122 :VESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTLDVEFAQNSGIQSIN T0329 211 :FRSV 2go7A 182 :FLES T0329 219 :KHGATVIVDTAEKLEEAIL 2go7A 186 :TYEGNHRIQALADISRIFE Number of specific fragments extracted= 12 number of extra gaps= 2 total=255 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2go7A/T0329-2go7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2go7A/T0329-2go7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2go7A read from 2go7A/T0329-2go7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2go7A in template set Warning: unaligning (T0329)Y3 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0329)V130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0329)V131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0329 4 :KAAI 2go7A 4 :TAFI T0329 10 :MDGTILDTSADLTSALNYAFEQTGHR 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIP T0329 38 :FTVEDIKNFFGS 2go7A 36 :YDKEKVREFIFK T0329 50 :GVVVAVTRAL 2go7A 49 :SVQDLLVRVA T0329 81 :P 2go7A 59 :E T0329 84 :VTQTEVNRVLEVFKPYYADHCQI 2go7A 60 :DRNLDVEVLNQVRAQSLAEKNAQ T0329 108 :TGPFPGILDLMKNLRQKGVKLA 2go7A 83 :VVLMPGAREVLAWADESGIQQF T0329 132 :SNKP 2go7A 107 :THKG T0329 137 :EAVQVLVEEL 2go7A 111 :NNAFTILKDL T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVN 2go7A 122 :VESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTLDVEFAQNSGIQSINFL T0329 211 :FRSVP 2go7A 184 :ESTYE T0329 222 :ATVIVDTAEKLEEAI 2go7A 189 :GNHRIQALADISRIF Number of specific fragments extracted= 12 number of extra gaps= 2 total=267 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2go7A/T0329-2go7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2go7A/T0329-2go7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2go7A read from 2go7A/T0329-2go7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2go7A in template set Warning: unaligning (T0329)Y3 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0329)V130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0329)V131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0329 4 :KAAI 2go7A 4 :TAFI T0329 10 :MDGTILDTSADLTSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRA 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIPYDKEKVREFIFKYSVQDLLVRVA T0329 80 :IPEAVTQTEVNRVLEV 2go7A 59 :EDRNLDVEVLNQVRAQ T0329 100 :YADHCQIKTGPFPGILDLMKNLRQKGVKLA 2go7A 75 :SLAEKNAQVVLMPGAREVLAWADESGIQQF T0329 132 :SNKP 2go7A 107 :THKG T0329 137 :EAVQVLVE 2go7A 111 :NNAFTILK T0329 145 :ELFPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGF 2go7A 120 :LGVESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTLDVEFAQNSGIQSINFLEST T0329 220 :HGATVIVDTAEKLEEAIL 2go7A 187 :YEGNHRIQALADISRIFE Number of specific fragments extracted= 8 number of extra gaps= 2 total=275 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fi1A/T0329-2fi1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fi1A expands to /projects/compbio/data/pdb/2fi1.pdb.gz 2fi1A:# T0329 read from 2fi1A/T0329-2fi1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fi1A read from 2fi1A/T0329-2fi1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fi1A to template set # found chain 2fi1A in template set T0329 1 :MKYKAAIFDMDGTILDTSADLTSALNYAFEQTGHR 2fi1A 4 :MKYHDYIWDLGGTLLDNYETSTAAFVETLALYGIT T0329 38 :FTVEDIKNFFGSGVVVAVTRALAYE 2fi1A 39 :QDHDSVYQALKVSTPFAIETFAPNL T0329 64 :GSS 2fi1A 64 :ENF T0329 86 :QTEVNRVLEV 2fi1A 67 :LEKYKENEAR T0329 104 :CQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNE 2fi1A 77 :ELEHPILFEGVSDLLEDISNQGGRHFLVSHRNDQ T0329 139 :VQVLVEEL 2fi1A 111 :VLEILEKT T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPR 2fi1A 120 :IAAYFTEVVTSSSGFKRKPNPESMLYLREKYQISS T0329 184 :CVYIGDSEIDIQTARNSEMDEIA 2fi1A 155 :GLVIGDRPIDIEAGQAAGLDTHL T0329 226 :VDTAEKLEEAI 2fi1A 178 :FTSIVNLRQVL Number of specific fragments extracted= 9 number of extra gaps= 0 total=284 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fi1A/T0329-2fi1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2fi1A/T0329-2fi1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fi1A read from 2fi1A/T0329-2fi1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fi1A in template set T0329 1 :MKYKAAIFDMDGTILDTSADLTSALNYAFEQTGHR 2fi1A 4 :MKYHDYIWDLGGTLLDNYETSTAAFVETLALYGIT T0329 38 :FTVEDIKNFFGSGVVVAVTRAL 2fi1A 39 :QDHDSVYQALKVSTPFAIETFA T0329 82 :EAVTQ 2fi1A 61 :PNLEN T0329 92 :VLEVFKPYYADHCQI 2fi1A 66 :FLEKYKENEARELEH T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNE 2fi1A 81 :PILFEGVSDLLEDISNQGGRHFLVSHRNDQ T0329 139 :VQVLVEEL 2fi1A 111 :VLEILEKT T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVP 2fi1A 120 :IAAYFTEVVTSSSGFKRKPNPESMLYLREKYQIS T0329 183 :KCVYIGDSEIDIQTARNSEMDEIA 2fi1A 154 :SGLVIGDRPIDIEAGQAAGLDTHL T0329 226 :VDTAEKLEEAI 2fi1A 178 :FTSIVNLRQVL Number of specific fragments extracted= 9 number of extra gaps= 0 total=293 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fi1A/T0329-2fi1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2fi1A/T0329-2fi1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fi1A read from 2fi1A/T0329-2fi1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fi1A in template set T0329 1 :MKYKAAIFDMDGTILDTSADLTSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRA 2fi1A 4 :MKYHDYIWDLGGTLLDNYETSTAAFVETLALYGITQDHDSVYQALKVSTPFAIETFAP T0329 82 :EAVT 2fi1A 62 :NLEN T0329 92 :VLEVFK 2fi1A 66 :FLEKYK T0329 99 :YYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNE 2fi1A 72 :ENEARELEHPILFEGVSDLLEDISNQGGRHFLVSHRNDQ T0329 139 :VQVLVE 2fi1A 111 :VLEILE T0329 145 :ELFPGSFDFALGEKSGIRRKPAPDMTSECVKVLGV 2fi1A 118 :TSIAAYFTEVVTSSSGFKRKPNPESMLYLREKYQI T0329 182 :DKCVYIGDSEIDIQTARNSEMDE 2fi1A 153 :SSGLVIGDRPIDIEAGQAAGLDT T0329 224 :VIVDTAEKLEEAI 2fi1A 176 :HLFTSIVNLRQVL Number of specific fragments extracted= 8 number of extra gaps= 0 total=301 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq5A/T0329-1qq5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qq5A expands to /projects/compbio/data/pdb/1qq5.pdb.gz 1qq5A:Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 646, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 648, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 650, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 652, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 654, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 764, because occupancy 0.440 <= existing 0.560 in 1qq5A Skipped atom 766, because occupancy 0.440 <= existing 0.560 in 1qq5A Skipped atom 768, because occupancy 0.440 <= existing 0.560 in 1qq5A Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 1361, because occupancy 0.510 <= existing 0.530 in 1qq5A Skipped atom 1363, because occupancy 0.510 <= existing 0.530 in 1qq5A Skipped atom 1463, because occupancy 0.510 <= existing 0.530 in 1qq5A Skipped atom 1465, because occupancy 0.510 <= existing 0.530 in 1qq5A Skipped atom 1752, because occupancy 0.280 <= existing 0.720 in 1qq5A Skipped atom 1754, because occupancy 0.280 <= existing 0.720 in 1qq5A Skipped atom 1756, because occupancy 0.280 <= existing 0.720 in 1qq5A Skipped atom 1758, because occupancy 0.280 <= existing 0.720 in 1qq5A Skipped atom 1793, because occupancy 0.490 <= existing 0.510 in 1qq5A Skipped atom 1795, because occupancy 0.490 <= existing 0.510 in 1qq5A Skipped atom 1797, because occupancy 0.490 <= existing 0.510 in 1qq5A Skipped atom 1820, because occupancy 0.460 <= existing 0.540 in 1qq5A Skipped atom 1822, because occupancy 0.460 <= existing 0.540 in 1qq5A Skipped atom 1824, because occupancy 0.460 <= existing 0.540 in 1qq5A Skipped atom 1826, because occupancy 0.460 <= existing 0.540 in 1qq5A Skipped atom 1828, because occupancy 0.460 <= existing 0.540 in 1qq5A # T0329 read from 1qq5A/T0329-1qq5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq5A read from 1qq5A/T0329-1qq5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qq5A to template set # found chain 1qq5A in template set T0329 1 :M 1qq5A 1 :M T0329 3 :YKAAIFDMDGTILDTSAD 1qq5A 2 :IKAVVFDAYGTLFDVQSV T0329 26 :NYAFEQTGHR 1qq5A 20 :ADATERAYPG T0329 38 :FTVEDIKNFFGSGVVVAVTRALAYEAGSSRESLVAFGTKDEQIPE 1qq5A 30 :RGEYITQVWRQKQLEYSWLRALMGRYADFWSVTREALAYTLGTLG T0329 83 :AVTQTEVNRVLEVFKP 1qq5A 76 :EPDESFLADMAQAYNR T0329 108 :TGPFPGILDLMKNL 1qq5A 92 :LTPYPDAAQCLAEL T0329 124 :KGVKLAVVSNKPNEAVQVLVEEL 1qq5A 106 :APLKRAILSNGAPDMLQALVANA T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNW 1qq5A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0329 210 :GFRSVPF 1qq5A 205 :GTIAPLT T0329 222 :ATVIVDTAEKLEEAILG 1qq5A 227 :PDFVVPALGDLPRLVRG Number of specific fragments extracted= 10 number of extra gaps= 0 total=311 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq5A/T0329-1qq5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1qq5A/T0329-1qq5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq5A read from 1qq5A/T0329-1qq5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq5A in template set T0329 1 :M 1qq5A 1 :M T0329 3 :YKAAIFDMDGTILDTS 1qq5A 2 :IKAVVFDAYGTLFDVQ T0329 19 :ADLTSA 1qq5A 21 :DATERA T0329 34 :HR 1qq5A 27 :YP T0329 37 :D 1qq5A 29 :G T0329 39 :TVEDIKNFFGSGVVVAVTRALAYEAGSSRESLV 1qq5A 30 :RGEYITQVWRQKQLEYSWLRALMGRYADFWSVT T0329 72 :AFGTKDEQIPEAVTQTEVNRV 1qq5A 65 :ALAYTLGTLGLEPDESFLADM T0329 101 :ADHCQI 1qq5A 86 :AQAYNR T0329 108 :TGPFPGILDLMKNL 1qq5A 92 :LTPYPDAAQCLAEL T0329 124 :KGVKLAVVSNKPNEAVQVLVEEL 1qq5A 106 :APLKRAILSNGAPDMLQALVANA T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNW 1qq5A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0329 210 :GFRSVPFLQ 1qq5A 204 :SGTIAPLTM T0329 221 :GATVIVDTAEKLEEAIL 1qq5A 226 :APDFVVPALGDLPRLVR Number of specific fragments extracted= 13 number of extra gaps= 0 total=324 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq5A/T0329-1qq5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1qq5A/T0329-1qq5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq5A read from 1qq5A/T0329-1qq5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq5A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1qq5A)M1 T0329 3 :YKAAIFDMDGTILDTS 1qq5A 2 :IKAVVFDAYGTLFDVQ T0329 19 :ADLTSA 1qq5A 21 :DATERA T0329 34 :HRHDFTVEDIKNFFGSGVVVAVTRALAYEAGSSRESLVAFGTKDEQIPEAVTQTEVNRVLE 1qq5A 27 :YPGRGEYITQVWRQKQLEYSWLRALMGRYADFWSVTREALAYTLGTLGLEPDESFLADMAQ T0329 104 :CQIKTGPFPGILDLMKNL 1qq5A 88 :AYNRLTPYPDAAQCLAEL T0329 124 :KGVKLAVVSNKPNEAVQVLVE 1qq5A 106 :APLKRAILSNGAPDMLQALVA T0329 145 :ELFPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNW 1qq5A 128 :AGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0329 212 :RSVPFLQKH 1qq5A 193 :LSQEALARE T0329 221 :GATVIVDTAEKLEEAIL 1qq5A 226 :APDFVVPALGDLPRLVR Number of specific fragments extracted= 8 number of extra gaps= 0 total=332 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qyiA/T0329-1qyiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qyiA expands to /projects/compbio/data/pdb/1qyi.pdb.gz 1qyiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0329 read from 1qyiA/T0329-1qyiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qyiA read from 1qyiA/T0329-1qyiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qyiA to template set # found chain 1qyiA in template set T0329 1 :M 1qyiA 1 :M T0329 4 :KAAIFDMDGTILDTSADL 1qyiA 2 :KKILFDVDGVFLSEERCF T0329 22 :TSALNYAFEQ 1qyiA 22 :SALTVYELLM T0329 32 :TGHRHDF 1qyiA 35 :YLGLHSH T0329 39 :TVEDIKNFFGSGV 1qyiA 48 :TDNDIQDIRNRIF T0329 52 :VVAVTRALAYE 1qyiA 63 :DKILNKLKSLG T0329 64 :GSSRESLVAFG 1qyiA 74 :LNSNWDMLFIV T0329 75 :TKDE 1qyiA 91 :DILK T0329 83 :AVTQTEVNRVLEVFKPY 1qyiA 95 :KLSHDEIEAFMYQDEPV T0329 100 :YADH 1qyiA 207 :YIYQ T0329 105 :QIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1qyiA 211 :EIILRPVDEVKVLLNDLKGAGFELGIATGRPYTETVVPFENL T0329 147 :FPGSF 1qyiA 254 :LLPYF T0329 152 :DFALG 1qyiA 261 :DFIAT T0329 167 :PDMTSECVKVLG 1qyiA 266 :ASDVLEAENMYP T0329 179 :VPRDKCVYIGDSEIDIQTARNSEMDEIAVNW 1qyiA 313 :VNKDDVFIVGDSLADLLSAQKIGATFIGTLT T0329 210 :GFRSVPFLQKHGATVIVDTAEKLEEAILG 1qyiA 347 :GKDAAGELEAHHADYVINHLGELRGVLDN Number of specific fragments extracted= 16 number of extra gaps= 0 total=348 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qyiA/T0329-1qyiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1qyiA/T0329-1qyiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qyiA read from 1qyiA/T0329-1qyiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qyiA in template set T0329 4 :KAAIFDMDGTILDTSADLTSALNYAFEQT 1qyiA 2 :KKILFDVDGVFLSEERCFDVSALTVYELL T0329 49 :SGVVVAVTRAL 1qyiA 95 :KLSHDEIEAFM T0329 64 :GSSRESLVAFGTKDEQIPEAVT 1qyiA 106 :YQDEPVELKLQNISTNLADCFN T0329 86 :QTEVNRVLEVFKPYYADHCQI 1qyiA 141 :KVGKNNIYAALEEFATTELHV T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1qyiA 213 :ILRPVDEVKVLLNDLKGAGFELGIATGRPYTETVVPFENL T0329 147 :FPGSF 1qyiA 254 :LLPYF T0329 152 :DFALG 1qyiA 261 :DFIAT T0329 167 :PDMTSECVKVLG 1qyiA 266 :ASDVLEAENMYP T0329 179 :VPRDKCVYIGDSEIDIQTARNSEMDEIAVNW 1qyiA 313 :VNKDDVFIVGDSLADLLSAQKIGATFIGTLT T0329 210 :GFRSVPFLQKHGATVIVDTAEKLEEAI 1qyiA 347 :GKDAAGELEAHHADYVINHLGELRGVL T0329 237 :LG 1qyiA 376 :LL Number of specific fragments extracted= 11 number of extra gaps= 0 total=359 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qyiA/T0329-1qyiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1qyiA/T0329-1qyiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qyiA read from 1qyiA/T0329-1qyiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qyiA in template set T0329 4 :KAAIFDMDGTILDTSADLTSALNYAFEQT 1qyiA 2 :KKILFDVDGVFLSEERCFDVSALTVYELL T0329 33 :GHRHDFT 1qyiA 39 :HSHIDWE T0329 40 :VEDIKNFFGSGVVVAVTRAL 1qyiA 53 :QDIRNRIFQKDKILNKLKSL T0329 60 :AYEAGSSRESLVAFGTKDEQIPEAVTQTEVNRVLEVFKPYYADHCQI 1qyiA 145 :NNIYAALEEFATTELHVSDATLFSLKGALWTLAQEVYQEWYLGSKLY T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1qyiA 213 :ILRPVDEVKVLLNDLKGAGFELGIATGRPYTETVVPFE T0329 145 :ELFPGSF 1qyiA 252 :LGLLPYF T0329 152 :DFALGE 1qyiA 261 :DFIATA T0329 158 :KSGIRRKPAPDMTSECVK 1qyiA 278 :QARPLGKPNPFSYIAALY T0329 179 :VPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRS 1qyiA 313 :VNKDDVFIVGDSLADLLSAQKIGATFIGTLTGLKG T0329 214 :VPFLQKHGATVIVDTAEKLEEAI 1qyiA 351 :AGELEAHHADYVINHLGELRGVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=369 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l7mA/T0329-1l7mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l7mA expands to /projects/compbio/data/pdb/1l7m.pdb.gz 1l7mA:Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 108, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 110, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 114, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 116, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 118, because occupancy 0.500 <= existing 0.500 in 1l7mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 785, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 787, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 791, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 1l7mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1526, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1528, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1530, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1532, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1534, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1536, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1538, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1540, because occupancy 0.500 <= existing 0.500 in 1l7mA # T0329 read from 1l7mA/T0329-1l7mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l7mA read from 1l7mA/T0329-1l7mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l7mA to template set # found chain 1l7mA in template set T0329 2 :KYKAAIFDMDGTILDTSAD 1l7mA 4 :KKKLILFDFDSTLVNNETI T0329 26 :NYAFEQTGHR 1l7mA 23 :DEIAREAGVE T0329 49 :SGVVVAVTRALAYE 1l7mA 33 :EEVKKITKEAMEGK T0329 64 :GSSRESLVAFGTKDE 1l7mA 47 :LNFEQSLRKRVSLLK T0329 83 :AVTQTEVNRVLEV 1l7mA 62 :DLPIEKVEKAIKR T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1l7mA 75 :ITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKL T0329 147 :FPGSFDFALGEK 1l7mA 115 :LDYAFANRLIVK T0329 160 :GIRR 1l7mA 138 :VLKE T0329 164 :K 1l7mA 144 :K T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 1l7mA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAF T0329 212 :RSVPFLQKH 1l7mA 185 :CAKPILKEK T0329 222 :ATVIVD 1l7mA 194 :ADICIE T0329 228 :TAEKLEE 1l7mA 202 :DLREILK Number of specific fragments extracted= 13 number of extra gaps= 0 total=382 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l7mA/T0329-1l7mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1l7mA/T0329-1l7mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l7mA read from 1l7mA/T0329-1l7mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l7mA in template set T0329 2 :KYKAAIFDMDGTILDTS 1l7mA 4 :KKKLILFDFDSTLVNNE T0329 24 :ALNYAFEQTGH 1l7mA 21 :TIDEIAREAGV T0329 40 :VEDIKNFF 1l7mA 32 :EEEVKKIT T0329 48 :GSGVVVAVTRAL 1l7mA 46 :KLNFEQSLRKRV T0329 82 :EAVTQTEVNR 1l7mA 58 :SLLKDLPIEK T0329 100 :YADHCQI 1l7mA 68 :VEKAIKR T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1l7mA 75 :ITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKL T0329 147 :FPGSFDFALGEKS 1l7mA 115 :LDYAFANRLIVKD T0329 161 :IRR 1l7mA 137 :EVL T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSE 1l7mA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0329 203 :DEIAV 1l7mA 180 :LKIAF T0329 212 :RSVPFLQKH 1l7mA 185 :CAKPILKEK T0329 222 :ATVIVD 1l7mA 194 :ADICIE T0329 228 :TAEKLEEAI 1l7mA 202 :DLREILKYI Number of specific fragments extracted= 14 number of extra gaps= 0 total=396 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l7mA/T0329-1l7mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1l7mA/T0329-1l7mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l7mA read from 1l7mA/T0329-1l7mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l7mA in template set T0329 2 :KYKAAIFDMDGTILDTS 1l7mA 4 :KKKLILFDFDSTLVNNE T0329 24 :ALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRALAY 1l7mA 21 :TIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVS T0329 80 :IPEAVTQTEVNRVLE 1l7mA 59 :LLKDLPIEKVEKAIK T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1l7mA 74 :RITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKE T0329 145 :ELFPGSFDFALGEKS 1l7mA 113 :LGLDYAFANRLIVKD T0329 160 :GIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSE 1l7mA 138 :VLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0329 203 :DEIAV 1l7mA 180 :LKIAF T0329 212 :RSVPFL 1l7mA 185 :CAKPIL T0329 219 :KHGATVIVDT 1l7mA 191 :KEKADICIEK Number of specific fragments extracted= 9 number of extra gaps= 0 total=405 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0cA/T0329-2b0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b0cA expands to /projects/compbio/data/pdb/2b0c.pdb.gz 2b0cA:# T0329 read from 2b0cA/T0329-2b0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0cA read from 2b0cA/T0329-2b0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b0cA to template set # found chain 2b0cA in template set T0329 4 :KAAIFDMDGTILD 2b0cA 8 :MLYIFDLGNVIVD T0329 17 :TSADLTSALNYAF 2b0cA 22 :DFNRVLGAWSDLT T0329 37 :DFTVEDIKNF 2b0cA 35 :RIPLASLKKS T0329 49 :SGVVVAVTRALAYE 2b0cA 45 :FHMGEAFHQHERGE T0329 64 :GSSRESLVAFGTKDEQ 2b0cA 59 :ISDEAFAEALCHEMAL T0329 83 :AVTQTEVNRVLEV 2b0cA 75 :PLSYEQFSHGWQA T0329 106 :IKTGPFPGILDLMKNLRQKGVKLAVVSN 2b0cA 88 :VFVALRPEVIAIMHKLREQGHRVVVLSN T0329 135 :PNEAVQVL 2b0cA 127 :EYPEIRDA T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNADNIEGANQLGITSIL T0329 211 :FRSVPF 2b0cA 191 :VKDKTT T0329 232 :LEEAIL 2b0cA 197 :IPDYFA Number of specific fragments extracted= 11 number of extra gaps= 0 total=416 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0cA/T0329-2b0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2b0cA/T0329-2b0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0cA read from 2b0cA/T0329-2b0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b0cA in template set T0329 3 :YKAAIFDMDGTILDTS 2b0cA 7 :KMLYIFDLGNVIVDID T0329 19 :ADLTSALNYAF 2b0cA 24 :NRVLGAWSDLT T0329 37 :DFTVEDIKNFFGSG 2b0cA 35 :RIPLASLKKSFHMG T0329 53 :VAVTRAL 2b0cA 49 :EAFHQHE T0329 80 :IPEAVTQTEVNRVLEVF 2b0cA 56 :RGEISDEAFAEALCHEM T0329 97 :KPYYADHCQIK 2b0cA 78 :YEQFSHGWQAV T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPN 2b0cA 90 :VALRPEVIAIMHKLREQGHRVVVLSNTNR T0329 137 :EAVQVL 2b0cA 129 :PEIRDA T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRSVPFLQ 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNADNIEGANQLGITSILVKDKTTIPDYFA Number of specific fragments extracted= 9 number of extra gaps= 0 total=425 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0cA/T0329-2b0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2b0cA/T0329-2b0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0cA read from 2b0cA/T0329-2b0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b0cA in template set T0329 5 :AAIFDMDGTILDT 2b0cA 9 :LYIFDLGNVIVDI T0329 18 :SADLTSALNYAF 2b0cA 23 :FNRVLGAWSDLT T0329 37 :DFTVEDIKNFFGSGVVVAVT 2b0cA 35 :RIPLASLKKSFHMGEAFHQH T0329 79 :QIPEAVTQTEVNRVLEVF 2b0cA 55 :ERGEISDEAFAEALCHEM T0329 97 :KPYYADHCQI 2b0cA 78 :YEQFSHGWQA T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSNKP 2b0cA 89 :FVALRPEVIAIMHKLREQGHRVVVLSNTN T0329 137 :EAVQVL 2b0cA 129 :PEIRDA T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRS 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNADNIEGANQLGITSILVKDKTTI T0329 233 :EEAI 2b0cA 198 :PDYF Number of specific fragments extracted= 9 number of extra gaps= 0 total=434 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rqlA/T0329-1rqlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rqlA expands to /projects/compbio/data/pdb/1rql.pdb.gz 1rqlA:# T0329 read from 1rqlA/T0329-1rqlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rqlA read from 1rqlA/T0329-1rqlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rqlA to template set # found chain 1rqlA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1rqlA)K5 T0329 3 :YKAAIFDMDGTILDTSADL 1rqlA 6 :IEAVIFDWAGTTVDYGCFA T0329 22 :TSALNYAFEQTGHR 1rqlA 26 :LEVFMEIFHKRGVA T0329 38 :FTVEDIKNFFGSGVVVAVTRALAY 1rqlA 40 :ITAEEARKPMGLLKIDHVRALTEM T0329 64 :GSSRESLVAFGTK 1rqlA 64 :PRIASEWNRVFRQ T0329 83 :AVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1rqlA 77 :LPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0329 147 :FPGS 1rqlA 142 :LQGY T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGV 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0329 180 :PRDKCVYIGDSEIDIQTARNSEMDEIAVNWG 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0329 211 :FRSVPFLQKHG 1rqlA 212 :GLTEEEVENMD T0329 222 :ATVIVDTAEKLEEAILG 1rqlA 242 :AHFTIETMQELESVMEH Number of specific fragments extracted= 10 number of extra gaps= 0 total=444 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rqlA/T0329-1rqlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1rqlA/T0329-1rqlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rqlA read from 1rqlA/T0329-1rqlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rqlA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1rqlA)K5 T0329 3 :YKAAIFDMDGTILDTS 1rqlA 6 :IEAVIFDWAGTTVDYG T0329 19 :ADLTSALNYAFEQTGHR 1rqlA 23 :FAPLEVFMEIFHKRGVA T0329 38 :FTVEDIKNFFGSGVVVAVTRAL 1rqlA 40 :ITAEEARKPMGLLKIDHVRALT T0329 68 :ESLVAFGTKDEQIPEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1rqlA 62 :EMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0329 147 :FPGS 1rqlA 142 :LQGY T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGV 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0329 180 :PRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFR 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0329 213 :SVPFLQKHGATVIVDTAEKLEEAI 1rqlA 233 :VRNRFVENGAHFTIETMQELESVM Number of specific fragments extracted= 8 number of extra gaps= 0 total=452 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rqlA/T0329-1rqlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1rqlA/T0329-1rqlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rqlA read from 1rqlA/T0329-1rqlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rqlA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1rqlA)K5 T0329 3 :YKAAIFDMDGTILDTSADL 1rqlA 6 :IEAVIFDWAGTTVDYGCFA T0329 22 :TSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRALAY 1rqlA 26 :LEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPR T0329 72 :AFGTKDEQIPEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1rqlA 66 :IASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAK T0329 145 :ELFPGSFDFALGEKSGIRRKPAPDMTSECVKVLGV 1rqlA 141 :ALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGV T0329 180 :PRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFR 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0329 213 :SVPF 1rqlA 214 :TEEE T0329 217 :LQKHGATVIVDTAEKLEEAIL 1rqlA 237 :FVENGAHFTIETMQELESVME Number of specific fragments extracted= 7 number of extra gaps= 0 total=459 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fezA/T0329-1fezA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fezA expands to /projects/compbio/data/pdb/1fez.pdb.gz 1fezA:# T0329 read from 1fezA/T0329-1fezA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fezA read from 1fezA/T0329-1fezA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fezA to template set # found chain 1fezA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1fezA)K5 T0329 3 :YKAAIFDMDGTILDTSADL 1fezA 6 :IEAVIFDWAGTTVDYGCFA T0329 22 :TSALNYAFEQTGHR 1fezA 26 :LEVFMEIFHKRGVA T0329 38 :FTVEDIKNFFGSGVVVAVTRALAYE 1fezA 40 :ITAEEARKPMGLLKIDHVRALTEMP T0329 64 :GSSRESLVAFGT 1fezA 65 :RIASEWNRVFRQ T0329 83 :AVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1fezA 77 :LPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0329 147 :FPGS 1fezA 142 :LQGY T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGV 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0329 180 :PRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRS 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSE T0329 214 :VPFLQKHGATVIVDTAEKLEEAIL 1fezA 234 :RNRFVENGAHFTIETMQELESVME Number of specific fragments extracted= 9 number of extra gaps= 0 total=468 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fezA/T0329-1fezA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1fezA/T0329-1fezA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fezA read from 1fezA/T0329-1fezA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fezA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1fezA)K5 T0329 3 :YKAAIFDMDGTILDTS 1fezA 6 :IEAVIFDWAGTTVDYG T0329 19 :ADLTSALNYAFEQTGHR 1fezA 23 :FAPLEVFMEIFHKRGVA T0329 38 :FTVEDIKNFFGSGVVVAVTRAL 1fezA 40 :ITAEEARKPMGLLKIDHVRALT T0329 68 :ESLVAFGTKDEQIPEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1fezA 62 :EMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0329 147 :FPGS 1fezA 142 :LQGY T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGVPR 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGVYP T0329 182 :DKCVYIGDSEIDIQTARNSEMDEIAVNWGFR 1fezA 179 :NHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0329 213 :SVPFLQKHGATVIVDTAEKLEEAI 1fezA 233 :VRNRFVENGAHFTIETMQELESVM Number of specific fragments extracted= 8 number of extra gaps= 0 total=476 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fezA/T0329-1fezA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1fezA/T0329-1fezA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fezA read from 1fezA/T0329-1fezA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fezA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1fezA)K5 T0329 3 :YKAAIFDMDGTILDTSADL 1fezA 6 :IEAVIFDWAGTTVDYGCFA T0329 22 :TSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRALAY 1fezA 26 :LEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPR T0329 72 :AFGTKDEQIPEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1fezA 66 :IASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAK T0329 145 :ELFP 1fezA 143 :QGYK T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGV 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0329 180 :PRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRS 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSE T0329 214 :VPFLQKHGATVIVDTAEKLEEAIL 1fezA 234 :RNRFVENGAHFTIETMQELESVME Number of specific fragments extracted= 7 number of extra gaps= 0 total=483 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zjjA/T0329-1zjjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zjjA expands to /projects/compbio/data/pdb/1zjj.pdb.gz 1zjjA:# T0329 read from 1zjjA/T0329-1zjjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjjA read from 1zjjA/T0329-1zjjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zjjA to template set # found chain 1zjjA in template set T0329 4 :KAAIFDMDGTILDT 1zjjA 2 :VAIIFDMDGVLYRG T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSN 1zjjA 16 :NRAIPGVRELIEFLKERGIPFAFLTN T0329 134 :KPNEAVQVLVEEL 1zjjA 45 :KTPEMYREKLLKM T0329 147 :FPGSFDFALGEK 1zjjA 59 :IDVSSSIIITSG T0329 160 :GI 1zjjA 187 :KP T0329 167 :PDMTSECVKVL 1zjjA 189 :NEPMYEVVREM T0329 179 :VPRDKCVYIGDSE 1zjjA 200 :FPGEELWMVGDRL T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFLQKHG 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDIKKSE T0329 222 :ATVIVDTAEKLEEAI 1zjjA 246 :PDLVLPSVYELIDYL Number of specific fragments extracted= 9 number of extra gaps= 0 total=492 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zjjA/T0329-1zjjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1zjjA/T0329-1zjjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjjA read from 1zjjA/T0329-1zjjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zjjA in template set T0329 4 :KAAIFDMDGTILD 1zjjA 2 :VAIIFDMDGVLYR T0329 17 :TSADLTSALNYAFE 1zjjA 18 :AIPGVRELIEFLKE T0329 32 :TGHRH 1zjjA 32 :RGIPF T0329 38 :FTVEDIKNFFGS 1zjjA 45 :KTPEMYREKLLK T0329 50 :GV 1zjjA 58 :GI T0329 74 :GTKDEQI 1zjjA 60 :DVSSSII T0329 98 :PYYADHCQIKTGP 1zjjA 71 :LATRLYMSKHLDP T0329 111 :FPGILDLMKNL 1zjjA 91 :GEGLVKEMQAL T0329 123 :QKG 1zjjA 112 :RQG T0329 126 :VKLAVVSN 1zjjA 119 :VKHVVVGL T0329 134 :KPNEAVQVLVEELFPGSFDFALGEKSGIRR 1zjjA 129 :DLTYEKLKYATLAIRNGATFIGTNPDATLP T0329 167 :PDMTSECVKVLG 1zjjA 168 :GSIIAALKVATN T0329 179 :VPRDKCVYIGDSE 1zjjA 200 :FPGEELWMVGDRL T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFLQK 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDIKK T0329 220 :HGATVIVDTAEKLEEAI 1zjjA 244 :YKPDLVLPSVYELIDYL Number of specific fragments extracted= 15 number of extra gaps= 0 total=507 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zjjA/T0329-1zjjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1zjjA/T0329-1zjjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjjA read from 1zjjA/T0329-1zjjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zjjA in template set T0329 4 :KAAIFDMDGTILD 1zjjA 2 :VAIIFDMDGVLYR T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSN 1zjjA 15 :GNRAIPGVRELIEFLKERGIPFAFLTN T0329 134 :KPNEAVQVLVE 1zjjA 45 :KTPEMYREKLL T0329 145 :ELFPGSFDFALGE 1zjjA 57 :MGIDVSSSIIITS T0329 168 :DMTSECVKVL 1zjjA 190 :EPMYEVVREM T0329 179 :VPRDKCVYIGDSE 1zjjA 200 :FPGEELWMVGDRL T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFL 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDI T0329 219 :KHGATVIVDTAEKLE 1zjjA 243 :EYKPDLVLPSVYELI Number of specific fragments extracted= 8 number of extra gaps= 0 total=515 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c4nA/T0329-2c4nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c4nA expands to /projects/compbio/data/pdb/2c4n.pdb.gz 2c4nA:# T0329 read from 2c4nA/T0329-2c4nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c4nA read from 2c4nA/T0329-2c4nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c4nA to template set # found chain 2c4nA in template set Warning: unaligning (T0329)L15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0329)D16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0329 1 :MKYKAAIFDMDGTI 2c4nA 1 :MTIKNVICDIDGVL T0329 17 :T 2c4nA 17 :D T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSN 2c4nA 18 :NVAVPGAAEFLHGIMDKGLPLVLLTN T0329 134 :KPNEAVQVLVEEL 2c4nA 47 :QTGQDLANRFATA T0329 147 :F 2c4nA 61 :V T0329 148 :PGSF 2c4nA 65 :DSVF T0329 152 :DFALGEK 2c4nA 86 :KAYVVGE T0329 159 :SGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSE 2c4nA 171 :PFYVGKPSPWIIRAALNKMQAHSEETVIVGDNL T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFLQKHG 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDIDSMP T0329 222 :ATVIVDTAEK 2c4nA 237 :PSWIYPSVAE Number of specific fragments extracted= 10 number of extra gaps= 1 total=525 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c4nA/T0329-2c4nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2c4nA/T0329-2c4nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c4nA read from 2c4nA/T0329-2c4nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c4nA in template set Warning: unaligning (T0329)L15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0329)D16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0329 1 :MKYKAAIFDMDGTI 2c4nA 1 :MTIKNVICDIDGVL T0329 17 :TSADLTSALNYAFEQ 2c4nA 20 :AVPGAAEFLHGIMDK T0329 33 :GHRH 2c4nA 35 :GLPL T0329 37 :DFTVEDIKNFFG 2c4nA 46 :SQTGQDLANRFA T0329 57 :RAL 2c4nA 58 :TAG T0329 73 :FGTKDEQI 2c4nA 61 :VDVPDSVF T0329 97 :KPYYADHCQI 2c4nA 72 :AMATADFLRR T0329 108 :TG 2c4nA 82 :QE T0329 110 :PFPGILDL 2c4nA 91 :GEGALIHE T0329 121 :LRQKGVKL 2c4nA 99 :LYKAGFTI T0329 129 :AVVSN 2c4nA 114 :VIVGE T0329 134 :KPNEAVQVLVEELFPGSFDFALGEKSGIRR 2c4nA 121 :SYNWDMMHKAAYFVANGARFIATNPDTHGR T0329 164 :KPAPDMTSECVKVLGVPRDKCVYIGDSE 2c4nA 176 :KPSPWIIRAALNKMQAHSEETVIVGDNL T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFLQK 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDIDS T0329 220 :HGATVIVDTAEKL 2c4nA 235 :FRPSWIYPSVAEI Number of specific fragments extracted= 15 number of extra gaps= 1 total=540 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c4nA/T0329-2c4nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2c4nA/T0329-2c4nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c4nA read from 2c4nA/T0329-2c4nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c4nA in template set Warning: unaligning (T0329)L15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0329)D16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0329 1 :MKYKAAIFDMDGTI 2c4nA 1 :MTIKNVICDIDGVL T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSNKP 2c4nA 17 :DNVAVPGAAEFLHGIMDKGLPLVLLTNYP T0329 136 :NEAVQVLVE 2c4nA 49 :GQDLANRFA T0329 145 :ELFPGSFDFALGE 2c4nA 59 :AGVDVPDSVFYTS T0329 159 :SGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSE 2c4nA 171 :PFYVGKPSPWIIRAALNKMQAHSEETVIVGDNL T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFL 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDI T0329 219 :KHGATVIVDTAEK 2c4nA 234 :PFRPSWIYPSVAE Number of specific fragments extracted= 7 number of extra gaps= 1 total=547 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq7A/T0329-1qq7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qq7A expands to /projects/compbio/data/pdb/1qq7.pdb.gz 1qq7A:Bad short name: C2 for alphabet: pdb_atoms Bad short name: C1 for alphabet: pdb_atoms Bad short name: O1 for alphabet: pdb_atoms Bad short name: O2 for alphabet: pdb_atoms Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1459, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1621, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1623, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1625, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1627, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1629, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1631, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1641, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1647, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1659, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1661, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1663, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1665, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1667, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1673, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1675, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1677, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1679, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1681, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1683, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1685, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1687, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1689, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1691, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1693, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1695, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1697, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1699, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1752, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1789, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1791, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1793, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1820, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1822, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1824, because occupancy 0.500 <= existing 0.500 in 1qq7A # T0329 read from 1qq7A/T0329-1qq7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq7A read from 1qq7A/T0329-1qq7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qq7A to template set # found chain 1qq7A in template set Warning: unaligning (T0329)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0329)M10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0329 1 :M 1qq7A 1 :M T0329 3 :YKAAI 1qq7A 2 :IKAVV T0329 11 :DGTILDTSAD 1qq7A 10 :YGTLFDVQSV T0329 26 :NYAFEQTGHR 1qq7A 20 :ADATERAYPG T0329 39 :TVEDI 1qq7A 30 :RGEYI T0329 44 :KNFFGSGVVVAVTRALAYEAGSSRESLVAFGTKDEQIPE 1qq7A 36 :QVWRQKQLEYSWLRALMGRYADFWSVTREALAYTLGTLG T0329 83 :AVTQTEVNRVLEVFKP 1qq7A 76 :EPDESFLADMAQAYNR T0329 108 :TGPFPGILDLMKNL 1qq7A 92 :LTPYPDAAQCLAEL T0329 124 :KGVKLAVVSNKPNEAVQVLVEEL 1qq7A 106 :APLKRAILSNGAPDMLQALVANA T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNW 1qq7A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0329 212 :RSVPFLQKHG 1qq7A 193 :LSQEALAREL T0329 222 :ATVIVDTAEKLEEAILG 1qq7A 227 :PDFVVPALGDLPRLVRG Number of specific fragments extracted= 12 number of extra gaps= 0 total=559 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq7A/T0329-1qq7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1qq7A/T0329-1qq7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq7A read from 1qq7A/T0329-1qq7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq7A in template set Warning: unaligning (T0329)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0329)M10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0329 1 :M 1qq7A 1 :M T0329 3 :YKAAI 1qq7A 2 :IKAVV T0329 11 :DGTILDTS 1qq7A 10 :YGTLFDVQ T0329 19 :ADLTSA 1qq7A 21 :DATERA T0329 34 :HR 1qq7A 27 :YP T0329 37 :D 1qq7A 29 :G T0329 39 :TVEDIKNFFGSGVVVAVTRALAYEAGSSRESLV 1qq7A 30 :RGEYITQVWRQKQLEYSWLRALMGRYADFWSVT T0329 72 :AFGTKDEQIPEAVTQTEVNRV 1qq7A 65 :ALAYTLGTLGLEPDESFLADM T0329 101 :ADHCQI 1qq7A 86 :AQAYNR T0329 108 :TGPFPGILDLMKNL 1qq7A 92 :LTPYPDAAQCLAEL T0329 124 :KGVKLAVVSNKPNEAVQVLVEEL 1qq7A 106 :APLKRAILSNGAPDMLQALVANA T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNW 1qq7A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0329 210 :GF 1qq7A 205 :GT T0329 221 :GATVIVDTAEKLEEAIL 1qq7A 226 :APDFVVPALGDLPRLVR Number of specific fragments extracted= 14 number of extra gaps= 0 total=573 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq7A/T0329-1qq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1qq7A/T0329-1qq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq7A read from 1qq7A/T0329-1qq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq7A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1qq7A)M1 Warning: unaligning (T0329)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0329)M10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0329 3 :YKAAI 1qq7A 2 :IKAVV T0329 11 :DGTILDTS 1qq7A 10 :YGTLFDVQ T0329 22 :TSALNYA 1qq7A 20 :ADATERA T0329 34 :HRHDFTVEDIKNFFGSGVVVAVTRALAYEAGSSRESLVAFGTKDEQIPEAVTQTEVNRVLE 1qq7A 27 :YPGRGEYITQVWRQKQLEYSWLRALMGRYADFWSVTREALAYTLGTLGLEPDESFLADMAQ T0329 104 :CQIKTGPFPGILDLMKNL 1qq7A 88 :AYNRLTPYPDAAQCLAEL T0329 124 :KGVKLAVVSNKPNEAVQVLVE 1qq7A 106 :APLKRAILSNGAPDMLQALVA T0329 145 :ELFPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNW 1qq7A 128 :AGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0329 212 :RSVPFLQKH 1qq7A 193 :LSQEALARE T0329 221 :GATVIVDTAEKLEEAIL 1qq7A 226 :APDFVVPALGDLPRLVR Number of specific fragments extracted= 9 number of extra gaps= 0 total=582 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zs9A/T0329-1zs9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zs9A expands to /projects/compbio/data/pdb/1zs9.pdb.gz 1zs9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0329 read from 1zs9A/T0329-1zs9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zs9A read from 1zs9A/T0329-1zs9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zs9A to template set # found chain 1zs9A in template set T0329 3 :YKAAIFDMDGTILD 1zs9A 10 :VTVILLDIEGTTTP T0329 17 :TSADLTSALNYAFEQTGHR 1zs9A 31 :LFPYIEENVKEYLQTHWEE T0329 49 :SGVVVAVTRALAYE 1zs9A 50 :EECQQDVSLLRKQA T0329 71 :VAFGTKDEQI 1zs9A 64 :EEDAHLDGAV T0329 81 :PEAVTQTEVNRVLEVFKPY 1zs9A 78 :ASGNGVDDLQQMIQAVVDN T0329 103 :HC 1zs9A 121 :AF T0329 105 :QIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1zs9A 126 :RMKAEFFADVVPAVRKWREAGMKVYIYSSGSVEAQKLLFGHS T0329 147 :FPGSFDFALGEKSGIRRK 1zs9A 172 :ILELVDGHFDTKIGHKVE T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWG 1zs9A 190 :SESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRP T0329 211 :FRSVPFLQKHG 1zs9A 237 :GLTDDEKTYYS T0329 225 :IVDTAEK 1zs9A 248 :LITSFSE Number of specific fragments extracted= 11 number of extra gaps= 0 total=593 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zs9A/T0329-1zs9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1zs9A/T0329-1zs9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zs9A read from 1zs9A/T0329-1zs9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zs9A in template set Warning: unaligning (T0329)A83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0329)T85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0329 3 :YKAAIFDMDGTILD 1zs9A 10 :VTVILLDIEGTTTP T0329 17 :TSADLTSALNYAFEQT 1zs9A 31 :LFPYIEENVKEYLQTH T0329 34 :HRHDFTVEDIKNFF 1zs9A 77 :AASGNGVDDLQQMI T0329 49 :SGVVVAVTRAL 1zs9A 91 :QAVVDNVCWQM T0329 81 :PE 1zs9A 102 :SL T0329 86 :QTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1zs9A 107 :TTALKQLQGHMWRAAFTAGRMKAEFFADVVPAVRKWREAGMKVYIYSSGSVEAQKLLFGHS T0329 147 :FPGSFDFALGEKSGIRRK 1zs9A 172 :ILELVDGHFDTKIGHKVE T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFR 1zs9A 190 :SESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGN T0329 213 :SVPFLQKHG 1zs9A 239 :TDDEKTYYS T0329 225 :IVDTAEKL 1zs9A 248 :LITSFSEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=603 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zs9A/T0329-1zs9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1zs9A/T0329-1zs9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zs9A read from 1zs9A/T0329-1zs9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zs9A in template set Warning: unaligning (T0329)A83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0329)T85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0329 3 :YKAAIFDMDGTILDTS 1zs9A 10 :VTVILLDIEGTTTPIA T0329 19 :ADLTSALNYAFEQTGHRHDFTVEDIK 1zs9A 33 :PYIEENVKEYLQTHWEEEECQQDVSL T0329 49 :SGVVVAVTRAL 1zs9A 59 :LRKQAEEDAHL T0329 60 :AYEAGSSRESLVAFGTKDEQIPE 1zs9A 81 :NGVDDLQQMIQAVVDNVCWQMSL T0329 86 :QTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1zs9A 107 :TTALKQLQGHMWRAAFTAGRMKAEFFADVVPAVRKWREAGMKVYIYSSGSVEAQKLLFG T0329 145 :ELFPGSFDFALGEKSGIRR 1zs9A 170 :GDILELVDGHFDTKIGHKV T0329 166 :APDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFR 1zs9A 189 :ESESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGN T0329 213 :SVPFLQKHG 1zs9A 239 :TDDEKTYYS T0329 225 :IVDTAEK 1zs9A 248 :LITSFSE Number of specific fragments extracted= 9 number of extra gaps= 0 total=612 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zd3A/T0329-1zd3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zd3A expands to /projects/compbio/data/pdb/1zd3.pdb.gz 1zd3A:# T0329 read from 1zd3A/T0329-1zd3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zd3A read from 1zd3A/T0329-1zd3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zd3A to template set # found chain 1zd3A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1zd3A)T2 T0329 3 :YKAAIFDMDGTILDTSA 1zd3A 3 :LRAAVFDLDGVLALPAV T0329 22 :TSALNYAFEQTGHR 1zd3A 20 :FGVLGRTEEALALP T0329 40 :VEDIKNFFG 1zd3A 34 :RGLLNDAFQ T0329 49 :SGVVVAVTRALAYE 1zd3A 44 :GGPEGATTRLMKGE T0329 64 :GSSRESLVAFGT 1zd3A 58 :ITLSQWIPLMEE T0329 76 :KDEQIPEAVT 1zd3A 78 :AKVCLPKNFS T0329 89 :VNRVLEVFKPY 1zd3A 88 :IKEIFDKAISA T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSN 1zd3A 99 :RKINRPMLQAALMLRKKGFTTAILTN T0329 134 :KPNEAVQVLVEEL 1zd3A 131 :AERDGLAQLMCEL T0329 147 :F 1zd3A 145 :M T0329 150 :SFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 1zd3A 146 :HFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTIL T0329 211 :FRSVPFL 1zd3A 203 :VQDTDTA T0329 229 :AEKLEEAIL 1zd3A 210 :LKELEKVTG Number of specific fragments extracted= 13 number of extra gaps= 0 total=625 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zd3A/T0329-1zd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1zd3A/T0329-1zd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zd3A read from 1zd3A/T0329-1zd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zd3A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1zd3A)T2 T0329 3 :YKAAIFDMDGTIL 1zd3A 3 :LRAAVFDLDGVLA T0329 16 :DTSAD 1zd3A 18 :AVFGV T0329 25 :LNYAFEQTGHRHD 1zd3A 23 :LGRTEEALALPRG T0329 42 :DIKNFFG 1zd3A 36 :LLNDAFQ T0329 60 :AYEAGSSRESLVAFGT 1zd3A 43 :KGGPEGATTRLMKGEI T0329 88 :EVNRVLEVFKPYYADHCQIK 1zd3A 59 :TLSQWIPLMEENCRKCSETA T0329 108 :TGPFPG 1zd3A 80 :VCLPKN T0329 114 :ILDLMKNLRQKGVKLAVVSN 1zd3A 105 :MLQAALMLRKKGFTTAILTN T0329 134 :KPNEAVQVLVEEL 1zd3A 131 :AERDGLAQLMCEL T0329 147 :FP 1zd3A 145 :MH T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAV 1zd3A 147 :FDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILV T0329 212 :RSVPFL 1zd3A 204 :QDTDTA T0329 229 :AEKLEEAI 1zd3A 210 :LKELEKVT Number of specific fragments extracted= 13 number of extra gaps= 0 total=638 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zd3A/T0329-1zd3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1zd3A/T0329-1zd3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zd3A read from 1zd3A/T0329-1zd3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zd3A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1zd3A)T2 T0329 3 :YKAAIFDMDGTILDTSAD 1zd3A 3 :LRAAVFDLDGVLALPAVF T0329 24 :ALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRAL 1zd3A 22 :VLGRTEEALALPRGLLNDAFQKGGPEGATTRLMKGE T0329 83 :AVTQTEVNRVLEVFKP 1zd3A 58 :ITLSQWIPLMEENCRK T0329 99 :YYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKP 1zd3A 90 :EIFDKAISARKINRPMLQAALMLRKKGFTTAILTNTW T0329 136 :NEAVQVLVE 1zd3A 133 :RDGLAQLMC T0329 145 :ELF 1zd3A 143 :LKM T0329 150 :SFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAV 1zd3A 146 :HFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILV T0329 212 :RSVPFL 1zd3A 204 :QDTDTA T0329 229 :AEKLEEAI 1zd3A 210 :LKELEKVT Number of specific fragments extracted= 9 number of extra gaps= 0 total=647 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nnlA/T0329-1nnlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nnlA expands to /projects/compbio/data/pdb/1nnl.pdb.gz 1nnlA:# T0329 read from 1nnlA/T0329-1nnlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nnlA read from 1nnlA/T0329-1nnlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nnlA to template set # found chain 1nnlA in template set Warning: unaligning (T0329)V51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0329)S65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0329 4 :KAAIFDMDGTILDTSAD 1nnlA 15 :DAVCFDVDSTVIREEGI T0329 26 :NYAFEQTGHR 1nnlA 32 :DELAKICGVE T0329 49 :SG 1nnlA 42 :DA T0329 66 :SRESLVAFGTKD 1nnlA 58 :FKAALTERLALI T0329 83 :AVTQTEVNRVLEV 1nnlA 70 :QPSREQVQRLIAE T0329 106 :IKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1nnlA 83 :QPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKL T0329 147 :FPGS 1nnlA 125 :IPAT T0329 151 :FDFALG 1nnlA 131 :FANRLK T0329 159 :SGIRRK 1nnlA 153 :AESGGK T0329 167 :PDMTSECVKVLGVP 1nnlA 159 :GKVIKLLKEKFHFK T0329 183 :KCVYIGDSEIDIQT 1nnlA 173 :KIIMIGDGATDMEA T0329 200 :S 1nnlA 187 :C T0329 201 :EMDEIAVNWGFRSVPFLQKH 1nnlA 189 :PADAFIGFGGNVIRQQVKDN T0329 222 :ATVIVDTAEKL 1nnlA 209 :AKWYITDFVEL Number of specific fragments extracted= 14 number of extra gaps= 0 total=661 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nnlA/T0329-1nnlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1nnlA/T0329-1nnlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nnlA read from 1nnlA/T0329-1nnlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nnlA in template set Warning: unaligning (T0329)F38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0329)G50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0329 3 :YKAAIFDMDGTILDTS 1nnlA 14 :ADAVCFDVDSTVIREE T0329 24 :ALNYAFEQTGHRHD 1nnlA 30 :GIDELAKICGVEDA T0329 51 :VVVAVTRAL 1nnlA 58 :FKAALTERL T0329 78 :EQI 1nnlA 67 :ALI T0329 83 :AVTQTEVNRVLEV 1nnlA 70 :QPSREQVQRLIAE T0329 106 :IKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1nnlA 83 :QPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKL T0329 147 :FPGSFDFALGEKSGIRR 1nnlA 125 :IPATNVFANRLKFYFNG T0329 167 :PDMTSECVKVLGV 1nnlA 159 :GKVIKLLKEKFHF T0329 182 :DKCVYIGDSEIDIQTAR 1nnlA 172 :KKIIMIGDGATDMEACP T0329 201 :EMDEIAVNWGFRSVPFLQKH 1nnlA 189 :PADAFIGFGGNVIRQQVKDN T0329 222 :ATVIVDTAEKLE 1nnlA 209 :AKWYITDFVELL Number of specific fragments extracted= 11 number of extra gaps= 0 total=672 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nnlA/T0329-1nnlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1nnlA/T0329-1nnlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nnlA read from 1nnlA/T0329-1nnlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nnlA in template set Warning: unaligning (T0329)F38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0329)V51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0329 4 :KAAIFDMDGTILDTS 1nnlA 15 :DAVCFDVDSTVIREE T0329 24 :ALNYAFEQTGHRHD 1nnlA 30 :GIDELAKICGVEDA T0329 52 :VVAVTRALAYEAGS 1nnlA 58 :FKAALTERLALIQP T0329 85 :TQTEVNRVLEV 1nnlA 72 :SREQVQRLIAE T0329 106 :IKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1nnlA 83 :QPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVAS T0329 145 :ELFPGSFDFALGE 1nnlA 123 :LNIPATNVFANRL T0329 167 :PDMTSECVKVL 1nnlA 155 :SGGKGKVIKLL T0329 180 :PRDKCVYIGDSEIDIQ 1nnlA 170 :HFKKIIMIGDGATDME T0329 200 :S 1nnlA 186 :A T0329 201 :EMDEIAVNWGFRSVPFLQK 1nnlA 189 :PADAFIGFGGNVIRQQVKD T0329 221 :GATVIVDTAEKL 1nnlA 208 :NAKWYITDFVEL Number of specific fragments extracted= 11 number of extra gaps= 0 total=683 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u7pA/T0329-1u7pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u7pA expands to /projects/compbio/data/pdb/1u7p.pdb.gz 1u7pA:# T0329 read from 1u7pA/T0329-1u7pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u7pA read from 1u7pA/T0329-1u7pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u7pA to template set # found chain 1u7pA in template set T0329 3 :YKAAIFDMDGTILDTSAD 1u7pA 5 :PKLAVFDLDYTLWPFWVD T0329 36 :HDF 1u7pA 23 :THV T0329 75 :TKDEQIPEAV 1u7pA 27 :PPFHKSSDGT T0329 104 :CQIKTGPFPGILDLMKNLRQKGVKLAVVSN 1u7pA 41 :RGQNIQLYPEVPEVLGRLQSLGVPVAAASR T0329 134 :KPNEAVQVLVEEL 1u7pA 72 :SEIQGANQLLELF T0329 147 :FPGSFDFALGE 1u7pA 86 :LGKYFIQREIY T0329 161 :IRRK 1u7pA 97 :PGSK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNW 1u7pA 101 :VTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRD T0329 211 :FRSVPFLQKH 1u7pA 144 :GMSLQTLTQG T0329 229 :AEKLEEAILG 1u7pA 154 :LETFAKAQAG Number of specific fragments extracted= 10 number of extra gaps= 0 total=693 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u7pA/T0329-1u7pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1u7pA/T0329-1u7pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u7pA read from 1u7pA/T0329-1u7pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u7pA in template set T0329 2 :KYKAAIFDMDGTILDTS 1u7pA 4 :LPKLAVFDLDYTLWPFW T0329 20 :D 1u7pA 22 :D T0329 32 :TGHRHD 1u7pA 23 :THVDPP T0329 85 :TQTE 1u7pA 33 :SDGT T0329 105 :QIK 1u7pA 40 :RRG T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSN 1u7pA 45 :IQLYPEVPEVLGRLQSLGVPVAAASR T0329 134 :KPNEAVQVLVEEL 1u7pA 72 :SEIQGANQLLELF T0329 147 :FPGSFDFALGEKSGI 1u7pA 86 :LGKYFIQREIYPGSK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVN 1u7pA 101 :VTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIR T0329 210 :GFRSVPFLQKH 1u7pA 143 :DGMSLQTLTQG T0329 229 :AEKLEEA 1u7pA 154 :LETFAKA Number of specific fragments extracted= 11 number of extra gaps= 0 total=704 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u7pA/T0329-1u7pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1u7pA/T0329-1u7pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u7pA read from 1u7pA/T0329-1u7pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u7pA in template set T0329 3 :YKAAIFDMDGTILDTSAD 1u7pA 5 :PKLAVFDLDYTLWPFWVD T0329 33 :GHRHD 1u7pA 24 :HVDPP T0329 54 :A 1u7pA 30 :H T0329 79 :QIPEA 1u7pA 31 :KSSDG T0329 103 :HCQIKTGPFPGILDLMKNLRQKGVKLAVVSN 1u7pA 40 :RRGQNIQLYPEVPEVLGRLQSLGVPVAAASR T0329 134 :KPNEAVQVLVE 1u7pA 72 :SEIQGANQLLE T0329 145 :ELFPGSFDFALGEKSGI 1u7pA 84 :FDLGKYFIQREIYPGSK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVN 1u7pA 101 :VTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIR T0329 210 :GFRSVPFLQKH 1u7pA 143 :DGMSLQTLTQG T0329 229 :AEKLEEA 1u7pA 154 :LETFAKA Number of specific fragments extracted= 10 number of extra gaps= 0 total=714 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jud/T0329-1jud-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jud expands to /projects/compbio/data/pdb/1jud.pdb.gz 1jud:Warning: there is no chain 1jud will retry with 1judA # T0329 read from 1jud/T0329-1jud-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jud read from 1jud/T0329-1jud-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jud to template set # found chain 1jud in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1jud)Y3 Warning: unaligning (T0329)I236 because last residue in template chain is (1jud)F222 T0329 3 :YKAAIFDMDGTILDTSADL 1jud 4 :IKGIAFDLYGTLFDVHSVV T0329 26 :NYAFEQTGHR 1jud 23 :GRCDEAFPGR T0329 40 :VEDIKNFFGSGVVVAVTRALA 1jud 33 :GREISALWRQKQLEYTWLRSL T0329 61 :YEAGSSRESLVAFGTKDEQIPE 1jud 55 :NRYVNFQQATEDALRFTCRHLG T0329 83 :AVTQTEVNRVLEVFKP 1jud 78 :DLDARTRSTLCDAYLR T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1jud 94 :LAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHA T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRS 1jud 134 :LRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGNV T0329 220 :HGATVIVDTAEKLEEA 1jud 206 :QTPDWEVTSLRAVVEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=722 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jud/T0329-1jud-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1jud/T0329-1jud-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jud read from 1jud/T0329-1jud-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jud in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1jud)Y3 Warning: unaligning (T0329)I236 because last residue in template chain is (1jud)F222 T0329 3 :YKAAIFDMDGTILDTSADLTSAL 1jud 4 :IKGIAFDLYGTLFDVHSVVGRCD T0329 30 :EQTGHR 1jud 27 :EAFPGR T0329 40 :VEDIKNFFGSGVVVAVTRALAYEAGSSRE 1jud 33 :GREISALWRQKQLEYTWLRSLMNRYVNFQ T0329 69 :SLVAFGTKDEQIPEAVTQTEVNRVLE 1jud 64 :TEDALRFTCRHLGLDLDARTRSTLCD T0329 103 :HCQI 1jud 90 :AYLR T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1jud 94 :LAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHA T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRSVPF 1jud 134 :LRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGNVFEE T0329 218 :QKHGATVIVDTAEKLEEA 1jud 204 :MGQTPDWEVTSLRAVVEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=730 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jud/T0329-1jud-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1jud/T0329-1jud-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jud read from 1jud/T0329-1jud-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jud in template set T0329 3 :YKAAIFDMDGTILDTSADLTSALNY 1jud 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0329 34 :HRHDFTVEDIKNFFGSGVVVAVTRALAYEAGSSRESLVAFGTKDEQIPEAVTQTEVNRVLE 1jud 29 :FPGRGREISALWRQKQLEYTWLRSLMNRYVNFQQATEDALRFTCRHLGLDLDARTRSTLCD T0329 104 :CQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1jud 90 :AYLRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVS T0329 145 :ELFPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRSVPFL 1jud 132 :AGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGNVFEEM T0329 219 :KHGATVIVDTAEKLEEA 1jud 205 :GQTPDWEVTSLRAVVEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=735 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2feaA/T0329-2feaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2feaA expands to /projects/compbio/data/pdb/2fea.pdb.gz 2feaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 517, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 521, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 523, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1325, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1329, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 1566, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1570, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1572, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1574, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1576, because occupancy 0.300 <= existing 0.700 in 2feaA # T0329 read from 2feaA/T0329-2feaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2feaA read from 2feaA/T0329-2feaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2feaA to template set # found chain 2feaA in template set Warning: unaligning (T0329)V131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0329)S132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 Warning: unaligning (T0329)I161 because of BadResidue code BAD_PEPTIDE in next template residue (2feaA)C149 Warning: unaligning (T0329)R162 because of BadResidue code BAD_PEPTIDE at template residue (2feaA)C149 T0329 2 :KYKAAIFDMDGTILDTSAD 2feaA 4 :RKPFIICDFDGTITMNDNI T0329 26 :NYAFEQTGHR 2feaA 23 :INIMKTFAPP T0329 50 :GVVVAVTRALAYE 2feaA 33 :EWMALKDGVLSKT T0329 64 :GSSRESLVAFGT 2feaA 46 :LSIKEGVGRMFG T0329 83 :AVTQTEVNRVLEVFKPY 2feaA 58 :LLPSSLKEEITSFVLED T0329 108 :TGPFPGILDLMKNLRQKGVKLAV 2feaA 75 :AKIREGFREFVAFINEHEIPFYV T0329 133 :NKPNEAVQVLVEEL 2feaA 100 :GGMDFFVYPLLEGI T0329 147 :FPGSFDFALGEK 2feaA 115 :EKDRIYCNHASF T0329 159 :SG 2feaA 146 :QC T0329 163 :RK 2feaA 150 :CK T0329 171 :SECVKVL 2feaA 152 :PSVIHEL T0329 179 :VPRD 2feaA 159 :SEPN T0329 183 :KCVYIGDSEIDIQTARN 2feaA 164 :YIIMIGDSVTDVEAAKL T0329 202 :MDEIAVN 2feaA 181 :SDLCFAR T0329 211 :FRSVPFLQKHGATVI 2feaA 188 :DYLLNECREQNLNHL T0329 226 :VDTAEKLEEAILG 2feaA 204 :YQDFYEIRKEIEN Number of specific fragments extracted= 16 number of extra gaps= 2 total=751 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2feaA/T0329-2feaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2feaA/T0329-2feaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2feaA read from 2feaA/T0329-2feaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2feaA in template set Warning: unaligning (T0329)V131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0329)S132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 T0329 2 :KYKAAIFDMDGTILDTS 2feaA 4 :RKPFIICDFDGTITMND T0329 24 :ALNYAFEQTGHR 2feaA 21 :NIINIMKTFAPP T0329 39 :TVEDIKNFFGS 2feaA 33 :EWMALKDGVLS T0329 50 :GVVVAVTRAL 2feaA 47 :SIKEGVGRMF T0329 82 :EAVTQTEVNRVLEVFKPY 2feaA 57 :GLLPSSLKEEITSFVLED T0329 108 :TGPFPGILDLMKNLRQKGVKLAV 2feaA 75 :AKIREGFREFVAFINEHEIPFYV T0329 133 :NKPNEAVQVLVEEL 2feaA 100 :GGMDFFVYPLLEGI T0329 147 :FPGSFDFALGEKSGIRR 2feaA 115 :EKDRIYCNHASFDNDYI T0329 170 :TSECVKVL 2feaA 151 :KPSVIHEL T0329 179 :VPRD 2feaA 159 :SEPN T0329 183 :KCVYIGDSEIDIQTARN 2feaA 164 :YIIMIGDSVTDVEAAKL T0329 202 :MDEIAVN 2feaA 181 :SDLCFAR T0329 211 :FRSVPFLQKHGATVI 2feaA 188 :DYLLNECREQNLNHL T0329 226 :VDTAEKLEEAILG 2feaA 204 :YQDFYEIRKEIEN Number of specific fragments extracted= 14 number of extra gaps= 1 total=765 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2feaA/T0329-2feaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2feaA/T0329-2feaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2feaA read from 2feaA/T0329-2feaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2feaA in template set Warning: unaligning (T0329)V131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0329)S132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 Warning: unaligning (T0329)I161 because of BadResidue code BAD_PEPTIDE in next template residue (2feaA)C149 Warning: unaligning (T0329)R162 because of BadResidue code BAD_PEPTIDE at template residue (2feaA)C149 T0329 3 :YKAAIFDMDGTILDTS 2feaA 5 :KPFIICDFDGTITMND T0329 24 :ALNYAFEQT 2feaA 21 :NIINIMKTF T0329 34 :HRHDFTVEDIKNFFGSGVVVAVTRAL 2feaA 30 :APPEWMALKDGVLSKTLSIKEGVGRM T0329 77 :DEQIPEAVTQTEVNRVLEV 2feaA 56 :FGLLPSSLKEEITSFVLED T0329 108 :TGPFPGILDLMKNLRQKGVKLAV 2feaA 75 :AKIREGFREFVAFINEHEIPFYV T0329 133 :NKPNEAVQVLVE 2feaA 100 :GGMDFFVYPLLE T0329 145 :ELFPGSFDFALGE 2feaA 113 :IVEKDRIYCNHAS T0329 158 :KSG 2feaA 145 :NQC T0329 163 :R 2feaA 150 :C T0329 170 :TSECVKVL 2feaA 151 :KPSVIHEL T0329 179 :VPRD 2feaA 159 :SEPN T0329 183 :KCVYIGDSEIDIQTARN 2feaA 164 :YIIMIGDSVTDVEAAKL T0329 202 :MDEIAVN 2feaA 181 :SDLCFAR T0329 214 :VPFLQKHGATVI 2feaA 191 :LNECREQNLNHL T0329 226 :VDTAEKLEEAILGE 2feaA 204 :YQDFYEIRKEIENV Number of specific fragments extracted= 15 number of extra gaps= 2 total=780 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j97A/T0329-1j97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j97A expands to /projects/compbio/data/pdb/1j97.pdb.gz 1j97A:Bad short name: BE for alphabet: pdb_atoms Bad short name: F1 for alphabet: pdb_atoms Bad short name: F2 for alphabet: pdb_atoms Bad short name: F3 for alphabet: pdb_atoms # T0329 read from 1j97A/T0329-1j97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j97A read from 1j97A/T0329-1j97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j97A to template set # found chain 1j97A in template set Warning: unaligning (T0329)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0329)M10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0329 2 :KYKAAI 1j97A 4 :KKKLIL T0329 11 :DGTILDTSAD 1j97A 13 :DSTLVNNETI T0329 26 :NYAFEQTGHR 1j97A 23 :DEIAREAGVE T0329 49 :SGVVVAVTRALAYE 1j97A 33 :EEVKKITKEAMEGK T0329 64 :GSSRESLVAFGTKDE 1j97A 47 :LNFEQSLRKRVSLLK T0329 83 :AVTQTEVNRVLEV 1j97A 62 :DLPIEKVEKAIKR T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1j97A 75 :ITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKL T0329 147 :FPGSFDFALGEK 1j97A 115 :LDYAFANRLIVK T0329 161 :IRR 1j97A 139 :LKE T0329 164 :K 1j97A 144 :K T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 1j97A 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAF T0329 212 :RSVPFLQKH 1j97A 185 :CAKPILKEK T0329 222 :ATVIVD 1j97A 194 :ADICIE T0329 228 :TAEKLEE 1j97A 202 :DLREILK Number of specific fragments extracted= 14 number of extra gaps= 0 total=794 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j97A/T0329-1j97A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1j97A/T0329-1j97A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j97A read from 1j97A/T0329-1j97A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j97A in template set Warning: unaligning (T0329)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0329)M10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0329 2 :KYKAAI 1j97A 4 :KKKLIL T0329 11 :DGTILDTS 1j97A 13 :DSTLVNNE T0329 24 :ALNYAFEQTGHR 1j97A 21 :TIDEIAREAGVE T0329 41 :EDIKNFF 1j97A 33 :EEVKKIT T0329 48 :GSGVVVAVTRAL 1j97A 46 :KLNFEQSLRKRV T0329 78 :EQIPE 1j97A 58 :SLLKD T0329 84 :VTQTEVNRVLE 1j97A 63 :LPIEKVEKAIK T0329 106 :I 1j97A 74 :R T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1j97A 75 :ITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKL T0329 147 :FPGSFDFALGEKS 1j97A 115 :LDYAFANRLIVKD T0329 161 :IRR 1j97A 137 :EVL T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSE 1j97A 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0329 203 :DEIAV 1j97A 180 :LKIAF T0329 212 :RSVPFLQKH 1j97A 185 :CAKPILKEK T0329 222 :ATVIVD 1j97A 194 :ADICIE T0329 228 :TAEKLEEA 1j97A 202 :DLREILKY Number of specific fragments extracted= 16 number of extra gaps= 0 total=810 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j97A/T0329-1j97A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1j97A/T0329-1j97A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j97A read from 1j97A/T0329-1j97A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j97A in template set Warning: unaligning (T0329)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0329)M10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0329 2 :KYKAAI 1j97A 4 :KKKLIL T0329 11 :DGTILDTS 1j97A 13 :DSTLVNNE T0329 24 :ALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRALA 1j97A 21 :TIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRV T0329 79 :QIPEAVTQTEVNRVLE 1j97A 58 :SLLKDLPIEKVEKAIK T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1j97A 74 :RITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKE T0329 145 :ELFPGSFDFALGEKS 1j97A 113 :LGLDYAFANRLIVKD T0329 160 :GIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSE 1j97A 138 :VLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0329 203 :DEIAV 1j97A 180 :LKIAF T0329 212 :RSVPFL 1j97A 185 :CAKPIL T0329 219 :KHGATVIVDT 1j97A 191 :KEKADICIEK Number of specific fragments extracted= 10 number of extra gaps= 0 total=820 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjrA/T0329-1vjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vjrA expands to /projects/compbio/data/pdb/1vjr.pdb.gz 1vjrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 172, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 173, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 177, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 178, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 180, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 181, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 183, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 184, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 186, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 187, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1601, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1616, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1868, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1872, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1874, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1876, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1878, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1880, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1912, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1914, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1916, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1918, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1920, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1922, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1930, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1938, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 1vjrA # T0329 read from 1vjrA/T0329-1vjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjrA read from 1vjrA/T0329-1vjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vjrA to template set # found chain 1vjrA in template set T0329 3 :YKAAIFDMDGTILD 1vjrA 5 :IELFILDMDGTFYL T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSN 1vjrA 19 :DDSLLPGSLEFLETLKEKNKRFVFFTN T0329 135 :PNEAVQVLVEEL 1vjrA 94 :GTPQLKKVFEAY T0329 147 :F 1vjrA 107 :H T0329 148 :PGSFDFALGEK 1vjrA 111 :EENPDFVVLGF T0329 159 :SGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSE 1vjrA 178 :DLIAGKPNPLVVDVISEKFGVPKERMAMVGDRL T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFLQKHG 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDLERAE T0329 222 :ATVIVDTAEKLEEAI 1vjrA 244 :PDFVFKNLGELAKAV Number of specific fragments extracted= 8 number of extra gaps= 0 total=828 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjrA/T0329-1vjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1vjrA/T0329-1vjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjrA read from 1vjrA/T0329-1vjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjrA in template set T0329 3 :YKAAIFDMDGTIL 1vjrA 5 :IELFILDMDGTFY T0329 17 :TSADLTSALNY 1vjrA 22 :LLPGSLEFLET T0329 29 :FEQTGHRHD 1vjrA 33 :LKEKNKRFV T0329 47 :FGSGVVVAVTRALAYEAGSS 1vjrA 47 :SSLGAQDYVRKLRNMGVDVP T0329 77 :DEQI 1vjrA 67 :DDAV T0329 92 :VLEVFKPYYADHCQI 1vjrA 73 :SGEITAEHMLKRFGR T0329 108 :TG 1vjrA 88 :CR T0329 110 :PFPGILDLMK 1vjrA 94 :GTPQLKKVFE T0329 123 :QKGVKL 1vjrA 104 :AYGHVI T0329 129 :AVVSN 1vjrA 116 :FVVLG T0329 134 :KPNEAVQVLVEELFPGSFDFALGEKSG 1vjrA 124 :TLTYERLKKACILLRKGKFYIATHPDI T0329 161 :IRRKPAPDMTSECVKVLGVPRDKCVYIGDSE 1vjrA 180 :IAGKPNPLVVDVISEKFGVPKERMAMVGDRL T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFLQK 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDLER T0329 220 :HGATVIVDTAEKLEEAI 1vjrA 242 :TKPDFVFKNLGELAKAV Number of specific fragments extracted= 14 number of extra gaps= 0 total=842 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjrA/T0329-1vjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1vjrA/T0329-1vjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjrA read from 1vjrA/T0329-1vjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjrA in template set T0329 2 :KYKAAIFDMDGTILD 1vjrA 4 :KIELFILDMDGTFYL T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSNKP 1vjrA 19 :DDSLLPGSLEFLETLKEKNKRFVFFTNNS T0329 136 :NEAVQVLVE 1vjrA 51 :AQDYVRKLR T0329 145 :ELFPGSFDFALGE 1vjrA 61 :MGVDVPDDAVVTS T0329 160 :GIRRKPAPDMTSECVKVLGVPRDKCVYIGDSE 1vjrA 179 :LIAGKPNPLVVDVISEKFGVPKERMAMVGDRL T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFLQKH 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDLERA T0329 221 :GATVIVDTAEKLEEAI 1vjrA 243 :KPDFVFKNLGELAKAV Number of specific fragments extracted= 7 number of extra gaps= 0 total=849 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aq6A/T0329-1aq6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1aq6A expands to /projects/compbio/data/pdb/1aq6.pdb.gz 1aq6A:# T0329 read from 1aq6A/T0329-1aq6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aq6A read from 1aq6A/T0329-1aq6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1aq6A to template set # found chain 1aq6A in template set T0329 1 :M 1aq6A 1 :M T0329 3 :YKAAIFDMDGTILDTSAD 1aq6A 2 :IKAVVFDAYGTLFDVQSV T0329 22 :TSALNYA 1aq6A 20 :ADATERA T0329 33 :GHR 1aq6A 27 :YPG T0329 38 :FTVEDIKNFFGSGVVVAVTRALAYEAGSSRESLVAFGTKDEQIPE 1aq6A 30 :RGEYITQVWRQKQLEYSWLRALMGRYADFWGVTREALAYTLGTLG T0329 83 :AVTQTEVNRVLEVFKP 1aq6A 76 :EPDESFLADMAQAYNR T0329 108 :TGPFPGILDLMKNL 1aq6A 92 :LTPYPDAAQCLAEL T0329 124 :KGVKLAVVSNKPNEAVQVLVEEL 1aq6A 106 :APLKRAILSNGAPDMLQALVANA T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNW 1aq6A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0329 210 :GFRSVPFLQKHG 1aq6A 205 :GTIAPLTMFKAL T0329 222 :ATVIVDTAEKLEEAILG 1aq6A 227 :PDFVVPALGDLPRLVRG Number of specific fragments extracted= 11 number of extra gaps= 0 total=860 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aq6A/T0329-1aq6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1aq6A/T0329-1aq6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aq6A read from 1aq6A/T0329-1aq6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aq6A in template set T0329 1 :M 1aq6A 1 :M T0329 3 :YKAAIFDMDGTILDTS 1aq6A 2 :IKAVVFDAYGTLFDVQ T0329 19 :ADLTSA 1aq6A 21 :DATERA T0329 34 :HR 1aq6A 27 :YP T0329 37 :D 1aq6A 29 :G T0329 39 :TVEDIKNFFGSGVVVAVTRALAYEAGSSRE 1aq6A 30 :RGEYITQVWRQKQLEYSWLRALMGRYADFW T0329 69 :SLVAFGTKDEQIPEAVTQTEVNRVL 1aq6A 62 :TREALAYTLGTLGLEPDESFLADMA T0329 102 :DHCQI 1aq6A 87 :QAYNR T0329 108 :TGPFPGILDLMKNL 1aq6A 92 :LTPYPDAAQCLAEL T0329 124 :KGVKLAVVSNKPNEAVQVLVEEL 1aq6A 106 :APLKRAILSNGAPDMLQALVANA T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNW 1aq6A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0329 210 :GFR 1aq6A 204 :SGT T0329 221 :GATVIVDTAEKLEEAILG 1aq6A 226 :APDFVVPALGDLPRLVRG Number of specific fragments extracted= 13 number of extra gaps= 0 total=873 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aq6A/T0329-1aq6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1aq6A/T0329-1aq6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aq6A read from 1aq6A/T0329-1aq6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aq6A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1aq6A)M1 T0329 3 :YKAAIFDMDGTILDTS 1aq6A 2 :IKAVVFDAYGTLFDVQ T0329 19 :ADLTSA 1aq6A 21 :DATERA T0329 34 :HRHDFTVEDIKNFFGSGVVVAVTRALAYEAGSSRESLVAFGTKDEQIPEAVTQTEVNRVLE 1aq6A 27 :YPGRGEYITQVWRQKQLEYSWLRALMGRYADFWGVTREALAYTLGTLGLEPDESFLADMAQ T0329 104 :CQIKTGPFPGILDLMKNL 1aq6A 88 :AYNRLTPYPDAAQCLAEL T0329 124 :KGVKLAVVSNKPNEAVQVLVE 1aq6A 106 :APLKRAILSNGAPDMLQALVA T0329 145 :ELFPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNW 1aq6A 128 :AGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0329 212 :RSVPFLQKH 1aq6A 193 :LSQEALARE T0329 221 :GATVIVDTAEKLEEAIL 1aq6A 226 :APDFVVPALGDLPRLVR Number of specific fragments extracted= 8 number of extra gaps= 0 total=881 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wviA/T0329-1wviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wviA expands to /projects/compbio/data/pdb/1wvi.pdb.gz 1wviA:# T0329 read from 1wviA/T0329-1wviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wviA read from 1wviA/T0329-1wviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wviA to template set # found chain 1wviA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1wviA)T1002 T0329 3 :YKAAIFDMDGTILDT 1wviA 1003 :YKGYLIDLDGTIYKG T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSN 1wviA 1018 :KDRIPAGEDFVKRLQERQLPYILVTN T0329 134 :KPNEAVQVLVEEL 1wviA 1047 :RTPEMVQEMLATS T0329 147 :F 1wviA 1062 :I T0329 148 :PGSF 1wviA 1066 :LETI T0329 152 :DFALGEK 1wviA 1088 :TAYVIGE T0329 159 :SGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSE 1wviA 1176 :PIIIGKPEAVIMNKALDRLGVKRHEAIMVGDNY T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFLQKHG 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEVPALP T0329 222 :ATVIVDTAEK 1wviA 1242 :PDFVLSSLAE Number of specific fragments extracted= 9 number of extra gaps= 0 total=890 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wviA/T0329-1wviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1wviA/T0329-1wviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wviA read from 1wviA/T0329-1wviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wviA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1wviA)T1002 T0329 3 :YKAAIFDMDGTILD 1wviA 1003 :YKGYLIDLDGTIYK T0329 17 :TSADLTSALNYAFEQT 1wviA 1020 :RIPAGEDFVKRLQERQ T0329 37 :DFTVEDIKNFFGSGV 1wviA 1046 :TRTPEMVQEMLATSF T0329 73 :FGTKDEQI 1wviA 1062 :IKTPLETI T0329 92 :VLEVFKPYYADHCQIK 1wviA 1072 :ATLATIDYMNDMKRGK T0329 108 :TGPFPGILDLM 1wviA 1091 :VIGETGLKKAV T0329 122 :RQKGVK 1wviA 1102 :AEAGYR T0329 128 :LAVVSN 1wviA 1115 :YVVVGL T0329 134 :KPNEAVQVLVEELFPGSFDFALGEKSG 1wviA 1123 :NLTYEKLTLATLAIQKGAVFIGTNPDL T0329 162 :RRKPAPDMTSECVKVLGVPRDKCVYIGDSE 1wviA 1179 :IGKPEAVIMNKALDRLGVKRHEAIMVGDNY T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFLQK 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEVPA T0329 220 :HGATVIVDTAEK 1wviA 1240 :IQPDFVLSSLAE Number of specific fragments extracted= 12 number of extra gaps= 0 total=902 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wviA/T0329-1wviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1wviA/T0329-1wviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wviA read from 1wviA/T0329-1wviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wviA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1wviA)T1002 T0329 3 :YKAAIFDMDGTILDT 1wviA 1003 :YKGYLIDLDGTIYKG T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSN 1wviA 1018 :KDRIPAGEDFVKRLQERQLPYILVTN T0329 134 :KPNEAVQVLVE 1wviA 1047 :RTPEMVQEMLA T0329 145 :ELFPGSFDFALGE 1wviA 1060 :FNIKTPLETIYTA T0329 162 :RRKPAPDMTSECVKVLGVPRDKCVYIGDSE 1wviA 1179 :IGKPEAVIMNKALDRLGVKRHEAIMVGDNY T0329 192 :IDIQTARNSEMDEIAVNWGFRSVPFLQK 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEVPA T0329 220 :HGATVIVDTAEK 1wviA 1240 :IQPDFVLSSLAE Number of specific fragments extracted= 7 number of extra gaps= 0 total=909 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvhA/T0329-1lvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lvhA expands to /projects/compbio/data/pdb/1lvh.pdb.gz 1lvhA:Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0329 read from 1lvhA/T0329-1lvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvhA read from 1lvhA/T0329-1lvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lvhA to template set # found chain 1lvhA in template set Warning: unaligning (T0329)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0329)M10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0329 1 :M 1lvhA 1 :M T0329 3 :YKAAI 1lvhA 2 :FKAVL T0329 11 :DGTILDTSADLTSALNYAFEQTGHR 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGIN T0329 37 :DFTVEDIKNFFGSGVVVAVTRALAYE 1lvhA 35 :GVDRQFNEQLKGVSREDSLQKILDLA T0329 82 :E 1lvhA 61 :D T0329 83 :AVTQTEVNRVLEVFKPYYADHC 1lvhA 63 :KVSAEEFKELAKRKNDNYVKMI T0329 105 :QIKTGPFPGILDLMKNLRQKGVKLAVVSNK 1lvhA 87 :VSPADVYPGILQLLKDLRSNKIKIALASAS T0329 137 :EAVQVLVEEL 1lvhA 117 :KNGPFLLERM T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 1lvhA 128 :LTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIG T0329 211 :FRSVPFLQKH 1lvhA 188 :VGRPEDLGDD T0329 222 :A 1lvhA 198 :I T0329 224 :VIVDTAEK 1lvhA 199 :VIVPDTSH T0329 232 :LEEAILG 1lvhA 212 :LKEVWLQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=922 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvhA/T0329-1lvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1lvhA/T0329-1lvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvhA read from 1lvhA/T0329-1lvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lvhA in template set Warning: unaligning (T0329)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0329)M10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0329 1 :M 1lvhA 1 :M T0329 3 :YKAAI 1lvhA 2 :FKAVL T0329 11 :DGTILDTSADLTSALNYAFEQTGHR 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGIN T0329 37 :DFTVEDIKNFFGSGVVVAVTRAL 1lvhA 35 :GVDRQFNEQLKGVSREDSLQKIL T0329 78 :EQIPEAVTQTEVNRVLEVFKPYYADHCQI 1lvhA 58 :DLADKKVSAEEFKELAKRKNDNYVKMIQD T0329 108 :TG 1lvhA 87 :VS T0329 110 :PFPGILDLMKNLRQKGVKLAVVSNK 1lvhA 92 :VYPGILQLLKDLRSNKIKIALASAS T0329 137 :EAVQVLVEEL 1lvhA 117 :KNGPFLLERM T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAV 1lvhA 128 :LTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGV T0329 212 :RSVPFLQK 1lvhA 189 :GRPEDLGD T0329 222 :ATVIVDTAEK 1lvhA 197 :DIVIVPDTSH T0329 232 :LEEAILG 1lvhA 212 :LKEVWLQ Number of specific fragments extracted= 12 number of extra gaps= 0 total=934 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvhA/T0329-1lvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1lvhA/T0329-1lvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvhA read from 1lvhA/T0329-1lvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lvhA in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1lvhA)M1 Warning: unaligning (T0329)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0329)M10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0329 3 :YKAAI 1lvhA 2 :FKAVL T0329 11 :DGTILDTSADLTSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVT 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQK T0329 76 :KDEQIPEAVTQTEVNRVLEVFKPYYADHCQI 1lvhA 56 :ILDLADKKVSAEEFKELAKRKNDNYVKMIQD T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSNK 1lvhA 89 :PADVYPGILQLLKDLRSNKIKIALASAS T0329 137 :EAVQVLVE 1lvhA 117 :KNGPFLLE T0329 145 :ELFPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAV 1lvhA 126 :MNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGV T0329 212 :RSVPFL 1lvhA 189 :GRPEDL T0329 220 :HGATVIVDT 1lvhA 195 :GDDIVIVPD T0329 229 :AEKLEEAILGE 1lvhA 209 :LEFLKEVWLQK Number of specific fragments extracted= 9 number of extra gaps= 0 total=943 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkuA/T0329-1rkuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rkuA expands to /projects/compbio/data/pdb/1rku.pdb.gz 1rkuA:Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1094, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1096, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1098, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 1rkuA # T0329 read from 1rkuA/T0329-1rkuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkuA read from 1rkuA/T0329-1rkuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rkuA to template set # found chain 1rkuA in template set Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0329 3 :YKAAI 1rkuA 1 :MEIAC T0329 10 :MDGTILDT 1rkuA 8 :LEGVLVPE T0329 24 :ALNYAFEQTGHR 1rkuA 16 :IWIAFAEKTGID T0329 45 :NFF 1rkuA 28 :ALK T0329 48 :GSGVVVAVTRALAY 1rkuA 40 :DVLMKQRLRILDEH T0329 83 :AVTQTEVNRVLEV 1rkuA 54 :GLKLGDIQEVIAT T0329 108 :TGPFPGILDLMKNLRQK 1rkuA 67 :LKPLEGAVEFVDWLRER T0329 126 :VKLAVVSNKPNEAVQVLVEEL 1rkuA 84 :FQVVILSDTFYEFSQPLMRQL T0329 147 :FPGSFDFALGEKSGIR 1rkuA 106 :FPTLLCHKLEIDDSDR T0329 163 :RKPAPDMTSECVK 1rkuA 130 :KDPKRQSVIAFKS T0329 180 :PRDKCVYIGDSEIDIQTARNSEMDEIA 1rkuA 143 :LYYRVIAAGDSYNDTTMLSEAHAGILF T0329 211 :FRSVPFLQKHG 1rkuA 170 :HAPENVIREFP T0329 224 :VIVDTAEKLEEAILG 1rkuA 183 :PAVHTYEDLKREFLK Number of specific fragments extracted= 13 number of extra gaps= 1 total=956 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkuA/T0329-1rkuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1rkuA/T0329-1rkuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkuA read from 1rkuA/T0329-1rkuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rkuA in template set Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0329 3 :YKAAI 1rkuA 1 :MEIAC T0329 10 :MDGTILDT 1rkuA 8 :LEGVLVPE T0329 24 :ALNYAFEQTGHR 1rkuA 16 :IWIAFAEKTGID T0329 74 :GTKDEQIPEAVTQTEVNRVLEVFKPY 1rkuA 28 :ALKATTRDIPDYDVLMKQRLRILDEH T0329 100 :YADHCQI 1rkuA 60 :IQEVIAT T0329 108 :TGPFPGILDLMKNLRQK 1rkuA 67 :LKPLEGAVEFVDWLRER T0329 126 :VKLAVVSNKPNEAVQVLVEEL 1rkuA 84 :FQVVILSDTFYEFSQPLMRQL T0329 147 :FPGSFDFALGEKSGI 1rkuA 106 :FPTLLCHKLEIDDSD T0329 162 :RRK 1rkuA 128 :RQK T0329 168 :DMTSECVKVL 1rkuA 131 :DPKRQSVIAF T0329 181 :RDKCVYIGDSEIDIQTARNSE 1rkuA 144 :YYRVIAAGDSYNDTTMLSEAH T0329 203 :DEIAVN 1rkuA 165 :AGILFH T0329 212 :RSVPFLQKHGATVIVDTAEKLEEAI 1rkuA 171 :APENVIREFPQFPAVHTYEDLKREF Number of specific fragments extracted= 13 number of extra gaps= 1 total=969 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkuA/T0329-1rkuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1rkuA/T0329-1rkuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkuA read from 1rkuA/T0329-1rkuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rkuA in template set Warning: unaligning (T0329)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0329)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0329 4 :KAAI 1rkuA 2 :EIAC T0329 10 :MDGTILDT 1rkuA 8 :LEGVLVPE T0329 24 :ALNYAFEQTGH 1rkuA 16 :IWIAFAEKTGI T0329 77 :DEQIPEAVTQTEVNRVLEVFKPYY 1rkuA 27 :DALKATTRDIPDYDVLMKQRLRIL T0329 101 :ADHCQIKTGPFPGILDLMKNLRQK 1rkuA 60 :IQEVIATLKPLEGAVEFVDWLRER T0329 126 :VKLAVVSNKPNEAVQVLVE 1rkuA 84 :FQVVILSDTFYEFSQPLMR T0329 145 :ELFPGSFDFALGEKS 1rkuA 104 :LGFPTLLCHKLEIDD T0329 160 :GIRRK 1rkuA 127 :LRQKD T0329 169 :MTSECVKVL 1rkuA 132 :PKRQSVIAF T0329 181 :RDKCVYIGDSEIDIQTARNSE 1rkuA 144 :YYRVIAAGDSYNDTTMLSEAH T0329 203 :DEIAVNW 1rkuA 165 :AGILFHA T0329 213 :SVPFLQKHGATVIVDTAEKLEEAI 1rkuA 172 :PENVIREFPQFPAVHTYEDLKREF Number of specific fragments extracted= 12 number of extra gaps= 1 total=981 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wr8A/T0329-1wr8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wr8A expands to /projects/compbio/data/pdb/1wr8.pdb.gz 1wr8A:# T0329 read from 1wr8A/T0329-1wr8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wr8A read from 1wr8A/T0329-1wr8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wr8A to template set # found chain 1wr8A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1wr8A)K2 T0329 3 :YKAAIFDMDGTIL 1wr8A 3 :IKAISIDIDGTIT T0329 105 :QIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1wr8A 16 :YPNRMIHEKALEAIRRAESLGIPIMLVTGNTVQFAEAASILI T0329 147 :FPGSF 1wr8A 59 :TSGPV T0329 152 :DFALGEK 1wr8A 68 :GGAISYK T0329 159 :SGIRRK 1wr8A 149 :KPWINK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 1wr8A 155 :GSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVGYKVAV T0329 211 :FRSVPFLQKH 1wr8A 195 :AQAPKILKEN T0329 222 :ATVIVDT 1wr8A 205 :ADYVTKK T0329 229 :AEKLEEA 1wr8A 221 :IYHILEK Number of specific fragments extracted= 9 number of extra gaps= 0 total=990 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wr8A/T0329-1wr8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1wr8A/T0329-1wr8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wr8A read from 1wr8A/T0329-1wr8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wr8A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1wr8A)K2 T0329 3 :YKAAIFDMDGTILD 1wr8A 3 :IKAISIDIDGTITY T0329 17 :TSADLTSALNYAFE 1wr8A 21 :IHEKALEAIRRAES T0329 32 :TGHRH 1wr8A 35 :LGIPI T0329 38 :FTVEDIKNFFGS 1wr8A 45 :NTVQFAEAASIL T0329 83 :AVTQTEVNRVLEVFKPY 1wr8A 80 :LASMDEEWILWNEIRKR T0329 104 :CQI 1wr8A 97 :FPN T0329 108 :TGPFPGI 1wr8A 100 :ARTSYTM T0329 124 :KG 1wr8A 117 :RE T0329 133 :NKPNEAVQVLVEEL 1wr8A 119 :TINVETVREIINEL T0329 147 :FP 1wr8A 134 :LN T0329 150 :SFDFALGEKSGI 1wr8A 142 :GFAIHVKKPWIN T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEM 1wr8A 155 :GSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVGY T0329 204 :EIAV 1wr8A 191 :KVAV T0329 211 :FRSVPFLQKH 1wr8A 195 :AQAPKILKEN T0329 222 :ATVIVDT 1wr8A 205 :ADYVTKK T0329 229 :AEKLEEAI 1wr8A 221 :IYHILEKF Number of specific fragments extracted= 16 number of extra gaps= 0 total=1006 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wr8A/T0329-1wr8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1wr8A/T0329-1wr8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wr8A read from 1wr8A/T0329-1wr8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wr8A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1wr8A)K2 T0329 3 :YKAAIFDMDGTIL 1wr8A 3 :IKAISIDIDGTIT T0329 105 :QIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1wr8A 16 :YPNRMIHEKALEAIRRAESLGIPIMLVTGNTVQFAEAASI T0329 145 :ELFPGSF 1wr8A 57 :IGTSGPV T0329 152 :DFALG 1wr8A 68 :GGAIS T0329 163 :RKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEI 1wr8A 151 :WINKGSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVGYKVA T0329 209 :W 1wr8A 194 :V T0329 211 :FRSVPFL 1wr8A 195 :AQAPKIL T0329 219 :KHGATVIVDT 1wr8A 202 :KENADYVTKK T0329 229 :AEKLEEA 1wr8A 221 :IYHILEK Number of specific fragments extracted= 9 number of extra gaps= 0 total=1015 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ymqA/T0329-1ymqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ymqA expands to /projects/compbio/data/pdb/1ymq.pdb.gz 1ymqA:# T0329 read from 1ymqA/T0329-1ymqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ymqA read from 1ymqA/T0329-1ymqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ymqA to template set # found chain 1ymqA in template set Warning: unaligning (T0329)Y3 because first residue in template chain is (1ymqA)T2 T0329 4 :KAAIFDMDGTILDTSA 1ymqA 3 :KALFFDIDGTLVSFET T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSN 1ymqA 19 :HRIPSSTIEALEAAHAKGLKIFIATG T0329 134 :KPNEAVQVLVEEL 1ymqA 85 :IPQEEVKAMAAFC T0329 147 :FPG 1ymqA 99 :KKG T0329 151 :FDFALGEK 1ymqA 102 :VPCIFVEE T0329 159 :SGIRRK 1ymqA 183 :AKGDTK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 1ymqA 189 :QKGIDEIIRHFGIKLEETMSFGDGGNDISMLRHAAIGVAM T0329 211 :FRSVPFLQKH 1ymqA 229 :GQAKEDVKAA T0329 222 :ATVIVDTAEK 1ymqA 239 :ADYVTAPIDE T0329 232 :LEEAIL 1ymqA 251 :ISKAMK Number of specific fragments extracted= 10 number of extra gaps= 0 total=1025 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ymqA/T0329-1ymqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1ymqA/T0329-1ymqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ymqA read from 1ymqA/T0329-1ymqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ymqA in template set Warning: unaligning (T0329)Y3 because first residue in template chain is (1ymqA)T2 T0329 4 :KAAIFDMDGTILDTS 1ymqA 3 :KALFFDIDGTLVSFE T0329 19 :ADLTSALNYAFEQT 1ymqA 23 :SSTIEALEAAHAKG T0329 34 :HR 1ymqA 83 :SA T0329 38 :FTVEDIKNFF 1ymqA 85 :IPQEEVKAMA T0329 56 :TRAL 1ymqA 95 :AFCE T0329 94 :EV 1ymqA 99 :KK T0329 96 :FKPYYADHCQIKTGPF 1ymqA 117 :PNEMVKKIFYDFLHVN T0329 112 :P 1ymqA 135 :P T0329 118 :MKNLRQKGV 1ymqA 139 :FEEASNKEV T0329 130 :VVSNK 1ymqA 149 :QMTPF T0329 135 :PNEAVQVL 1ymqA 155 :TEEEEKEV T0329 147 :FPGSFDFALGEKSGI 1ymqA 174 :WYPAFADVTAKGDTK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSE 1ymqA 189 :QKGIDEIIRHFGIKLEETMSFGDGGNDISMLRHAA T0329 205 :IAVNWGFR 1ymqA 224 :IGVAMGQA T0329 214 :VPFLQKH 1ymqA 232 :KEDVKAA T0329 222 :ATVIVDTAEK 1ymqA 239 :ADYVTAPIDE T0329 232 :LEEAI 1ymqA 251 :ISKAM Number of specific fragments extracted= 17 number of extra gaps= 0 total=1042 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ymqA/T0329-1ymqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1ymqA/T0329-1ymqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ymqA read from 1ymqA/T0329-1ymqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ymqA in template set Warning: unaligning (T0329)Y3 because first residue in template chain is (1ymqA)T2 T0329 4 :KAAIFDMDGTILDT 1ymqA 3 :KALFFDIDGTLVSF T0329 106 :IKTGPFPGILDLMKNLRQKGVKLAVVSNKP 1ymqA 17 :ETHRIPSSTIEALEAAHAKGLKIFIATGRP T0329 137 :E 1ymqA 54 :S T0329 141 :VLVEE 1ymqA 55 :ELQDR T0329 149 :GSFDFALGE 1ymqA 60 :NLIDGYITM T0329 162 :RRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSE 1ymqA 184 :KGDTKQKGIDEIIRHFGIKLEETMSFGDGGNDISMLRHAA T0329 205 :IAVNWGFRSVPFL 1ymqA 224 :IGVAMGQAKEDVK T0329 220 :HGATVIVDTAEK 1ymqA 237 :AAADYVTAPIDE Number of specific fragments extracted= 8 number of extra gaps= 0 total=1050 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkqA/T0329-1rkqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rkqA expands to /projects/compbio/data/pdb/1rkq.pdb.gz 1rkqA:Skipped atom 294, because occupancy 0.500 <= existing 0.500 in 1rkqA Skipped atom 296, because occupancy 0.500 <= existing 0.500 in 1rkqA Skipped atom 1588, because occupancy 0.500 <= existing 0.500 in 1rkqA Skipped atom 1590, because occupancy 0.500 <= existing 0.500 in 1rkqA Skipped atom 1592, because occupancy 0.500 <= existing 0.500 in 1rkqA # T0329 read from 1rkqA/T0329-1rkqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkqA read from 1rkqA/T0329-1rkqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rkqA to template set # found chain 1rkqA in template set T0329 2 :KYKAAIFDMDGTI 1rkqA 3 :AIKLIAIDMDGTL T0329 104 :CQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1rkqA 16 :LLPDHTISPAVKNAIAAARARGVNVVLTTGRPYAGVHNYLKEL T0329 147 :FPGSFDFALGEK 1rkqA 60 :MEQPGDYCITYN T0329 159 :SGIRRK 1rkqA 193 :DKRVNK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 1rkqA 199 :GTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGVGVAV T0329 211 :FRSVPFLQKH 1rkqA 239 :DNAIPSVKEV T0329 222 :ATVIVDTAEK 1rkqA 249 :ANFVTKSNLE T0329 232 :LEEAIL 1rkqA 261 :VAFAIE Number of specific fragments extracted= 8 number of extra gaps= 0 total=1058 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkqA/T0329-1rkqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1rkqA/T0329-1rkqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkqA read from 1rkqA/T0329-1rkqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rkqA in template set Warning: unaligning (T0329)A54 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rkqA)S101 Warning: unaligning (T0329)V55 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rkqA)S101 T0329 2 :KYKAAIFDMDGTILD 1rkqA 3 :AIKLIAIDMDGTLLL T0329 17 :TSADLTSALNYAFEQT 1rkqA 22 :ISPAVKNAIAAARARG T0329 34 :HR 1rkqA 87 :TA T0329 38 :FTVEDIKNFF 1rkqA 89 :LSYDDYRFLE T0329 53 :V 1rkqA 99 :K T0329 56 :TRALA 1rkqA 102 :REVGS T0329 63 :AGSSRESLVAFGT 1rkqA 124 :SYYTVHESFVATI T0329 76 :KDEQIPEAV 1rkqA 142 :EAEKMDPNT T0329 85 :TQTEVNRVLEVFKPYYADHC 1rkqA 160 :EPAILDQAIARIPQEVKEKY T0329 149 :GSFDFALGEKSGI 1rkqA 186 :PYFLEILDKRVNK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSE 1rkqA 199 :GTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAG T0329 205 :IAVNW 1rkqA 234 :VGVAV T0329 211 :FRSVPFLQKH 1rkqA 239 :DNAIPSVKEV T0329 222 :ATVIVDTA 1rkqA 249 :ANFVTKSN Number of specific fragments extracted= 14 number of extra gaps= 1 total=1072 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkqA/T0329-1rkqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1rkqA/T0329-1rkqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkqA read from 1rkqA/T0329-1rkqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rkqA in template set T0329 2 :KYKAAIFDM 1rkqA 3 :AIKLIAIDM T0329 100 :YADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1rkqA 12 :DGTLLLPDHTISPAVKNAIAAARARGVNVVLTTGRPYAGVHNYLK T0329 145 :ELFPGSFDFALGE 1rkqA 58 :LHMEQPGDYCITY T0329 166 :APDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSE 1rkqA 198 :KGTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAG T0329 205 :IAVNWG 1rkqA 234 :VGVAVD T0329 212 :RSVPFLQK 1rkqA 240 :NAIPSVKE T0329 221 :GATVIVDT 1rkqA 248 :VANFVTKS Number of specific fragments extracted= 7 number of extra gaps= 0 total=1079 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf2A/T0329-1nf2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nf2A expands to /projects/compbio/data/pdb/1nf2.pdb.gz 1nf2A:# T0329 read from 1nf2A/T0329-1nf2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nf2A read from 1nf2A/T0329-1nf2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nf2A to template set # found chain 1nf2A in template set T0329 1 :M 1nf2A 1 :M T0329 3 :YKAAIFDMDGTILDTSADLTSALNYAFEQTGHRHDF 1nf2A 2 :YRVFVFDLDGTLLNDNLEISEKDRRNIEKLSRKCYV T0329 83 :AVTQTEVNRVLEVFKPY 1nf2A 82 :KIPPEVAKDIIEYIKPL T0329 100 :YADHCQIKTGPFPGILDLMK 1nf2A 122 :YARHSNVDYRVEPNLSELVS T0329 123 :QK 1nf2A 142 :KM T0329 133 :N 1nf2A 144 :G T0329 134 :KPNEAVQVLVEEL 1nf2A 152 :DTPERLDELKEIL T0329 147 :FPGSFDFALGEK 1nf2A 168 :FKDVVKVFKSFP T0329 159 :SGIRRK 1nf2A 186 :PKNVDK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 1nf2A 192 :GKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVAM T0329 211 :FRSVPFLQKH 1nf2A 232 :ENAIEKVKEA T0329 222 :ATVIVDTAEK 1nf2A 242 :SDIVTLTNND T0329 232 :LEEAILG 1nf2A 254 :VSYVLER Number of specific fragments extracted= 13 number of extra gaps= 0 total=1092 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf2A/T0329-1nf2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1nf2A/T0329-1nf2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nf2A read from 1nf2A/T0329-1nf2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nf2A in template set T0329 1 :M 1nf2A 1 :M T0329 3 :YKAAIFDMDGTILD 1nf2A 2 :YRVFVFDLDGTLLN T0329 17 :TSADLTSALNYAFEQT 1nf2A 20 :ISEKDRRNIEKLSRKC T0329 34 :HR 1nf2A 81 :EK T0329 38 :FTVEDIKNF 1nf2A 83 :IPPEVAKDI T0329 55 :VTRAL 1nf2A 92 :IEYIK T0329 81 :PEAV 1nf2A 97 :PLNV T0329 85 :TQTEVNRVLE 1nf2A 115 :DNEEIKSYAR T0329 103 :HCQIKTGPFPGILDLMK 1nf2A 125 :HSNVDYRVEPNLSELVS T0329 123 :QKG 1nf2A 142 :KMG T0329 132 :SN 1nf2A 145 :TT T0329 134 :KPNEAVQVLVEEL 1nf2A 152 :DTPERLDELKEIL T0329 147 :FPGSFDF 1nf2A 168 :FKDVVKV T0329 154 :ALGEKSGI 1nf2A 183 :EIVPKNVD T0329 166 :APDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEI 1nf2A 191 :KGKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVA T0329 211 :FRSVPFLQKH 1nf2A 232 :ENAIEKVKEA T0329 222 :ATVIVDTAE 1nf2A 242 :SDIVTLTNN Number of specific fragments extracted= 17 number of extra gaps= 0 total=1109 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf2A/T0329-1nf2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1nf2A/T0329-1nf2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nf2A read from 1nf2A/T0329-1nf2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nf2A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1nf2A)M1 T0329 3 :YKAAIFDM 1nf2A 2 :YRVFVFDL T0329 100 :YADHCQIKTGPFPGILDLMKNLRQK 1nf2A 10 :DGTLLNDNLEISEKDRRNIEKLSRK T0329 126 :VKLAVVSNKPNEAVQVLVEELFPGSFDFALGE 1nf2A 35 :CYVVFASGRMLVSTLNVEKKYFKRTFPTIAYN T0329 160 :GIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEI 1nf2A 185 :VPKNVDKGKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVA Number of specific fragments extracted= 4 number of extra gaps= 0 total=1113 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nrwA/T0329-1nrwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nrwA expands to /projects/compbio/data/pdb/1nrw.pdb.gz 1nrwA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 128, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 130, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 1nrwA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 646, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 648, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1007, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1015, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 1nrwA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2199, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2201, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2203, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2205, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2207, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2209, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2211, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2213, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2215, because occupancy 0.500 <= existing 0.500 in 1nrwA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0329 read from 1nrwA/T0329-1nrwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nrwA read from 1nrwA/T0329-1nrwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nrwA to template set # found chain 1nrwA in template set Warning: unaligning (T0329)Y3 because first residue in template chain is (1nrwA)M1 T0329 4 :KAAIFDMDGTILDTSADLTSALNYAFEQTGHRHD 1nrwA 2 :KLIAIDLDGTLLNSKHQVSLENENALRQAQRDGI T0329 38 :F 1nrwA 37 :V T0329 39 :TVEDIKNFF 1nrwA 83 :DKKRAYDIL T0329 48 :GSGVVVAVTRALAYE 1nrwA 115 :GRELLDVELDRFRSA T0329 64 :GS 1nrwA 130 :NP T0329 83 :AVTQTEVNRVLEVFKPY 1nrwA 132 :EADLSVLKQAAEVQYSQ T0329 100 :YAD 1nrwA 157 :FQE T0329 104 :CQIKTGPF 1nrwA 160 :LFEADEPI T0329 133 :NKPNEAVQVLVEEL 1nrwA 176 :SFFKEKLEAGWKRY T0329 147 :FPGSFDFALGEK 1nrwA 191 :HAEDLTLVSSAE T0329 159 :SGIRRK 1nrwA 209 :SRKASK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 1nrwA 215 :GQALKRLAKQLNIPLEETAAVGDSLNDKSMLEAAGKGVAM T0329 211 :FRSVPFLQKH 1nrwA 255 :GNAREDIKSI T0329 222 :ATVIVDTAEK 1nrwA 265 :ADAVTLTNDE T0329 232 :LEEAIL 1nrwA 277 :VAHMMK Number of specific fragments extracted= 15 number of extra gaps= 0 total=1128 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nrwA/T0329-1nrwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1nrwA/T0329-1nrwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nrwA read from 1nrwA/T0329-1nrwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nrwA in template set Warning: unaligning (T0329)Y3 because first residue in template chain is (1nrwA)M1 T0329 4 :KAAIFDMDGTILDTS 1nrwA 2 :KLIAIDLDGTLLNSK T0329 19 :ADLTSALNYAFEQT 1nrwA 21 :LENENALRQAQRDG T0329 36 :HDFTVEDIKNFF 1nrwA 111 :TPQNGRELLDVE T0329 52 :VVAVTRAL 1nrwA 123 :LDRFRSAN T0329 82 :EAVTQTEVNRVLEVFKPY 1nrwA 131 :PEADLSVLKQAAEVQYSQ T0329 100 :YADHCQI 1nrwA 157 :FQELFEA T0329 108 :TGPF 1nrwA 164 :DEPI T0329 133 :NKPNEAVQVLVEEL 1nrwA 176 :SFFKEKLEAGWKRY T0329 147 :FPGSFDFALGEKS 1nrwA 191 :HAEDLTLVSSAEH T0329 160 :GIRRK 1nrwA 210 :RKASK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSE 1nrwA 215 :GQALKRLAKQLNIPLEETAAVGDSLNDKSMLEAAG T0329 203 :DEIAV 1nrwA 250 :KGVAM T0329 211 :FRSVPFLQKH 1nrwA 255 :GNAREDIKSI T0329 222 :ATVIVDTAEK 1nrwA 265 :ADAVTLTNDE Number of specific fragments extracted= 14 number of extra gaps= 0 total=1142 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nrwA/T0329-1nrwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1nrwA/T0329-1nrwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nrwA read from 1nrwA/T0329-1nrwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nrwA in template set Warning: unaligning (T0329)Y3 because first residue in template chain is (1nrwA)M1 T0329 4 :KAAIFDMDGTI 1nrwA 2 :KLIAIDLDGTL T0329 104 :CQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1nrwA 13 :LNSKHQVSLENENALRQAQRDGIEVVVSTGRAHFDVMSIFE T0329 145 :ELFP 1nrwA 55 :LGIK T0329 152 :DFALGE 1nrwA 59 :TWVISA T0329 166 :APDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSE 1nrwA 214 :KGQALKRLAKQLNIPLEETAAVGDSLNDKSMLEAAG T0329 205 :IAVNWGF 1nrwA 250 :KGVAMGN T0329 213 :SVPFLQ 1nrwA 257 :AREDIK T0329 220 :HGATVI 1nrwA 263 :SIADAV Number of specific fragments extracted= 8 number of extra gaps= 0 total=1150 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj5A/T0329-1vj5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vj5A expands to /projects/compbio/data/pdb/1vj5.pdb.gz 1vj5A:# T0329 read from 1vj5A/T0329-1vj5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vj5A read from 1vj5A/T0329-1vj5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vj5A to template set # found chain 1vj5A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1vj5A)T2 T0329 3 :YKAAIFDMDGTILDTSA 1vj5A 3 :LRAAVFDLDGVLALPAV T0329 22 :TSALNYAFEQTGHR 1vj5A 20 :FGVLGRTEEALALP T0329 40 :VEDIKNFFG 1vj5A 34 :RGLLNDAFQ T0329 49 :SGVVVAVTRALAYE 1vj5A 44 :GGPEGATTRLMKGE T0329 64 :GSSRESLVAFGTK 1vj5A 58 :ITLSQWIPLMEEN T0329 77 :DEQIPEAVT 1vj5A 79 :KVCLPKNFS T0329 89 :VNRVLEVFKPY 1vj5A 88 :IKEIFDKAISA T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSN 1vj5A 99 :RKINRPMLQAALMLRKKGFTTAILTN T0329 134 :KPNEAVQVLVEEL 1vj5A 131 :AERDGLAQLMCEL T0329 147 :F 1vj5A 145 :M T0329 150 :SFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 1vj5A 146 :HFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTIL T0329 211 :FRSVPFL 1vj5A 203 :VQDTDTA T0329 229 :AEKLEEAIL 1vj5A 210 :LKELEKVTG Number of specific fragments extracted= 13 number of extra gaps= 0 total=1163 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj5A/T0329-1vj5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1vj5A/T0329-1vj5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vj5A read from 1vj5A/T0329-1vj5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vj5A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1vj5A)T2 T0329 3 :YKAAIFDMDGTIL 1vj5A 3 :LRAAVFDLDGVLA T0329 16 :DTSA 1vj5A 18 :AVFG T0329 24 :ALNYAFEQTGHRHD 1vj5A 22 :VLGRTEEALALPRG T0329 42 :DIKNFFG 1vj5A 36 :LLNDAFQ T0329 60 :AYEAGSSRESLVAFGTKDEQIPEAVTQTEVNRVLEV 1vj5A 43 :KGGPEGATTRLMKGEITLSQWIPLMEENCRKCSETA T0329 96 :FKPYYADHCQI 1vj5A 88 :IKEIFDKAISA T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSN 1vj5A 99 :RKINRPMLQAALMLRKKGFTTAILTN T0329 134 :KPNEAVQVLVEEL 1vj5A 131 :AERDGLAQLMCEL T0329 147 :FP 1vj5A 145 :MH T0329 151 :FDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAV 1vj5A 147 :FDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILV T0329 212 :RSVPFL 1vj5A 204 :QDTDTA T0329 229 :AEKLEEAI 1vj5A 210 :LKELEKVT Number of specific fragments extracted= 12 number of extra gaps= 0 total=1175 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj5A/T0329-1vj5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1vj5A/T0329-1vj5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vj5A read from 1vj5A/T0329-1vj5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vj5A in template set Warning: unaligning (T0329)K2 because first residue in template chain is (1vj5A)T2 T0329 3 :YKAAIFDMDGTILDTSAD 1vj5A 3 :LRAAVFDLDGVLALPAVF T0329 24 :ALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRALAYEAGSSRES 1vj5A 22 :VLGRTEEALALPRGLLNDAFQKGGPEGATTRLMKGEITLSQWIPLM T0329 70 :LVAFGTKDEQIPEAVTQ 1vj5A 72 :RKCSETAKVCLPKNFSI T0329 93 :L 1vj5A 89 :K T0329 99 :YYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKP 1vj5A 90 :EIFDKAISARKINRPMLQAALMLRKKGFTTAILTNTW T0329 136 :NEAVQVLVE 1vj5A 133 :RDGLAQLMC T0329 145 :ELF 1vj5A 143 :LKM T0329 150 :SFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAV 1vj5A 146 :HFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILV T0329 212 :RSVPFL 1vj5A 204 :QDTDTA T0329 229 :AEKLEEAI 1vj5A 210 :LKELEKVT Number of specific fragments extracted= 10 number of extra gaps= 0 total=1185 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k1eA/T0329-1k1eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1k1eA expands to /projects/compbio/data/pdb/1k1e.pdb.gz 1k1eA:# T0329 read from 1k1eA/T0329-1k1eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k1eA read from 1k1eA/T0329-1k1eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1k1eA to template set # found chain 1k1eA in template set T0329 3 :YKAAIFDMDGTILDT 1k1eA 8 :IKFVITDVDGVLTDG T0329 112 :PGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1k1eA 38 :VRDGLGIKMLMDADIQVAVLSGRDSPILRRRIADL T0329 151 :FDFALGE 1k1eA 74 :IKLFFLG T0329 161 :IRRK 1k1eA 81 :KLEK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 1k1eA 85 :ETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACGTSFAV T0329 211 :FRSVPFLQKH 1k1eA 125 :ADAPIYVKNA T0329 222 :ATVIVDT 1k1eA 135 :VDHVLST T0329 229 :AEKLEEAI 1k1eA 148 :FREMSDMI Number of specific fragments extracted= 8 number of extra gaps= 0 total=1193 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k1eA/T0329-1k1eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1k1eA/T0329-1k1eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k1eA read from 1k1eA/T0329-1k1eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k1eA in template set T0329 3 :YKAAIFDMDGTILD 1k1eA 8 :IKFVITDVDGVLTD T0329 112 :PGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1k1eA 38 :VRDGLGIKMLMDADIQVAVLSGRDSPILRRRIADL T0329 147 :FP 1k1eA 74 :IK T0329 153 :FALGEKSGI 1k1eA 76 :LFFLGKLEK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSE 1k1eA 85 :ETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACG T0329 203 :DEIAV 1k1eA 120 :TSFAV T0329 210 :GFRSVPFL 1k1eA 125 :ADAPIYVK T0329 219 :KH 1k1eA 133 :NA T0329 222 :ATVIVDT 1k1eA 135 :VDHVLST T0329 229 :AEKLEEAI 1k1eA 148 :FREMSDMI Number of specific fragments extracted= 10 number of extra gaps= 0 total=1203 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k1eA/T0329-1k1eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1k1eA/T0329-1k1eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k1eA read from 1k1eA/T0329-1k1eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k1eA in template set T0329 2 :KYKAAIFDMDGTILDTS 1k1eA 7 :NIKFVITDVDGVLTDGQ T0329 51 :VVVA 1k1eA 30 :GEAI T0329 112 :PGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1k1eA 38 :VRDGLGIKMLMDADIQVAVLSGRDSPILRRRIA T0329 145 :ELFP 1k1eA 72 :LGIK T0329 153 :FALGEKSG 1k1eA 76 :LFFLGKLE T0329 166 :APDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSE 1k1eA 84 :KETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACG T0329 205 :IAVNWGFRSVPFL 1k1eA 120 :TSFAVADAPIYVK T0329 220 :HGATVIVDT 1k1eA 133 :NAVDHVLST Number of specific fragments extracted= 8 number of extra gaps= 0 total=1211 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b8eA/T0329-2b8eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b8eA expands to /projects/compbio/data/pdb/2b8e.pdb.gz 2b8eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0329 read from 2b8eA/T0329-2b8eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b8eA read from 2b8eA/T0329-2b8eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b8eA to template set # found chain 2b8eA in template set Warning: unaligning (T0329)E191 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0329)I192 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0329)D193 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0329)G210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0329)F211 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 Warning: unaligning (T0329)L237 because last residue in template chain is (2b8eA)Q663 T0329 3 :YKAAIFD 2b8eA 418 :VTAVIFD T0329 14 :ILDTSADLTSALNYAFEQTGHRHD 2b8eA 439 :LVPLNGDERELLRLAAIAERRSEH T0329 49 :SGVVVAVTRALAYE 2b8eA 463 :PIAEAIVKKALEHG T0329 64 :GSS 2b8eA 477 :IEL T0329 67 :RESLVAF 2b8eA 503 :KRLMEDF T0329 82 :E 2b8eA 510 :G T0329 83 :AVTQT 2b8eA 512 :AVSNE T0329 89 :VNRVLEVFKPY 2b8eA 517 :VELALEKLERE T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 2b8eA 548 :DTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISREL T0329 151 :FDFAL 2b8eA 588 :LDLVI T0329 161 :IRRK 2b8eA 593 :AEVL T0329 167 :PDMTSECVKVLGV 2b8eA 597 :PHQKSEEVKKLQA T0329 181 :RDKCVYIGDS 2b8eA 610 :KEVVAFVGDG T0329 194 :IQTARNSEMDEIA 2b8eA 623 :APALAQADLGIAV T0329 212 :R 2b8eA 646 :G T0329 223 :TVIV 2b8eA 647 :DIVL T0329 227 :DTAEKLEEAI 2b8eA 653 :DDLRDVVAAI Number of specific fragments extracted= 17 number of extra gaps= 2 total=1228 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b8eA/T0329-2b8eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2b8eA/T0329-2b8eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b8eA read from 2b8eA/T0329-2b8eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b8eA in template set Warning: unaligning (T0329)E191 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0329)I192 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0329)D193 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0329)N208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0329)W209 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0329 3 :YKAAIFD 2b8eA 418 :VTAVIFD T0329 14 :ILDTSADLTSALNYAFEQT 2b8eA 439 :LVPLNGDERELLRLAAIAE T0329 33 :GHRHD 2b8eA 476 :GIELG T0329 51 :VVVAVTRAL 2b8eA 502 :NKRLMEDFG T0329 82 :EAVTQT 2b8eA 511 :VAVSNE T0329 92 :VLEVFKPYYADHC 2b8eA 517 :VELALEKLEREAK T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 2b8eA 548 :DTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISREL T0329 147 :F 2b8eA 588 :L T0329 152 :DFALG 2b8eA 589 :DLVIA T0329 158 :K 2b8eA 594 :E T0329 160 :GI 2b8eA 595 :VL T0329 167 :PDMTSECVKVLG 2b8eA 597 :PHQKSEEVKKLQ T0329 181 :RDKCVYIGDS 2b8eA 610 :KEVVAFVGDG T0329 194 :IQTARNSE 2b8eA 623 :APALAQAD T0329 203 :DEIAV 2b8eA 631 :LGIAV T0329 210 :G 2b8eA 646 :G T0329 223 :TVIV 2b8eA 647 :DIVL T0329 227 :DTAEKLEEAI 2b8eA 653 :DDLRDVVAAI Number of specific fragments extracted= 18 number of extra gaps= 2 total=1246 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b8eA/T0329-2b8eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2b8eA/T0329-2b8eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b8eA read from 2b8eA/T0329-2b8eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b8eA in template set Warning: unaligning (T0329)E191 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0329)I192 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0329)D193 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0329)N208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0329)W209 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0329 3 :YKAAIFD 2b8eA 418 :VTAVIFD T0329 14 :ILDTSADLTSALNYAFEQTGHRHDFTVEDIKN 2b8eA 439 :LVPLNGDERELLRLAAIAERRSEHPIAEAIVK T0329 59 :LAYEAGSSRES 2b8eA 471 :KALEHGIELGE T0329 70 :LVAFG 2b8eA 503 :KRLME T0329 79 :QIPEAVTQTEVNRVLEVFKP 2b8eA 508 :DFGVAVSNEVELALEKLERE T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 2b8eA 547 :SDTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISR T0329 145 :ELFP 2b8eA 586 :LNLD T0329 154 :ALGEKS 2b8eA 590 :LVIAEV T0329 166 :APDMTSECVKVLG 2b8eA 596 :LPHQKSEEVKKLQ T0329 181 :RDKCVYIGDS 2b8eA 610 :KEVVAFVGDG T0329 194 :IQTARNSE 2b8eA 623 :APALAQAD T0329 203 :DEIAV 2b8eA 631 :LGIAV T0329 210 :G 2b8eA 646 :G T0329 223 :TVIV 2b8eA 647 :DIVL T0329 227 :DTAEKLEEAI 2b8eA 653 :DDLRDVVAAI Number of specific fragments extracted= 15 number of extra gaps= 2 total=1261 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek1A/T0329-1ek1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ek1A expands to /projects/compbio/data/pdb/1ek1.pdb.gz 1ek1A:# T0329 read from 1ek1A/T0329-1ek1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek1A read from 1ek1A/T0329-1ek1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ek1A to template set # found chain 1ek1A in template set Warning: unaligning (T0329)K4 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0329)S18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 Warning: unaligning (T0329)V53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0329)I80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)Q90 T0329 5 :AAIFDMDGTILD 1ek1A 5 :VAAFDLDGVLAL T0329 17 :T 1ek1A 18 :S T0329 54 :AVTRALAYE 1ek1A 49 :PTEQLMKGK T0329 64 :GS 1ek1A 58 :IT T0329 74 :GTKDEQ 1ek1A 60 :FSQWVP T0329 105 :QIKTGPFPGILDLMKNLRQKGVKLAVVSN 1ek1A 96 :MAARSINRPMLQAAIALKKKGFTTCIVTN T0329 134 :KPNEAVQVLVEEL 1ek1A 131 :DKRDSLAQMMCEL T0329 149 :GSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDE 1ek1A 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVT Number of specific fragments extracted= 8 number of extra gaps= 0 total=1269 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek1A/T0329-1ek1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1ek1A/T0329-1ek1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek1A read from 1ek1A/T0329-1ek1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ek1A in template set Warning: unaligning (T0329)K4 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0329)L21 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 Warning: unaligning (T0329)G50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0329)Q86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)Q90 Warning: unaligning (T0329)G109 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)Q90 T0329 5 :AAIFDMDGTIL 1ek1A 5 :VAAFDLDGVLA T0329 18 :SAD 1ek1A 16 :LPS T0329 51 :VVVAVTRAL 1ek1A 49 :PTEQLMKGK T0329 78 :EQIPEAVT 1ek1A 58 :ITFSQWVP T0329 110 :PFPG 1ek1A 91 :IFSQ T0329 114 :ILDLMKNLRQKGVKLAVVSN 1ek1A 105 :MLQAAIALKKKGFTTCIVTN T0329 134 :KPNEAVQVLVEEL 1ek1A 131 :DKRDSLAQMMCEL T0329 149 :GSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMD 1ek1A 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMV Number of specific fragments extracted= 8 number of extra gaps= 0 total=1277 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek1A/T0329-1ek1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1ek1A/T0329-1ek1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek1A read from 1ek1A/T0329-1ek1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ek1A in template set Warning: unaligning (T0329)K4 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0329)T39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0329)Q79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)Q90 T0329 5 :AAIFDMDGTIL 1ek1A 5 :VAAFDLDGVLA T0329 40 :VEDIKNFFGSG 1ek1A 49 :PTEQLMKGKIT T0329 73 :FGTKDE 1ek1A 60 :FSQWVP T0329 101 :ADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKP 1ek1A 92 :FSQAMAARSINRPMLQAAIALKKKGFTTCIVTNNW T0329 136 :NEAVQVLVE 1ek1A 133 :RDSLAQMMC T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMD 1ek1A 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMV Number of specific fragments extracted= 6 number of extra gaps= 0 total=1283 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdeA/T0329-2bdeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bdeA expands to /projects/compbio/data/pdb/2bde.pdb.gz 2bdeA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0329 read from 2bdeA/T0329-2bdeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bdeA read from 2bdeA/T0329-2bdeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bdeA to template set # found chain 2bdeA in template set T0329 2 :KYKAAIFDMDGTILD 2bdeA 16 :KIKLIGLDMDHTLIR T0329 17 :TSADLTSALNYAFEQTGHRHDF 2bdeA 33 :SKNFESLVYDLVKERLAESFHY T0329 39 :TVEDIKNFF 2bdeA 101 :SFSDQKKIY T0329 49 :SGVVVAVTRALA 2bdeA 130 :IAFCILYGQLVD T0329 63 :AGSSRESL 2bdeA 150 :MPSYQAIA T0329 87 :TEVNRVLEVFKPY 2bdeA 158 :QDVQYCVDKVHSD T0329 100 :YADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 2bdeA 177 :IIKNLKKYVIREKEVVEGLKHFIRYGKKIFILTNSEYSYSKLLLDYA T0329 147 :F 2bdeA 225 :S T0329 148 :PGSFDFALGEK 2bdeA 235 :QGLFEFVITLA T0329 170 :TSECVKVLGVPRDKCVYIGDSE 2bdeA 284 :AKKFTEDLGVGGDEILYIGDHI T0329 192 :IDI 2bdeA 307 :GDI T0329 195 :QTARNSEMDEIAVNW 2bdeA 311 :RLKKDCNWRTALVVE T0329 228 :TAEKLEEA 2bdeA 326 :ELGEEIAS Number of specific fragments extracted= 13 number of extra gaps= 0 total=1296 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdeA/T0329-2bdeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2bdeA/T0329-2bdeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bdeA read from 2bdeA/T0329-2bdeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bdeA in template set T0329 2 :KYKAAIFDMDGTILDTS 2bdeA 16 :KIKLIGLDMDHTLIRYN T0329 19 :ADLTSALNYAFEQT 2bdeA 35 :NFESLVYDLVKERL T0329 35 :R 2bdeA 98 :K T0329 37 :DFTVEDIKNFFGSG 2bdeA 99 :QISFSDQKKIYRSI T0329 51 :VVVAVTRAL 2bdeA 129 :SIAFCILYG T0329 68 :ESLVAFGTKDEQIPE 2bdeA 138 :QLVDLKDTNPDKMPS T0329 89 :VNRVLEVFKPYYADHCQI 2bdeA 153 :YQAIAQDVQYCVDKVHSD T0329 107 :KTG 2bdeA 180 :NLK T0329 110 :PFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEELFPG 2bdeA 187 :REKEVVEGLKHFIRYGKKIFILTNSEYSYSKLLLDYALSP T0329 150 :SFDFALGE 2bdeA 237 :LFEFVITL T0329 167 :PDMTS 2bdeA 248 :PRFFY T0329 172 :ECVKVLGVPRDKCVYIGDSE 2bdeA 286 :KFTEDLGVGGDEILYIGDHI T0329 192 :IDIQ 2bdeA 307 :GDIL T0329 196 :TARNSEMDEIAVNWG 2bdeA 312 :LKKDCNWRTALVVEE T0329 229 :AEKLE 2bdeA 327 :LGEEI Number of specific fragments extracted= 15 number of extra gaps= 0 total=1311 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdeA/T0329-2bdeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2bdeA/T0329-2bdeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bdeA read from 2bdeA/T0329-2bdeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bdeA in template set T0329 2 :KYKAAIFDMDGTILDTSAD 2bdeA 16 :KIKLIGLDMDHTLIRYNSK T0329 21 :LTSALNYAFEQTGHRH 2bdeA 40 :VYDLVKERLAESFHYP T0329 37 :DFTVEDIKNFFGSGV 2bdeA 101 :SFSDQKKIYRSIYVD T0329 52 :VVAVTRALAYEAGSSRESLVAFGTKDEQIPEAVTQTEVNRVLEVFKPYYADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 2bdeA 129 :SIAFCILYGQLVDLKDTNPDKMPSYQAIAQDVQYCVDKVHSDGTLKNIIIKNLKKYVIREKEVVEGLKHFIRYGKKIFILTNSEYSYSKLLLD T0329 146 :LFPGSFDFALGE 2bdeA 233 :HWQGLFEFVITL T0329 170 :TSECVKVLGVPRDKCVYIGDSE 2bdeA 284 :AKKFTEDLGVGGDEILYIGDHI T0329 192 :IDIQ 2bdeA 307 :GDIL T0329 196 :TARNSEMDEIAVNWG 2bdeA 312 :LKKDCNWRTALVVEE T0329 229 :AEKLEEA 2bdeA 327 :LGEEIAS Number of specific fragments extracted= 9 number of extra gaps= 0 total=1320 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g09A/T0329-2g09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2g09A expands to /projects/compbio/data/pdb/2g09.pdb.gz 2g09A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 2g09A Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 2g09A Skipped atom 1944, because occupancy 0.500 <= existing 0.500 in 2g09A Skipped atom 1946, because occupancy 0.500 <= existing 0.500 in 2g09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0329 read from 2g09A/T0329-2g09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g09A read from 2g09A/T0329-2g09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2g09A to template set # found chain 2g09A in template set Warning: unaligning (T0329)A5 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0329 6 :AIFDMDGTILDT 2g09A 46 :IITDFDMTLSRF T0329 18 :SADLTSALNYAFEQTGHR 2g09A 82 :RRKLLQLKEQYYAIEVDP T0329 37 :DFTVEDIKNFFGSGVVVAVTRALAY 2g09A 100 :VLTVEEKFPYMVEWYTKSHGLLIEQ T0329 83 :AVTQTEVNRVLEVFK 2g09A 125 :GIPKAKLKEIVADSD T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 2g09A 140 :VMLKEGYENFFGKLQQHGIPVFIFSAGIGDVLEEVIRQA T0329 147 :FPGSFDFALGEK 2g09A 180 :VYHSNVKVVSNF T0329 159 :SG 2g09A 219 :KN T0329 167 :PDMT 2g09A 221 :TDYF T0329 175 :KVLG 2g09A 225 :SQLK T0329 180 :PRDKCVYIGDSEIDIQTARNSE 2g09A 229 :DNSNIILLGDSQGDLRMADGVA T0329 202 :MDEIAVNW 2g09A 255 :ILKIGYLN T0329 212 :RS 2g09A 263 :DR T0329 214 :VPFLQKH 2g09A 269 :LEKYMDS T0329 222 :ATVIV 2g09A 276 :YDIVL T0329 227 :DTAEKLEEAIL 2g09A 284 :ESLEVVNSILQ Number of specific fragments extracted= 15 number of extra gaps= 1 total=1335 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g09A/T0329-2g09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2g09A/T0329-2g09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g09A read from 2g09A/T0329-2g09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g09A in template set Warning: unaligning (T0329)A5 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0329 6 :AIFDMDGTILD 2g09A 46 :IITDFDMTLSR T0329 18 :SADLTSALNYAFEQTGHR 2g09A 82 :RRKLLQLKEQYYAIEVDP T0329 37 :DFTVEDIKNFFGSGVVVAVTRAL 2g09A 100 :VLTVEEKFPYMVEWYTKSHGLLI T0329 81 :PEAVTQTEVNRVLEVFK 2g09A 123 :EQGIPKAKLKEIVADSD T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 2g09A 140 :VMLKEGYENFFGKLQQHGIPVFIFSAGIGDVLEEVIRQA T0329 147 :FPGSFDFA 2g09A 181 :YHSNVKVV T0329 155 :LGEKSGIRRK 2g09A 203 :FKGELIHVFN T0329 170 :TSECV 2g09A 213 :KHDGA T0329 175 :KVLG 2g09A 225 :SQLK T0329 179 :V 2g09A 230 :N T0329 182 :DKCVYIGDSEIDIQTAR 2g09A 231 :SNIILLGDSQGDLRMAD T0329 201 :EMD 2g09A 248 :GVA T0329 204 :EIAVNW 2g09A 257 :KIGYLN T0329 212 :RSVPFLQK 2g09A 263 :DRVDELLE T0329 220 :H 2g09A 275 :S T0329 222 :ATVIV 2g09A 276 :YDIVL Number of specific fragments extracted= 16 number of extra gaps= 1 total=1351 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g09A/T0329-2g09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2g09A/T0329-2g09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g09A read from 2g09A/T0329-2g09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g09A in template set Warning: unaligning (T0329)A5 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0329 6 :AIFDMDGTILDTS 2g09A 46 :IITDFDMTLSRFS T0329 19 :ADLTSALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTR 2g09A 83 :RKLLQLKEQYYAIEVDPVLTVEEKFPYMVEWYTKSHGLL T0329 80 :IPEAVTQTEVNRVLE 2g09A 122 :IEQGIPKAKLKEIVA T0329 105 :QIKTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 2g09A 137 :DSDVMLKEGYENFFGKLQQHGIPVFIFSAGIGDVLEEVIR T0329 145 :ELFPGSFDFALGE 2g09A 178 :AGVYHSNVKVVSN T0329 174 :VKVLG 2g09A 224 :FSQLK T0329 182 :DKCVYIGDSEIDIQT 2g09A 231 :SNIILLGDSQGDLRM T0329 199 :NSEMD 2g09A 246 :ADGVA T0329 204 :EIAVNWGFRSVPFLQ 2g09A 255 :ILKIGYLNDRVDELL T0329 230 :EKLEE 2g09A 270 :EKYMD Number of specific fragments extracted= 10 number of extra gaps= 1 total=1361 Will force an alignment to be made, even if fragment is small Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q92A/T0329-1q92A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q92A expands to /projects/compbio/data/pdb/1q92.pdb.gz 1q92A:# T0329 read from 1q92A/T0329-1q92A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q92A read from 1q92A/T0329-1q92A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q92A to template set # found chain 1q92A in template set Warning: unaligning (T0329)T32 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0329)G33 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F61 Warning: unaligning (T0329)V40 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0329)E41 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0329)G50 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)G74 Warning: unaligning (T0329)V51 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0329)L59 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0329)A60 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0329)F111 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0329)P112 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0329)L121 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0329)R122 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0329)L146 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0329)M202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0329)D203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0329)N208 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0329)W209 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0329)I225 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0329)V226 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 T0329 4 :KAAIFDMDGTILDTSADL 1q92A 36 :LRVLVDMDGVLADFEGGF T0329 26 :NYAFEQ 1q92A 54 :LRKFRA T0329 34 :HRHD 1q92A 62 :PDQP T0329 38 :FT 1q92A 67 :IA T0329 42 :D 1q92A 71 :D T0329 49 :S 1q92A 72 :R T0329 52 :VVAVTRA 1q92A 75 :FWVSEQY T0329 61 :YE 1q92A 84 :LR T0329 64 :GSSRESLVAFGTKDE 1q92A 86 :PGLSEKAISIWESKN T0329 104 :CQIKTGP 1q92A 101 :FFFELEP T0329 113 :GILDLMKN 1q92A 110 :GAVEAVKE T0329 123 :QKG 1q92A 120 :SLQ T0329 126 :VKLAVVSN 1q92A 124 :TDVFICTS T0329 134 :KPNEAVQVLVEE 1q92A 138 :YCPYEKYAWVEK T0329 147 :FPGSFDFALGEKSGIRRKPA 1q92A 152 :GPDFLEQIVLTRDKTVVSAD T0329 185 :VYIGDSE 1q92A 172 :LLIDDRP T0329 201 :E 1q92A 188 :S T0329 204 :EIAV 1q92A 191 :HVLF T0329 210 :GFRSVP 1q92A 201 :HLQLQP T0329 222 :ATV 1q92A 207 :PRR T0329 227 :DTAEK 1q92A 212 :HSWAD T0329 232 :LEEAILG 1q92A 218 :WKAILDS Number of specific fragments extracted= 22 number of extra gaps= 10 total=1383 Will force an alignment to be made, even if fragment is small Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q92A/T0329-1q92A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1q92A/T0329-1q92A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q92A read from 1q92A/T0329-1q92A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q92A in template set Warning: unaligning (T0329)A28 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0329)V40 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0329)E41 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0329)F47 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)G74 Warning: unaligning (T0329)G48 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0329)T56 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0329)R57 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0329)F111 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0329)P112 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0329)L121 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0329)R122 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0329)L146 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0329)M202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0329)D203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0329)N208 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0329)W209 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0329)I225 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0329)V226 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 T0329 3 :YKAAIFDMDGTILDTSADLTSALNY 1q92A 35 :ALRVLVDMDGVLADFEGGFLRKFRA T0329 33 :GHRH 1q92A 63 :DQPF T0329 38 :FT 1q92A 67 :IA T0329 42 :D 1q92A 71 :D T0329 49 :SGVVVAV 1q92A 75 :FWVSEQY T0329 58 :AL 1q92A 84 :LR T0329 86 :QTEVNRVLEVFK 1q92A 86 :PGLSEKAISIWE T0329 102 :DHCQI 1q92A 100 :NFFFE T0329 108 :TGP 1q92A 105 :LEP T0329 113 :GILDLMKN 1q92A 110 :GAVEAVKE T0329 123 :Q 1q92A 120 :S T0329 124 :KGVKLAVVSN 1q92A 122 :QNTDVFICTS T0329 134 :KPNEAVQVLVEE 1q92A 138 :YCPYEKYAWVEK T0329 147 :FPGSFDFALGEKSGIRRKPA 1q92A 152 :GPDFLEQIVLTRDKTVVSAD T0329 185 :VYIGDSE 1q92A 172 :LLIDDRP T0329 201 :E 1q92A 188 :S T0329 204 :EIAV 1q92A 191 :HVLF T0329 210 :GFRSVPF 1q92A 200 :QHLQLQP T0329 222 :ATV 1q92A 207 :PRR T0329 227 :DTAEK 1q92A 212 :HSWAD T0329 232 :LEEAI 1q92A 218 :WKAIL Number of specific fragments extracted= 21 number of extra gaps= 10 total=1404 Will force an alignment to be made, even if fragment is small Number of alignments=131 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q92A/T0329-1q92A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1q92A/T0329-1q92A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q92A read from 1q92A/T0329-1q92A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q92A in template set Warning: unaligning (T0329)A28 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0329)F47 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F61 Warning: unaligning (T0329)D77 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0329)E78 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0329)P81 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)G74 Warning: unaligning (T0329)E82 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0329)N90 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0329)R91 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0329)F111 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0329)P112 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0329)L121 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0329)R122 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0329)E145 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0329)L146 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F151 Warning: unaligning (T0329)M202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0329)D203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0329)N208 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0329)W209 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 T0329 5 :AAIFDMDGTILDTSADLTSALNY 1q92A 37 :RVLVDMDGVLADFEGGFLRKFRA T0329 48 :GSG 1q92A 62 :PDQ T0329 73 :FGTK 1q92A 65 :PFIA T0329 79 :QI 1q92A 71 :DR T0329 83 :AVTQTEV 1q92A 75 :FWVSEQY T0329 92 :VLEVFKPYYADHCQI 1q92A 84 :LRPGLSEKAISIWES T0329 107 :KTGP 1q92A 104 :ELEP T0329 113 :GILDLMKN 1q92A 110 :GAVEAVKE T0329 123 :Q 1q92A 120 :S T0329 124 :KGVKLAVVSNKP 1q92A 122 :QNTDVFICTSPI T0329 136 :NEAVQVLVE 1q92A 140 :PYEKYAWVE T0329 147 :FPGSFDFALGEKSGIRRKPA 1q92A 152 :GPDFLEQIVLTRDKTVVSAD T0329 185 :VYIGDSE 1q92A 172 :LLIDDRP T0329 201 :E 1q92A 188 :S T0329 204 :EIAV 1q92A 191 :HVLF T0329 210 :GFR 1q92A 197 :CHN Number of specific fragments extracted= 16 number of extra gaps= 9 total=1420 Will force an alignment to be made, even if fragment is small Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5sA/T0329-1f5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f5sA expands to /projects/compbio/data/pdb/1f5s.pdb.gz 1f5sA:Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1f5sA # T0329 read from 1f5sA/T0329-1f5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f5sA read from 1f5sA/T0329-1f5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f5sA to template set # found chain 1f5sA in template set T0329 2 :KYKAAIFDMDGTILDTSAD 1f5sA 4 :KKKLILFDFDSTLVNNETI T0329 26 :NYAFEQTGHR 1f5sA 23 :DEIAREAGVE T0329 49 :SGVVVAVTRALAYE 1f5sA 33 :EEVKKITKEAMEGK T0329 64 :GSSRESLVAFGTKDE 1f5sA 47 :LNFEQSLRKRVSLLK T0329 83 :AVTQTEVNRVLEV 1f5sA 62 :DLPIEKVEKAIKR T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1f5sA 75 :ITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKL T0329 147 :FPGSFDFALGEK 1f5sA 115 :LDYAFANRLIVK T0329 159 :SGIRRK 1f5sA 139 :LKENAK T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIA 1f5sA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAF T0329 212 :RSVPFLQKH 1f5sA 185 :CAKPILKEK T0329 222 :ATVIVD 1f5sA 194 :ADICIE T0329 228 :TAEKLEEA 1f5sA 202 :DLREILKY Number of specific fragments extracted= 12 number of extra gaps= 0 total=1432 Will force an alignment to be made, even if fragment is small Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5sA/T0329-1f5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1f5sA/T0329-1f5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f5sA read from 1f5sA/T0329-1f5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f5sA in template set T0329 2 :KYKAAIFDMDGTILDTS 1f5sA 4 :KKKLILFDFDSTLVNNE T0329 24 :ALNYAFEQTGHR 1f5sA 21 :TIDEIAREAGVE T0329 41 :EDIKNFF 1f5sA 33 :EEVKKIT T0329 48 :GSGVVVAVTRAL 1f5sA 46 :KLNFEQSLRKRV T0329 78 :EQIPE 1f5sA 58 :SLLKD T0329 84 :VTQTEVNRVLE 1f5sA 63 :LPIEKVEKAIK T0329 106 :I 1f5sA 74 :R T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVEEL 1f5sA 75 :ITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKL T0329 147 :FPGSFDFALGEKS 1f5sA 115 :LDYAFANRLIVKD T0329 161 :IRR 1f5sA 137 :EVL T0329 167 :PDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSE 1f5sA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0329 203 :DEIAV 1f5sA 180 :LKIAF T0329 212 :RSVPFLQKH 1f5sA 185 :CAKPILKEK T0329 222 :ATVIVD 1f5sA 194 :ADICIE T0329 228 :TAEKLEEAI 1f5sA 202 :DLREILKYI Number of specific fragments extracted= 15 number of extra gaps= 0 total=1447 Will force an alignment to be made, even if fragment is small Number of alignments=134 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5sA/T0329-1f5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1f5sA/T0329-1f5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f5sA read from 1f5sA/T0329-1f5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f5sA in template set T0329 2 :KYKAAIFDMDGTILDTS 1f5sA 4 :KKKLILFDFDSTLVNNE T0329 24 :ALNYAFEQTGHRHDFTVEDIKNFFGSGVVVAVTRALAY 1f5sA 21 :TIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVS T0329 80 :IPEAVTQTEVNRVLE 1f5sA 59 :LLKDLPIEKVEKAIK T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSNKPNEAVQVLVE 1f5sA 74 :RITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKE T0329 145 :ELFPGSFDFALGEKS 1f5sA 113 :LGLDYAFANRLIVKD T0329 160 :GIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMD 1f5sA 138 :VLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLK T0329 205 :IAV 1f5sA 182 :IAF T0329 212 :RSVPFL 1f5sA 185 :CAKPIL T0329 219 :KHGATVIVDT 1f5sA 191 :KEKADICIEK Number of specific fragments extracted= 9 number of extra gaps= 0 total=1456 Will force an alignment to be made, even if fragment is small Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cqzA/T0329-1cqzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cqzA expands to /projects/compbio/data/pdb/1cqz.pdb.gz 1cqzA:# T0329 read from 1cqzA/T0329-1cqzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cqzA read from 1cqzA/T0329-1cqzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cqzA to template set # found chain 1cqzA in template set Warning: unaligning (T0329)K4 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0329)V51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 T0329 5 :AAIFDMDGTILD 1cqzA 5 :VAAFDLDGVLAL T0329 49 :SG 1cqzA 17 :PS T0329 100 :YAD 1cqzA 96 :MAA T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSN 1cqzA 99 :RSINRPMLQAAIALKKKGFTTCIVTN T0329 134 :KPNEAVQVLVEEL 1cqzA 131 :DKRDSLAQMMCEL T0329 148 :PGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAV 1cqzA 144 :SQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILV T0329 211 :FRSVPFLQK 1cqzA 204 :HNTASALRE Number of specific fragments extracted= 7 number of extra gaps= 0 total=1463 Will force an alignment to be made, even if fragment is small Number of alignments=136 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cqzA/T0329-1cqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1cqzA/T0329-1cqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cqzA read from 1cqzA/T0329-1cqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cqzA in template set Warning: unaligning (T0329)K4 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0329)L21 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0329)R35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)Q90 Warning: unaligning (T0329)Q86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0329 5 :AAIFDMDGTILD 1cqzA 5 :VAAFDLDGVLAL T0329 19 :AD 1cqzA 17 :PS T0329 33 :GH 1cqzA 61 :SQ T0329 87 :TEVNRVLE 1cqzA 91 :IFSQAMAA T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSN 1cqzA 99 :RSINRPMLQAAIALKKKGFTTCIVTN T0329 134 :KPNEAVQVLVEE 1cqzA 131 :DKRDSLAQMMCE T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVN 1cqzA 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVH T0329 212 :RSVPFLQK 1cqzA 205 :NTASALRE Number of specific fragments extracted= 8 number of extra gaps= 0 total=1471 Will force an alignment to be made, even if fragment is small Number of alignments=137 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cqzA/T0329-1cqzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1cqzA/T0329-1cqzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cqzA read from 1cqzA/T0329-1cqzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cqzA in template set Warning: unaligning (T0329)K4 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0329)F47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)G48 Warning: unaligning (T0329)L59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)Q90 Warning: unaligning (T0329)Q86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0329 5 :AAIFDMDGTILDTS 1cqzA 5 :VAAFDLDGVLALPS T0329 48 :GSGVVVAVTR 1cqzA 49 :PTEQLMKGKI T0329 58 :A 1cqzA 62 :Q T0329 87 :TEVNRVL 1cqzA 91 :IFSQAMA T0329 107 :KTGPFPGILDLMKNLRQKGVKLAVVSNKP 1cqzA 98 :ARSINRPMLQAAIALKKKGFTTCIVTNNW T0329 136 :NEAVQVLVE 1cqzA 133 :RDSLAQMMC T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWG 1cqzA 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNT T0329 214 :VPFL 1cqzA 207 :ASAL Number of specific fragments extracted= 8 number of extra gaps= 0 total=1479 Will force an alignment to be made, even if fragment is small Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cr6B/T0329-1cr6B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cr6B expands to /projects/compbio/data/pdb/1cr6.pdb.gz 1cr6B:# T0329 read from 1cr6B/T0329-1cr6B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cr6B read from 1cr6B/T0329-1cr6B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cr6B to template set # found chain 1cr6B in template set Warning: unaligning (T0329)K4 because first residue in template chain is (1cr6B)R4 T0329 5 :AAIFDMDGTILDTSA 1cr6B 5 :VAAFDLDGVLALPSI T0329 26 :NYAFEQTGHRHDF 1cr6B 20 :AGAFRRSEEALAL T0329 49 :SGVVVAVTRALAYE 1cr6B 44 :EFPEGPTEQLMKGK T0329 64 :GSSRES 1cr6B 58 :ITFSQW T0329 70 :LVAFGTKDEQIPEAVT 1cr6B 72 :RKSSKACGANLPENFS T0329 92 :VLEVFKPYYAD 1cr6B 88 :ISQIFSQAMAA T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSN 1cr6B 99 :RSINRPMLQAAIALKKKGFTTCIVTN T0329 134 :KPNEAVQVLVEEL 1cr6B 131 :DKRDSLAQMMCEL T0329 149 :GSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFR 1cr6B 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTAS Number of specific fragments extracted= 9 number of extra gaps= 0 total=1488 Will force an alignment to be made, even if fragment is small Number of alignments=139 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cr6B/T0329-1cr6B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1cr6B/T0329-1cr6B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cr6B read from 1cr6B/T0329-1cr6B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cr6B in template set Warning: unaligning (T0329)K4 because first residue in template chain is (1cr6B)R4 T0329 5 :AAIFDMDGTILD 1cr6B 5 :VAAFDLDGVLAL T0329 19 :ADLTSALNYAFEQT 1cr6B 17 :PSIAGAFRRSEEAL T0329 37 :DFTVEDIKNFFGS 1cr6B 45 :FPEGPTEQLMKGK T0329 50 :GVVVAVTRAL 1cr6B 59 :TFSQWVPLMD T0329 71 :VAFGTKDEQIPEAVTQTEV 1cr6B 69 :ESYRKSSKACGANLPENFS T0329 96 :FKPYYADHCQI 1cr6B 88 :ISQIFSQAMAA T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSNKP 1cr6B 99 :RSINRPMLQAAIALKKKGFTTCIVTNNW T0329 136 :NEAVQVLVEEL 1cr6B 133 :RDSLAQMMCEL T0329 148 :PGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFR 1cr6B 144 :SQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTAS Number of specific fragments extracted= 9 number of extra gaps= 0 total=1497 Will force an alignment to be made, even if fragment is small Number of alignments=140 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cr6B/T0329-1cr6B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1cr6B/T0329-1cr6B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cr6B read from 1cr6B/T0329-1cr6B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cr6B in template set Warning: unaligning (T0329)K4 because first residue in template chain is (1cr6B)R4 T0329 5 :AAIFDMDGTILD 1cr6B 5 :VAAFDLDGVLAL T0329 19 :ADLTSALNYAFEQTGHRH 1cr6B 17 :PSIAGAFRRSEEALALPR T0329 37 :DFTVEDIKNFFGSGVVVAVT 1cr6B 47 :EGPTEQLMKGKITFSQWVPL T0329 59 :L 1cr6B 67 :M T0329 66 :SRESLVAFGTKDEQIPEAVTQTEV 1cr6B 68 :DESYRKSSKACGANLPENFSISQI T0329 101 :ADHCQIKTGPFPGILDLMKNLRQKGVKLAVVSNKP 1cr6B 92 :FSQAMAARSINRPMLQAAIALKKKGFTTCIVTNNW T0329 136 :NEAVQVLVE 1cr6B 133 :RDSLAQMMC T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFR 1cr6B 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTAS Number of specific fragments extracted= 8 number of extra gaps= 0 total=1505 Will force an alignment to be made, even if fragment is small Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mh9A/T0329-1mh9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mh9A expands to /projects/compbio/data/pdb/1mh9.pdb.gz 1mh9A:# T0329 read from 1mh9A/T0329-1mh9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh9A read from 1mh9A/T0329-1mh9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mh9A to template set # found chain 1mh9A in template set Warning: unaligning (T0329)V214 because of BadResidue code BAD_PEPTIDE in next template residue (1mh9A)P206 Warning: unaligning (T0329)P215 because of BadResidue code BAD_PEPTIDE at template residue (1mh9A)P206 T0329 4 :KAAIFDMDGTILDT 1mh9A 36 :LRVLVDMDGVLADF T0329 22 :TSALNYAFEQTGHRHD 1mh9A 50 :EGGFLRKFRARFPDQP T0329 38 :FTVED 1mh9A 67 :IALED T0329 49 :SGVVVAVTRALAYE 1mh9A 72 :RRGFWVSEQYGRLR T0329 64 :GSSRESLVAFGTKDE 1mh9A 86 :PGLSEKAISIWESKN T0329 104 :CQIKTGPFPGILDLMKNLRQKG 1mh9A 101 :FFFELEPLPGAVEAVKEMASLQ T0329 126 :VKLAVVSN 1mh9A 124 :TDVFICTS T0329 134 :KPNEAVQVLVEEL 1mh9A 138 :YCPYEKYAWVEKY T0329 147 :FPGSFDFALGEKSGIRRKPA 1mh9A 152 :GPDFLEQIVLTRDKTVVSAD T0329 185 :VYIGDSE 1mh9A 172 :LLIDDRP T0329 201 :EMDEIAVNW 1mh9A 188 :SWEHVLFTA T0329 210 :GFRS 1mh9A 201 :HLQL T0329 222 :ATVIVDTAEK 1mh9A 207 :PRRRLHSWAD T0329 232 :LEEAILG 1mh9A 218 :WKAILDS Number of specific fragments extracted= 14 number of extra gaps= 1 total=1519 Will force an alignment to be made, even if fragment is small Number of alignments=142 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mh9A/T0329-1mh9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1mh9A/T0329-1mh9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh9A read from 1mh9A/T0329-1mh9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mh9A in template set Warning: unaligning (T0329)P215 because of BadResidue code BAD_PEPTIDE in next template residue (1mh9A)P206 Warning: unaligning (T0329)H220 because of BadResidue code BAD_PEPTIDE at template residue (1mh9A)P206 T0329 3 :YKAAIFDMDGTILDTSADLTSALNYA 1mh9A 35 :ALRVLVDMDGVLADFEGGFLRKFRAR T0329 33 :GHRH 1mh9A 63 :DQPF T0329 38 :FTVED 1mh9A 67 :IALED T0329 47 :FGSGVVVAVTRAL 1mh9A 73 :RGFWVSEQYGRLR T0329 86 :QTEVNRVLEVFK 1mh9A 86 :PGLSEKAISIWE T0329 102 :DHCQI 1mh9A 100 :NFFFE T0329 108 :TGPFPGILDLMKNLRQ 1mh9A 105 :LEPLPGAVEAVKEMAS T0329 124 :KGVKLAVVSN 1mh9A 122 :QNTDVFICTS T0329 134 :KPNEAVQVLVEEL 1mh9A 138 :YCPYEKYAWVEKY T0329 147 :FPGSFDFALGEKSGIRRKPA 1mh9A 152 :GPDFLEQIVLTRDKTVVSAD T0329 185 :VYIGDSE 1mh9A 172 :LLIDDRP T0329 201 :EMDEIAVNW 1mh9A 188 :SWEHVLFTA T0329 210 :GFRSV 1mh9A 200 :QHLQL T0329 222 :ATVIVDTAEK 1mh9A 207 :PRRRLHSWAD T0329 232 :LEEAI 1mh9A 218 :WKAIL Number of specific fragments extracted= 15 number of extra gaps= 1 total=1534 Will force an alignment to be made, even if fragment is small Number of alignments=143 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mh9A/T0329-1mh9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 1mh9A/T0329-1mh9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh9A read from 1mh9A/T0329-1mh9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mh9A in template set T0329 5 :AAIFDMDGTILDTSADLTSALNYA 1mh9A 37 :RVLVDMDGVLADFEGGFLRKFRAR T0329 47 :FGSG 1mh9A 61 :FPDQ T0329 73 :FGTKDEQIPEAVTQTEVNRVLEVFKPYYADHCQI 1mh9A 65 :PFIALEDRRGFWVSEQYGRLRPGLSEKAISIWES T0329 107 :KTGPFPGILDLMKNLRQ 1mh9A 104 :ELEPLPGAVEAVKEMAS T0329 124 :KGVKLAVVSNKP 1mh9A 122 :QNTDVFICTSPI T0329 136 :NEAVQVLVE 1mh9A 140 :PYEKYAWVE T0329 145 :ELFPGSFDFALGEKSGIRRKPA 1mh9A 150 :YFGPDFLEQIVLTRDKTVVSAD T0329 185 :VYIGDSE 1mh9A 172 :LLIDDRP T0329 201 :EMDEIAVNWGFR 1mh9A 188 :SWEHVLFTACHN Number of specific fragments extracted= 9 number of extra gaps= 0 total=1543 Will force an alignment to be made, even if fragment is small Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bduA/T0329-2bduA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bduA expands to /projects/compbio/data/pdb/2bdu.pdb.gz 2bduA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1944, because occupancy 0.350 <= existing 0.650 in 2bduA Skipped atom 1946, because occupancy 0.350 <= existing 0.650 in 2bduA Skipped atom 1948, because occupancy 0.350 <= existing 0.650 in 2bduA Skipped atom 1950, because occupancy 0.350 <= existing 0.650 in 2bduA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0329 read from 2bduA/T0329-2bduA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bduA read from 2bduA/T0329-2bduA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bduA to template set # found chain 2bduA in template set Warning: unaligning (T0329)V131 because of BadResidue code BAD_PEPTIDE in next template residue (2bduA)S164 Warning: unaligning (T0329)S132 because of BadResidue code BAD_PEPTIDE at template residue (2bduA)S164 Warning: unaligning (T0329)C184 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bduA)I234 Warning: unaligning (T0329)V185 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bduA)I234 Warning: unaligning (T0329)V226 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bduA)D263 Warning: unaligning (T0329)D227 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bduA)D263 T0329 5 :AAIFDMDGTILDT 2bduA 45 :QIITDFDMTLSRF T0329 18 :SADLTSALNYAFEQTGHR 2bduA 82 :RRKLLQLKEQYYAIEVDP T0329 37 :DFTVEDIKNFFGSGVVVAVTRALAY 2bduA 100 :VLTVEEKFPYMVEWYTKSHGLLIEQ T0329 83 :AVTQTEVNRVLEVFK 2bduA 125 :GIPKAKLKEIVADSD T0329 108 :TGPFPGILDLMKNLRQKGVKLAV 2bduA 140 :VMLKEGYENFFGKLQQHGIPVFI T0329 133 :NKPNEAVQVLVEEL 2bduA 165 :AGIGDVLEEVIRQA T0329 147 :FPGSFDFALGE 2bduA 181 :YHSNVKVVSNF T0329 159 :SG 2bduA 219 :KN T0329 167 :PDMT 2bduA 221 :TDYF T0329 175 :KVLG 2bduA 225 :SQLK T0329 180 :PRDK 2bduA 229 :DNSN T0329 186 :YIGDSEIDIQTARNS 2bduA 235 :LLGDSQGDLRMADGV T0329 201 :EMDEIAVNW 2bduA 251 :NVEHILKIG T0329 224 :VI 2bduA 260 :YL T0329 228 :TAEKLEEAILG 2bduA 264 :RVDELLEKYMD Number of specific fragments extracted= 15 number of extra gaps= 3 total=1558 Will force an alignment to be made, even if fragment is small Number of alignments=145 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bduA/T0329-2bduA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2bduA/T0329-2bduA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bduA read from 2bduA/T0329-2bduA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bduA in template set Warning: unaligning (T0329)V131 because of BadResidue code BAD_PEPTIDE in next template residue (2bduA)S164 Warning: unaligning (T0329)S132 because of BadResidue code BAD_PEPTIDE at template residue (2bduA)S164 Warning: unaligning (T0329)C184 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bduA)I234 Warning: unaligning (T0329)V185 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bduA)I234 Warning: unaligning (T0329)F211 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bduA)D263 Warning: unaligning (T0329)R212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bduA)D263 T0329 5 :AAIFDMDGTILD 2bduA 45 :QIITDFDMTLSR T0329 17 :TSADLTSALNYAFEQT 2bduA 77 :VTDECRRKLLQLKEQY T0329 33 :GHR 2bduA 97 :VDP T0329 37 :DFTVEDIKNFFGSGVVVAVTRAL 2bduA 100 :VLTVEEKFPYMVEWYTKSHGLLI T0329 81 :PEAVTQTEVNRVLEVFK 2bduA 123 :EQGIPKAKLKEIVADSD T0329 108 :TGPFPGILDLMKNLRQKGVKLAV 2bduA 140 :VMLKEGYENFFGKLQQHGIPVFI T0329 133 :NKPNEAVQVLVEEL 2bduA 165 :AGIGDVLEEVIRQA T0329 147 :FPGSFDFALGE 2bduA 181 :YHSNVKVVSNF T0329 158 :KSGIRR 2bduA 206 :ELIHVF T0329 167 :PDMTS 2bduA 214 :HDGAL T0329 174 :VKVLG 2bduA 224 :FSQLK T0329 179 :V 2bduA 230 :N T0329 182 :DK 2bduA 231 :SN T0329 186 :YIGDSEIDIQT 2bduA 235 :LLGDSQGDLRM T0329 199 :NSEMD 2bduA 246 :ADGVA T0329 204 :EIAVN 2bduA 257 :KIGYL T0329 213 :SVPFLQK 2bduA 264 :RVDELLE T0329 222 :ATVIV 2bduA 276 :YDIVL Number of specific fragments extracted= 18 number of extra gaps= 3 total=1576 Will force an alignment to be made, even if fragment is small Number of alignments=146 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bduA/T0329-2bduA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0329 read from 2bduA/T0329-2bduA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bduA read from 2bduA/T0329-2bduA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bduA in template set Warning: unaligning (T0329)V131 because of BadResidue code BAD_PEPTIDE in next template residue (2bduA)S164 Warning: unaligning (T0329)S132 because of BadResidue code BAD_PEPTIDE at template residue (2bduA)S164 Warning: unaligning (T0329)C184 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bduA)I234 Warning: unaligning (T0329)V185 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bduA)I234 Warning: unaligning (T0329)F211 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bduA)D263 Warning: unaligning (T0329)R212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bduA)D263 T0329 5 :AAIFDMDGTILDTS 2bduA 45 :QIITDFDMTLSRFS T0329 19 :ADLTSALNYAFEQT 2bduA 79 :DECRRKLLQLKEQY T0329 42 :DIKNFF 2bduA 93 :YAIEVD T0329 78 :EQIPEAVTQTEVNRVLEVFKPYYADHCQI 2bduA 99 :PVLTVEEKFPYMVEWYTKSHGLLIEQGIP T0329 107 :KTGPFPGILDLMKNLRQKGVKLAV 2bduA 139 :DVMLKEGYENFFGKLQQHGIPVFI T0329 133 :NKPNEAVQVLVE 2bduA 165 :AGIGDVLEEVIR T0329 145 :ELFPGSFDFALGE 2bduA 178 :AGVYHSNVKVVSN T0329 174 :VKVLG 2bduA 224 :FSQLK T0329 182 :DK 2bduA 231 :SN T0329 186 :YIGDSEIDI 2bduA 235 :LLGDSQGDL T0329 199 :NSEMD 2bduA 246 :ADGVA T0329 204 :EIAVNWG 2bduA 255 :ILKIGYL T0329 213 :SVPFLQK 2bduA 264 :RVDELLE T0329 231 :K 2bduA 271 :K Number of specific fragments extracted= 14 number of extra gaps= 3 total=1590 Will force an alignment to be made, even if fragment is small Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cr6A/T0329-1cr6A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cr6A expands to /projects/compbio/data/pdb/1cr6.pdb.gz 1cr6A:# T0329 read from 1cr6A/T0329-1cr6A-t06-local-adpstyle5.a2m # 1cr6A read from 1cr6A/T0329-1cr6A-t06-local-adpstyle5.a2m # adding 1cr6A to template set # found chain 1cr6A in template set Warning: unaligning (T0329)K4 because first residue in template chain is (1cr6A)R4 Warning: unaligning (T0329)L25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cr6A)G48 Warning: unaligning (T0329)V53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cr6A)G48 Warning: unaligning (T0329)S69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cr6A)Q90 Warning: unaligning (T0329)E94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cr6A)Q90 T0329 5 :AAIFDMDGTILD 1cr6A 5 :VAAFDLDGVLAL T0329 23 :SA 1cr6A 17 :PS T0329 54 :AVTRALAYE 1cr6A 49 :PTEQLMKGK T0329 64 :GSSRE 1cr6A 58 :ITFSQ T0329 95 :VFKPYYAD 1cr6A 91 :IFSQAMAA T0329 108 :TGPFPGILDLMKNLRQKGVKLAVVSN 1cr6A 99 :RSINRPMLQAAIALKKKGFTTCIVTN T0329 134 :KPNEAVQVLVEEL 1cr6A 128 :DDGDKRDSLAQMM T0329 147 :FPGSFDFALGEKSGIRRKPAPDMTSECVKVLGVPRDKCVYIGDSEIDIQTARNSEMDEIAVNWGFRSVPFLQKHG 1cr6A 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASALRELEKVT Number of specific fragments extracted= 8 number of extra gaps= 0 total=1598 Will force an alignment to be made, even if fragment is small Number of alignments=148 # command:CPU_time= 40.555 sec, elapsed time= 43.568 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 148 Adding 28441 constraints to all_contacts Done adding distance constraints # command:CPU_time= 40.740 sec, elapsed time= 43.763 sec. # command:Reading probabilities from T0329.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 81.261 Optimizing... Probability sum: -402.631, CN propb: -402.631 weights: 0.400 constraints: 527 # command:CPU_time= 220.988 sec, elapsed time= 224.340 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 527 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 527 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 3891 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 3891 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 22147 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 22147 # command:CPU_time= 221.468 sec, elapsed time= 225.167 sec. # command: