parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0341/ # command:# Making conformation for sequence T0341 numbered 1 through 259 Created new target T0341 from T0341.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0341/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0341//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0341/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0341//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0341/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0341/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0341/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j97A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 1j97A/merged-good-all-a2m # 1j97A read from 1j97A/merged-good-all-a2m # adding 1j97A to template set # found chain 1j97A in template set Warning: unaligning (T0341)V12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0341)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0341 6 :ALKAVL 1j97A 4 :KKKLIL # choosing archetypes in rotamer library T0341 15 :NGTLHIED 1j97A 13 :DSTLVNNE T0341 31 :ALKRLRATS 1j97A 21 :TIDEIAREA T0341 51 :ETKKDLLERLKK 1j97A 30 :GVEEEVKKITKE T0341 63 :LEF 1j97A 47 :LNF T0341 76 :LTAARNLIEQKQ 1j97A 50 :EQSLRKRVSLLK T0341 96 :DRALPEFTGVQ 1j97A 62 :DLPIEKVEKAI T0341 119 :PEHFHYQLLNQAFRLLLD 1j97A 73 :KRITPTEGAEETIKELKN T0341 137 :GAPL 1j97A 92 :GYVV T0341 141 :IAIHKARYYKRKDGLALG 1j97A 97 :VVSGGFDIAVNKIKEKLG T0341 162 :FVTAL 1j97A 115 :LDYAF T0341 170 :TDTK 1j97A 130 :LTGD T0341 174 :AMVV 1j97A 138 :VLKE T0341 182 :KTFFLEALRDADCAPEEAVMIGDD 1j97A 145 :GEILEKIAKIEGINLEDTVAVGDG T0341 207 :RDDVDGAQNIG 1j97A 169 :ANDISMFKKAG T0341 219 :LGILVK 1j97A 180 :LKIAFC T0341 229 :KAADEEKI 1j97A 186 :AKPILKEK T0341 240 :PYLTCE 1j97A 194 :ADICIE T0341 246 :SFPHA 1j97A 202 :DLREI Number of specific fragments extracted= 19 number of extra gaps= 0 total=19 Number of alignments=1 # 1j97A read from 1j97A/merged-good-all-a2m # found chain 1j97A in template set Warning: unaligning (T0341)V12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0341)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0341 5 :RALKAVL 1j97A 3 :KKKKLIL T0341 15 :NGTLHIED 1j97A 13 :DSTLVNNE T0341 31 :ALKRLRAT 1j97A 21 :TIDEIARE T0341 39 :SV 1j97A 30 :GV T0341 53 :KKDLLERLKKL 1j97A 32 :EEEVKKITKEA T0341 69 :EDEIFTSLTAARNLIEQKQ 1j97A 43 :MEGKLNFEQSLRKRVSLLK T0341 96 :DRALPEFTGVQ 1j97A 62 :DLPIEKVEKAI T0341 119 :PEHFHYQLLNQAFRLLLD 1j97A 73 :KRITPTEGAEETIKELKN T0341 137 :GAPL 1j97A 92 :GYVV T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYA 1j97A 97 :VVSGGFDIAVNKIKEKLGLDYAFANRLIV T0341 170 :TDTKAMVVG 1j97A 132 :GDVEGEVLK T0341 179 :K 1j97A 144 :K T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1j97A 145 :GEILEKIAKIEGINLEDTVAVGDGAN T0341 209 :DVDGAQNIG 1j97A 171 :DISMFKKAG T0341 219 :LGILVKT 1j97A 180 :LKIAFCA T0341 233 :EEKINPPPYLTCE 1j97A 187 :KPILKEKADICIE T0341 246 :SFPHAV 1j97A 202 :DLREIL Number of specific fragments extracted= 17 number of extra gaps= 0 total=36 Number of alignments=2 # 1j97A read from 1j97A/merged-good-all-a2m # found chain 1j97A in template set Warning: unaligning (T0341)V12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0341)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0341 6 :ALKAVL 1j97A 4 :KKKLIL T0341 15 :NGTLHIEDA 1j97A 13 :DSTLVNNET T0341 24 :AVPGAQEALKRLRATSVM 1j97A 31 :VEEEVKKITKEAMEGKLN T0341 56 :LLERLKK 1j97A 49 :FEQSLRK T0341 63 :LEFEISEDE 1j97A 59 :LLKDLPIEK T0341 112 :AVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYY 1j97A 68 :VEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIA T0341 163 :VTALEYATD 1j97A 106 :VNKIKEKLG T0341 176 :VVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1j97A 139 :LKENAKGEILEKIAKIEGINLEDTVAVGDGAN T0341 209 :DVDGAQNIGMLGIL 1j97A 171 :DISMFKKAGLKIAF T0341 227 :KYKAADEEK 1j97A 185 :CAKPILKEK T0341 240 :PYLTCES 1j97A 194 :ADICIEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=47 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c4nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c4nA expands to /projects/compbio/data/pdb/2c4n.pdb.gz 2c4nA:# T0341 read from 2c4nA/merged-good-all-a2m # 2c4nA read from 2c4nA/merged-good-all-a2m # adding 2c4nA to template set # found chain 2c4nA in template set Warning: unaligning (T0341)R5 because first residue in template chain is (2c4nA)M1 Warning: unaligning (T0341)H19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0341)I20 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0341 6 :ALKAVLVDLNGTL 2c4nA 2 :TIKNVICDIDGVL T0341 21 :EDAAVPGAQEALKRLRATSVMVRFVTNTTKETKKDLLERLKKLEFEISEDEIFTSLTAARNLIEQKQVRPMLLLD 2c4nA 17 :DNVAVPGAAEFLHGIMDKGLPLVLLTNYPSQTGQDLANRFATAGVDVPDSVFYTSAMATADFLRRQEGKKAYVVG T0341 96 :DRALPEFTGVQT 2c4nA 93 :GALIHELYKAGF T0341 108 :QDPNAVVIGL 2c4nA 109 :VNPDFVIVGE T0341 119 :PEHFHYQLLNQAFRLLLDGAPLIAIHKARYY 2c4nA 119 :TRSYNWDMMHKAAYFVANGARFIATNPDTHG T0341 153 :DGLALGPGPFVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPH 2c4nA 150 :RGFYPACGALCAGIEKISGRKPFYVGKPSPWIIRAALNKMQAHSEETVIVGDNLRTDILAGFQAGLETILVLSGVSSLDDIDSMPFRPSWIYPSVAE Number of specific fragments extracted= 6 number of extra gaps= 1 total=53 Number of alignments=4 # 2c4nA read from 2c4nA/merged-good-all-a2m # found chain 2c4nA in template set Warning: unaligning (T0341)R5 because first residue in template chain is (2c4nA)M1 Warning: unaligning (T0341)H19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0341)I20 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0341 6 :ALKAVLVDLNGTL 2c4nA 2 :TIKNVICDIDGVL T0341 21 :EDAAVPGAQEALKRLRATSVMVRFVTNTTKETKKDLLERLKKLEFEISEDEIFTSLTAARNLIEQKQVRPMLLLD 2c4nA 17 :DNVAVPGAAEFLHGIMDKGLPLVLLTNYPSQTGQDLANRFATAGVDVPDSVFYTSAMATADFLRRQEGKKAYVVG T0341 96 :DRALPEFTGVQ 2c4nA 93 :GALIHELYKAG T0341 107 :TQDPNAVVIGL 2c4nA 108 :DVNPDFVIVGE T0341 119 :PEHFHYQLLNQAFRLLLDGAPLIAIHKARY 2c4nA 119 :TRSYNWDMMHKAAYFVANGARFIATNPDTH T0341 149 :YKRKDGLALGP 2c4nA 159 :LCAGIEKISGR T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPH 2c4nA 170 :KPFYVGKPSPWIIRAALNKMQAHSEETVIVGDNLRTDILAGFQAGLETILVLSGVSSLDDIDSMPFRPSWIYPSVAE Number of specific fragments extracted= 7 number of extra gaps= 1 total=60 Number of alignments=5 # 2c4nA read from 2c4nA/merged-good-all-a2m # found chain 2c4nA in template set Warning: unaligning (T0341)H19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0341)I20 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0341 7 :LKAVLVDLNGTL 2c4nA 3 :IKNVICDIDGVL T0341 21 :EDAAVPGAQEALKRLRATSVMVRFVTNTTKETKKDLLERLKKLEFEISEDEIFTSLTAARNLIEQKQVRPMLLLDDRALPEFTG 2c4nA 17 :DNVAVPGAAEFLHGIMDKGLPLVLLTNYPSQTGQDLANRFATAGVDVPDSVFYTSAMATADFLRRQEGKKAYVVGEGALIHELY T0341 107 :TQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYY 2c4nA 107 :TDVNPDFVIVGETRSYNWDMMHKAAYFVANGARFIATNPDTHG T0341 153 :DGLALGPGPFVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPH 2c4nA 150 :RGFYPACGALCAGIEKISGRKPFYVGKPSPWIIRAALNKMQAHSEETVIVGDNLRTDILAGFQAGLETILVLSGVSSLDDIDSMPFRPSWIYPSVAE Number of specific fragments extracted= 4 number of extra gaps= 1 total=64 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gfhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 2gfhA/merged-good-all-a2m # 2gfhA read from 2gfhA/merged-good-all-a2m # adding 2gfhA to template set # found chain 2gfhA in template set Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0341)E66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gfhA)C67 Warning: unaligning (T0341)E71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0341 4 :RRALKAVL 2gfhA 3 :LSRVRAVF T0341 14 :LNGTLHIEDAAVPGAQEAL 2gfhA 13 :LDNTLIDTAGASRRGMLEV T0341 33 :KRLR 2gfhA 33 :KLLQ T0341 37 :ATSVM 2gfhA 38 :KYHYK T0341 51 :ETKKDLLE 2gfhA 43 :EEAEIICD T0341 59 :RLKKLEF 2gfhA 55 :KLSKECF T0341 72 :IF 2gfhA 68 :IT T0341 74 :TSLTAARNLIEQKQVRPML 2gfhA 71 :VRTSHWEEAIQETKGGADN T0341 96 :DRALPEFTGVQTQDPN 2gfhA 90 :RKLAEECYFLWKSTRL T0341 119 :PEHFHYQLLNQAFRLLLDGAPL 2gfhA 106 :QHMILADDVKAMLTELRKEVRL T0341 141 :IAIHKARYYKRKDGLALG 2gfhA 129 :LLTNGDRQTQREKIEACA T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGML 2gfhA 147 :CQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTLETDIQGGLNAGLK T0341 220 :GILVKTGK 2gfhA 206 :TVWINKSG T0341 231 :ADEEKINPPPYLTCESFPHAVDHILQHL 2gfhA 214 :RVPLTSSPMPHYMVSSVLELPALLQSID Number of specific fragments extracted= 14 number of extra gaps= 1 total=78 Number of alignments=7 # 2gfhA read from 2gfhA/merged-good-all-a2m # found chain 2gfhA in template set Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0341)E66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gfhA)C67 Warning: unaligning (T0341)E71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0341 4 :RRALKAVL 2gfhA 3 :LSRVRAVF T0341 14 :LNGTLHIEDAAVPGAQE 2gfhA 13 :LDNTLIDTAGASRRGML T0341 31 :ALKRLRAT 2gfhA 31 :VIKLLQSK T0341 39 :SV 2gfhA 40 :HY T0341 50 :KETKKDLLERLKKLE 2gfhA 42 :KEEAEIICDKVQVKL T0341 65 :F 2gfhA 61 :F T0341 72 :IFTSL 2gfhA 68 :ITDVR T0341 77 :TAARNLIE 2gfhA 74 :SHWEEAIQ T0341 85 :QKQVRPMLLLDDRALPEFTGVQT 2gfhA 83 :TKGGADNRKLAEECYFLWKSTRL T0341 119 :PEHFHYQLLNQAFRLLLDGAPL 2gfhA 106 :QHMILADDVKAMLTELRKEVRL T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYA 2gfhA 129 :LLTNGDRQTQREKIEACACQSYFDAIVIG T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGML 2gfhA 158 :GEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTLETDIQGGLNAGLK T0341 220 :GILVKT 2gfhA 206 :TVWINK T0341 229 :KAADEEKINPPPYLTCESFPHAVDHILQHL 2gfhA 212 :SGRVPLTSSPMPHYMVSSVLELPALLQSID Number of specific fragments extracted= 14 number of extra gaps= 1 total=92 Number of alignments=8 # 2gfhA read from 2gfhA/merged-good-all-a2m # found chain 2gfhA in template set Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0341)E66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gfhA)C67 Warning: unaligning (T0341)E71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0341 5 :RALKAVL 2gfhA 4 :SRVRAVF T0341 14 :LNGTLHIEDAAVPGAQEALKRLRATSVMV 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLLQSKYHY T0341 46 :TNTTKETKKDLLERLKKLEF 2gfhA 42 :KEEAEIICDKVQVKLSKECF T0341 72 :IF 2gfhA 68 :IT T0341 74 :TSLTAARNLIEQKQ 2gfhA 71 :VRTSHWEEAIQETK T0341 96 :DRALPEFTGVQTQDPNAVVIGLAPEHFHYQLLNQAFRL 2gfhA 85 :GGADNRKLAEECYFLWKSTRLQHMILADDVKAMLTELR T0341 135 :LDGAPLIAIHKARYYKRKDGLALGPGPFVTAL 2gfhA 123 :KEVRLLLLTNGDRQTQREKIEACACQSYFDAI T0341 170 :TDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGML 2gfhA 155 :VIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTLETDIQGGLNAGLK T0341 220 :GILVKTGKYKAA 2gfhA 206 :TVWINKSGRVPL T0341 235 :KINPPPYLTCESFPHAVDHILQHL 2gfhA 218 :TSSPMPHYMVSSVLELPALLQSID Number of specific fragments extracted= 10 number of extra gaps= 1 total=102 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wr8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0341 read from 1wr8A/merged-good-all-a2m # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0341)A6 because first residue in template chain is (1wr8A)K2 T0341 7 :LKAVLVDLNGTLHI 1wr8A 3 :IKAISIDIDGTITY T0341 21 :EDAAVPGAQEALKRLRATSVMVRFVTN 1wr8A 18 :NRMIHEKALEAIRRAESLGIPIMLVTG T0341 51 :ETKKDLLERLKKLEFEIS 1wr8A 45 :NTVQFAEAASILIGTSGP T0341 69 :EDEIFTS 1wr8A 74 :KKKRIFL T0341 86 :KQVRPM 1wr8A 81 :ASMDEE T0341 96 :DRALPEFTGVQTQDP 1wr8A 87 :WILWNEIRKRFPNAR T0341 111 :N 1wr8A 116 :M T0341 119 :PEHFHYQLLNQAFR 1wr8A 117 :RETINVETVREIIN T0341 136 :D 1wr8A 131 :E T0341 137 :GAPL 1wr8A 133 :NLNL T0341 141 :IAIHKARYYKR 1wr8A 138 :AVDSGFAIHVK T0341 154 :GLALG 1wr8A 149 :KPWIN T0341 162 :F 1wr8A 154 :K T0341 182 :KTFFLEALRDADCAPEEAVMIGDD 1wr8A 155 :GSGIEKASEFLGIKPKEVAHVGDG T0341 207 :RDDVDGAQNIG 1wr8A 179 :ENDLDAFKVVG T0341 219 :LGILVK 1wr8A 190 :YKVAVA T0341 227 :KYKAADEEK 1wr8A 196 :QAPKILKEN T0341 240 :PYLTCES 1wr8A 205 :ADYVTKK T0341 247 :FPHAVDHILQHL 1wr8A 217 :GAEAIYHILEKF Number of specific fragments extracted= 19 number of extra gaps= 0 total=121 Number of alignments=10 # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0341)A6 because first residue in template chain is (1wr8A)K2 T0341 7 :LKAVLVDLNGTLHIEDAAV 1wr8A 3 :IKAISIDIDGTITYPNRMI T0341 26 :PGAQEALKRLRATSVMVRFVTNTT 1wr8A 23 :EKALEAIRRAESLGIPIMLVTGNT T0341 53 :KKDLLERLKKLE 1wr8A 47 :VQFAEAASILIG T0341 65 :FEISEDEIFTSL 1wr8A 62 :PVVAEDGGAISY T0341 119 :PEHFHYQLLNQAFRLLLD 1wr8A 78 :IFLASMDEEWILWNEIRK T0341 137 :GAP 1wr8A 99 :NAR T0341 146 :ARYYKRKDGLALGPG 1wr8A 121 :NVETVREIINELNLN T0341 163 :VTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1wr8A 136 :LVAVDSGFAIHVKKPWINKGSGIEKASEFLGIKPKEVAHVGDGEN T0341 209 :DVDGAQNIG 1wr8A 181 :DLDAFKVVG T0341 219 :LGILV 1wr8A 190 :YKVAV T0341 226 :GKYKAADEEK 1wr8A 195 :AQAPKILKEN T0341 240 :PYLTCES 1wr8A 205 :ADYVTKK T0341 247 :FPHAVDHILQHL 1wr8A 217 :GAEAIYHILEKF Number of specific fragments extracted= 13 number of extra gaps= 0 total=134 Number of alignments=11 # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0341)A6 because first residue in template chain is (1wr8A)K2 T0341 7 :LKAVLVDLNGTLHIEDA 1wr8A 3 :IKAISIDIDGTITYPNR T0341 24 :AVPGAQEALKRLRATSVMVRFVTNT 1wr8A 21 :IHEKALEAIRRAESLGIPIMLVTGN T0341 52 :TKKDLLERLKKLEFEIS 1wr8A 46 :TVQFAEAASILIGTSGP T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAF 1wr8A 105 :TMPDRRAGLVIMRETINVETVREIINE T0341 135 :LDGAPLIAIHKA 1wr8A 132 :LNLNLVAVDSGF T0341 155 :LALGP 1wr8A 150 :PWINK T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1wr8A 155 :GSGIEKASEFLGIKPKEVAHVGDGEN T0341 209 :DVDGAQNIGM 1wr8A 181 :DLDAFKVVGY T0341 220 :GILV 1wr8A 191 :KVAV T0341 226 :GKYKAADEEK 1wr8A 195 :AQAPKILKEN T0341 240 :PYLTCES 1wr8A 205 :ADYVTKK T0341 247 :FPHAVDHILQHL 1wr8A 217 :GAEAIYHILEKF Number of specific fragments extracted= 12 number of extra gaps= 0 total=146 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qyiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 1qyiA/merged-good-all-a2m # 1qyiA read from 1qyiA/merged-good-all-a2m # adding 1qyiA to template set # found chain 1qyiA in template set T0341 8 :KAVLVDLNGTLHIEDAAVPGAQEALKRLR 1qyiA 2 :KKILFDVDGVFLSEERCFDVSALTVYELL T0341 37 :ATSVMVRFVTNTTKETKKDLLE 1qyiA 33 :KCYLGLHSHIDWETLTDNDIQD T0341 59 :RLKKLEF 1qyiA 68 :KLKSLGL T0341 73 :FTSLTAARNLIEQK 1qyiA 75 :NSNWDMLFIVFSIH T0341 87 :QVRPML 1qyiA 139 :NVKVGK T0341 96 :DRALPEFTGVQTQDP 1qyiA 145 :NNIYAALEEFATTEL T0341 112 :A 1qyiA 211 :E T0341 119 :PEHFHYQLLNQAFRLLLD 1qyiA 212 :IILRPVDEVKVLLNDLKG T0341 137 :GAPL 1qyiA 231 :GFEL T0341 141 :IAIHKARYYKRKDGLALG 1qyiA 236 :IATGRPYTETVVPFENLG T0341 162 :FVTAL 1qyiA 254 :LLPYF T0341 167 :EYATDTKAM 1qyiA 261 :DFIATASDV T0341 176 :VVGKPEKTFFLEALR 1qyiA 281 :PLGKPNPFSYIAALY T0341 193 :D 1qyiA 310 :D T0341 194 :CAPEEAVMIGDD 1qyiA 313 :VNKDDVFIVGDS T0341 207 :RDDVDGAQNIGMLGILVKTGKYKAAD 1qyiA 325 :LADLLSAQKIGATFIGTLTGLKGKDA T0341 233 :EEKIN 1qyiA 354 :LEAHH T0341 240 :PYLTCESFPHAVDHI 1qyiA 359 :ADYVINHLGELRGVL Number of specific fragments extracted= 18 number of extra gaps= 0 total=164 Number of alignments=13 # 1qyiA read from 1qyiA/merged-good-all-a2m # found chain 1qyiA in template set T0341 8 :KAVLVDLNGTLHIEDA 1qyiA 2 :KKILFDVDGVFLSEER T0341 26 :PGAQEAL 1qyiA 131 :QLPLQFL T0341 38 :TSV 1qyiA 138 :DNV T0341 50 :KETKKDLLERLK 1qyiA 141 :KVGKNNIYAALE T0341 77 :TAARNLIEQKQVRPMLL 1qyiA 153 :EFATTELHVSDATLFSL T0341 96 :DRALPEFTGVQ 1qyiA 171 :GALWTLAQEVY T0341 108 :QDPNAVVIGLAPEHFHYQLLNQAFRLLLD 1qyiA 201 :TTFKTGYIYQEIILRPVDEVKVLLNDLKG T0341 137 :GAPL 1qyiA 231 :GFEL T0341 141 :IAIHKARYYKRKDGLALGPGPFV 1qyiA 236 :IATGRPYTETVVPFENLGLLPYF T0341 164 :TALEYA 1qyiA 261 :DFIATA T0341 170 :TDTKAM 1qyiA 277 :PQARPL T0341 178 :GKPEKTFFLEALR 1qyiA 283 :GKPNPFSYIAALY T0341 193 :DCAPEE 1qyiA 296 :GNNRDK T0341 199 :AVMIGDDCR 1qyiA 318 :VFIVGDSLA T0341 209 :DVDGAQNIGMLGILVKTGKYKAADEEKIN 1qyiA 327 :DLLSAQKIGATFIGTLTGLKGKDAAGELE T0341 238 :PPPYLTCESFPHAVDHI 1qyiA 357 :HHADYVINHLGELRGVL Number of specific fragments extracted= 16 number of extra gaps= 0 total=180 Number of alignments=14 # 1qyiA read from 1qyiA/merged-good-all-a2m # found chain 1qyiA in template set T0341 8 :KAVLVDLNGTLHIEDAAVPGAQEALKRL 1qyiA 2 :KKILFDVDGVFLSEERCFDVSALTVYEL T0341 37 :ATSV 1qyiA 60 :FQKD T0341 55 :DLLERLKKLEFEISEDEIFTSLTAARNLIEQKQ 1qyiA 64 :KILNKLKSLGLNSNWDMLFIVFSIHLIDILKKL T0341 95 :DDRALPEFTG 1qyiA 97 :SHDEIEAFMY T0341 117 :LAPEHFHYQLLNQAFRLLLDGAPLIAIHKA 1qyiA 212 :IILRPVDEVKVLLNDLKGAGFELGIATGRP T0341 147 :RYYKRKDGLALGPGPFVTALEY 1qyiA 253 :GLLPYFEADFIATASDVLEAEN T0341 170 :TDTKAMVVGKPEKTFFLEALR 1qyiA 275 :MYPQARPLGKPNPFSYIAALY T0341 194 :CAPEEAVMIGDDCR 1qyiA 313 :VNKDDVFIVGDSLA T0341 209 :DVDGAQNIGMLGILVKTGKYKAADEE 1qyiA 327 :DLLSAQKIGATFIGTLTGLKGKDAAG T0341 237 :NPPPYLTCESFPHAVDHI 1qyiA 356 :AHHADYVINHLGELRGVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=190 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rqlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rqlA expands to /projects/compbio/data/pdb/1rql.pdb.gz 1rqlA:# T0341 read from 1rqlA/merged-good-all-a2m # 1rqlA read from 1rqlA/merged-good-all-a2m # adding 1rqlA to template set # found chain 1rqlA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1rqlA)K5 T0341 7 :LKAVLVDLNGTLHIE 1rqlA 6 :IEAVIFDWAGTTVDY T0341 23 :AAVPGAQEALKRLRATSVM 1rqlA 21 :GCFAPLEVFMEIFHKRGVA T0341 51 :ETKKD 1rqlA 40 :ITAEE T0341 56 :LLERLKK 1rqlA 53 :KIDHVRA T0341 63 :LEF 1rqlA 61 :TEM T0341 76 :LTAARNLIEQKQVRPMLLLDDRALPEFTGVQTQDPN 1rqlA 64 :PRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILP T0341 119 :PEHFHYQLLNQAFRLLLD 1rqlA 100 :RYASPINAVKEVIASLRE T0341 137 :GAPLIAIHKARYYK 1rqlA 119 :GIKIGSTTGYTREM T0341 151 :RKDGLALGPGPF 1rqlA 139 :EAALQGYKPDFL T0341 170 :TDTKAMVVGKPEKTFFLEALRDADC 1rqlA 151 :VTPDDVPAGRPYPWMCYKNAMELGV T0341 195 :APEEAVMIGDD 1rqlA 177 :PMNHMIKVGDT T0341 207 :RDDVDGAQNIGMLGILVKT 1rqlA 188 :VSDMKEGRNAGMWTVGVIL T0341 226 :GKYKAADEEKI 1rqlA 211 :LGLTEEEVENM T0341 240 :PYLTCESFPHAVDHILQH 1rqlA 242 :AHFTIETMQELESVMEHI Number of specific fragments extracted= 14 number of extra gaps= 0 total=204 Number of alignments=16 # 1rqlA read from 1rqlA/merged-good-all-a2m # found chain 1rqlA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1rqlA)K5 T0341 7 :LKAVLVDLNGTLHIEDAAV 1rqlA 6 :IEAVIFDWAGTTVDYGCFA T0341 26 :PGAQE 1rqlA 26 :LEVFM T0341 33 :KRLRATSV 1rqlA 31 :EIFHKRGV T0341 50 :KETKKDLL 1rqlA 39 :AITAEEAR T0341 58 :ERLKKLEFE 1rqlA 55 :DHVRALTEM T0341 77 :TAARNLIEQKQVR 1rqlA 64 :PRIASEWNRVFRQ T0341 90 :PMLLLDDRALPEFTGVQTQDPN 1rqlA 78 :PTEADIQEMYEEFEEILFAILP T0341 119 :PEHFHYQLLNQAFRLLLD 1rqlA 100 :RYASPINAVKEVIASLRE T0341 137 :GAPL 1rqlA 119 :GIKI T0341 141 :IAIHKARYYKRKDGLAL 1rqlA 124 :STTGYTREMMDIVAKEA T0341 158 :GPG 1rqlA 144 :GYK T0341 163 :VTALEYA 1rqlA 147 :PDFLVTP T0341 173 :KAMVVGKPEKTFFLEALRDADC 1rqlA 154 :DDVPAGRPYPWMCYKNAMELGV T0341 195 :APEEAVMIGDDCR 1rqlA 177 :PMNHMIKVGDTVS T0341 209 :DVDGAQNIGMLGILVKTG 1rqlA 190 :DMKEGRNAGMWTVGVILG T0341 227 :KYKAADE 1rqlA 212 :GLTEEEV T0341 237 :NPPPYLTCESFPHAVDHILQH 1rqlA 239 :ENGAHFTIETMQELESVMEHI Number of specific fragments extracted= 17 number of extra gaps= 0 total=221 Number of alignments=17 # 1rqlA read from 1rqlA/merged-good-all-a2m # found chain 1rqlA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1rqlA)K5 T0341 7 :LKAVLVDLNGTLHIEDAAVP 1rqlA 6 :IEAVIFDWAGTTVDYGCFAP T0341 53 :KKDLLERLKKLEFEISEDEIFTSL 1rqlA 26 :LEVFMEIFHKRGVAITAEEARKPM T0341 77 :TAARNL 1rqlA 55 :DHVRAL T0341 83 :IEQKQVRPMLLLDDRALPEFTGVQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKAR 1rqlA 66 :IASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTR T0341 161 :PFVTALEYATD 1rqlA 131 :EMMDIVAKEAA T0341 172 :TKAMVVGKPEKTFFLEALRDADC 1rqlA 153 :PDDVPAGRPYPWMCYKNAMELGV T0341 195 :APEEAVMIGDDCR 1rqlA 177 :PMNHMIKVGDTVS T0341 209 :DVDGAQNIGMLGILVKTG 1rqlA 190 :DMKEGRNAGMWTVGVILG T0341 227 :KYKAADEEKI 1rqlA 212 :GLTEEEVENM T0341 237 :NPPPYLTCESFPHAVDHIL 1rqlA 239 :ENGAHFTIETMQELESVME Number of specific fragments extracted= 10 number of extra gaps= 0 total=231 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ek1A expands to /projects/compbio/data/pdb/1ek1.pdb.gz 1ek1A:# T0341 read from 1ek1A/merged-good-all-a2m # 1ek1A read from 1ek1A/merged-good-all-a2m # adding 1ek1A to template set # found chain 1ek1A in template set Warning: unaligning (T0341)K8 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0341)V25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 Warning: unaligning (T0341)R97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 T0341 9 :AVLVDLNGTLHI 1ek1A 5 :VAAFDLDGVLAL T0341 23 :AA 1ek1A 17 :PS T0341 98 :ALPEFTGVQTQDP 1ek1A 49 :PTEQLMKGKITFS T0341 111 :N 1ek1A 96 :M T0341 119 :PEHFHYQLLNQAFRLLLD 1ek1A 97 :AARSINRPMLQAAIALKK T0341 137 :GAPL 1ek1A 116 :GFTT T0341 141 :IAIHK 1ek1A 121 :IVTNN T0341 146 :ARYYKRKDGL 1ek1A 132 :KRDSLAQMMC T0341 158 :G 1ek1A 142 :E T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1ek1A 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDF T0341 207 :RDDVDGAQNIGMLG 1ek1A 187 :GSNLKPARDMGMVT Number of specific fragments extracted= 11 number of extra gaps= 0 total=242 Number of alignments=19 # 1ek1A read from 1ek1A/merged-good-all-a2m # found chain 1ek1A in template set Warning: unaligning (T0341)K8 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0341)A23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 T0341 9 :AVLVDLNGTLHIED 1ek1A 5 :VAAFDLDGVLALPS T0341 24 :AVPGAQEALKRLRATSVMVRFVTNT 1ek1A 101 :INRPMLQAAIALKKKGFTTCIVTNN T0341 49 :TKETKKDLLERLKKLE 1ek1A 132 :KRDSLAQMMCELSQHF T0341 65 :FEISED 1ek1A 149 :FLIESC T0341 71 :EIFTS 1ek1A 157 :GMIKP T0341 77 :TAARNLIEQKQVR 1ek1A 164 :QIYNFLLDTLKAK T0341 90 :PMLLLDDRALPEFTGVQ 1ek1A 181 :VFLDDFGSNLKPARDMG T0341 107 :TQDPNAV 1ek1A 300 :PPEIEEY T0341 119 :PEHFHYQLLNQAFRLL 1ek1A 307 :AMELLCKEMVTFLDKL T0341 136 :D 1ek1A 323 :G T0341 137 :GAPL 1ek1A 325 :PQAV T0341 141 :IAIHKARYYKRKDGLALG 1ek1A 330 :IGHDWAGVMVWNMALFYP T0341 161 :PFVTALE 1ek1A 348 :ERVRAVA T0341 182 :KTFFLEALRDA 1ek1A 443 :EEEIEFYIQQF T0341 193 :DCA 1ek1A 482 :KIL T0341 218 :MLGILVKTGKYKAADEEKI 1ek1A 485 :VPALMVTAEKDIVLRPEMS T0341 237 :NPPPYLTCE 1ek1A 511 :PFLKRGHIE T0341 246 :SFPHAVDHILQHL 1ek1A 529 :KPTEVNQILIKWL Number of specific fragments extracted= 18 number of extra gaps= 0 total=260 Number of alignments=20 # 1ek1A read from 1ek1A/merged-good-all-a2m # found chain 1ek1A in template set Warning: unaligning (T0341)K8 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0341)V25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 Warning: unaligning (T0341)A98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0341)P110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)Q90 T0341 9 :AVLVDLNGTLHI 1ek1A 5 :VAAFDLDGVLAL T0341 23 :AA 1ek1A 17 :PS T0341 99 :LPEF 1ek1A 49 :PTEQ T0341 111 :NAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKR 1ek1A 91 :IFSQAMAARSINRPMLQAAIALKKKGFTTCIVTNNWLDDGD T0341 155 :LALGPGPFVTALEYATD 1ek1A 132 :KRDSLAQMMCELSQHFD T0341 172 :TKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1ek1A 153 :SCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGS T0341 209 :DVDGAQNIGMLG 1ek1A 189 :NLKPARDMGMVT Number of specific fragments extracted= 7 number of extra gaps= 0 total=267 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nnlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0341 read from 1nnlA/merged-good-all-a2m # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0341)K53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0341)T74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0341 7 :LKAVLVDLNGTLHIED 1nnlA 14 :ADAVCFDVDSTVIREE T0341 31 :ALKRLRAT 1nnlA 30 :GIDELAKI T0341 39 :SVM 1nnlA 39 :GVE T0341 51 :ET 1nnlA 42 :DA T0341 75 :SLTAARNLIEQKQVRPM 1nnlA 58 :FKAALTERLALIQPSRE T0341 98 :ALPEFTGV 1nnlA 75 :QVQRLIAE T0341 119 :PEHFHYQLLNQAFRLLLD 1nnlA 83 :QPPHLTPGIRELVSRLQE T0341 137 :GAPL 1nnlA 102 :NVQV T0341 141 :IAIHKARYYKRKDGLALGPGP 1nnlA 107 :LISGGFRSIVEHVASKLNIPA T0341 174 :AMVVGKP 1nnlA 145 :GFDETQP T0341 181 :EKTFFLEALRDA 1nnlA 154 :ESGGKGKVIKLL T0341 195 :APEEAVMIGDD 1nnlA 170 :HFKKIIMIGDG T0341 207 :RDDVDG 1nnlA 181 :ATDMEA T0341 217 :GML 1nnlA 189 :PAD T0341 220 :GILVKTGKYKAADEEK 1nnlA 193 :FIGFGGNVIRQQVKDN T0341 240 :PYLTCESFPHA 1nnlA 209 :AKWYITDFVEL Number of specific fragments extracted= 16 number of extra gaps= 0 total=283 Number of alignments=22 # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0341)K53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0341)E66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0341 6 :ALKAVLVDLNGTLHIED 1nnlA 13 :SADAVCFDVDSTVIREE T0341 31 :ALKRLRAT 1nnlA 30 :GIDELAKI T0341 39 :SV 1nnlA 39 :GV T0341 50 :KET 1nnlA 41 :EDA T0341 75 :SLTAARNLIEQKQVR 1nnlA 58 :FKAALTERLALIQPS T0341 96 :DRALPEFTGV 1nnlA 73 :REQVQRLIAE T0341 119 :PEHFHYQLLNQAFRLLLD 1nnlA 83 :QPPHLTPGIRELVSRLQE T0341 137 :GAPL 1nnlA 102 :NVQV T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYA 1nnlA 107 :LISGGFRSIVEHVASKLNIPATNVFANRL T0341 170 :TDTKAMVVG 1nnlA 139 :FNGEYAGFD T0341 179 :K 1nnlA 158 :K T0341 182 :KTFFLEALRDA 1nnlA 159 :GKVIKLLKEKF T0341 195 :APEEAVMIGDDCR 1nnlA 170 :HFKKIIMIGDGAT T0341 209 :DVDGAQNIG 1nnlA 183 :DMEACPPAD T0341 219 :LGILVKTGKYKAADEEK 1nnlA 192 :AFIGFGGNVIRQQVKDN T0341 240 :PYLTCESFPHA 1nnlA 209 :AKWYITDFVEL Number of specific fragments extracted= 16 number of extra gaps= 0 total=299 Number of alignments=23 # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0341)E51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0341 2 :AARRALKAVLVDLNGTLHIED 1nnlA 9 :KLFYSADAVCFDVDSTVIREE T0341 28 :AQEALKRL 1nnlA 30 :GIDELAKI T0341 52 :TKKDLLERLKKLEFE 1nnlA 58 :FKAALTERLALIQPS T0341 107 :TQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKA 1nnlA 73 :REQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGF T0341 160 :GPFVTALEYATD 1nnlA 113 :RSIVEHVASKLN T0341 180 :PEKTFFLEALRDA 1nnlA 157 :GKGKVIKLLKEKF T0341 195 :APEEAVMIGDDCR 1nnlA 170 :HFKKIIMIGDGAT T0341 209 :DV 1nnlA 183 :DM T0341 219 :LGILVKTGKYKAADEEK 1nnlA 192 :AFIGFGGNVIRQQVKDN T0341 240 :PYLTCESFPHA 1nnlA 209 :AKWYITDFVEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=309 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zd3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zd3A expands to /projects/compbio/data/pdb/1zd3.pdb.gz 1zd3A:# T0341 read from 1zd3A/merged-good-all-a2m # 1zd3A read from 1zd3A/merged-good-all-a2m # adding 1zd3A to template set # found chain 1zd3A in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1zd3A)T2 T0341 7 :LKAVLVDLNGTLHI 1zd3A 3 :LRAAVFDLDGVLAL T0341 23 :AAVPGAQE 1zd3A 17 :PAVFGVLG T0341 33 :KRLRATSVM 1zd3A 25 :RTEEALALP T0341 51 :ET 1zd3A 34 :RG T0341 56 :LLERLKKLEF 1zd3A 36 :LLNDAFQKGG T0341 69 :ED 1zd3A 46 :PE T0341 71 :EIFTSLTAARNLIEQK 1zd3A 59 :TLSQWIPLMEENCRKC T0341 87 :QVRPM 1zd3A 79 :KVCLP T0341 96 :DR 1zd3A 84 :KN T0341 98 :ALPEFTGVQ 1zd3A 88 :IKEIFDKAI T0341 119 :PEHFHYQLLNQAFRLLLD 1zd3A 97 :SARKINRPMLQAALMLRK T0341 137 :GAPL 1zd3A 116 :GFTT T0341 141 :IAIHK 1zd3A 121 :ILTNT T0341 148 :YYKRKDGLAL 1zd3A 130 :RAERDGLAQL T0341 158 :G 1zd3A 142 :E T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1zd3A 143 :LKMHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDI T0341 207 :RDDVDGAQNIGMLGI 1zd3A 187 :GANLKPARDLGMVTI T0341 243 :TCESFPHAVDHILQHL 1zd3A 202 :LVQDTDTALKELEKVT Number of specific fragments extracted= 18 number of extra gaps= 0 total=327 Number of alignments=25 # 1zd3A read from 1zd3A/merged-good-all-a2m # found chain 1zd3A in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1zd3A)T2 T0341 7 :LKAVLVDLNGTLHIEDAA 1zd3A 3 :LRAAVFDLDGVLALPAVF T0341 27 :GAQE 1zd3A 21 :GVLG T0341 33 :KRLRATSVM 1zd3A 25 :RTEEALALP T0341 50 :KETKKDLL 1zd3A 34 :RGLLNDAF T0341 63 :LEF 1zd3A 46 :PEG T0341 77 :TAARNLIEQKQVRPMLLLD 1zd3A 49 :ATTRLMKGEITLSQWIPLM T0341 96 :DRALPEFTGVQ 1zd3A 69 :ENCRKCSETAK T0341 107 :TQDPNAVVIGLAPEHFHYQLLNQAFRLLLD 1zd3A 85 :NFSIKEIFDKAISARKINRPMLQAALMLRK T0341 137 :GAPL 1zd3A 116 :GFTT T0341 141 :IAIHK 1zd3A 121 :ILTNT T0341 146 :ARYYKRKDGLALGPG 1zd3A 132 :ERDGLAQLMCELKMH T0341 163 :VTALEYA 1zd3A 147 :FDFLIES T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1zd3A 154 :CQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGA T0341 209 :DVDGAQNIGM 1zd3A 189 :NLKPARDLGM T0341 240 :PYLTCESFPHAVDHILQHL 1zd3A 199 :VTILVQDTDTALKELEKVT Number of specific fragments extracted= 15 number of extra gaps= 0 total=342 Number of alignments=26 # 1zd3A read from 1zd3A/merged-good-all-a2m # found chain 1zd3A in template set T0341 7 :LKAVLVDLNGTLHI 1zd3A 3 :LRAAVFDLDGVLAL T0341 21 :EDAAVPGAQE 1zd3A 19 :VFGVLGRTEE T0341 31 :ALKRLRATS 1zd3A 36 :LLNDAFQKG T0341 40 :VM 1zd3A 58 :IT T0341 49 :TKETKKDLLERLKK 1zd3A 60 :LSQWIPLMEENCRK T0341 63 :LEFEISED 1zd3A 78 :AKVCLPKN T0341 73 :FTSLTAARNLIEQ 1zd3A 86 :FSIKEIFDKAISA T0341 119 :PEHFHYQLLNQAFRLLLDGAPLIAIHKARYY 1zd3A 99 :RKINRPMLQAALMLRKKGFTTAILTNTWLDD T0341 153 :DGLALGPGPFVTALEYATD 1zd3A 130 :RAERDGLAQLMCELKMHFD T0341 172 :TKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1zd3A 153 :SCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGA T0341 209 :DVDGAQNIGMLG 1zd3A 189 :NLKPARDLGMVT T0341 242 :LTCESFPHAVDHILQH 1zd3A 201 :ILVQDTDTALKELEKV Number of specific fragments extracted= 12 number of extra gaps= 0 total=354 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l7mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0341 read from 1l7mA/merged-good-all-a2m # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set T0341 6 :ALKAVLVDLNGTLHIED 1l7mA 4 :KKKLILFDFDSTLVNNE T0341 31 :ALKRLRATS 1l7mA 21 :TIDEIAREA T0341 51 :ETKKDLLERLKK 1l7mA 30 :GVEEEVKKITKE T0341 63 :LEF 1l7mA 47 :LNF T0341 76 :LTAARNLIEQKQ 1l7mA 50 :EQSLRKRVSLLK T0341 96 :DRALPEFTGVQ 1l7mA 62 :DLPIEKVEKAI T0341 119 :PEHFHYQLLNQAFRLLLD 1l7mA 73 :KRITPTEGAEETIKELKN T0341 137 :GAPL 1l7mA 92 :GYVV T0341 141 :IAIHKARYYKRKDGLALG 1l7mA 97 :VVSGGFDIAVNKIKEKLG T0341 162 :FVTAL 1l7mA 115 :LDYAF T0341 170 :TDT 1l7mA 130 :LTG T0341 173 :KAMVVG 1l7mA 137 :EVLKEN T0341 182 :KTFFLEALRDADCAPEEAVMIGDD 1l7mA 145 :GEILEKIAKIEGINLEDTVAVGDG T0341 207 :RDDVDGAQNIG 1l7mA 169 :ANDISMFKKAG T0341 219 :LGILVK 1l7mA 180 :LKIAFC T0341 229 :KAADEEKI 1l7mA 186 :AKPILKEK T0341 240 :PYLTCE 1l7mA 194 :ADICIE T0341 246 :SFPHAV 1l7mA 202 :DLREIL Number of specific fragments extracted= 18 number of extra gaps= 0 total=372 Number of alignments=28 # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set Warning: unaligning (T0341)R5 because first residue in template chain is (1l7mA)K3 T0341 6 :ALKAVLVDLNGTLHIED 1l7mA 4 :KKKLILFDFDSTLVNNE T0341 31 :ALKRLRAT 1l7mA 21 :TIDEIARE T0341 39 :SV 1l7mA 30 :GV T0341 53 :KKDLLERLKKL 1l7mA 32 :EEEVKKITKEA T0341 69 :EDEIFTSLTAARNLIEQKQ 1l7mA 43 :MEGKLNFEQSLRKRVSLLK T0341 96 :DRALPEFTGVQ 1l7mA 62 :DLPIEKVEKAI T0341 119 :PEHFHYQLLNQAFRLLLD 1l7mA 73 :KRITPTEGAEETIKELKN T0341 137 :GAPL 1l7mA 92 :GYVV T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYA 1l7mA 97 :VVSGGFDIAVNKIKEKLGLDYAFANRLIV T0341 170 :TDTKAMVVG 1l7mA 132 :GDVEGEVLK T0341 179 :K 1l7mA 144 :K T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1l7mA 145 :GEILEKIAKIEGINLEDTVAVGDGAN T0341 209 :DVDGAQNIG 1l7mA 171 :DISMFKKAG T0341 219 :LGILVKT 1l7mA 180 :LKIAFCA T0341 233 :EEKINPPPYLTCE 1l7mA 187 :KPILKEKADICIE T0341 246 :SFPHAV 1l7mA 202 :DLREIL Number of specific fragments extracted= 16 number of extra gaps= 0 total=388 Number of alignments=29 # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set T0341 6 :ALKAVLVDLNGTLHIEDA 1l7mA 4 :KKKLILFDFDSTLVNNET T0341 24 :AVPGAQEALKRLRATSVM 1l7mA 31 :VEEEVKKITKEAMEGKLN T0341 53 :KKDLLERLKKLEFEISEDEIFT 1l7mA 49 :FEQSLRKRVSLLKDLPIEKVEK T0341 115 :IGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKA 1l7mA 71 :AIKRITPTEGAEETIKELKNRGYVVAVVSGGF T0341 160 :GPFVTALEYATD 1l7mA 103 :DIAVNKIKEKLG T0341 181 :EKTFFLEALRDADCAPEEAVMIGDDCR 1l7mA 144 :KGEILEKIAKIEGINLEDTVAVGDGAN T0341 209 :DVDGAQNIGMLGIL 1l7mA 171 :DISMFKKAGLKIAF T0341 227 :KYKAADEEK 1l7mA 185 :CAKPILKEK T0341 240 :PYLTCES 1l7mA 194 :ADICIEK Number of specific fragments extracted= 9 number of extra gaps= 0 total=397 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cqzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cqzA expands to /projects/compbio/data/pdb/1cqz.pdb.gz 1cqzA:# T0341 read from 1cqzA/merged-good-all-a2m # 1cqzA read from 1cqzA/merged-good-all-a2m # adding 1cqzA to template set # found chain 1cqzA in template set Warning: unaligning (T0341)K8 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0341)V25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0341)I67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)G48 Warning: unaligning (T0341)E71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)Q90 Warning: unaligning (T0341)D96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0341 9 :AVLVDLNGTLHI 1cqzA 5 :VAAFDLDGVLAL T0341 23 :AA 1cqzA 17 :PS T0341 68 :SED 1cqzA 49 :PTE T0341 97 :RALPEFTGVQT 1cqzA 91 :IFSQAMAARSI T0341 124 :YQLLNQAFRLLLD 1cqzA 102 :NRPMLQAAIALKK T0341 137 :GAPL 1cqzA 116 :GFTT T0341 141 :IAIHK 1cqzA 121 :IVTNN T0341 146 :ARYYKRKDGLA 1cqzA 132 :KRDSLAQMMCE T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1cqzA 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDF T0341 207 :RDDVDGAQNIGMLGILVK 1cqzA 187 :GSNLKPARDMGMVTILVH T0341 245 :ESFPHAVDHILQHL 1cqzA 205 :NTASALRELEKVTG Number of specific fragments extracted= 11 number of extra gaps= 0 total=408 Number of alignments=31 # 1cqzA read from 1cqzA/merged-good-all-a2m # found chain 1cqzA in template set Warning: unaligning (T0341)K8 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0341)A23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0341)I72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)Q90 Warning: unaligning (T0341)D96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0341 9 :AVLVDLNGTLHIED 1cqzA 5 :VAAFDLDGVLALPS T0341 61 :KKLEFEISEDE 1cqzA 52 :QLMKGKITFSQ T0341 97 :RALPEFT 1cqzA 91 :IFSQAMA T0341 120 :EHFHYQLLNQAFRLLLD 1cqzA 98 :ARSINRPMLQAAIALKK T0341 137 :GAPL 1cqzA 116 :GFTT T0341 141 :IAIHKARY 1cqzA 121 :IVTNNWLD T0341 149 :YKRKDGLALG 1cqzA 135 :SLAQMMCELS T0341 161 :PFVTALEYA 1cqzA 145 :QHFDFLIES T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1cqzA 154 :CQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGS T0341 209 :DVDGAQNIGMLGILVKT 1cqzA 189 :NLKPARDMGMVTILVHN T0341 246 :SFPHAVDHILQHL 1cqzA 206 :TASALRELEKVTG Number of specific fragments extracted= 11 number of extra gaps= 0 total=419 Number of alignments=32 # 1cqzA read from 1cqzA/merged-good-all-a2m # found chain 1cqzA in template set Warning: unaligning (T0341)K8 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0341)V25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0341)I67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)G48 Warning: unaligning (T0341)P110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0341 9 :AVLVDLNGTLHI 1cqzA 5 :VAAFDLDGVLAL T0341 23 :AA 1cqzA 17 :PS T0341 68 :SEDE 1cqzA 49 :PTEQ T0341 85 :QKQ 1cqzA 53 :LMK T0341 111 :NAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKR 1cqzA 91 :IFSQAMAARSINRPMLQAAIALKKKGFTTCIVTNNWLDDGD T0341 155 :LALGPGPFVTALEYATD 1cqzA 132 :KRDSLAQMMCELSQHFD T0341 172 :TKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1cqzA 153 :SCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGS T0341 209 :DVDGAQNIGMLGILVK 1cqzA 189 :NLKPARDMGMVTILVH T0341 245 :ESFPHAVDHILQHL 1cqzA 205 :NTASALRELEKVTG Number of specific fragments extracted= 9 number of extra gaps= 0 total=428 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wviA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wviA expands to /projects/compbio/data/pdb/1wvi.pdb.gz 1wviA:# T0341 read from 1wviA/merged-good-all-a2m # 1wviA read from 1wviA/merged-good-all-a2m # adding 1wviA to template set # found chain 1wviA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1wviA)T1002 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEALKRLRATSVMVRFVTNTTKETKKDLLERLKK 1wviA 1003 :YKGYLIDLDGTIYKGKDRIPAGEDFVKRLQERQLPYILVTNNTTRTPEMVQEMLAT T0341 63 :LEFEISEDEIFTSLTAARNLIEQKQVRPM 1wviA 1060 :FNIKTPLETIYTATLATIDYMNDMKRGKT T0341 92 :LLLD 1wviA 1090 :YVIG T0341 96 :DRALPEFTGVQT 1wviA 1095 :TGLKKAVAEAGY T0341 108 :QDPNAVVIGL 1wviA 1111 :ENPAYVVVGL T0341 119 :PEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPH 1wviA 1121 :DTNLTYEKLTLATLAIQKGAVFIGTNPDLNIPTERGLLPGAGAILFLLEKATRVKPIIIGKPEAVIMNKALDRLGVKRHEAIMVGDNYLTDITAGIKNDIATLLVTTGFTKPEEVPALPIQPDFVLSSLAE Number of specific fragments extracted= 6 number of extra gaps= 0 total=434 Number of alignments=34 # 1wviA read from 1wviA/merged-good-all-a2m # found chain 1wviA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1wviA)T1002 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEALKRLRATSVMVRFVTNTTKETKKDLLERL 1wviA 1003 :YKGYLIDLDGTIYKGKDRIPAGEDFVKRLQERQLPYILVTNNTTRTPEMVQEML T0341 61 :KKLEFEISEDEIFTSLTAARNLIEQKQVR 1wviA 1058 :TSFNIKTPLETIYTATLATIDYMNDMKRG T0341 90 :PMLLLD 1wviA 1088 :TAYVIG T0341 96 :DRALPEFTGVQ 1wviA 1095 :TGLKKAVAEAG T0341 107 :TQDPNAVVIGL 1wviA 1110 :SENPAYVVVGL T0341 119 :PEHFHYQLLNQAFRLLLDGAPLIAIHKARY 1wviA 1121 :DTNLTYEKLTLATLAIQKGAVFIGTNPDLN T0341 149 :YKRKDGLAL 1wviA 1163 :AILFLLEKA T0341 158 :GP 1wviA 1173 :RV T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPH 1wviA 1175 :KPIIIGKPEAVIMNKALDRLGVKRHEAIMVGDNYLTDITAGIKNDIATLLVTTGFTKPEEVPALPIQPDFVLSSLAE Number of specific fragments extracted= 9 number of extra gaps= 0 total=443 Number of alignments=35 # 1wviA read from 1wviA/merged-good-all-a2m # found chain 1wviA in template set T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEALKRLRATSVMVRFVTNTTKETKKDLLERLKK 1wviA 1003 :YKGYLIDLDGTIYKGKDRIPAGEDFVKRLQERQLPYILVTNNTTRTPEMVQEMLAT T0341 63 :LEFEISEDEIFTSLTAARNLIEQKQVRPMLLLDDRALPEFTG 1wviA 1060 :FNIKTPLETIYTATLATIDYMNDMKRGKTAYVIGETGLKKAV T0341 107 :TQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPH 1wviA 1109 :DSENPAYVVVGLDTNLTYEKLTLATLAIQKGAVFIGTNPDLNIPTERGLLPGAGAILFLLEKATRVKPIIIGKPEAVIMNKALDRLGVKRHEAIMVGDNYLTDITAGIKNDIATLLVTTGFTKPEEVPALPIQPDFVLSSLAE Number of specific fragments extracted= 3 number of extra gaps= 0 total=446 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zjjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zjjA expands to /projects/compbio/data/pdb/1zjj.pdb.gz 1zjjA:# T0341 read from 1zjjA/merged-good-all-a2m # 1zjjA read from 1zjjA/merged-good-all-a2m # adding 1zjjA to template set # found chain 1zjjA in template set T0341 8 :KAVLVDLNGTLHIEDAAVPGAQEALKRLRATSVMVRFVTNTTKETKKDLLERLKKLEFEISEDEIFTSLTAARNLIEQK 1zjjA 2 :VAIIFDMDGVLYRGNRAIPGVRELIEFLKERGIPFAFLTNNSTKTPEMYREKLLKMGIDVSSSIIITSGLATRLYMSKH T0341 87 :QVRPMLLLD 1zjjA 82 :DPGKIFVIG T0341 96 :DRALPEFTGVQTQDP 1zjjA 92 :EGLVKEMQALGWGIV T0341 111 :NAVVIGLAPEH 1zjjA 120 :KHVVVGLDPDL T0341 123 :HYQLLNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKAMVVGKPEKTFFLEALRDAD 1zjjA 131 :TYEKLKYATLAIRNGATFIGTNPDATLPGEEGIYPGAGSIIAALKVATNVEPIIIGKPNEPMYEVVREMFP T0341 197 :EEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPHAV 1zjjA 203 :EELWMVGDRLDTDIAFAKKFGMKAIMVLTGVSSLEDIKKSEYKPDLVLPSVYELI Number of specific fragments extracted= 6 number of extra gaps= 0 total=452 Number of alignments=37 # 1zjjA read from 1zjjA/merged-good-all-a2m # found chain 1zjjA in template set T0341 9 :AVLVDLNGTLHIEDAAVPGAQEALKRLRATSVMVRFVTNTTKETKKDLLERLKKLEFEISEDEIFTSLTAARNLIE 1zjjA 3 :AIIFDMDGVLYRGNRAIPGVRELIEFLKERGIPFAFLTNNSTKTPEMYREKLLKMGIDVSSSIIITSGLATRLYMS T0341 85 :QKQVRPMLLLD 1zjjA 80 :HLDPGKIFVIG T0341 96 :DRALPEFTGVQ 1zjjA 92 :EGLVKEMQALG T0341 107 :TQDPN 1zjjA 125 :GLDPD T0341 119 :PEHFHYQLLNQAF 1zjjA 130 :LTYEKLKYATLAI T0341 135 :LDGAPLIAIHKARY 1zjjA 143 :RNGATFIGTNPDAT T0341 149 :YKRKDGLAL 1zjjA 169 :SIIAALKVA T0341 158 :GP 1zjjA 179 :NV T0341 173 :KAMVVGKPEKTFFLEALRDAD 1zjjA 181 :EPIIIGKPNEPMYEVVREMFP T0341 196 :PEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPHAV 1zjjA 202 :GEELWMVGDRLDTDIAFAKKFGMKAIMVLTGVSSLEDIKKSEYKPDLVLPSVYELI Number of specific fragments extracted= 10 number of extra gaps= 0 total=462 Number of alignments=38 # 1zjjA read from 1zjjA/merged-good-all-a2m # found chain 1zjjA in template set T0341 9 :AVLVDLNGTLHIEDAAVPGAQEALKRLRATSVMVRFVTNTTKETKKDLLERLKKLEFEISEDEIFTSLTAARNLIEQKQVRPMLLLDDRALPEFTG 1zjjA 3 :AIIFDMDGVLYRGNRAIPGVRELIEFLKERGIPFAFLTNNSTKTPEMYREKLLKMGIDVSSSIIITSGLATRLYMSKHLDPGKIFVIGGEGLVKEM T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKAMVVGKPEKTFFLEALRDAD 1zjjA 113 :QGSWKEVKHVVVGLDPDLTYEKLKYATLAIRNGATFIGTNPDATLPGEEGIYPGAGSIIAALKVATNVEPIIIGKPNEPMYEVVREMFP T0341 196 :PEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPHA 1zjjA 202 :GEELWMVGDRLDTDIAFAKKFGMKAIMVLTGVSSLEDIKKSEYKPDLVLPSVYEL Number of specific fragments extracted= 3 number of extra gaps= 0 total=465 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2go7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 2go7A/merged-good-all-a2m # 2go7A read from 2go7A/merged-good-all-a2m # adding 2go7A to template set # found chain 2go7A in template set Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0341)A142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0341)I143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0341 8 :KAVL 2go7A 4 :TAFI T0341 14 :LNGTLHIEDAAVPGAQE 2go7A 10 :LDGTLLDSYEAILSGIE T0341 33 :KRLRATSVM 2go7A 27 :ETFAQFSIP T0341 51 :ETKKDLLERLKKLEF 2go7A 36 :YDKEKVREFIFKYSV T0341 76 :LTAARNLIEQKQVRP 2go7A 51 :QDLLVRVAEDRNLDV T0341 96 :DRALPEFTGVQTQDP 2go7A 66 :EVLNQVRAQSLAEKN T0341 119 :PEHFHYQLLNQAFRLLLD 2go7A 81 :AQVVLMPGAREVLAWADE T0341 137 :GAPLI 2go7A 100 :GIQQF T0341 144 :HKARYYKRKDGLALG 2go7A 107 :THKGNNAFTILKDLG T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 2go7A 122 :VESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDR T0341 207 :RDDVDGAQNIGMLGILV 2go7A 166 :TLDVEFAQNSGIQSINF T0341 234 :EKINPPPYLTCESFPHAVDH 2go7A 183 :LESTYEGNHRIQALADISRI Number of specific fragments extracted= 12 number of extra gaps= 2 total=477 Number of alignments=40 # 2go7A read from 2go7A/merged-good-all-a2m # found chain 2go7A in template set Warning: unaligning (T0341)L7 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0341)A142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0341)I143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0341 8 :KAVL 2go7A 4 :TAFI T0341 14 :LNGTLHIEDA 2go7A 10 :LDGTLLDSYE T0341 27 :GAQEALKRLRAT 2go7A 20 :AILSGIEETFAQ T0341 39 :SV 2go7A 33 :SI T0341 50 :KETKKDLLERLKKLEFE 2go7A 35 :PYDKEKVREFIFKYSVQ T0341 77 :TAARNLIEQKQVRP 2go7A 52 :DLLVRVAEDRNLDV T0341 96 :DRALPEFTGVQTQDP 2go7A 66 :EVLNQVRAQSLAEKN T0341 119 :PEHFHYQLLNQAFRLLLD 2go7A 81 :AQVVLMPGAREVLAWADE T0341 137 :GAPLI 2go7A 100 :GIQQF T0341 144 :HKARYYKRKDGLALGPGPFVTALEYA 2go7A 107 :THKGNNAFTILKDLGVESYFTEILTS T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 2go7A 133 :QSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTL T0341 209 :DVDGAQNIGMLGILVKTGKYK 2go7A 168 :DVEFAQNSGIQSINFLESTYE T0341 240 :PYLTCESFPHAVDH 2go7A 189 :GNHRIQALADISRI Number of specific fragments extracted= 13 number of extra gaps= 2 total=490 Number of alignments=41 # 2go7A read from 2go7A/merged-good-all-a2m # found chain 2go7A in template set Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0341)I141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0341)A142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0341 8 :KAVL 2go7A 4 :TAFI T0341 14 :LNGTLHIEDAAVPGAQEALKRLRATSVM 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIPYD T0341 53 :KKDLLERLKK 2go7A 38 :KEKVREFIFK T0341 74 :TSLTAARNLIEQ 2go7A 48 :YSVQDLLVRVAE T0341 96 :DRALPEFTGVQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPL 2go7A 60 :DRNLDVEVLNQVRAQSLAEKNAQVVLMPGAREVLAWADESGIQQF T0341 143 :IHKARYYKR 2go7A 107 :THKGNNAFT T0341 153 :DGLALGPGPFVTAL 2go7A 116 :ILKDLGVESYFTEI T0341 170 :TDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 2go7A 130 :LTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTL T0341 209 :DVDGAQNIGMLGILV 2go7A 168 :DVEFAQNSGIQSINF T0341 234 :EKINPPPYLTCESFPHAVDH 2go7A 183 :LESTYEGNHRIQALADISRI Number of specific fragments extracted= 10 number of extra gaps= 2 total=500 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ys9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0341/1ys9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0341/1ys9A/merged-good-all-a2m.gz for input Trying 1ys9A/merged-good-all-a2m Error: Couldn't open file 1ys9A/merged-good-all-a2m or 1ys9A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nrwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0341 read from 1nrwA/merged-good-all-a2m # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0341)L7 because first residue in template chain is (1nrwA)M1 T0341 8 :KAVLVDLNGTLHIED 1nrwA 2 :KLIAIDLDGTLLNSK T0341 23 :AAVPGAQEALKRLRATSVMVRFVTN 1nrwA 18 :QVSLENENALRQAQRDGIEVVVSTG T0341 51 :ETKKDLLERLKKLEFEIS 1nrwA 43 :RAHFDVMSIFEPLGIKTW T0341 69 :ED 1nrwA 72 :PE T0341 71 :E 1nrwA 83 :D T0341 76 :LTAARNLIEQK 1nrwA 84 :KKRAYDILSWL T0341 87 :QVRPMLL 1nrwA 132 :EADLSVL T0341 96 :DRALPEFTGVQT 1nrwA 139 :KQAAEVQYSQSG T0341 108 :QDP 1nrwA 155 :NSF T0341 113 :VVIGL 1nrwA 171 :NILGF T0341 121 :HFHYQLLNQAFRLLLD 1nrwA 176 :SFFKEKLEAGWKRYEH T0341 137 :G 1nrwA 193 :E T0341 141 :IAIHKARYY 1nrwA 197 :LVSSAEHNF T0341 155 :LALG 1nrwA 210 :RKAS T0341 162 :F 1nrwA 214 :K T0341 182 :KTFFLEALRDADCAPEEAVMIGDD 1nrwA 215 :GQALKRLAKQLNIPLEETAAVGDS T0341 207 :RDDVDGAQNIG 1nrwA 239 :LNDKSMLEAAG T0341 219 :LGILV 1nrwA 250 :KGVAM T0341 226 :GKYKAADEEK 1nrwA 255 :GNAREDIKSI T0341 240 :PYLTCESF 1nrwA 265 :ADAVTLTN Number of specific fragments extracted= 20 number of extra gaps= 0 total=520 Number of alignments=43 # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0341)L7 because first residue in template chain is (1nrwA)M1 T0341 8 :KAVLVDLNGTLHIEDAAV 1nrwA 2 :KLIAIDLDGTLLNSKHQV T0341 26 :PGAQEALKRLRATSVMVRFVTNTT 1nrwA 21 :LENENALRQAQRDGIEVVVSTGRA T0341 53 :KKDLLERLKKLEFE 1nrwA 45 :HFDVMSIFEPLGIK T0341 67 :ISEDEIFTSL 1nrwA 62 :ISANGAVIHD T0341 87 :QVRPML 1nrwA 73 :EGRLYH T0341 119 :PEHFHYQLLNQAFRLLLD 1nrwA 79 :HETIDKKRAYDILSWLES T0341 137 :GAP 1nrwA 98 :NYY T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYATDTKAMVVGKPE 1nrwA 173 :LGFSFFKEKLEAGWKRYEHAEDLTLVSSAEHNFELSSRKAS T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1nrwA 215 :GQALKRLAKQLNIPLEETAAVGDSLN T0341 209 :DVDGAQNIG 1nrwA 241 :DKSMLEAAG T0341 219 :LGILV 1nrwA 250 :KGVAM T0341 226 :GKYKAADEEK 1nrwA 255 :GNAREDIKSI T0341 240 :PYLTCESFPH 1nrwA 265 :ADAVTLTNDE T0341 250 :AVDHILQH 1nrwA 277 :VAHMMKHL Number of specific fragments extracted= 14 number of extra gaps= 0 total=534 Number of alignments=44 # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0341)L7 because first residue in template chain is (1nrwA)M1 T0341 8 :KAVLVDLNGTLHIEDA 1nrwA 2 :KLIAIDLDGTLLNSKH T0341 24 :AVPGAQEALKRLRATSVMVRFVTNT 1nrwA 19 :VSLENENALRQAQRDGIEVVVSTGR T0341 52 :TKKDLLERLKKLEFEI 1nrwA 44 :AHFDVMSIFEPLGIKT T0341 115 :IGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPF 1nrwA 77 :YHHETIDKKRAYDILSWLESENYYYEVFTGSAIYTPQNGRELLDVELD T0341 165 :ALEYAT 1nrwA 125 :RFRSAN T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1nrwA 215 :GQALKRLAKQLNIPLEETAAVGDSLN T0341 209 :DVDGAQNIG 1nrwA 241 :DKSMLEAAG T0341 219 :LGILV 1nrwA 250 :KGVAM T0341 226 :GKYKAADEEK 1nrwA 255 :GNAREDIKSI T0341 240 :PYLT 1nrwA 265 :ADAV Number of specific fragments extracted= 10 number of extra gaps= 0 total=544 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yv9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0341/1yv9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0341/1yv9A/merged-good-all-a2m.gz for input Trying 1yv9A/merged-good-all-a2m Error: Couldn't open file 1yv9A/merged-good-all-a2m or 1yv9A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rdfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rdfA expands to /projects/compbio/data/pdb/1rdf.pdb.gz 1rdfA:# T0341 read from 1rdfA/merged-good-all-a2m # 1rdfA read from 1rdfA/merged-good-all-a2m # adding 1rdfA to template set # found chain 1rdfA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0341)A195 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0341 7 :LKAVLVDLNGTLHIED 1rdfA 6 :IEAVIFDWAGTTVDYG T0341 23 :AAVPGAQE 1rdfA 23 :FAPLEVFM T0341 33 :KRLRATSVM 1rdfA 31 :EIFHKRGVA T0341 51 :ETKKDL 1rdfA 40 :ITAEEA T0341 64 :EF 1rdfA 48 :PM T0341 66 :EISED 1rdfA 51 :LLKID T0341 71 :EIFTSLTAARNLIEQKQVRPMLLLDDRALPEFTGVQTQDPN 1rdfA 59 :ALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILP T0341 119 :PEHFHYQLLNQAFRLLLD 1rdfA 100 :RYASPINAVKEVIASLRE T0341 137 :GAPLIAIHK 1rdfA 119 :GIKIGSTTG T0341 146 :ARYYKRKDGLALGPGPF 1rdfA 134 :DIVAKEAALQGYKPDFL T0341 170 :TDTKAMVVGKPEKTFFLEALRDADC 1rdfA 151 :VTPDDVPAGRPYPWMCYKNAMELGV T0341 196 :PEEAVMIGDD 1rdfA 178 :MNHMIKVGDT T0341 207 :RDDVDGAQNIGMLGILVKT 1rdfA 188 :VSDMKEGRNAGMWTVGVIL T0341 226 :GKYKAADEEKI 1rdfA 211 :LGLTEEEVENM T0341 237 :N 1rdfA 241 :G T0341 240 :PYLTCESFPHA 1rdfA 242 :AHFTIETMQEL T0341 251 :VDHILQHLL 1rdfA 256 :MEHIEKQEL Number of specific fragments extracted= 17 number of extra gaps= 1 total=561 Number of alignments=46 # 1rdfA read from 1rdfA/merged-good-all-a2m # found chain 1rdfA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0341)A195 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0341 7 :LKAVLVDLNGTLHIEDAAV 1rdfA 6 :IEAVIFDWAGTTVDYGCFA T0341 26 :PGAQE 1rdfA 26 :LEVFM T0341 33 :KRLRATSV 1rdfA 31 :EIFHKRGV T0341 50 :KETKKDL 1rdfA 39 :AITAEEA T0341 63 :LEFEISEDEIFTSLTAARNLIEQKQVRPMLLLD 1rdfA 50 :PLLKIDHVRALTEMPRIASEWNRVFRQLPTEAD T0341 96 :DRALPEFTGVQTQDPN 1rdfA 84 :QEMYEEFEEILFAILP T0341 119 :PEHFHYQLLNQAFRLLLD 1rdfA 100 :RYASPINAVKEVIASLRE T0341 137 :GAPL 1rdfA 119 :GIKI T0341 141 :IAIHKARYYKRKDGLAL 1rdfA 124 :STTGYTREMMDIVAKEA T0341 158 :GPG 1rdfA 144 :GYK T0341 163 :VTALEYA 1rdfA 147 :PDFLVTP T0341 173 :KAMVVGKPEKTFFLEALRDADC 1rdfA 154 :DDVPAGRPYPWMCYKNAMELGV T0341 196 :PEEAVMIGDDCR 1rdfA 178 :MNHMIKVGDTVS T0341 209 :DVDGAQNIGMLGILVKTG 1rdfA 190 :DMKEGRNAGMWTVGVILG T0341 229 :KAADEEKI 1rdfA 211 :LGLTEEEV T0341 240 :PYLTCESFPH 1rdfA 242 :AHFTIETMQE T0341 250 :AVDHILQHLL 1rdfA 255 :VMEHIEKQEL Number of specific fragments extracted= 17 number of extra gaps= 1 total=578 Number of alignments=47 # 1rdfA read from 1rdfA/merged-good-all-a2m # found chain 1rdfA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0341)A195 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0341 7 :LKAVLVDLNGTLHIEDAAVP 1rdfA 6 :IEAVIFDWAGTTVDYGCFAP T0341 53 :KKDLLERLKKLEFEISEDEIFTSL 1rdfA 26 :LEVFMEIFHKRGVAITAEEARKPM T0341 86 :KQVRPMLLL 1rdfA 50 :PLLKIDHVR T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKAR 1rdfA 88 :EEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTR T0341 161 :PFVTALEYATD 1rdfA 131 :EMMDIVAKEAA T0341 172 :TKAMVVGKPEKTFFLEALRDADC 1rdfA 153 :PDDVPAGRPYPWMCYKNAMELGV T0341 196 :PEEAVMIGDDCR 1rdfA 178 :MNHMIKVGDTVS T0341 209 :DVDGAQNIGMLGILVKTG 1rdfA 190 :DMKEGRNAGMWTVGVILG T0341 227 :KYKAADEEKI 1rdfA 212 :GLTEEEVENM T0341 237 :NPPPYLTCESFPH 1rdfA 239 :ENGAHFTIETMQE T0341 250 :AVDHILQHL 1rdfA 255 :VMEHIEKQE Number of specific fragments extracted= 11 number of extra gaps= 1 total=589 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fdrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 2fdrA/merged-good-all-a2m # 2fdrA read from 2fdrA/merged-good-all-a2m # adding 2fdrA to template set # found chain 2fdrA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0341 7 :LKAVL 2fdrA 4 :FDLII T0341 14 :LNGTLHIEDAAVPGAQE 2fdrA 11 :CDGVLVDSEIIAAQVES T0341 33 :KRLRATSVM 2fdrA 28 :RLLTEAGYP T0341 51 :ETKKDLLERLKKLEF 2fdrA 37 :ISVEEMGERFAGMTW T0341 76 :LTAARNLIEQKQVRPMLLLDDRALPEFTGVQT 2fdrA 52 :KNILLQVESEASIPLSASLLDKSEKLLDMRLE T0341 119 :PEHFHYQLLNQAFRLL 2fdrA 84 :RDVKIIDGVKFALSRL T0341 137 :GAPL 2fdrA 100 :TTPR T0341 141 :IAIHKARYYKRKDGLALG 2fdrA 105 :ICSNSSSHRLDMMLTKVG T0341 162 :FVTALE 2fdrA 123 :LKPYFA T0341 168 :YATDTKAMV 2fdrA 130 :HIYSAKDLG T0341 177 :VGKPEKTFFLEALRDADCAPEEAVMIGDD 2fdrA 141 :RVKPKPDIFLHGAAQFGVSPDRVVVVEDS T0341 207 :RDDVDGAQNIGMLGILVKTGKYKAADEEKI 2fdrA 170 :VHGIHGARAAGMRVIGFTGASHTYPSHADR T0341 237 :N 2fdrA 204 :G T0341 240 :PYLTCESFPHAVDHILQHL 2fdrA 205 :AETVISRMQDLPAVIAAMA Number of specific fragments extracted= 14 number of extra gaps= 1 total=603 Number of alignments=49 # 2fdrA read from 2fdrA/merged-good-all-a2m # found chain 2fdrA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0341 7 :LKAVL 2fdrA 4 :FDLII T0341 14 :LNGTLHIEDAAVPGAQE 2fdrA 11 :CDGVLVDSEIIAAQVES T0341 33 :KRLRATSV 2fdrA 28 :RLLTEAGY T0341 50 :KETKKDLLERLKKLEFE 2fdrA 36 :PISVEEMGERFAGMTWK T0341 77 :TAARNLIEQKQVRPM 2fdrA 53 :NILLQVESEASIPLS T0341 96 :DRALPEFTGVQTQDPN 2fdrA 68 :ASLLDKSEKLLDMRLE T0341 119 :PEHFHYQLLNQAFRLL 2fdrA 84 :RDVKIIDGVKFALSRL T0341 137 :GAPL 2fdrA 100 :TTPR T0341 141 :IAIHKARYYKRKDGLALGPGPFV 2fdrA 105 :ICSNSSSHRLDMMLTKVGLKPYF T0341 164 :TALEYA 2fdrA 129 :PHIYSA T0341 173 :KAMVVG 2fdrA 135 :KDLGAD T0341 179 :KPEKTFFLEALRDADCAPEEAVMIGDDCR 2fdrA 143 :KPKPDIFLHGAAQFGVSPDRVVVVEDSVH T0341 209 :DVDGAQNIGMLGILVKTGKYKAADEEKI 2fdrA 172 :GIHGARAAGMRVIGFTGASHTYPSHADR T0341 237 :N 2fdrA 204 :G T0341 240 :PYLTCESFPHAVDHILQHL 2fdrA 205 :AETVISRMQDLPAVIAAMA Number of specific fragments extracted= 15 number of extra gaps= 1 total=618 Number of alignments=50 # 2fdrA read from 2fdrA/merged-good-all-a2m # found chain 2fdrA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0341 7 :LKAVL 2fdrA 4 :FDLII T0341 14 :LNGTLHIEDAA 2fdrA 11 :CDGVLVDSEII T0341 52 :TKKDLLERLKKLEFEISEDEI 2fdrA 22 :AAQVESRLLTEAGYPISVEEM T0341 88 :VRPMLLLDDRALPEFTG 2fdrA 43 :GERFAGMTWKNILLQVE T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAF 2fdrA 72 :DKSEKLLDMRLERDVKIIDGVKFALSR T0341 135 :LDGAPLIAIHKARYYKRKDGLALGPGPFV 2fdrA 99 :LTTPRCICSNSSSHRLDMMLTKVGLKPYF T0341 168 :YATDTKA 2fdrA 135 :KDLGADR T0341 178 :GKPEKTFFLEALRDADCAPEEAVMIGDDCR 2fdrA 142 :VKPKPDIFLHGAAQFGVSPDRVVVVEDSVH T0341 209 :DVDGAQNIGMLGILVKTGKYKAADEE 2fdrA 172 :GIHGARAAGMRVIGFTGASHTYPSHA T0341 237 :NPPPYLTCESFPHAVDHILQ 2fdrA 202 :DAGAETVISRMQDLPAVIAA Number of specific fragments extracted= 10 number of extra gaps= 1 total=628 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 1lvhA/merged-good-all-a2m # 1lvhA read from 1lvhA/merged-good-all-a2m # adding 1lvhA to template set # found chain 1lvhA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1lvhA)M1 Warning: unaligning (T0341)V12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0341)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0341 7 :LKAVL 1lvhA 2 :FKAVL T0341 15 :NGTLHIEDAAVPGAQE 1lvhA 10 :DGVITDTAEYHFRAWK T0341 33 :KRLRATSVM 1lvhA 26 :ALAEEIGIN T0341 50 :KETKKDLLERLKKL 1lvhA 46 :GVSREDSLQKILDL T0341 64 :EFEISE 1lvhA 61 :DKKVSA T0341 93 :LLDDRALPEFTGVQTQDPNAV 1lvhA 67 :EEFKELAKRKNDNYVKMIQDV T0341 119 :PEHFHYQLLNQAFRLLLD 1lvhA 88 :SPADVYPGILQLLKDLRS T0341 137 :GAPLIAIHKARYY 1lvhA 107 :KIKIALASASKNG T0341 151 :RKDGLALG 1lvhA 120 :PFLLERMN T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1lvhA 128 :LTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDS T0341 207 :RDDVDGAQNIGMLGILVK 1lvhA 172 :QAGIQAIKDSGALPIGVG T0341 229 :KAADEEK 1lvhA 190 :RPEDLGD T0341 240 :PYLTCESFPHA 1lvhA 197 :DIVIVPDTSHY T0341 251 :VDHILQHL 1lvhA 209 :LEFLKEVW Number of specific fragments extracted= 14 number of extra gaps= 0 total=642 Number of alignments=52 # 1lvhA read from 1lvhA/merged-good-all-a2m # found chain 1lvhA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1lvhA)M1 Warning: unaligning (T0341)V12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0341)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0341 7 :LKAVL 1lvhA 2 :FKAVL T0341 15 :NGTLHIEDAAVPGAQE 1lvhA 10 :DGVITDTAEYHFRAWK T0341 33 :KRLRATS 1lvhA 26 :ALAEEIG T0341 50 :KETKKDLLERLKKLE 1lvhA 46 :GVSREDSLQKILDLA T0341 71 :EIFTSLTAARNLIEQKQ 1lvhA 61 :DKKVSAEEFKELAKRKN T0341 96 :DRALPEFTGV 1lvhA 78 :DNYVKMIQDV T0341 119 :PEHFHYQLLNQAFRLLLD 1lvhA 88 :SPADVYPGILQLLKDLRS T0341 137 :GAPLIAIHKA 1lvhA 107 :KIKIALASAS T0341 148 :YYKRKDGLALGPGPFVTALEYA 1lvhA 117 :KNGPFLLERMNLTGYFDAIADP T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRD 1lvhA 139 :AEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAG T0341 210 :VDGAQNIGMLGILVKT 1lvhA 175 :IQAIKDSGALPIGVGR T0341 229 :KAADEEKI 1lvhA 191 :PEDLGDDI T0341 242 :LTCESFPHA 1lvhA 199 :VIVPDTSHY T0341 251 :VDHILQHLL 1lvhA 209 :LEFLKEVWL Number of specific fragments extracted= 14 number of extra gaps= 0 total=656 Number of alignments=53 # 1lvhA read from 1lvhA/merged-good-all-a2m # found chain 1lvhA in template set Warning: unaligning (T0341)V12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0341)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0341 7 :LKAVL 1lvhA 2 :FKAVL T0341 15 :NGTLHIED 1lvhA 10 :DGVITDTA T0341 26 :PGAQEALKRLR 1lvhA 18 :EYHFRAWKALA T0341 37 :ATSV 1lvhA 30 :EIGI T0341 47 :NTTKETKKDLLERLKK 1lvhA 43 :QLKGVSREDSLQKILD T0341 63 :LEFEISEDEIFTSLTAARNLIEQKQ 1lvhA 60 :ADKKVSAEEFKELAKRKNDNYVKMI T0341 114 :VIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYY 1lvhA 85 :QDVSPADVYPGILQLLKDLRSNKIKIALASASKNGP T0341 152 :KDGLALGPGPFVTAL 1lvhA 121 :FLLERMNLTGYFDAI T0341 170 :TDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1lvhA 136 :ADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQA T0341 209 :DVDGAQNIGMLGILVK 1lvhA 174 :GIQAIKDSGALPIGVG T0341 229 :KAADEEK 1lvhA 190 :RPEDLGD T0341 240 :PYLTCESFPH 1lvhA 197 :DIVIVPDTSH T0341 250 :AVDHILQH 1lvhA 212 :LKEVWLQK Number of specific fragments extracted= 13 number of extra gaps= 0 total=669 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 1f5sA/merged-good-all-a2m # 1f5sA read from 1f5sA/merged-good-all-a2m # adding 1f5sA to template set # found chain 1f5sA in template set T0341 5 :RALKAVLVDLNGTLHIED 1f5sA 3 :KKKKLILFDFDSTLVNNE T0341 31 :ALKRLRATS 1f5sA 21 :TIDEIAREA T0341 51 :ETKKDLLERLKK 1f5sA 30 :GVEEEVKKITKE T0341 70 :DEIFTSLTAARNLIEQKQ 1f5sA 44 :EGKLNFEQSLRKRVSLLK T0341 96 :DRALPEFTGVQ 1f5sA 62 :DLPIEKVEKAI T0341 119 :PEHFHYQLLNQAFRLLLD 1f5sA 73 :KRITPTEGAEETIKELKN T0341 137 :GAPL 1f5sA 92 :GYVV T0341 141 :IAIHKARYYKRKDGLALG 1f5sA 97 :VVSGGFDIAVNKIKEKLG T0341 162 :FVTAL 1f5sA 115 :LDYAF T0341 173 :K 1f5sA 133 :D T0341 174 :AMVV 1f5sA 137 :EVLK T0341 182 :KTFFLEALRDADCAPEEAVMIGDD 1f5sA 145 :GEILEKIAKIEGINLEDTVAVGDG T0341 207 :RDDVDGAQNIG 1f5sA 169 :ANDISMFKKAG T0341 219 :LGILVK 1f5sA 180 :LKIAFC T0341 229 :KAADEEKI 1f5sA 186 :AKPILKEK T0341 240 :PYLTCE 1f5sA 194 :ADICIE T0341 246 :SFPHAV 1f5sA 202 :DLREIL Number of specific fragments extracted= 17 number of extra gaps= 0 total=686 Number of alignments=55 # 1f5sA read from 1f5sA/merged-good-all-a2m # found chain 1f5sA in template set T0341 5 :RALKAVLVDLNGTLHIED 1f5sA 3 :KKKKLILFDFDSTLVNNE T0341 31 :ALKRLRAT 1f5sA 21 :TIDEIARE T0341 39 :SV 1f5sA 30 :GV T0341 53 :KKDLLERLKKL 1f5sA 32 :EEEVKKITKEA T0341 69 :EDEIFTSLTAARNLIEQKQ 1f5sA 43 :MEGKLNFEQSLRKRVSLLK T0341 96 :DRALPEFTGVQ 1f5sA 62 :DLPIEKVEKAI T0341 119 :PEHFHYQLLNQAFRLLLD 1f5sA 73 :KRITPTEGAEETIKELKN T0341 137 :GAPL 1f5sA 92 :GYVV T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYA 1f5sA 97 :VVSGGFDIAVNKIKEKLGLDYAFANRLIV T0341 170 :TDTKAMVVG 1f5sA 132 :GDVEGEVLK T0341 179 :K 1f5sA 144 :K T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1f5sA 145 :GEILEKIAKIEGINLEDTVAVGDGAN T0341 209 :DVDGAQNIG 1f5sA 171 :DISMFKKAG T0341 219 :LGILVKT 1f5sA 180 :LKIAFCA T0341 233 :EEKINPPPYLTCE 1f5sA 187 :KPILKEKADICIE T0341 246 :SFPHAV 1f5sA 202 :DLREIL Number of specific fragments extracted= 16 number of extra gaps= 0 total=702 Number of alignments=56 # 1f5sA read from 1f5sA/merged-good-all-a2m # found chain 1f5sA in template set T0341 6 :ALKAVLVDLNGTLHIEDA 1f5sA 4 :KKKLILFDFDSTLVNNET T0341 24 :AVPGAQEALKRLRATSVM 1f5sA 31 :VEEEVKKITKEAMEGKLN T0341 56 :LLERLKK 1f5sA 49 :FEQSLRK T0341 63 :LEFEISEDE 1f5sA 59 :LLKDLPIEK T0341 112 :AVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKA 1f5sA 68 :VEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGF T0341 160 :GPFVTALEYATD 1f5sA 103 :DIAVNKIKEKLG T0341 178 :GKPEKTFFLEALRDADCAPEEAVMIGDDCR 1f5sA 141 :ENAKGEILEKIAKIEGINLEDTVAVGDGAN T0341 209 :DVDGAQNIGMLGIL 1f5sA 171 :DISMFKKAGLKIAF T0341 227 :KYKAADEEK 1f5sA 185 :CAKPILKEK T0341 240 :PYLTCES 1f5sA 194 :ADICIEK Number of specific fragments extracted= 10 number of extra gaps= 0 total=712 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b8eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 2b8eA/merged-good-all-a2m # 2b8eA read from 2b8eA/merged-good-all-a2m # adding 2b8eA to template set # found chain 2b8eA in template set Warning: unaligning (T0341)R207 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0341)D208 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0341)D209 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0341)K224 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0341)T225 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0341 6 :ALKAVLVD 2b8eA 417 :KVTAVIFD T0341 18 :LHIEDAAVPGAQEALKRLR 2b8eA 439 :LVPLNGDERELLRLAAIAE T0341 38 :TSVM 2b8eA 458 :RRSE T0341 50 :KETKKDLLERLKKLEFEISED 2b8eA 462 :HPIAEAIVKKALEHGIELGEP T0341 80 :RNLIEQKQVRPM 2b8eA 503 :KRLMEDFGVAVS T0341 96 :DRALPEFTGVQTQDPNAVVIGL 2b8eA 515 :NEVELALEKLEREAKTAVIVAR T0341 119 :PE 2b8eA 537 :NG T0341 121 :HFHYQLLNQAFRLLLD 2b8eA 548 :DTLKESAKPAVQELKR T0341 137 :GAPL 2b8eA 565 :GIKV T0341 141 :IAIHKARYYKRKDGLALG 2b8eA 570 :MITGDNWRSAEAISRELN T0341 162 :FV 2b8eA 588 :LD T0341 169 :ATDTKA 2b8eA 590 :LVIAEV T0341 181 :EKTFFLEALRDA 2b8eA 596 :LPHQKSEEVKKL T0341 193 :D 2b8eA 610 :K T0341 197 :EEAVMIGDD 2b8eA 611 :EVVAFVGDG T0341 210 :VDGAQNIG 2b8eA 623 :APALAQAD T0341 219 :LGILV 2b8eA 631 :LGIAV T0341 226 :G 2b8eA 646 :G T0341 241 :YLTC 2b8eA 647 :DIVL T0341 245 :ESFPHAVDHI 2b8eA 653 :DDLRDVVAAI Number of specific fragments extracted= 20 number of extra gaps= 2 total=732 Number of alignments=58 # 2b8eA read from 2b8eA/merged-good-all-a2m # found chain 2b8eA in template set Warning: unaligning (T0341)S75 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)D496 Warning: unaligning (T0341)L76 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D496 Warning: unaligning (T0341)C206 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0341)R207 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0341)D209 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0341)K224 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0341)T225 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0341 5 :RALKAVLVDLNGTLHIEDA 2b8eA 416 :EKVTAVIFDKTGTLTKGKP T0341 24 :AVPGAQEAL 2b8eA 449 :LLRLAAIAE T0341 38 :TSVM 2b8eA 458 :RRSE T0341 50 :KETKKDLLERLKKLE 2b8eA 462 :HPIAEAIVKKALEHG T0341 65 :FEISEDEIFT 2b8eA 485 :VEVIAGEGVV T0341 80 :RNLIEQKQVRPM 2b8eA 503 :KRLMEDFGVAVS T0341 96 :DRALPEFTGVQ 2b8eA 515 :NEVELALEKLE T0341 121 :HFHYQLLNQAFRLLLD 2b8eA 548 :DTLKESAKPAVQELKR T0341 137 :GAPL 2b8eA 565 :GIKV T0341 141 :IAIHKARYYKRKDGLALGPG 2b8eA 570 :MITGDNWRSAEAISRELNLD T0341 166 :LEYA 2b8eA 590 :LVIA T0341 173 :KAMVVGK 2b8eA 594 :EVLPHQK T0341 182 :KTFFLEAL 2b8eA 601 :SEEVKKLQ T0341 193 :D 2b8eA 610 :K T0341 197 :EEAVMIGDD 2b8eA 611 :EVVAFVGDG T0341 210 :VDGAQNIG 2b8eA 623 :APALAQAD T0341 219 :LGILV 2b8eA 631 :LGIAV T0341 226 :G 2b8eA 646 :G T0341 241 :YLTC 2b8eA 647 :DIVL T0341 245 :ESFPHAVDHI 2b8eA 653 :DDLRDVVAAI Number of specific fragments extracted= 20 number of extra gaps= 3 total=752 Number of alignments=59 # 2b8eA read from 2b8eA/merged-good-all-a2m # found chain 2b8eA in template set Warning: unaligning (T0341)C206 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0341)R207 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0341)D209 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0341)K224 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0341)T225 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0341 2 :AARRALKAVLVDLNGTL 2b8eA 413 :EVAEKVTAVIFDKTGTL T0341 19 :HIEDAAVPGAQEALKRLRATS 2b8eA 440 :VPLNGDERELLRLAAIAERRS T0341 49 :TKETKKDLLERLKKLEFEISEDE 2b8eA 461 :EHPIAEAIVKKALEHGIELGEPE T0341 119 :PEHFHYQLLNQAFRLLLDGAPLIAIHKAR 2b8eA 548 :DTLKESAKPAVQELKRMGIKVGMITGDNW T0341 161 :PFVTALEYATDTKAMVVG 2b8eA 577 :RSAEAISRELNLDLVIAE T0341 180 :PEKTFFLEALRDA 2b8eA 595 :VLPHQKSEEVKKL T0341 193 :D 2b8eA 610 :K T0341 197 :EEAVMIGDD 2b8eA 611 :EVVAFVGDG T0341 211 :DGAQNIGMLGILV 2b8eA 623 :APALAQADLGIAV T0341 226 :G 2b8eA 646 :G T0341 241 :YLTC 2b8eA 647 :DIVL T0341 245 :ESFPHAVDHI 2b8eA 653 :DDLRDVVAAI Number of specific fragments extracted= 12 number of extra gaps= 2 total=764 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vj5A expands to /projects/compbio/data/pdb/1vj5.pdb.gz 1vj5A:# T0341 read from 1vj5A/merged-good-all-a2m # 1vj5A read from 1vj5A/merged-good-all-a2m # adding 1vj5A to template set # found chain 1vj5A in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1vj5A)T2 T0341 7 :LKAVLVDLNGTLHI 1vj5A 3 :LRAAVFDLDGVLAL T0341 21 :EDAAVPGAQE 1vj5A 19 :VFGVLGRTEE T0341 31 :ALKRLRATS 1vj5A 36 :LLNDAFQKG T0341 49 :TKETKKDLLERL 1vj5A 56 :GEITLSQWIPLM T0341 76 :LTAARNLIEQKQVRPM 1vj5A 68 :EENCRKCSETAKVCLP T0341 96 :DR 1vj5A 84 :KN T0341 98 :ALPEFTGVQ 1vj5A 88 :IKEIFDKAI T0341 119 :PEHFHYQLLNQAFRLLLD 1vj5A 97 :SARKINRPMLQAALMLRK T0341 137 :GAPL 1vj5A 116 :GFTT T0341 141 :IAIHK 1vj5A 121 :ILTNT T0341 146 :ARYYKRKDGLA 1vj5A 132 :ERDGLAQLMCE T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1vj5A 143 :LKMHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDI T0341 207 :RDDVDGAQNIGMLGI 1vj5A 187 :GANLKPARDLGMVTI T0341 243 :TCESFPHAVDHILQHL 1vj5A 202 :LVQDTDTALKELEKVT Number of specific fragments extracted= 14 number of extra gaps= 0 total=778 Number of alignments=61 # 1vj5A read from 1vj5A/merged-good-all-a2m # found chain 1vj5A in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1vj5A)T2 T0341 7 :LKAVLVDLNGTLHIEDAAV 1vj5A 3 :LRAAVFDLDGVLALPAVFG T0341 26 :PGAQE 1vj5A 24 :GRTEE T0341 31 :ALKRLRATS 1vj5A 36 :LLNDAFQKG T0341 50 :KETKKDLLERLK 1vj5A 57 :EITLSQWIPLME T0341 77 :TAARNLIEQKQVR 1vj5A 69 :ENCRKCSETAKVC T0341 107 :TQDPNAVVIGLAPEHFHYQLLNQAFRLLLD 1vj5A 85 :NFSIKEIFDKAISARKINRPMLQAALMLRK T0341 137 :GAPL 1vj5A 116 :GFTT T0341 141 :IAIHK 1vj5A 121 :ILTNT T0341 146 :ARYYKRKDGLALGPG 1vj5A 132 :ERDGLAQLMCELKMH T0341 163 :VTALEYA 1vj5A 147 :FDFLIES T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1vj5A 154 :CQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGA T0341 209 :DVDGAQNIGMLG 1vj5A 189 :NLKPARDLGMVT T0341 242 :LTCESFPHAVDHILQHL 1vj5A 201 :ILVQDTDTALKELEKVT Number of specific fragments extracted= 13 number of extra gaps= 0 total=791 Number of alignments=62 # 1vj5A read from 1vj5A/merged-good-all-a2m # found chain 1vj5A in template set T0341 7 :LKAVLVDLNGTLHIEDA 1vj5A 3 :LRAAVFDLDGVLALPAV T0341 24 :AVPGAQE 1vj5A 22 :VLGRTEE T0341 31 :ALKRLRATS 1vj5A 36 :LLNDAFQKG T0341 50 :KETKKDLLERLKK 1vj5A 57 :EITLSQWIPLMEE T0341 63 :LEFEISED 1vj5A 78 :AKVCLPKN T0341 73 :FTSLTAARNLIEQ 1vj5A 86 :FSIKEIFDKAISA T0341 119 :PEHFHYQLLNQAFRLLLDGAPLIAIHKARYY 1vj5A 99 :RKINRPMLQAALMLRKKGFTTAILTNTWLDD T0341 153 :DGLALGPGPFVTALEYATD 1vj5A 130 :RAERDGLAQLMCELKMHFD T0341 172 :TKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1vj5A 153 :SCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGA T0341 209 :DVDGAQNIGMLG 1vj5A 189 :NLKPARDLGMVT T0341 242 :LTCESFPHAVDHILQH 1vj5A 201 :ILVQDTDTALKELEKV Number of specific fragments extracted= 11 number of extra gaps= 0 total=802 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o08A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0341 read from 1o08A/merged-good-all-a2m # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0341)A6 because first residue in template chain is (1o08A)M1001 Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0341 7 :LKAVL 1o08A 1002 :FKAVL T0341 14 :LNGTLHI 1o08A 1009 :LDGVITD T0341 24 :AVPGAQEAL 1o08A 1016 :TAEYHFRAW T0341 33 :KRLRATSVM 1o08A 1026 :ALAEEIGIN T0341 51 :ETKKDLLERLKKLEF 1o08A 1047 :VSREDSLQKILDLAD T0341 87 :QVRPMLL 1o08A 1063 :KVSAEEF T0341 96 :DRALPEFTGVQTQDPN 1o08A 1070 :KELAKRKNDNYVKMIQ T0341 116 :GL 1o08A 1086 :DV T0341 119 :PEHFHYQLLNQAFRLLLD 1o08A 1088 :SPADVYPGILQLLKDLRS T0341 137 :GAPLIAIHKARYY 1o08A 1107 :KIKIALASASKNG T0341 151 :RKDGLALG 1o08A 1120 :PFLLERMN T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1o08A 1128 :LTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDS T0341 207 :RDDVDGAQNIGMLGILVK 1o08A 1172 :QAGIQAIKDSGALPIGVG T0341 229 :KAADEEK 1o08A 1190 :RPEDLGD T0341 240 :PYLTCESFPHA 1o08A 1197 :DIVIVPDTSHY T0341 251 :VDHILQHL 1o08A 1209 :LEFLKEVW Number of specific fragments extracted= 16 number of extra gaps= 1 total=818 Number of alignments=64 # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0341)A6 because first residue in template chain is (1o08A)M1001 Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0341 7 :LKAVL 1o08A 1002 :FKAVL T0341 14 :LNGTLHIE 1o08A 1009 :LDGVITDT T0341 25 :VPGAQEAL 1o08A 1017 :AEYHFRAW T0341 33 :KRLRATSVM 1o08A 1026 :ALAEEIGIN T0341 50 :KETKKDLLERLKKLEFE 1o08A 1046 :GVSREDSLQKILDLADK T0341 73 :FTSLTAARNLIEQKQ 1o08A 1063 :KVSAEEFKELAKRKN T0341 96 :DRALPEFTGV 1o08A 1078 :DNYVKMIQDV T0341 119 :PEHFHYQLLNQAFRLLLD 1o08A 1088 :SPADVYPGILQLLKDLRS T0341 137 :GAPLIAIHKA 1o08A 1107 :KIKIALASAS T0341 148 :YYKRKDGLALGPGPFVTALEYA 1o08A 1117 :KNGPFLLERMNLTGYFDAIADP T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1o08A 1139 :AEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQA T0341 209 :DVDGAQNIGMLGILVKT 1o08A 1174 :GIQAIKDSGALPIGVGR T0341 229 :KAADEEKI 1o08A 1191 :PEDLGDDI T0341 242 :LTCESFPHA 1o08A 1199 :VIVPDTSHY T0341 251 :VDHILQHL 1o08A 1209 :LEFLKEVW Number of specific fragments extracted= 15 number of extra gaps= 1 total=833 Number of alignments=65 # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0341 7 :LKAVL 1o08A 1002 :FKAVL T0341 14 :LNGTLH 1o08A 1009 :LDGVIT T0341 23 :AAVPGAQEALKRLR 1o08A 1015 :DTAEYHFRAWKALA T0341 37 :ATSVM 1o08A 1030 :EIGIN T0341 46 :TNTTKETKKDLLERLKKLEF 1o08A 1042 :EQLKGVSREDSLQKILDLAD T0341 66 :EISEDEIFTSLTAARNLIEQKQV 1o08A 1063 :KVSAEEFKELAKRKNDNYVKMIQ T0341 115 :IGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYK 1o08A 1086 :DVSPADVYPGILQLLKDLRSNKIKIALASASKNGPF T0341 153 :DGLALGPGPFVTAL 1o08A 1122 :LLERMNLTGYFDAI T0341 170 :TDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1o08A 1136 :ADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQA T0341 209 :DVDGAQNIGMLGILV 1o08A 1174 :GIQAIKDSGALPIGV T0341 228 :YKAADEEK 1o08A 1189 :GRPEDLGD T0341 240 :PYLTCESFPHA 1o08A 1197 :DIVIVPDTSHY T0341 251 :VDHILQ 1o08A 1209 :LEFLKE Number of specific fragments extracted= 13 number of extra gaps= 1 total=846 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l6rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0341 read from 1l6rA/merged-good-all-a2m # 1l6rA read from 1l6rA/merged-good-all-a2m # found chain 1l6rA in training set Warning: unaligning (T0341)R5 because first residue in template chain is (1l6rA)H0 T0341 6 :ALKAVLVDLNGTLHIEDA 1l6rA 1 :MIRLAAIDVDGNLTDRDR T0341 24 :AVPGAQEALKRLRATSVMVRFVTN 1l6rA 20 :ISTKAIESIRSAEKKGLTVSLLSG T0341 51 :ETKKDLLERLKKLEFEIS 1l6rA 44 :NVIPVVYALKIFLGINGP T0341 69 :EDEI 1l6rA 74 :DGSI T0341 119 :PEHFHYQLLNQAFRLLLDGAPL 1l6rA 78 :KKFFSNEGTNKFLEEMSKRTSM T0341 145 :K 1l6rA 101 :S T0341 148 :YYKRKDGLA 1l6rA 102 :ILTNRWREA T0341 157 :LGPGPFVTALEYATDTKAM 1l6rA 116 :IDPEDVDYVRKEAESRGFV T0341 176 :VVGKPEKTFFLEALRDADCAPEEAVMIGDD 1l6rA 146 :NRGEDKAFAVNKLKEMYSLEYDEILVIGDS T0341 207 :RDDVDG 1l6rA 176 :NNDMPM T0341 214 :QNIGMLGIL 1l6rA 182 :FQLPVRKAC T0341 225 :TGKYKAADEEK 1l6rA 191 :PANATDNIKAV T0341 240 :PYLTCES 1l6rA 202 :SDFVSDY Number of specific fragments extracted= 13 number of extra gaps= 0 total=859 Number of alignments=67 # 1l6rA read from 1l6rA/merged-good-all-a2m # found chain 1l6rA in training set Warning: unaligning (T0341)R5 because first residue in template chain is (1l6rA)H0 T0341 6 :ALKAVLVDLNGTLHIEDAAV 1l6rA 1 :MIRLAAIDVDGNLTDRDRLI T0341 26 :PGAQEALKRLRATSVMVRFVTNTT 1l6rA 22 :TKAIESIRSAEKKGLTVSLLSGNV T0341 53 :KKDLLERLKKLEFE 1l6rA 46 :IPVVYALKIFLGIN T0341 67 :ISEDEIFTSL 1l6rA 63 :FGENGGIMFD T0341 87 :QVRP 1l6rA 74 :DGSI T0341 119 :PEHFHYQLLNQAFRLLLDGAP 1l6rA 78 :KKFFSNEGTNKFLEEMSKRTS T0341 146 :ARYYKRKDGLALG 1l6rA 120 :DVDYVRKEAESRG T0341 163 :VTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1l6rA 133 :FVIFYSGYSWHLMNRGEDKAFAVNKLKEMYSLEYDEILVIGDSNN T0341 209 :DVDGAQ 1l6rA 178 :DMPMFQ T0341 216 :IGMLGILV 1l6rA 184 :LPVRKACP T0341 226 :GKYKAADEEK 1l6rA 192 :ANATDNIKAV T0341 240 :PYLTCE 1l6rA 202 :SDFVSD T0341 246 :SFPH 1l6rA 209 :SYGE T0341 250 :AVDHILQ 1l6rA 214 :IGQIFKH Number of specific fragments extracted= 14 number of extra gaps= 0 total=873 Number of alignments=68 # 1l6rA read from 1l6rA/merged-good-all-a2m # found chain 1l6rA in training set T0341 7 :LKAVLVDLNGTLHIEDA 1l6rA 2 :IRLAAIDVDGNLTDRDR T0341 24 :AVPGAQEALKRLRATSVMVRFVTNT 1l6rA 20 :ISTKAIESIRSAEKKGLTVSLLSGN T0341 52 :TKKDLLERLKKLEFEIS 1l6rA 45 :VIPVVYALKIFLGINGP T0341 117 :LAPEHFHYQLLNQAFRL 1l6rA 78 :KKFFSNEGTNKFLEEMS T0341 135 :LD 1l6rA 95 :KR T0341 144 :HKARYYKRKDG 1l6rA 97 :TSMRSILTNRW T0341 155 :LALGPGPFVTALEYATD 1l6rA 114 :FDIDPEDVDYVRKEAES T0341 178 :GKPEKTFFLEALRDADCAPEEAVMIGDDCR 1l6rA 148 :GEDKAFAVNKLKEMYSLEYDEILVIGDSNN T0341 209 :D 1l6rA 178 :D T0341 211 :DGAQNIGMLGIL 1l6rA 179 :MPMFQLPVRKAC T0341 225 :TGKYKAADEEK 1l6rA 191 :PANATDNIKAV T0341 240 :PYLTCE 1l6rA 202 :SDFVSD Number of specific fragments extracted= 12 number of extra gaps= 0 total=885 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ah5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 2ah5A/merged-good-all-a2m # 2ah5A read from 2ah5A/merged-good-all-a2m # adding 2ah5A to template set # found chain 2ah5A in template set Warning: unaligning (T0341)R4 because first residue in template chain is (2ah5A)M1 Warning: unaligning (T0341)H144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0341)K145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0341 5 :RALKAVLVDLNGTLHI 2ah5A 2 :TSITAIFFDLDGTLVD T0341 24 :AVPGAQEALKRLRAT 2ah5A 18 :SSIGIHNAFTYTFKE T0341 39 :SVM 2ah5A 34 :GVP T0341 50 :KETKKD 2ah5A 37 :SPDAKT T0341 60 :LKKLEF 2ah5A 43 :IRGFMG T0341 73 :FT 2ah5A 49 :PP T0341 79 :ARNLIEQ 2ah5A 51 :LESSFAT T0341 87 :QVRPMLL 2ah5A 58 :CLSKDQI T0341 96 :DRALPEFTGVQTQDPN 2ah5A 65 :SEAVQIYRSYYKAKGI T0341 119 :PEHFHYQLLNQAFRLLLDGAPL 2ah5A 81 :YEAQLFPQIIDLLEELSSSYPL T0341 141 :IAI 2ah5A 104 :ITT T0341 146 :ARYYKRKDGLALG 2ah5A 109 :DTSTAQDMAKNLE T0341 162 :FVTALEYATDTKAMVVGK 2ah5A 122 :IHHFFDGIYGSSPEAPHK T0341 182 :KTFFLEALRDADCAPEEAVMIGDD 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDT T0341 207 :RDDVDGAQNIGMLGILVKTGKYKAADEEKIN 2ah5A 164 :KFDMLGARETGIQKLAITWGFGEQADLLNYQ T0341 240 :PYLTCESFPHAVDH 2ah5A 195 :PDYIAHKPLEVLAY Number of specific fragments extracted= 16 number of extra gaps= 1 total=901 Number of alignments=70 # 2ah5A read from 2ah5A/merged-good-all-a2m # found chain 2ah5A in template set Warning: unaligning (T0341)R4 because first residue in template chain is (2ah5A)M1 Warning: unaligning (T0341)H144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0341)K145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0341 5 :RALKAVLVDLNGTLHIE 2ah5A 2 :TSITAIFFDLDGTLVDS T0341 25 :VPGAQEALKRLRAT 2ah5A 19 :SIGIHNAFTYTFKE T0341 39 :SVM 2ah5A 34 :GVP T0341 50 :KETKKDLLE 2ah5A 37 :SPDAKTIRG T0341 63 :LEF 2ah5A 46 :FMG T0341 77 :TAARNLIEQKQVRPML 2ah5A 49 :PPLESSFATCLSKDQI T0341 96 :DRALPEFTGVQTQDPN 2ah5A 65 :SEAVQIYRSYYKAKGI T0341 119 :PEHFHYQLLNQAFRLLLDGAPL 2ah5A 81 :YEAQLFPQIIDLLEELSSSYPL T0341 141 :IAI 2ah5A 104 :ITT T0341 146 :ARYYKRKDGLALGPGPFVTALEYA 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGIYGS T0341 173 :KAMVVGK 2ah5A 133 :SPEAPHK T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKF T0341 209 :DVDGAQNIGMLGILVKTGKYKAADEEKIN 2ah5A 166 :DMLGARETGIQKLAITWGFGEQADLLNYQ T0341 240 :PYLTCESFPHAVDH 2ah5A 195 :PDYIAHKPLEVLAY Number of specific fragments extracted= 14 number of extra gaps= 1 total=915 Number of alignments=71 # 2ah5A read from 2ah5A/merged-good-all-a2m # found chain 2ah5A in template set Warning: unaligning (T0341)H144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0341)K145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0341 5 :RALKAVLVDLNGTLHIEDAAVPGAQEALKRLRATSVM 2ah5A 2 :TSITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVPSP T0341 49 :TKETKKD 2ah5A 39 :DAKTIRG T0341 56 :LLERLKK 2ah5A 51 :LESSFAT T0341 66 :EISEDEIFTSLTAARNLIE 2ah5A 58 :CLSKDQISEAVQIYRSYYK T0341 113 :VVIGLAPEHFHYQLLNQAFRL 2ah5A 77 :AKGIYEAQLFPQIIDLLEELS T0341 135 :LDGAPLIAI 2ah5A 98 :SSYPLYITT T0341 146 :ARYYKRKDGLALGPGPFVTAL 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGI T0341 170 :TDTKAMVVGK 2ah5A 130 :YGSSPEAPHK T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKF T0341 209 :DVDGAQNIGMLGILVKTGKYKAADEEK 2ah5A 166 :DMLGARETGIQKLAITWGFGEQADLLN T0341 238 :PPPYLTCESFPHAVD 2ah5A 193 :YQPDYIAHKPLEVLA Number of specific fragments extracted= 11 number of extra gaps= 1 total=926 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zs9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 1zs9A/merged-good-all-a2m # 1zs9A read from 1zs9A/merged-good-all-a2m # adding 1zs9A to template set # found chain 1zs9A in template set Warning: unaligning (T0341)Q87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0341)R89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0341 2 :AARRALKAVLVDLNGTLHIED 1zs9A 5 :SVPAEVTVILLDIEGTTTPIA T0341 23 :AAVPGAQEAL 1zs9A 30 :ILFPYIEENV T0341 33 :KRLRATSVM 1zs9A 41 :EYLQTHWEE T0341 51 :ETKKDLLERLKKL 1zs9A 50 :EECQQDVSLLRKQ T0341 64 :EFEIS 1zs9A 74 :PIPAA T0341 69 :EDEIFTSLTAARNLIEQK 1zs9A 83 :VDDLQQMIQAVVDNVCWQ T0341 90 :PMLL 1zs9A 107 :TTAL T0341 96 :DRALPEFTGVQTQDPN 1zs9A 111 :KQLQGHMWRAAFTAGR T0341 119 :PEHFHYQLLNQAFRLLLD 1zs9A 127 :MKAEFFADVVPAVRKWRE T0341 137 :GAPL 1zs9A 146 :GMKV T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYATDTKA 1zs9A 151 :IYSSGSVEAQKLLFGHSTEGDILELVDGHFDTKI T0341 177 :VGKPEKTFFLEALRDADCAPEEAVMIGDD 1zs9A 185 :GHKVESESYRKIADSIGCSTNNILFLTDV T0341 207 :RDDVDGAQNIGMLGILVKTGKY 1zs9A 214 :TREASAAEEADVHVAVVVRPGN T0341 229 :KAADEEKIN 1zs9A 239 :TDDEKTYYS T0341 243 :TCESFPHA 1zs9A 248 :LITSFSEL Number of specific fragments extracted= 15 number of extra gaps= 0 total=941 Number of alignments=73 # 1zs9A read from 1zs9A/merged-good-all-a2m # found chain 1zs9A in template set Warning: unaligning (T0341)D96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0341)A98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0341 2 :AARRALKAVLVDLNGTLHIEDA 1zs9A 5 :SVPAEVTVILLDIEGTTTPIAF T0341 24 :AVPGAQEALKRLRAT 1zs9A 48 :EEEECQQDVSLLRKQ T0341 45 :VTNTTKETKKDLLERLK 1zs9A 78 :ASGNGVDDLQQMIQAVV T0341 77 :TAARNLIE 1zs9A 95 :DNVCWQMS T0341 99 :LPEFTGVQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLD 1zs9A 107 :TTALKQLQGHMWRAAFTAGRMKAEFFADVVPAVRKWRE T0341 137 :GAPL 1zs9A 146 :GMKV T0341 141 :IAIHKARYYKRKDGLAL 1zs9A 151 :IYSSGSVEAQKLLFGHS T0341 158 :GPGPFVTALEYA 1zs9A 171 :DILELVDGHFDT T0341 173 :KAM 1zs9A 183 :KIG T0341 178 :GKPEKTFFLEALRDADCAPEEAVMIGDDCR 1zs9A 186 :HKVESESYRKIADSIGCSTNNILFLTDVTR T0341 209 :DVDGAQNIGMLGILVKTGKYKAADEEK 1zs9A 216 :EASAAEEADVHVAVVVRPGNAGLTDDE T0341 236 :IN 1zs9A 246 :YS T0341 243 :TCESFPHA 1zs9A 248 :LITSFSEL Number of specific fragments extracted= 13 number of extra gaps= 0 total=954 Number of alignments=74 # 1zs9A read from 1zs9A/merged-good-all-a2m # found chain 1zs9A in template set Warning: unaligning (T0341)P90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0341)D96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0341 2 :AARRALKAVLVDLNGTLHIEDA 1zs9A 5 :SVPAEVTVILLDIEGTTTPIAF T0341 24 :AVPGAQEALKRLRA 1zs9A 31 :LFPYIEENVKEYLQ T0341 38 :TS 1zs9A 47 :WE T0341 46 :TNTTKETKKDLLERLKKLE 1zs9A 49 :EEECQQDVSLLRKQAEEDA T0341 66 :EISEDEIFTSLTAARNLIEQKQVR 1zs9A 80 :GNGVDDLQQMIQAVVDNVCWQMSL T0341 97 :RALPEFTGVQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYY 1zs9A 107 :TTALKQLQGHMWRAAFTAGRMKAEFFADVVPAVRKWREAGMKVYIYSSGSVEA T0341 163 :VTALEYATD 1zs9A 160 :QKLLFGHST T0341 172 :TKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1zs9A 180 :FDTKIGHKVESESYRKIADSIGCSTNNILFLTDVTR T0341 209 :DVDGAQNIGMLGILVKTGKYKAADEE 1zs9A 216 :EASAAEEADVHVAVVVRPGNAGLTDD T0341 242 :LTCESFPH 1zs9A 247 :SLITSFSE Number of specific fragments extracted= 10 number of extra gaps= 0 total=964 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x42A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 1x42A/merged-good-all-a2m # 1x42A read from 1x42A/merged-good-all-a2m # adding 1x42A to template set # found chain 1x42A in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1x42A)M1 Warning: unaligning (T0341)L258 because last residue in template chain is (1x42A)N230 T0341 7 :LKAVLVDLNGTLHI 1x42A 2 :IRAVFFDFVGTLLS T0341 22 :DAAVPGAQE 1x42A 16 :VEGEAKTHL T0341 33 :KRLRAT 1x42A 25 :KIMEEV T0341 39 :SVM 1x42A 33 :DYP T0341 51 :ETKKDLLERLKKL 1x42A 36 :LNPKTLLDEYEKL T0341 64 :EFEIS 1x42A 58 :GKPYR T0341 72 :IFTSLTAARNLIEQKQVRPM 1x42A 65 :RDIEEEVMRKLAEKYGFKYP T0341 96 :DRALPEFTGVQT 1x42A 85 :ENFWEIHLRMHQ T0341 119 :PEHFHYQLLNQAFRLLLDGAPL 1x42A 97 :RYGELYPEVVEVLKSLKGKYHV T0341 141 :IAIHKARYYKRKDGLALG 1x42A 120 :MITDSDTEYLMAHLDALG T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEK 1x42A 138 :IKDLFDSITTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNPVKDCGGSKNLGMTSILLDRKGEKREFWDK T0341 240 :PYLTCESFPHAVDHILQH 1x42A 212 :CDFIVSDLREVIKIVDEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=976 Number of alignments=76 # 1x42A read from 1x42A/merged-good-all-a2m # found chain 1x42A in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1x42A)M1 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEALKRLR 1x42A 2 :IRAVFFDFVGTLLSVEGEAKTHLKIMEEVL T0341 39 :SV 1x42A 33 :DY T0341 50 :KETKKDLLERLK 1x42A 35 :PLNPKTLLDEYE T0341 77 :TAARNLIEQKQVRPMLLLDDRALPEFTGVQ 1x42A 47 :KLTREAFSNYAGKPYRPIRDIEEEVMRKLA T0341 107 :TQDPNAVVIGLA 1x42A 84 :PENFWEIHLRMH T0341 119 :PEHFHYQLLNQAFRLLLDGAPL 1x42A 97 :RYGELYPEVVEVLKSLKGKYHV T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYA 1x42A 120 :MITDSDTEYLMAHLDALGIKDLFDSITTS T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEK 1x42A 149 :EEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNPVKDCGGSKNLGMTSILLDRKGEKREFWDK T0341 240 :PYLTCESFPHAVDHILQH 1x42A 212 :CDFIVSDLREVIKIVDEL Number of specific fragments extracted= 9 number of extra gaps= 0 total=985 Number of alignments=77 # 1x42A read from 1x42A/merged-good-all-a2m # found chain 1x42A in template set Warning: unaligning (T0341)L258 because last residue in template chain is (1x42A)N230 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEALKRLRAT 1x42A 2 :IRAVFFDFVGTLLSVEGEAKTHLKIMEEVLGD T0341 49 :TKETKKDLLERLKK 1x42A 34 :YPLNPKTLLDEYEK T0341 63 :LEFEISE 1x42A 57 :AGKPYRP T0341 75 :SLTAARNLIEQ 1x42A 64 :IRDIEEEVMRK T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAFRL 1x42A 85 :ENFWEIHLRMHQRYGELYPEVVEVLKSLK T0341 135 :LDGAPLIAIHKARYYKRKDGLALGPGPFVTAL 1x42A 114 :GKYHVGMITDSDTEYLMAHLDALGIKDLFDSI T0341 170 :TDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEK 1x42A 146 :TTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNPVKDCGGSKNLGMTSILLDRKGEKREFWDK T0341 240 :PYLTCESFPHAVDHILQH 1x42A 212 :CDFIVSDLREVIKIVDEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=993 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b0cA expands to /projects/compbio/data/pdb/2b0c.pdb.gz 2b0cA:# T0341 read from 2b0cA/merged-good-all-a2m # 2b0cA read from 2b0cA/merged-good-all-a2m # adding 2b0cA to template set # found chain 2b0cA in template set T0341 9 :AVLVDLNGTLHIED 2b0cA 9 :LYIFDLGNVIVDID T0341 25 :VPGAQ 2b0cA 23 :FNRVL T0341 33 :KRLRAT 2b0cA 28 :GAWSDL T0341 41 :M 2b0cA 35 :R T0341 51 :ETKKDLLER 2b0cA 36 :IPLASLKKS T0341 65 :FEIS 2b0cA 45 :FHMG T0341 69 :EDEIFTSLTAARNLIEQKQVRPML 2b0cA 55 :ERGEISDEAFAEALCHEMALPLSY T0341 96 :DRALPEFTG 2b0cA 79 :EQFSHGWQA T0341 119 :PEHFHYQLLNQAFRLLLD 2b0cA 88 :VFVALRPEVIAIMHKLRE T0341 137 :GAPL 2b0cA 107 :GHRV T0341 141 :IAIHKARYYKRKDGLALG 2b0cA 112 :VLSNTNRLHTTFWPEEYP T0341 161 :PFVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 2b0cA 130 :EIRDAADHIYLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDN T0341 207 :RDDVDGAQNIGMLG 2b0cA 175 :ADNIEGANQLGITS T0341 242 :LTCESFPHAVDHIL 2b0cA 189 :ILVKDKTTIPDYFA Number of specific fragments extracted= 14 number of extra gaps= 0 total=1007 Number of alignments=79 # 2b0cA read from 2b0cA/merged-good-all-a2m # found chain 2b0cA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (2b0cA)A6 T0341 7 :LKAVLVDLNGTLHIEDA 2b0cA 7 :KMLYIFDLGNVIVDIDF T0341 26 :PGAQ 2b0cA 24 :NRVL T0341 33 :KRLRAT 2b0cA 28 :GAWSDL T0341 50 :KETKKDLLERLKKLEFEISEDEIFTSL 2b0cA 35 :RIPLASLKKSFHMGEAFHQHERGEISD T0341 77 :TAARNLIEQKQVRPML 2b0cA 63 :AFAEALCHEMALPLSY T0341 96 :DRALPEFTG 2b0cA 79 :EQFSHGWQA T0341 119 :PEHFHYQLLNQAFRLLLD 2b0cA 88 :VFVALRPEVIAIMHKLRE T0341 137 :GAPL 2b0cA 107 :GHRV T0341 141 :IAIHKARYYKRKDGLAL 2b0cA 112 :VLSNTNRLHTTFWPEEY T0341 158 :GPGPFVTALEYA 2b0cA 130 :EIRDAADHIYLS T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 2b0cA 142 :QDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNAD T0341 209 :DVDGAQNIGMLGILV 2b0cA 177 :NIEGANQLGITSILV T0341 245 :ESFPHAVDHI 2b0cA 192 :KDKTTIPDYF Number of specific fragments extracted= 13 number of extra gaps= 0 total=1020 Number of alignments=80 # 2b0cA read from 2b0cA/merged-good-all-a2m # found chain 2b0cA in template set T0341 9 :AVLVDLNGTLHIED 2b0cA 9 :LYIFDLGNVIVDID T0341 25 :VPGAQEALKRL 2b0cA 23 :FNRVLGAWSDL T0341 36 :RATSVM 2b0cA 54 :HERGEI T0341 52 :TKKDLLERLKK 2b0cA 60 :SDEAFAEALCH T0341 63 :LEFEISEDE 2b0cA 72 :MALPLSYEQ T0341 79 :ARNLIEQ 2b0cA 81 :FSHGWQA T0341 117 :LAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKRKDG 2b0cA 88 :VFVALRPEVIAIMHKLREQGHRVVVLSNTNRLHTTFWP T0341 155 :LALGPGPFVTAL 2b0cA 127 :EYPEIRDAADHI T0341 170 :TDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 2b0cA 139 :YLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNAD T0341 209 :DVDGAQNIGMLG 2b0cA 177 :NIEGANQLGITS T0341 242 :LTCESFPHAVDHI 2b0cA 189 :ILVKDKTTIPDYF Number of specific fragments extracted= 11 number of extra gaps= 0 total=1031 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0341 read from 1rkqA/merged-good-all-a2m # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set Warning: unaligning (T0341)R4 because first residue in template chain is (1rkqA)S1 Warning: unaligning (T0341)L133 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rkqA)S101 Warning: unaligning (T0341)L134 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rkqA)S101 T0341 5 :RALKAVLVDLNGTLHI 1rkqA 2 :LAIKLIAIDMDGTLLL T0341 21 :EDAAVPGAQEALKRLRATSVMVRFVTN 1rkqA 19 :DHTISPAVKNAIAAARARGVNVVLTTG T0341 51 :ETK 1rkqA 46 :RPY T0341 96 :DRALPEFTGVQTQDP 1rkqA 49 :AGVHNYLKELHMEQP T0341 119 :PEHFHYQLLNQAFR 1rkqA 86 :QTALSYDDYRFLEK T0341 135 :LD 1rkqA 102 :RE T0341 137 :G 1rkqA 105 :G T0341 139 :PLIAIHKARYYKRKD 1rkqA 115 :TLYTANRDISYYTVH T0341 154 :GLALGPGP 1rkqA 143 :AEKMDPNT T0341 164 :TALEYATDT 1rkqA 162 :AILDQAIAR T0341 173 :KAM 1rkqA 173 :QEV T0341 177 :VGKPEKTFFLEALRDADCAPEEAVMIGDD 1rkqA 194 :KRVNKGTGVKSLADVLGIKPEEIMAIGDQ T0341 207 :RDDVDGAQNIGM 1rkqA 223 :ENDIAMIEYAGV T0341 222 :LVKTGKYKAADEEK 1rkqA 235 :GVAVDNAIPSVKEV T0341 240 :PYLTCESFPH 1rkqA 249 :ANFVTKSNLE Number of specific fragments extracted= 15 number of extra gaps= 1 total=1046 Number of alignments=82 # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set Warning: unaligning (T0341)L133 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rkqA)S101 Warning: unaligning (T0341)L134 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rkqA)S101 T0341 5 :RALKAVLVDLNGTLHIEDAAV 1rkqA 2 :LAIKLIAIDMDGTLLLPDHTI T0341 26 :PGAQEALKRLRATSVMVRFVTNTTKETKKDLLERL 1rkqA 24 :PAVKNAIAAARARGVNVVLTTGRPYAGVHNYLKEL T0341 61 :KKLEFEISEDEIFTSL 1rkqA 62 :QPGDYCITYNGALVQK T0341 85 :QKQVRPML 1rkqA 78 :AADGSTVA T0341 119 :PEHFHYQLLNQAFR 1rkqA 86 :QTALSYDDYRFLEK T0341 135 :LD 1rkqA 102 :RE T0341 137 :GAP 1rkqA 105 :GSH T0341 149 :YKRKDGLALG 1rkqA 163 :ILDQAIARIP T0341 168 :YA 1rkqA 190 :EI T0341 173 :KAMVVGK 1rkqA 192 :LDKRVNK T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1rkqA 199 :GTGVKSLADVLGIKPEEIMAIGDQEN T0341 209 :DVDGAQNIG 1rkqA 225 :DIAMIEYAG T0341 219 :LGILV 1rkqA 234 :VGVAV T0341 226 :GKYKAADEEK 1rkqA 239 :DNAIPSVKEV T0341 240 :PYLTCESFPH 1rkqA 249 :ANFVTKSNLE T0341 250 :AVDHILQHL 1rkqA 261 :VAFAIEKYV Number of specific fragments extracted= 16 number of extra gaps= 1 total=1062 Number of alignments=83 # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set Warning: unaligning (T0341)F131 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rkqA)S101 Warning: unaligning (T0341)R132 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rkqA)S101 T0341 6 :ALKAVLVDLNGTLHIEDA 1rkqA 3 :AIKLIAIDMDGTLLLPDH T0341 24 :AVPGAQEALKRLRATSVMVRFVTNTTKET 1rkqA 22 :ISPAVKNAIAAARARGVNVVLTTGRPYAG T0341 56 :LLERLKKLEFEISE 1rkqA 51 :VHNYLKELHMEQPG T0341 116 :GLAPEHFHYQLLNQA 1rkqA 85 :AQTALSYDDYRFLEK T0341 133 :LLLD 1rkqA 102 :REVG T0341 137 :GAPLIAIHKARY 1rkqA 113 :RTTLYTANRDIS T0341 161 :PFVTALEYATDTKAMVVG 1rkqA 125 :YYTVHESFVATIPLVFCE T0341 180 :PEKTFFLEALRDA 1rkqA 159 :DEPAILDQAIARI T0341 193 :DCAPEEAVMIGDDCR 1rkqA 210 :GIKPEEIMAIGDQEN T0341 209 :DVDGAQNIGM 1rkqA 225 :DIAMIEYAGV T0341 222 :LVKTGKYKAADEEK 1rkqA 235 :GVAVDNAIPSVKEV T0341 240 :PYLTCESFPH 1rkqA 249 :ANFVTKSNLE Number of specific fragments extracted= 12 number of extra gaps= 1 total=1074 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1swvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1swvA expands to /projects/compbio/data/pdb/1swv.pdb.gz 1swvA:# T0341 read from 1swvA/merged-good-all-a2m # 1swvA read from 1swvA/merged-good-all-a2m # adding 1swvA to template set # found chain 1swvA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1swvA)K5 T0341 7 :LKAVLVDLNGTLHI 1swvA 6 :IEAVIFAWAGTTVD T0341 21 :EDAAVPGAQ 1swvA 22 :CFAPLEVFM T0341 33 :KRLRATSVM 1swvA 31 :EIFHKRGVA T0341 51 :ETKKD 1swvA 40 :ITAEE T0341 56 :LLERLKKL 1swvA 56 :HVRALTEM T0341 76 :LTAARNLIEQKQVRPMLLLDDRALPEFTGVQTQDPN 1swvA 64 :PRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILP T0341 119 :PEHFHYQLLNQAFRLLLD 1swvA 100 :RYASPINGVKEVIASLRE T0341 137 :GAPL 1swvA 119 :GIKI T0341 141 :IAIHKARYYK 1swvA 124 :STTGYTREMM T0341 151 :RKDGLALGPGPF 1swvA 139 :EAALQGYKPDFL T0341 170 :TDTKAMVVGKPEKTFFLEALRDADC 1swvA 151 :VTPDDVPAGRPYPWMCYKNAMELGV T0341 195 :APEEAVMIGDD 1swvA 177 :PMNHMIKVGDT T0341 207 :RDDVDGAQNIGMLGILVKT 1swvA 188 :VSDMKEGRNAGMWTVGVIL T0341 227 :KYKAADEEKI 1swvA 212 :GLTEEEVENM T0341 240 :PYLTCESFPHAVDHILQHL 1swvA 242 :AHFTIETMQELESVMEHIE Number of specific fragments extracted= 15 number of extra gaps= 0 total=1089 Number of alignments=85 # 1swvA read from 1swvA/merged-good-all-a2m # found chain 1swvA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1swvA)K5 T0341 7 :LKAVLVDLNGTLHIED 1swvA 6 :IEAVIFAWAGTTVDYG T0341 23 :AAVPGAQE 1swvA 24 :APLEVFME T0341 34 :RLRATSVMV 1swvA 32 :IFHKRGVAI T0341 50 :KETK 1swvA 41 :TAEE T0341 54 :KDLLERLKKLE 1swvA 54 :IDHVRALTEMP T0341 77 :TAARNLIEQKQVRPMLLLDDRALPEFTGVQTQDPN 1swvA 65 :RIASEWNRVFRQLPTEADIQEMYEEFEEILFAILP T0341 119 :PEHFHYQLLNQAFRLLLD 1swvA 100 :RYASPINGVKEVIASLRE T0341 137 :GAPL 1swvA 119 :GIKI T0341 141 :IAIHKARYYKRKDGLAL 1swvA 124 :STTGYTREMMDIVAKEA T0341 158 :GPG 1swvA 144 :GYK T0341 163 :VTALEYA 1swvA 147 :PDFLVTP T0341 173 :KAMVVGKPEKTFFLEALRDADC 1swvA 154 :DDVPAGRPYPWMCYKNAMELGV T0341 195 :APEEAVMIGDDCR 1swvA 177 :PMNHMIKVGDTVS T0341 209 :DVDGAQNIGMLGILVKTG 1swvA 190 :DMKEGRNAGMWTVGVILG T0341 227 :KYKAADEEKI 1swvA 212 :GLTEEEVENM T0341 240 :PYLTCESFPHAVDHILQHL 1swvA 242 :AHFTIETMQELESVMEHIE Number of specific fragments extracted= 16 number of extra gaps= 0 total=1105 Number of alignments=86 # 1swvA read from 1swvA/merged-good-all-a2m # found chain 1swvA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1swvA)K5 T0341 7 :LKAVLVDLNGTLHIED 1swvA 6 :IEAVIFAWAGTTVDYG T0341 49 :TKETKKDLLERLKKLEFEISEDEIF 1swvA 22 :CFAPLEVFMEIFHKRGVAITAEEAR T0341 74 :TSLTAARNLIEQKQV 1swvA 51 :LLKIDHVRALTEMPR T0341 89 :RPMLLLDDRALPEFTGVQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKA 1swvA 72 :RVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYT T0341 160 :GPFVTALEYATD 1swvA 130 :REMMDIVAKEAA T0341 172 :TKAMVVGKPEKTFFLEALRDADC 1swvA 153 :PDDVPAGRPYPWMCYKNAMELGV T0341 195 :APEEAVMIGDDCR 1swvA 177 :PMNHMIKVGDTVS T0341 209 :DVDGAQNIGMLGILVKTG 1swvA 190 :DMKEGRNAGMWTVGVILG T0341 227 :KYKAADEE 1swvA 212 :GLTEEEVE T0341 237 :NPPPYLTCESFPHAVDHIL 1swvA 239 :ENGAHFTIETMQELESVME Number of specific fragments extracted= 10 number of extra gaps= 0 total=1115 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jud/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jud expands to /projects/compbio/data/pdb/1jud.pdb.gz 1jud:Warning: there is no chain 1jud will retry with 1judA # T0341 read from 1jud/merged-good-all-a2m # 1jud read from 1jud/merged-good-all-a2m # adding 1jud to template set # found chain 1jud in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1jud)Y3 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEA 1jud 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0341 32 :LKRLRAT 1jud 37 :SALWRQK T0341 56 :LLERLKKLEF 1jud 44 :QLEYTWLRSL T0341 69 :EDEIFTSLTAARNLIEQK 1jud 54 :MNRYVNFQQATEDALRFT T0341 87 :QVRPM 1jud 76 :GLDLD T0341 96 :DRALPEFTGVQ 1jud 81 :ARTRSTLCDAY T0341 119 :PEHFHYQLLNQAFRLLLD 1jud 92 :LRLAPFSEVPDSLRELKR T0341 137 :GAPL 1jud 111 :GLKL T0341 141 :IAIHKARYYKRKDGLALG 1jud 116 :ILSNGSPQSIDAVVSHAG T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1jud 134 :LRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSN T0341 207 :RDDVDGAQNIGMLGILVKT 1jud 178 :AWDATGARYFGFPTCWINR T0341 229 :KAADEEKINPPPYLTCESFPHAVD 1jud 197 :TGNVFEEMGQTPDWEVTSLRAVVE Number of specific fragments extracted= 12 number of extra gaps= 0 total=1127 Number of alignments=88 # 1jud read from 1jud/merged-good-all-a2m # found chain 1jud in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1jud)Y3 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEA 1jud 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0341 32 :LKRLRAT 1jud 37 :SALWRQK T0341 52 :TKKDLLERLKKLEFE 1jud 44 :QLEYTWLRSLMNRYV T0341 70 :DEIFTSLTAARNLIEQKQVRPM 1jud 59 :NFQQATEDALRFTCRHLGLDLD T0341 96 :DRALPEFTGVQ 1jud 81 :ARTRSTLCDAY T0341 119 :PEHFHYQLLNQAFRLLLD 1jud 92 :LRLAPFSEVPDSLRELKR T0341 137 :GAPL 1jud 111 :GLKL T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYA 1jud 116 :ILSNGSPQSIDAVVSHAGLRDGFDHLLSV T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1jud 145 :DPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAW T0341 209 :DVDGAQNIGMLGILVKT 1jud 180 :DATGARYFGFPTCWINR T0341 229 :KAADEEKINPPPYLTCESFPHAVD 1jud 197 :TGNVFEEMGQTPDWEVTSLRAVVE Number of specific fragments extracted= 11 number of extra gaps= 0 total=1138 Number of alignments=89 # 1jud read from 1jud/merged-good-all-a2m # found chain 1jud in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1jud)Y3 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEA 1jud 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0341 49 :TKETKKDLLERLKKL 1jud 29 :FPGRGREISALWRQK T0341 75 :SLTAARNLIEQKQVRPMLLLDDRALPEFTG 1jud 44 :QLEYTWLRSLMNRYVNFQQATEDALRFTCR T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTAL 1jud 80 :DARTRSTLCDAYLRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHAGLRDGFDHL T0341 170 :TDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1jud 142 :LSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAW T0341 209 :DVDGAQNIGMLGILVKTGKYKAAD 1jud 180 :DATGARYFGFPTCWINRTGNVFEE T0341 236 :INPPPYLTCESFPHAVD 1jud 204 :MGQTPDWEVTSLRAVVE Number of specific fragments extracted= 7 number of extra gaps= 0 total=1145 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 1vjrA/merged-good-all-a2m # 1vjrA read from 1vjrA/merged-good-all-a2m # adding 1vjrA to template set # found chain 1vjrA in template set Warning: unaligning (T0341)A2 because of BadResidue code BAD_PEPTIDE at template residue (1vjrA)H0 T0341 3 :ARRALKAVLVDLNGTLHIEDAAVPGAQEALKRLRATSVMVRFVTNTTKETKKDLLERLKKLEFEISEDEIFTSLTAAR 1vjrA 1 :VLDKIELFILDMDGTFYLDDSLLPGSLEFLETLKEKNKRFVFFTNNSSLGAQDYVRKLRNMGVDVPDDAVVTSGEITA T0341 81 :NLIEQKQVRPMLLLD 1vjrA 80 :HMLKRFGRCRIFLLG T0341 96 :DRALPEFTGVQT 1vjrA 96 :PQLKKVFEAYGH T0341 108 :QDPNAVVIGL 1vjrA 112 :ENPDFVVLGF T0341 119 :PEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTK 1vjrA 122 :DKTLTYERLKKACILLRKGKFYIATHPDINCPSKEGPVPDAGSIMAAIEASTGRK T0341 174 :AMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPHAVDHI 1vjrA 178 :DLIAGKPNPLVVDVISEKFGVPKERMAMVGDRLYTDVKLGKNAGIVSILVLTGETTPEDLERAETKPDFVFKNLGELAKAV Number of specific fragments extracted= 6 number of extra gaps= 1 total=1151 Number of alignments=91 # 1vjrA read from 1vjrA/merged-good-all-a2m # found chain 1vjrA in template set T0341 3 :ARRALKAVLVDLNGTLHIEDAAVPGAQEALKRLRATSVMVRFVTNTTKETKKDLLERLKKLEFEISEDEIFTSL 1vjrA 1 :VLDKIELFILDMDGTFYLDDSLLPGSLEFLETLKEKNKRFVFFTNNSSLGAQDYVRKLRNMGVDVPDDAVVTSG T0341 77 :TAARNLIEQKQVRPMLLLD 1vjrA 76 :ITAEHMLKRFGRCRIFLLG T0341 96 :DRALPEFTGVQ 1vjrA 96 :PQLKKVFEAYG T0341 107 :TQDPNAVVIGL 1vjrA 111 :EENPDFVVLGF T0341 119 :PEHFHYQLLNQAFRLLLDGAPLIAIHKARY 1vjrA 122 :DKTLTYERLKKACILLRKGKFYIATHPDIN T0341 149 :YKRKDGLALGPG 1vjrA 165 :IMAAIEASTGRK T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPHAVDHI 1vjrA 177 :PDLIAGKPNPLVVDVISEKFGVPKERMAMVGDRLYTDVKLGKNAGIVSILVLTGETTPEDLERAETKPDFVFKNLGELAKAV Number of specific fragments extracted= 7 number of extra gaps= 0 total=1158 Number of alignments=92 # 1vjrA read from 1vjrA/merged-good-all-a2m # found chain 1vjrA in template set Warning: unaligning (T0341)A2 because of BadResidue code BAD_PEPTIDE at template residue (1vjrA)H0 T0341 3 :ARRALKAVLVDLNGTLHIEDAAVPGAQEALKRLRATSVMVRFVTNTTKETKKDLLERLKKLEFEISEDEIFTSLTAARNLIEQKQVRPMLLLDDRALPEFTG 1vjrA 1 :VLDKIELFILDMDGTFYLDDSLLPGSLEFLETLKEKNKRFVFFTNNSSLGAQDYVRKLRNMGVDVPDDAVVTSGEITAEHMLKRFGRCRIFLLGTPQLKKVF T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQ 1vjrA 110 :DEENPDFVVLGFDKTLTYERLKKAC T0341 132 :RLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTK 1vjrA 135 :ILLRKGKFYIATHPDINCPSKEGPVPDAGSIMAAIEASTGRK T0341 174 :AMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCRDDVDGAQNIGMLGILVKTGKYKAADEEKINPPPYLTCESFPHAVDHI 1vjrA 178 :DLIAGKPNPLVVDVISEKFGVPKERMAMVGDRLYTDVKLGKNAGIVSILVLTGETTPEDLERAETKPDFVFKNLGELAKAV Number of specific fragments extracted= 4 number of extra gaps= 1 total=1162 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zrn/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zrn expands to /projects/compbio/data/pdb/1zrn.pdb.gz 1zrn:Warning: there is no chain 1zrn will retry with 1zrnA # T0341 read from 1zrn/merged-good-all-a2m # 1zrn read from 1zrn/merged-good-all-a2m # adding 1zrn to template set # found chain 1zrn in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1zrn)Y3 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEA 1zrn 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0341 32 :LKRLRAT 1zrn 37 :SALWRQK T0341 52 :TKKDLLERLKKLEF 1zrn 44 :QLEYTWLRSLMNRY T0341 69 :EDEIFTSLTAARNLIEQKQVRPM 1zrn 58 :VNFQQATEDALRFTCRHLGLDLD T0341 96 :DRALPEFTGVQ 1zrn 81 :ARTRSTLCDAY T0341 119 :PEHFHYQLLNQAFRLLLD 1zrn 92 :LRLAPFSEVPDSLRELKR T0341 137 :GAPL 1zrn 111 :GLKL T0341 141 :IAIHKARYYKRKDGLALG 1zrn 116 :ILSNGSPQSIDAVVSHAG T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1zrn 134 :LRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASN T0341 207 :RDDVDGAQNIGMLGILVKT 1zrn 178 :AWDATGARYFGFPTCWINR T0341 229 :KAADEEKINPPPYLTCESFPHAVD 1zrn 197 :TGNVFEEMGQTPDWEVTSLRAVVE Number of specific fragments extracted= 11 number of extra gaps= 0 total=1173 Number of alignments=94 # 1zrn read from 1zrn/merged-good-all-a2m # found chain 1zrn in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1zrn)Y3 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEA 1zrn 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0341 32 :LKRLRAT 1zrn 37 :SALWRQK T0341 52 :TKKDLLERLKKLEFE 1zrn 44 :QLEYTWLRSLMNRYV T0341 70 :DEIFTSLTAARNLIEQKQVRPM 1zrn 59 :NFQQATEDALRFTCRHLGLDLD T0341 96 :DRALPEFTGVQ 1zrn 81 :ARTRSTLCDAY T0341 119 :PEHFHYQLLNQAFRLLLD 1zrn 92 :LRLAPFSEVPDSLRELKR T0341 137 :GAPL 1zrn 111 :GLKL T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYA 1zrn 116 :ILSNGSPQSIDAVVSHAGLRDGFDHLLSV T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1zrn 145 :DPVQVYKPDNRVYELAEQALGLDRSAILFVASNAW T0341 209 :DVDGAQNIGMLGILVKT 1zrn 180 :DATGARYFGFPTCWINR T0341 229 :KAADEEKINPPPYLTCESFPHAVD 1zrn 197 :TGNVFEEMGQTPDWEVTSLRAVVE Number of specific fragments extracted= 11 number of extra gaps= 0 total=1184 Number of alignments=95 # 1zrn read from 1zrn/merged-good-all-a2m # found chain 1zrn in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1zrn)Y3 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEA 1zrn 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0341 49 :TKETKKDLLERLKKL 1zrn 29 :FPGRGREISALWRQK T0341 75 :SLTAARNLIEQKQVRPMLLLDDRALPEFTG 1zrn 44 :QLEYTWLRSLMNRYVNFQQATEDALRFTCR T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTAL 1zrn 80 :DARTRSTLCDAYLRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHAGLRDGFDHL T0341 170 :TDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1zrn 142 :LSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAW T0341 209 :DVDGAQNIGMLGILVKTGKYKAAD 1zrn 180 :DATGARYFGFPTCWINRTGNVFEE T0341 236 :INPPPYLTCESFPHAVD 1zrn 204 :MGQTPDWEVTSLRAVVE Number of specific fragments extracted= 7 number of extra gaps= 0 total=1191 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pw5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0341/1pw5A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0341/1pw5A/merged-good-all-a2m.gz for input Trying 1pw5A/merged-good-all-a2m Error: Couldn't open file 1pw5A/merged-good-all-a2m or 1pw5A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u7pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u7pA expands to /projects/compbio/data/pdb/1u7p.pdb.gz 1u7pA:# T0341 read from 1u7pA/merged-good-all-a2m # 1u7pA read from 1u7pA/merged-good-all-a2m # adding 1u7pA to template set # found chain 1u7pA in template set Warning: unaligning (T0341)A3 because first residue in template chain is (1u7pA)M1 T0341 4 :RRALKAVLVDLNGTLHIEDAA 1u7pA 2 :TRLPKLAVFDLDYTLWPFWVD T0341 38 :TSVM 1u7pA 23 :THVD T0341 63 :LEFEISEDEIF 1u7pA 27 :PPFHKSSDGTV T0341 104 :GVQ 1u7pA 40 :RRG T0341 119 :PEHFHYQLLNQAFRLLLD 1u7pA 43 :QNIQLYPEVPEVLGRLQS T0341 137 :GAPL 1u7pA 62 :GVPV T0341 141 :IAIH 1u7pA 67 :AASR T0341 145 :KARYYKRKDGLALG 1u7pA 72 :SEIQGANQLLELFD T0341 162 :FVTALEYATDTK 1u7pA 86 :LGKYFIQREIYP T0341 178 :G 1u7pA 98 :G T0341 182 :KTFFLEALRDADCAPEEAVMIGDD 1u7pA 101 :VTHFERLHHKTGVPFSQMVFFDDE T0341 207 :RDDVDGAQNIGMLGILV 1u7pA 125 :NRNIIDVGRLGVTCIHI T0341 225 :TGKYKAADEEK 1u7pA 142 :RDGMSLQTLTQ T0341 250 :AVDHILQHL 1u7pA 153 :GLETFAKAQ Number of specific fragments extracted= 14 number of extra gaps= 0 total=1205 Number of alignments=97 # 1u7pA read from 1u7pA/merged-good-all-a2m # found chain 1u7pA in template set T0341 4 :RRALKAVLVDLNGTLHIEDAA 1u7pA 2 :TRLPKLAVFDLDYTLWPFWVD T0341 38 :TSV 1u7pA 23 :THV T0341 62 :KLEFEISEDEIFTSL 1u7pA 26 :DPPFHKSSDGTVRDR T0341 118 :APEHFHYQLLNQAFRLLLD 1u7pA 42 :GQNIQLYPEVPEVLGRLQS T0341 137 :GAPL 1u7pA 62 :GVPV T0341 141 :IAIH 1u7pA 67 :AASR T0341 145 :KARYYKRKDGLALGPGPFVTALEYATD 1u7pA 72 :SEIQGANQLLELFDLGKYFIQREIYPG T0341 178 :GK 1u7pA 99 :SK T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1u7pA 101 :VTHFERLHHKTGVPFSQMVFFDDENR T0341 209 :DVDGAQNIGMLGILVKT 1u7pA 127 :NIIDVGRLGVTCIHIRD T0341 230 :AADEEK 1u7pA 144 :GMSLQT T0341 247 :FPHAVDHILQHL 1u7pA 150 :LTQGLETFAKAQ Number of specific fragments extracted= 12 number of extra gaps= 0 total=1217 Number of alignments=98 # 1u7pA read from 1u7pA/merged-good-all-a2m # found chain 1u7pA in template set T0341 7 :LKAVLVDLNGTLHIEDAA 1u7pA 5 :PKLAVFDLDYTLWPFWVD T0341 38 :TSVM 1u7pA 23 :THVD T0341 107 :TQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARY 1u7pA 33 :SDGTVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASRTSEI T0341 149 :YKRKDGLALGPGPFV 1u7pA 76 :GANQLLELFDLGKYF T0341 172 :TKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1u7pA 91 :IQREIYPGSKVTHFERLHHKTGVPFSQMVFFDDENR T0341 209 :DVDGAQNIGMLGILV 1u7pA 127 :NIIDVGRLGVTCIHI T0341 225 :TGKYKAAD 1u7pA 142 :RDGMSLQT T0341 247 :FPHAVDHILQHL 1u7pA 150 :LTQGLETFAKAQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=1225 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0341 read from 1rkuA/merged-good-all-a2m # 1rkuA read from 1rkuA/merged-good-all-a2m # found chain 1rkuA in training set Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0341 8 :KAVL 1rkuA 2 :EIAC T0341 14 :LNGTLHI 1rkuA 8 :LEGVLVP T0341 27 :GAQE 1rkuA 15 :EIWI T0341 34 :RLRAT 1rkuA 19 :AFAEK T0341 39 :SVMVRFVTNTTKETKKDLLERL 1rkuA 25 :GIDALKATTRDIPDYDVLMKQR T0341 80 :RNLIEQKQVRP 1rkuA 47 :LRILDEHGLKL T0341 100 :PEFTGVQ 1rkuA 58 :GDIQEVI T0341 119 :PEHFHYQLLNQAFRLLLDGAPL 1rkuA 65 :ATLKPLEGAVEFVDWLRERFQV T0341 141 :IAIHKARYYKRKDGLALGPGPFV 1rkuA 88 :ILSDTFYEFSQPLMRQLGFPTLL T0341 173 :KAM 1rkuA 120 :DRV T0341 177 :VGK 1rkuA 128 :RQK T0341 183 :TFFLEALRDA 1rkuA 131 :DPKRQSVIAF T0341 193 :DC 1rkuA 144 :YY T0341 198 :EAVMIGDD 1rkuA 146 :RVIAAGDS T0341 207 :RDDVDGAQNIG 1rkuA 154 :YNDTTMLSEAH T0341 219 :LGILVK 1rkuA 165 :AGILFH T0341 228 :YKAADEEKINPPP 1rkuA 171 :APENVIREFPQFP T0341 243 :TCESFPHAVDHILQH 1rkuA 184 :AVHTYEDLKREFLKA Number of specific fragments extracted= 18 number of extra gaps= 1 total=1243 Number of alignments=100 # 1rkuA read from 1rkuA/merged-good-all-a2m # found chain 1rkuA in training set Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0341 8 :KAVL 1rkuA 2 :EIAC T0341 14 :LNGTLH 1rkuA 8 :LEGVLV T0341 50 :KETKKDLLERLKKLEFEISEDEIFTSLTAARNLIE 1rkuA 14 :PEIWIAFAEKTGIDALKATTRDIPDYDVLMKQRLR T0341 85 :QKQVRP 1rkuA 52 :EHGLKL T0341 96 :DRALPEF 1rkuA 58 :GDIQEVI T0341 119 :PEHFHYQLLNQAFRLLLDGAPL 1rkuA 65 :ATLKPLEGAVEFVDWLRERFQV T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYA 1rkuA 88 :ILSDTFYEFSQPLMRQLGFPTLLCHKLEI T0341 171 :DT 1rkuA 120 :DR T0341 173 :KAMVVGK 1rkuA 124 :GYQLRQK T0341 183 :TFFLEALRDA 1rkuA 131 :DPKRQSVIAF T0341 193 :DC 1rkuA 144 :YY T0341 198 :EAVMIGDDCR 1rkuA 146 :RVIAAGDSYN T0341 209 :DVDGAQNIG 1rkuA 156 :DTTMLSEAH T0341 219 :LGILVKT 1rkuA 165 :AGILFHA T0341 229 :KAADEEKINPPP 1rkuA 172 :PENVIREFPQFP T0341 243 :TCESFPHAVDHILQH 1rkuA 184 :AVHTYEDLKREFLKA Number of specific fragments extracted= 16 number of extra gaps= 1 total=1259 Number of alignments=101 # 1rkuA read from 1rkuA/merged-good-all-a2m # found chain 1rkuA in training set Warning: unaligning (T0341)V12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0341)D13 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0341 9 :AVL 1rkuA 3 :IAC T0341 14 :LNGTLHIE 1rkuA 8 :LEGVLVPE T0341 24 :A 1rkuA 16 :I T0341 28 :AQEALKRL 1rkuA 17 :WIAFAEKT T0341 49 :TKETKKDLLERLKKLEFEI 1rkuA 39 :YDVLMKQRLRILDEHGLKL T0341 110 :PNAVVIGLAPEHFHYQLLNQAFRL 1rkuA 58 :GDIQEVIATLKPLEGAVEFVDWLR T0341 135 :LDGAPLIAIHKA 1rkuA 82 :ERFQVVILSDTF T0341 160 :GPFVTALEYATD 1rkuA 94 :YEFSQPLMRQLG T0341 175 :MVVGKPEKTFFLEALRDA 1rkuA 123 :VGYQLRQKDPKRQSVIAF T0341 198 :EAVMIGDDCR 1rkuA 146 :RVIAAGDSYN T0341 209 :DVDGAQNIG 1rkuA 156 :DTTMLSEAH T0341 219 :LGILVK 1rkuA 165 :AGILFH T0341 228 :YKAADEEK 1rkuA 171 :APENVIRE T0341 238 :PPPYLTCESFPHAVDHILQ 1rkuA 179 :FPQFPAVHTYEDLKREFLK Number of specific fragments extracted= 14 number of extra gaps= 1 total=1273 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1te2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0341 read from 1te2A/merged-good-all-a2m # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0341)R5 because first residue in template chain is (1te2A)R5 Warning: unaligning (T0341)A156 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0341)L157 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0341 6 :ALKAVLVDLNGTLHIEDAAVPGAQE 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAEL T0341 33 :KRLRATSVM 1te2A 31 :DVMASLGVD T0341 46 :TNTT 1te2A 48 :DTLG T0341 51 :ETKKDLLERLKKLEF 1te2A 52 :LRIDMVVDLWYARQP T0341 86 :KQVRPMLLLDDRALPEFTGVQT 1te2A 67 :WNGPSRQEVVERVIARAISLVE T0341 119 :PEHFHYQLLNQAFRLLLD 1te2A 89 :ETRPLLPGVREAVALCKE T0341 137 :GAPL 1te2A 108 :GLLV T0341 141 :IAIHKARYYKRKDGL 1te2A 113 :LASASPLHMLEKVLT T0341 158 :G 1te2A 130 :D T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1te2A 131 :LRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDS T0341 207 :RDDVDGAQNIGMLGILVKTGKYKAADEEKI 1te2A 175 :VNGMIASKAARMRSIVVPAPEAQNDPRFVL T0341 240 :PYLTCESFPHA 1te2A 205 :ANVKLSSLTEL T0341 251 :VDHIL 1te2A 217 :AKDLL Number of specific fragments extracted= 13 number of extra gaps= 1 total=1286 Number of alignments=103 # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0341)R5 because first residue in template chain is (1te2A)R5 Warning: unaligning (T0341)A156 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0341)L157 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0341 6 :ALKAVLVDLNGTLHIEDAAVPGAQE 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAEL T0341 33 :KRLRATSVM 1te2A 31 :DVMASLGVD T0341 50 :KE 1te2A 40 :IS T0341 61 :KKLEFEISED 1te2A 42 :RRNELPDTLG T0341 73 :FTSLTAARNLIEQKQVR 1te2A 52 :LRIDMVVDLWYARQPWN T0341 90 :PMLLLDDRALPEFTGVQT 1te2A 71 :SRQEVVERVIARAISLVE T0341 119 :PEHFHYQLLNQAFRLLLD 1te2A 89 :ETRPLLPGVREAVALCKE T0341 137 :GAPL 1te2A 108 :GLLV T0341 141 :IAIHKARYYKRKDGL 1te2A 113 :LASASPLHMLEKVLT T0341 158 :GPGPFVTALEYA 1te2A 130 :DLRDSFDALASA T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1te2A 142 :EKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVN T0341 209 :DVDGAQNIGMLGILVKTGKYKAADEEKI 1te2A 177 :GMIASKAARMRSIVVPAPEAQNDPRFVL T0341 240 :PYLTCESFPHA 1te2A 205 :ANVKLSSLTEL T0341 251 :VDHI 1te2A 217 :AKDL Number of specific fragments extracted= 14 number of extra gaps= 1 total=1300 Number of alignments=104 # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0341)A156 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0341)L157 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0341 6 :ALKAVLVDLNGTLHIEDAAVPGA 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRA T0341 56 :LLERLKKLEFEISEDEIF 1te2A 29 :ELDVMASLGVDISRRNEL T0341 74 :TSLTAARNLIEQKQV 1te2A 52 :LRIDMVVDLWYARQP T0341 95 :DDRALPEFTGVQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYYKRKDGL 1te2A 67 :WNGPSRQEVVERVIARAISLVEETRPLLPGVREAVALCKEQGLLVGLASASPLHMLEKVLT T0341 158 :GPGPFVTAL 1te2A 130 :DLRDSFDAL T0341 170 :TDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1te2A 139 :ASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVN T0341 209 :DVDGAQNIGMLGILVKTGKYKAADEE 1te2A 177 :GMIASKAARMRSIVVPAPEAQNDPRF T0341 238 :PPPYLTCESFPHA 1te2A 203 :VLANVKLSSLTEL Number of specific fragments extracted= 8 number of extra gaps= 1 total=1308 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fezA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fezA expands to /projects/compbio/data/pdb/1fez.pdb.gz 1fezA:# T0341 read from 1fezA/merged-good-all-a2m # 1fezA read from 1fezA/merged-good-all-a2m # adding 1fezA to template set # found chain 1fezA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1fezA)K5 T0341 7 :LKAVLVDLNGTLHIED 1fezA 6 :IEAVIFDWAGTTVDYG T0341 23 :AAVPGAQE 1fezA 23 :FAPLEVFM T0341 33 :KRLRATSVMV 1fezA 31 :EIFHKRGVAI T0341 46 :T 1fezA 41 :T T0341 47 :NTTKETKKDLLERLKKL 1fezA 47 :KPMGLLKIDHVRALTEM T0341 76 :LTAARNLIEQKQVRPMLLLDDRALPEFTGVQTQDPN 1fezA 64 :PRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILP T0341 119 :PEHFHYQLLNQAFRLLLD 1fezA 100 :RYASPINAVKEVIASLRE T0341 137 :GAPLIAIHKARYYKRK 1fezA 119 :GIKIGSTTGYTREMMD T0341 153 :DGLALGPGPF 1fezA 141 :ALQGYKPDFL T0341 170 :TDTKAMVVGKPEKTFFLEALRDADC 1fezA 151 :VTPDDVPAGRPYPWMCYKNAMELGV T0341 195 :APEEAVMIGDD 1fezA 177 :PMNHMIKVGDT T0341 207 :RDDVDGAQNIGMLGILVKTGKY 1fezA 188 :VSDMKEGRNAGMWTVGVILGSS T0341 229 :KAADEEKI 1fezA 214 :TEEEVENM T0341 237 :N 1fezA 241 :G T0341 240 :PYLTCESFPHAVDHILQH 1fezA 242 :AHFTIETMQELESVMEHI Number of specific fragments extracted= 15 number of extra gaps= 0 total=1323 Number of alignments=106 # 1fezA read from 1fezA/merged-good-all-a2m # found chain 1fezA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1fezA)K5 T0341 7 :LKAVLVDLNGTLHIEDAAV 1fezA 6 :IEAVIFDWAGTTVDYGCFA T0341 26 :PGAQE 1fezA 26 :LEVFM T0341 33 :KRLRATSV 1fezA 31 :EIFHKRGV T0341 50 :KETKKDLL 1fezA 39 :AITAEEAR T0341 58 :ERLKKLE 1fezA 58 :RALTEMP T0341 77 :TAARNLIEQKQVRPMLLLDDRALPEFTGVQTQDPN 1fezA 65 :RIASEWNRVFRQLPTEADIQEMYEEFEEILFAILP T0341 119 :PEHFHYQLLNQAFRLLLD 1fezA 100 :RYASPINAVKEVIASLRE T0341 137 :GAPL 1fezA 119 :GIKI T0341 141 :IAIHKARYYKRKDGLAL 1fezA 124 :STTGYTREMMDIVAKEA T0341 158 :GPG 1fezA 144 :GYK T0341 163 :VTALEYA 1fezA 147 :PDFLVTP T0341 173 :KAMVVGKPEKTFFLEALRDADC 1fezA 154 :DDVPAGRPYPWMCYKNAMELGV T0341 195 :APEEAVMIGDDCR 1fezA 177 :PMNHMIKVGDTVS T0341 209 :DVDGAQNIGMLGILVKTGKY 1fezA 190 :DMKEGRNAGMWTVGVILGSS T0341 229 :KAADEEKI 1fezA 214 :TEEEVENM T0341 237 :N 1fezA 241 :G T0341 240 :PYLTCESFPHAVDHILQH 1fezA 242 :AHFTIETMQELESVMEHI Number of specific fragments extracted= 17 number of extra gaps= 0 total=1340 Number of alignments=107 # 1fezA read from 1fezA/merged-good-all-a2m # found chain 1fezA in template set T0341 7 :LKAVLVDLNGTLHIEDAAVP 1fezA 6 :IEAVIFDWAGTTVDYGCFAP T0341 53 :KKDLLERLKKLEFEISEDEIFTS 1fezA 26 :LEVFMEIFHKRGVAITAEEARKP T0341 76 :LTAARNL 1fezA 54 :IDHVRAL T0341 83 :IEQKQVRPMLLLDDRALPEFTGVQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKAR 1fezA 66 :IASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTR T0341 161 :PFVTALEYATD 1fezA 131 :EMMDIVAKEAA T0341 172 :TKAMVVGKPEKTFFLEALRDADC 1fezA 153 :PDDVPAGRPYPWMCYKNAMELGV T0341 195 :APEEAVMIGDDCR 1fezA 177 :PMNHMIKVGDTVS T0341 209 :DVDGAQNIGMLGILVKTGK 1fezA 190 :DMKEGRNAGMWTVGVILGS T0341 228 :YKAADEE 1fezA 213 :LTEEEVE T0341 237 :NPPPYLTCESFPHAVDHIL 1fezA 239 :ENGAHFTIETMQELESVME Number of specific fragments extracted= 10 number of extra gaps= 0 total=1350 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cr6B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cr6B expands to /projects/compbio/data/pdb/1cr6.pdb.gz 1cr6B:# T0341 read from 1cr6B/merged-good-all-a2m # 1cr6B read from 1cr6B/merged-good-all-a2m # adding 1cr6B to template set # found chain 1cr6B in template set Warning: unaligning (T0341)K8 because first residue in template chain is (1cr6B)R4 T0341 9 :AVLVDLNGTLHI 1cr6B 5 :VAAFDLDGVLAL T0341 23 :AAVPGAQE 1cr6B 17 :PSIAGAFR T0341 33 :KRLRATSVM 1cr6B 25 :RSEEALALP T0341 46 :TNTTKETK 1cr6B 41 :YQTEFPEG T0341 56 :LLERLKKLEF 1cr6B 49 :PTEQLMKGKI T0341 71 :EIFTSLTAARNLIEQK 1cr6B 59 :TFSQWVPLMDESYRKS T0341 87 :QVRPML 1cr6B 81 :NLPENF T0341 97 :RALPEFTGVQ 1cr6B 87 :SISQIFSQAM T0341 119 :PEHFHYQLLNQAFRLLLD 1cr6B 97 :AARSINRPMLQAAIALKK T0341 137 :GAPL 1cr6B 116 :GFTT T0341 141 :IAIHK 1cr6B 121 :IVTNN T0341 146 :ARYYKRKDGLA 1cr6B 132 :KRDSLAQMMCE T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1cr6B 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDF T0341 207 :RDDVDGAQNIGMLGILVKTGKYKAADEEKI 1cr6B 187 :GSNLKPARDMGMVTILVHNTASALRELEKV T0341 237 :NPPPYL 1cr6B 222 :PEAPLP Number of specific fragments extracted= 15 number of extra gaps= 0 total=1365 Number of alignments=109 # 1cr6B read from 1cr6B/merged-good-all-a2m # found chain 1cr6B in template set Warning: unaligning (T0341)K8 because first residue in template chain is (1cr6B)R4 T0341 9 :AVLVDLNGTLHIEDA 1cr6B 5 :VAAFDLDGVLALPSI T0341 33 :KRLRAT 1cr6B 51 :EQLMKG T0341 50 :KETKKDLLERLK 1cr6B 57 :KITFSQWVPLMD T0341 77 :TAARNLIEQKQVR 1cr6B 69 :ESYRKSSKACGAN T0341 90 :PMLLLDDRALPEF 1cr6B 84 :ENFSISQIFSQAM T0341 119 :PEHFHYQLLNQAFRLLLD 1cr6B 97 :AARSINRPMLQAAIALKK T0341 137 :GAPL 1cr6B 116 :GFTT T0341 141 :IAIHKARY 1cr6B 121 :IVTNNWLD T0341 149 :YKRKDGLALG 1cr6B 135 :SLAQMMCELS T0341 161 :PFVTALEYA 1cr6B 145 :QHFDFLIES T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1cr6B 154 :CQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGS T0341 209 :DVDGAQNIGMLGILVKT 1cr6B 189 :NLKPARDMGMVTILVHN T0341 229 :KAADEEKI 1cr6B 206 :TASALREL Number of specific fragments extracted= 13 number of extra gaps= 0 total=1378 Number of alignments=110 # 1cr6B read from 1cr6B/merged-good-all-a2m # found chain 1cr6B in template set Warning: unaligning (T0341)K8 because first residue in template chain is (1cr6B)R4 T0341 9 :AVLVDLNGTLHI 1cr6B 5 :VAAFDLDGVLAL T0341 23 :AAVPGAQEAL 1cr6B 17 :PSIAGAFRRS T0341 33 :KRLRATSVM 1cr6B 51 :EQLMKGKIT T0341 49 :TKETKKDLLERLKK 1cr6B 60 :FSQWVPLMDESYRK T0341 63 :LEFEISED 1cr6B 78 :CGANLPEN T0341 73 :FTSLTAARNLIEQ 1cr6B 86 :FSISQIFSQAMAA T0341 119 :PEHFHYQLLNQAFRLLLDGAPLIAIHKARYYK 1cr6B 99 :RSINRPMLQAAIALKKKGFTTCIVTNNWLDDG T0341 154 :GLALGPGPFVTALEY 1cr6B 131 :DKRDSLAQMMCELSQ T0341 172 :TKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1cr6B 153 :SCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGS T0341 209 :DVDGAQNIGMLGILVKTGKYKAADEE 1cr6B 189 :NLKPARDMGMVTILVHNTASALRELE T0341 235 :KINPPP 1cr6B 222 :PEAPLP Number of specific fragments extracted= 11 number of extra gaps= 0 total=1389 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2feaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 2feaA/merged-good-all-a2m # 2feaA read from 2feaA/merged-good-all-a2m # adding 2feaA to template set # found chain 2feaA in template set Warning: unaligning (T0341)R4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)T3 Warning: unaligning (T0341)A142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0341)I143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 T0341 5 :RAL 2feaA 4 :RKP T0341 9 :AVLVDLNGTLHI 2feaA 7 :FIICDFDGTITM T0341 22 :DAAVPGAQE 2feaA 19 :NDNIINIMK T0341 33 :KR 2feaA 28 :TF T0341 40 :VM 2feaA 30 :AP T0341 51 :ETKKDLLERLKKLEF 2feaA 32 :PEWMALKDGVLSKTL T0341 74 :TSLTAARNLIEQKQVRPM 2feaA 47 :SIKEGVGRMFGLLPSSLK T0341 96 :DRALPEFTGV 2feaA 65 :EEITSFVLED T0341 121 :HFHYQLLNQAFRLLLD 2feaA 75 :AKIREGFREFVAFINE T0341 137 :GAPL 2feaA 92 :EIPF T0341 141 :I 2feaA 97 :V T0341 144 :HKARYY 2feaA 100 :GGMDFF T0341 162 :FVTALEYATDTKAM 2feaA 106 :VYPLLEGIVEKDRI T0341 185 :FLEALRDA 2feaA 151 :KPSVIHEL T0341 194 :CAPE 2feaA 159 :SEPN T0341 198 :EAVMIGDD 2feaA 164 :YIIMIGDS T0341 207 :RDDVDGAQ 2feaA 172 :VTDVEAAK T0341 218 :MLGILVKT 2feaA 181 :SDLCFARD T0341 230 :AADEEKINPP 2feaA 191 :LNECREQNLN T0341 241 :YLTCESFPHAVDHILQ 2feaA 201 :HLPYQDFYEIRKEIEN Number of specific fragments extracted= 20 number of extra gaps= 2 total=1409 Number of alignments=112 # 2feaA read from 2feaA/merged-good-all-a2m # found chain 2feaA in template set Warning: unaligning (T0341)R4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)T3 Warning: unaligning (T0341)A142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0341)I143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 T0341 5 :RAL 2feaA 4 :RKP T0341 9 :AVLVDLNGTLHIED 2feaA 7 :FIICDFDGTITMND T0341 27 :GAQEALKRL 2feaA 21 :NIINIMKTF T0341 50 :KETKKDLLERLKKLEFEIS 2feaA 31 :PPEWMALKDGVLSKTLSIK T0341 77 :TAARNLIEQKQ 2feaA 50 :EGVGRMFGLLP T0341 96 :DRALPEFTGVQT 2feaA 61 :SSLKEEITSFVL T0341 119 :PEHFHYQLLNQAFRLLLD 2feaA 73 :EDAKIREGFREFVAFINE T0341 137 :GAPL 2feaA 92 :EIPF T0341 141 :I 2feaA 97 :V T0341 144 :HKARYYKRKDGLALGPGPFVTALEYATDTKAMVVG 2feaA 100 :GGMDFFVYPLLEGIVEKDRIYCNHASFDNDYIHID T0341 179 :K 2feaA 151 :K T0341 182 :KTFFLEA 2feaA 152 :PSVIHEL T0341 194 :CAPE 2feaA 159 :SEPN T0341 198 :EAVMIGDDCR 2feaA 164 :YIIMIGDSVT T0341 209 :DVDGAQN 2feaA 174 :DVEAAKL T0341 218 :MLGILVKT 2feaA 181 :SDLCFARD T0341 229 :KAADEEKINPPPYLTCESFPHAVDHILQ 2feaA 189 :YLLNECREQNLNHLPYQDFYEIRKEIEN Number of specific fragments extracted= 17 number of extra gaps= 2 total=1426 Number of alignments=113 # 2feaA read from 2feaA/merged-good-all-a2m # found chain 2feaA in template set Warning: unaligning (T0341)A142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0341)I143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 Warning: unaligning (T0341)V176 because of BadResidue code BAD_PEPTIDE in next template residue (2feaA)C149 Warning: unaligning (T0341)V177 because of BadResidue code BAD_PEPTIDE at template residue (2feaA)C149 T0341 9 :AVLVDLNGTLHIED 2feaA 7 :FIICDFDGTITMND T0341 24 :AVPGAQEA 2feaA 21 :NIINIMKT T0341 48 :TTKETKKDLLERLKKLEFE 2feaA 29 :FAPPEWMALKDGVLSKTLS T0341 83 :IEQKQVRPMLLLDDRALPEFTGVQTQ 2feaA 48 :IKEGVGRMFGLLPSSLKEEITSFVLE T0341 118 :APEHFHYQLLNQAFRLLLDGAPLI 2feaA 74 :DAKIREGFREFVAFINEHEIPFYV T0341 144 :H 2feaA 100 :G T0341 159 :PGPFVTAL 2feaA 102 :MDFFVYPL T0341 170 :TD 2feaA 110 :LE T0341 172 :TKAM 2feaA 144 :SNQC T0341 178 :GKP 2feaA 150 :CKP T0341 187 :EALRDA 2feaA 153 :SVIHEL T0341 196 :PEE 2feaA 161 :PNQ T0341 199 :AVMIGDDCR 2feaA 165 :IIMIGDSVT T0341 209 :DVDGAQN 2feaA 174 :DVEAAKL T0341 218 :MLGILVK 2feaA 181 :SDLCFAR T0341 235 :K 2feaA 196 :E T0341 237 :NPPPYLTCESFPHAVDHIL 2feaA 197 :QNLNHLPYQDFYEIRKEIE Number of specific fragments extracted= 17 number of extra gaps= 2 total=1443 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ymqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ymqA expands to /projects/compbio/data/pdb/1ymq.pdb.gz 1ymqA:# T0341 read from 1ymqA/merged-good-all-a2m # 1ymqA read from 1ymqA/merged-good-all-a2m # adding 1ymqA to template set # found chain 1ymqA in template set Warning: unaligning (T0341)L7 because first residue in template chain is (1ymqA)T2 T0341 8 :KAVLVDLNGTLHIED 1ymqA 3 :KALFFDIDGTLVSFE T0341 23 :AAVPGAQEALKRLRATSVMVRFVTNTT 1ymqA 20 :RIPSSTIEALEAAHAKGLKIFIATGRP T0341 50 :KETK 1ymqA 51 :NNLS T0341 59 :RLKKLEF 1ymqA 55 :ELQDRNL T0341 67 :IS 1ymqA 62 :ID T0341 69 :ED 1ymqA 76 :GE T0341 75 :SLTAARNLIEQKQVR 1ymqA 89 :EVKAMAAFCEKKGVP T0341 90 :PMLLLD 1ymqA 111 :NISVCQ T0341 96 :DRALPEFTGVQTQDP 1ymqA 119 :EMVKKIFYDFLHVNV T0341 119 :PEHFHYQLL 1ymqA 134 :IPTVSFEEA T0341 135 :LD 1ymqA 143 :SN T0341 137 :GAPLIAIHKARYYKRKDGLALGP 1ymqA 146 :EVIQMTPFITEEEEKEVLPSIPT T0341 161 :PFVTALEYATDTKAMV 1ymqA 173 :RWYPAFADVTAKGDTK T0341 182 :KTFFLEALRDADCAPEEAVMIGDD 1ymqA 189 :QKGIDEIIRHFGIKLEETMSFGDG T0341 207 :RDDVDGAQNIG 1ymqA 213 :GNDISMLRHAA T0341 221 :ILVKTGKYKAADEEK 1ymqA 224 :IGVAMGQAKEDVKAA T0341 240 :PYLTCESFPH 1ymqA 239 :ADYVTAPIDE T0341 250 :AVDHILQHL 1ymqA 251 :ISKAMKHFG Number of specific fragments extracted= 18 number of extra gaps= 0 total=1461 Number of alignments=115 # 1ymqA read from 1ymqA/merged-good-all-a2m # found chain 1ymqA in template set Warning: unaligning (T0341)L7 because first residue in template chain is (1ymqA)T2 T0341 8 :KAVLVDLNGTLHIED 1ymqA 3 :KALFFDIDGTLVSFE T0341 23 :AAV 1ymqA 19 :HRI T0341 26 :PGAQEALKRLRATSVMVRFVTNTT 1ymqA 23 :SSTIEALEAAHAKGLKIFIATGRP T0341 58 :ERLKKLE 1ymqA 54 :SELQDRN T0341 65 :FEISEDEIFTS 1ymqA 64 :GYITMNGAYCF T0341 119 :PEHFHYQLLNQAFRLLLD 1ymqA 82 :KSAIPQEEVKAMAAFCEK T0341 137 :GAP 1ymqA 101 :GVP T0341 140 :L 1ymqA 147 :V T0341 141 :IAIHK 1ymqA 149 :QMTPF T0341 146 :ARYYKRKDGLAL 1ymqA 155 :TEEEEKEVLPSI T0341 158 :GPGPFVTALEYA 1ymqA 173 :RWYPAFADVTAK T0341 173 :KAMV 1ymqA 185 :GDTK T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1ymqA 189 :QKGIDEIIRHFGIKLEETMSFGDGGN T0341 209 :DVDGAQNIG 1ymqA 215 :DISMLRHAA T0341 219 :LGILV 1ymqA 224 :IGVAM T0341 226 :GKYKAADEEK 1ymqA 229 :GQAKEDVKAA T0341 240 :PYLTCESFPH 1ymqA 239 :ADYVTAPIDE T0341 250 :AVDHILQHLL 1ymqA 251 :ISKAMKHFGI Number of specific fragments extracted= 18 number of extra gaps= 0 total=1479 Number of alignments=116 # 1ymqA read from 1ymqA/merged-good-all-a2m # found chain 1ymqA in template set Warning: unaligning (T0341)L7 because first residue in template chain is (1ymqA)T2 T0341 8 :KAVLVDLNGTLHIEDA 1ymqA 3 :KALFFDIDGTLVSFET T0341 24 :AVPGAQEALKRLRATSVMVRFVTNTTKET 1ymqA 21 :IPSSTIEALEAAHAKGLKIFIATGRPKAI T0341 58 :ERLKKLEF 1ymqA 54 :SELQDRNL T0341 66 :EISEDE 1ymqA 84 :AIPQEE T0341 76 :LTAARNLIEQKQVRPMLLLDD 1ymqA 90 :VKAMAAFCEKKGVPCIFVEEH T0341 172 :TKAM 1ymqA 184 :KGDT T0341 181 :EKTFFLEALRDADCAPEEAVMIGDDCR 1ymqA 188 :KQKGIDEIIRHFGIKLEETMSFGDGGN T0341 209 :DVDGAQNI 1ymqA 215 :DISMLRHA T0341 221 :ILVKTGKYKAADEEK 1ymqA 224 :IGVAMGQAKEDVKAA T0341 240 :PYLTCESFPH 1ymqA 239 :ADYVTAPIDE Number of specific fragments extracted= 10 number of extra gaps= 0 total=1489 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nf2A expands to /projects/compbio/data/pdb/1nf2.pdb.gz 1nf2A:# T0341 read from 1nf2A/merged-good-all-a2m # 1nf2A read from 1nf2A/merged-good-all-a2m # adding 1nf2A to template set # found chain 1nf2A in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1nf2A)M1 T0341 7 :LKAVLVDLNGTLHI 1nf2A 2 :YRVFVFDLDGTLLN T0341 21 :EDAAVPGAQEALKRLRAT 1nf2A 17 :NLEISEKDRRNIEKLSRK T0341 40 :VMVRFVTN 1nf2A 35 :CYVVFASG T0341 51 :ETKKDLLERLKKLEFEIS 1nf2A 43 :RMLVSTLNVEKKYFKRTF T0341 69 :ED 1nf2A 74 :EE T0341 71 :EIFTSLTAARNLIEQK 1nf2A 80 :NEKIPPEVAKDIIEYI T0341 96 :DRALPEFTGVQ 1nf2A 117 :EEIKSYARHSN T0341 119 :PEHFHYQLLNQAFR 1nf2A 128 :VDYRVEPNLSELVS T0341 138 :APLIAIHKARYYKRK 1nf2A 146 :TKLLLIDTPERLDEL T0341 154 :GLA 1nf2A 161 :KEI T0341 162 :FVTALE 1nf2A 164 :LSERFK T0341 175 :MVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1nf2A 185 :VPKNVDKGKALRFLRERMNWKKEEIVVFGDN T0341 207 :RDDVDGAQNIG 1nf2A 216 :ENDLFMFEEAG T0341 219 :LGILV 1nf2A 227 :LRVAM T0341 226 :GKYKAADEEK 1nf2A 232 :ENAIEKVKEA T0341 240 :PYLTCESFPH 1nf2A 242 :SDIVTLTNND Number of specific fragments extracted= 16 number of extra gaps= 0 total=1505 Number of alignments=118 # 1nf2A read from 1nf2A/merged-good-all-a2m # found chain 1nf2A in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1nf2A)M1 T0341 7 :LKAVLVDLNGTLHIEDAAV 1nf2A 2 :YRVFVFDLDGTLLNDNLEI T0341 26 :PGAQEALKRLRAT 1nf2A 22 :EKDRRNIEKLSRK T0341 40 :VMVRFVTNTTK 1nf2A 35 :CYVVFASGRML T0341 54 :KDLLERLKKLE 1nf2A 46 :VSTLNVEKKYF T0341 65 :FEISEDEIFTSL 1nf2A 61 :PTIAYNGAIVYL T0341 110 :PNAVVI 1nf2A 74 :EEGVIL T0341 119 :PEHFHYQLLNQAFRLLLD 1nf2A 80 :NEKIPPEVAKDIIEYIKP T0341 137 :GAP 1nf2A 99 :NVH T0341 141 :IAIHKARYYKRKDGLALGPG 1nf2A 110 :LYSEKDNEEIKSYARHSNVD T0341 163 :VTA 1nf2A 130 :YRV T0341 168 :YA 1nf2A 183 :EI T0341 173 :KAMVVGK 1nf2A 185 :VPKNVDK T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1nf2A 192 :GKALRFLRERMNWKKEEIVVFGDNEN T0341 209 :DVDGAQNIGMLGIL 1nf2A 218 :DLFMFEEAGLRVAM T0341 226 :GKYKAADEEK 1nf2A 232 :ENAIEKVKEA T0341 240 :PYLTCESFPH 1nf2A 242 :SDIVTLTNND T0341 250 :AVDHILQ 1nf2A 254 :VSYVLER Number of specific fragments extracted= 17 number of extra gaps= 0 total=1522 Number of alignments=119 # 1nf2A read from 1nf2A/merged-good-all-a2m # found chain 1nf2A in template set T0341 7 :LKAVLVDLNGTLHIEDA 1nf2A 2 :YRVFVFDLDGTLLNDNL T0341 24 :AVPGAQEALKRLRAT 1nf2A 20 :ISEKDRRNIEKLSRK T0341 40 :VMVRFVT 1nf2A 35 :CYVVFAS T0341 50 :KETKKDLLER 1nf2A 42 :GRMLVSTLNV T0341 83 :IEQKQVRPM 1nf2A 52 :EKKYFKRTF T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAFRL 1nf2A 140 :VSKMGTTKLLLIDTPERLDELKEILSERF T0341 135 :LD 1nf2A 169 :KD T0341 172 :TKAMVV 1nf2A 186 :PKNVDK T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1nf2A 192 :GKALRFLRERMNWKKEEIVVFGDNEN T0341 209 :DVDGAQNIGMLGI 1nf2A 218 :DLFMFEEAGLRVA Number of specific fragments extracted= 10 number of extra gaps= 0 total=1532 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0341 read from 1qq5A/merged-good-all-a2m # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set Warning: unaligning (T0341)A6 because first residue in template chain is (1qq5A)M1 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEA 1qq5A 2 :IKAVVFDAYGTLFDVQSVADATERA T0341 32 :LKRLRAT 1qq5A 35 :TQVWRQK T0341 52 :TKKDLLERLK 1qq5A 42 :QLEYSWLRAL T0341 69 :EDEIFTSLTAARNLIEQK 1qq5A 52 :MGRYADFWSVTREALAYT T0341 87 :QVRPM 1qq5A 74 :GLEPD T0341 96 :DRALPEFTGVQ 1qq5A 79 :ESFLADMAQAY T0341 119 :PEHFHYQLLNQAFRLLL 1qq5A 90 :NRLTPYPDAAQCLAELA T0341 137 :GAPL 1qq5A 107 :PLKR T0341 141 :IAIHKARYYKRKDGLALG 1qq5A 112 :ILSNGAPDMLQALVANAG T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1qq5A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSN T0341 207 :RDDVDGAQNIGMLGILVKT 1qq5A 174 :GFDVGGAKNFGFSVARVAR T0341 228 :YKAADEEKI 1qq5A 193 :LSQEALARE T0341 237 :N 1qq5A 226 :A T0341 240 :PYLTCESFPHAVDHILQH 1qq5A 227 :PDFVVPALGDLPRLVRGM Number of specific fragments extracted= 14 number of extra gaps= 0 total=1546 Number of alignments=121 # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set Warning: unaligning (T0341)A6 because first residue in template chain is (1qq5A)M1 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEA 1qq5A 2 :IKAVVFDAYGTLFDVQSVADATERA T0341 33 :KRLR 1qq5A 36 :QVWR T0341 50 :KETKKDLLERLKKLEFE 1qq5A 40 :QKQLEYSWLRALMGRYA T0341 70 :DEIFTSLTAARNLIEQKQVRPM 1qq5A 57 :DFWSVTREALAYTLGTLGLEPD T0341 96 :DRALPEFTGVQ 1qq5A 79 :ESFLADMAQAY T0341 119 :PEHFHYQLLNQAFRLLL 1qq5A 90 :NRLTPYPDAAQCLAELA T0341 137 :GAPL 1qq5A 107 :PLKR T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYA 1qq5A 112 :ILSNGAPDMLQALVANAGLTDSFDAVISV T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1qq5A 141 :DAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGF T0341 209 :DVDGAQNIGMLGILVKT 1qq5A 176 :DVGGAKNFGFSVARVAR T0341 228 :YKAADEEKI 1qq5A 193 :LSQEALARE T0341 237 :NPPPYLTCESFPHAVDHILQH 1qq5A 224 :AEAPDFVVPALGDLPRLVRGM Number of specific fragments extracted= 12 number of extra gaps= 0 total=1558 Number of alignments=122 # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEA 1qq5A 2 :IKAVVFDAYGTLFDVQSVADATERA T0341 49 :TKETKKDLLER 1qq5A 27 :YPGRGEYITQV T0341 75 :SLTAARNLIEQKQVRPMLLLDDRALPEFTG 1qq5A 38 :WRQKQLEYSWLRALMGRYADFWSVTREALA T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAFR 1qq5A 78 :DESFLADMAQAYNRLTPYPDAAQCLAEL T0341 135 :LDGAPLIAIHKARYYKRKDGLALGPGPFVTAL 1qq5A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAV T0341 170 :TDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1qq5A 138 :ISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGF T0341 209 :DVDGAQNIGMLGILVKT 1qq5A 176 :DVGGAKNFGFSVARVAR T0341 228 :YKAADEE 1qq5A 193 :LSQEALA T0341 235 :KINPPPYLTCESFPHAVDHIL 1qq5A 222 :TYAEAPDFVVPALGDLPRLVR Number of specific fragments extracted= 9 number of extra gaps= 0 total=1567 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fi1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fi1A expands to /projects/compbio/data/pdb/2fi1.pdb.gz 2fi1A:# T0341 read from 2fi1A/merged-good-all-a2m # 2fi1A read from 2fi1A/merged-good-all-a2m # adding 2fi1A to template set # found chain 2fi1A in template set Warning: unaligning (T0341)R5 because first residue in template chain is (2fi1A)M4 T0341 6 :ALKAVLVDLNGTLHIEDAAVPGAQE 2fi1A 5 :KYHDYIWDLGGTLLDNYETSTAAFV T0341 33 :KRLRATSVM 2fi1A 30 :ETLALYGIT T0341 51 :ETKKDLLERLKK 2fi1A 39 :QDHDSVYQALKV T0341 76 :LTAARN 2fi1A 53 :PFAIET T0341 86 :KQVRP 2fi1A 59 :FAPNL T0341 96 :DRALPEFTGVQTQDP 2fi1A 64 :ENFLEKYKENEAREL T0341 119 :PEHFHYQLLNQAFRLLLD 2fi1A 79 :EHPILFEGVSDLLEDISN T0341 137 :GAPLIAIHKARYYKRKDGLALG 2fi1A 98 :GGRHFLVSHRNDQVLEILEKTS T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADC 2fi1A 120 :IAAYFTEVVTSSSGFKRKPNPESMLYLREKYQI T0341 197 :EEAVMIGDD 2fi1A 153 :SSGLVIGDR T0341 207 :RDDVDGAQNIGMLG 2fi1A 162 :PIDIEAGQAAGLDT T0341 242 :LTCESFPHAVDHI 2fi1A 176 :HLFTSIVNLRQVL Number of specific fragments extracted= 12 number of extra gaps= 0 total=1579 Number of alignments=124 # 2fi1A read from 2fi1A/merged-good-all-a2m # found chain 2fi1A in template set Warning: unaligning (T0341)R5 because first residue in template chain is (2fi1A)M4 T0341 6 :ALKAVLVDLNGTLHIEDAAVPGAQE 2fi1A 5 :KYHDYIWDLGGTLLDNYETSTAAFV T0341 33 :KRLRATSV 2fi1A 30 :ETLALYGI T0341 50 :KETKKDLLERLKKLE 2fi1A 38 :TQDHDSVYQALKVST T0341 77 :TAARNLI 2fi1A 53 :PFAIETF T0341 87 :QVRP 2fi1A 60 :APNL T0341 96 :DRALPEFTGVQTQDP 2fi1A 64 :ENFLEKYKENEAREL T0341 119 :PEHFHYQLLNQAFRLLLD 2fi1A 79 :EHPILFEGVSDLLEDISN T0341 137 :GAPLIAIHKARYYKRKDGLALGPGPFVTALEYA 2fi1A 98 :GGRHFLVSHRNDQVLEILEKTSIAAYFTEVVTS T0341 173 :KAMVVGKPEKTFFLEALRDADC 2fi1A 131 :SSGFKRKPNPESMLYLREKYQI T0341 197 :EEAVMIGDDCR 2fi1A 153 :SSGLVIGDRPI T0341 209 :DVDGAQNIGM 2fi1A 164 :DIEAGQAAGL T0341 240 :PYLTCESFPHAVDHI 2fi1A 174 :DTHLFTSIVNLRQVL Number of specific fragments extracted= 12 number of extra gaps= 0 total=1591 Number of alignments=125 # 2fi1A read from 2fi1A/merged-good-all-a2m # found chain 2fi1A in template set T0341 6 :ALKAVLVDLNGTLHIEDAA 2fi1A 5 :KYHDYIWDLGGTLLDNYET T0341 52 :TKKDLLERLKKLEFEISEDE 2fi1A 24 :STAAFVETLALYGITQDHDS T0341 79 :ARNLIEQ 2fi1A 44 :VYQALKV T0341 98 :ALPEFTG 2fi1A 51 :STPFAIE T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAFRLLLDGAPLIAIHKARYY 2fi1A 67 :LEKYKENEARELEHPILFEGVSDLLEDISNQGGRHFLVSHRNDQV T0341 151 :RKDGLALGPGPFVTAL 2fi1A 112 :LEILEKTSIAAYFTEV T0341 170 :TDTKAMVVGKPEKTFFLEALRDADC 2fi1A 128 :VTSSSGFKRKPNPESMLYLREKYQI T0341 197 :EEAVMIGDDCR 2fi1A 153 :SSGLVIGDRPI T0341 209 :DVDGAQNIGMLG 2fi1A 164 :DIEAGQAAGLDT T0341 242 :LTCESFPHAVDHI 2fi1A 176 :HLFTSIVNLRQVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1601 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rlmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rlmA expands to /projects/compbio/data/pdb/1rlm.pdb.gz 1rlmA:# T0341 read from 1rlmA/merged-good-all-a2m # 1rlmA read from 1rlmA/merged-good-all-a2m # adding 1rlmA to template set # found chain 1rlmA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1rlmA)A2 T0341 7 :LKAVLVDLNGTLHIEDAAV 1rlmA 3 :VKVIVTDMDGTFLNDAKTY T0341 26 :PGAQEALKRLRATSVMVRFVTNTT 1rlmA 24 :PRFMAQYQELKKRGIKFVVASGNQ T0341 57 :LERLKKLEFEISED 1rlmA 48 :YYQLISFFPELKDE T0341 71 :EIFT 1rlmA 82 :GELT T0341 76 :LTAARNLIEQK 1rlmA 86 :RHESRIVIGEL T0341 87 :QVR 1rlmA 117 :NAP T0341 96 :DRALPEFTGVQT 1rlmA 120 :EAFVALMAKHYH T0341 108 :QDP 1rlmA 137 :KDY T0341 116 :G 1rlmA 152 :N T0341 119 :PEHFHYQLLNQAFRLLLDGAPLIAIHKARYY 1rlmA 153 :LPDEQIPLVIDKLHVALDGIMKPVTSGFGFI T0341 156 :ALG 1rlmA 187 :IPG T0341 162 :F 1rlmA 190 :L T0341 180 :PEKTFFLEALRDADCAPEEAVMIGDD 1rlmA 191 :HKANGISRLLKRWDLSPQNVVAIGDS T0341 207 :RDDVDGAQN 1rlmA 217 :GNDAEMLKM T0341 218 :MLGILVK 1rlmA 226 :ARYSFAM T0341 226 :GKYKAADEEK 1rlmA 233 :GNAAENIKQI T0341 240 :PYLTCESFPH 1rlmA 243 :ARYATDDNNH T0341 250 :AVDHILQ 1rlmA 258 :VIQAVLD Number of specific fragments extracted= 18 number of extra gaps= 0 total=1619 Number of alignments=127 # 1rlmA read from 1rlmA/merged-good-all-a2m # found chain 1rlmA in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1rlmA)A2 T0341 7 :LKAVLVDLNGTLHIEDAAV 1rlmA 3 :VKVIVTDMDGTFLNDAKTY T0341 26 :PGAQEALKRLRATSVMVRFVTNTT 1rlmA 24 :PRFMAQYQELKKRGIKFVVASGNQ T0341 96 :DRALPEFTGVQ 1rlmA 49 :YQLISFFPELK T0341 120 :EHFHYQLLNQAFRLLLD 1rlmA 82 :GELTRHESRIVIGELLK T0341 137 :GAP 1rlmA 101 :QLN T0341 140 :LIAIHKARYYKRKDGLAL 1rlmA 112 :AYVSENAPEAFVALMAKH T0341 158 :GPGPFVTALEYA 1rlmA 141 :EIDDVLFKFSLN T0341 170 :TDT 1rlmA 170 :DGI T0341 173 :KAMVVG 1rlmA 174 :KPVTSG T0341 179 :K 1rlmA 192 :K T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1rlmA 193 :ANGISRLLKRWDLSPQNVVAIGDSGN T0341 209 :DVDGAQNIGM 1rlmA 219 :DAEMLKMARY T0341 220 :GILV 1rlmA 229 :SFAM T0341 226 :GKYKAADEEK 1rlmA 233 :GNAAENIKQI T0341 240 :PYLTCESFPH 1rlmA 243 :ARYATDDNNH T0341 250 :AVDHILQ 1rlmA 258 :VIQAVLD Number of specific fragments extracted= 16 number of extra gaps= 0 total=1635 Number of alignments=128 # 1rlmA read from 1rlmA/merged-good-all-a2m # found chain 1rlmA in template set T0341 7 :LKAVLVDLNGTLHIEDA 1rlmA 3 :VKVIVTDMDGTFLNDAK T0341 24 :AVPGAQEALKRLRATSVMVRFVTNTTKE 1rlmA 22 :NQPRFMAQYQELKKRGIKFVVASGNQYY T0341 59 :RLKKLE 1rlmA 50 :QLISFF T0341 65 :FEISEDE 1rlmA 82 :GELTRHE T0341 76 :LTAARNLIEQKQV 1rlmA 89 :SRIVIGELLKDKQ T0341 89 :RPMLLLDDRALPEFTG 1rlmA 109 :LQSAYVSENAPEAFVA T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAFRL 1rlmA 141 :EIDDVLFKFSLNLPDEQIPLVIDKLHVAL T0341 135 :LDGAPLIAIHKA 1rlmA 170 :DGIMKPVTSGFG T0341 156 :ALGPG 1rlmA 187 :IPGLH T0341 162 :F 1rlmA 192 :K T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1rlmA 193 :ANGISRLLKRWDLSPQNVVAIGDSGN T0341 209 :DVDGAQNIGML 1rlmA 219 :DAEMLKMARYS T0341 223 :VKTGKYKAADEEK 1rlmA 230 :FAMGNAAENIKQI T0341 240 :PYLTCESFPH 1rlmA 243 :ARYATDDNNH Number of specific fragments extracted= 14 number of extra gaps= 0 total=1649 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ydfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0341/1ydfA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0341/1ydfA/merged-good-all-a2m.gz for input Trying 1ydfA/merged-good-all-a2m Error: Couldn't open file 1ydfA/merged-good-all-a2m or 1ydfA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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 # T0341 read from 1qq7A/merged-good-all-a2m # 1qq7A read from 1qq7A/merged-good-all-a2m # adding 1qq7A to template set # found chain 1qq7A in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1qq7A)M1 Warning: unaligning (T0341)V12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0341)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0341 7 :LKAVL 1qq7A 2 :IKAVV T0341 15 :NGTLHIEDAAVPGAQEA 1qq7A 10 :YGTLFDVQSVADATERA T0341 32 :LKRLRAT 1qq7A 35 :TQVWRQK T0341 52 :TKKDLLERLK 1qq7A 42 :QLEYSWLRAL T0341 69 :EDEIFTSLTAARNLIEQK 1qq7A 52 :MGRYADFWSVTREALAYT T0341 87 :QVRPM 1qq7A 74 :GLEPD T0341 96 :DRALPEFTGVQ 1qq7A 79 :ESFLADMAQAY T0341 119 :PEHFHYQLLNQAFRLLL 1qq7A 90 :NRLTPYPDAAQCLAELA T0341 137 :GAPL 1qq7A 107 :PLKR T0341 141 :IAIHKARYYKRKDGLALG 1qq7A 112 :ILSNGAPDMLQALVANAG T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1qq7A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSN T0341 207 :RDDVDGAQNIGMLGILVKT 1qq7A 174 :GFDVGGAKNFGFSVARVAR T0341 228 :YKAADEEKI 1qq7A 193 :LSQEALARE T0341 237 :N 1qq7A 226 :A T0341 240 :PYLTCESFPHAVDHILQH 1qq7A 227 :PDFVVPALGDLPRLVRGM Number of specific fragments extracted= 15 number of extra gaps= 0 total=1664 Number of alignments=130 # 1qq7A read from 1qq7A/merged-good-all-a2m # found chain 1qq7A in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1qq7A)M1 Warning: unaligning (T0341)V12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0341)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0341 7 :LKAVL 1qq7A 2 :IKAVV T0341 15 :NGTLHIEDAAVPGAQEA 1qq7A 10 :YGTLFDVQSVADATERA T0341 33 :KRLR 1qq7A 36 :QVWR T0341 50 :KETKKDLLERLKKLEFE 1qq7A 40 :QKQLEYSWLRALMGRYA T0341 70 :DEIFTSLTAARNLIEQKQVRPM 1qq7A 57 :DFWSVTREALAYTLGTLGLEPD T0341 96 :DRALPEFTGVQ 1qq7A 79 :ESFLADMAQAY T0341 119 :PEHFHYQLLNQAFRLLL 1qq7A 90 :NRLTPYPDAAQCLAELA T0341 137 :GAPL 1qq7A 107 :PLKR T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYA 1qq7A 112 :ILSNGAPDMLQALVANAGLTDSFDAVISV T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1qq7A 141 :DAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGF T0341 209 :DVDGAQNIGMLGILVKT 1qq7A 176 :DVGGAKNFGFSVARVAR T0341 228 :YKAADEEKI 1qq7A 193 :LSQEALARE T0341 237 :NPPPYLTCESFPHAVDHILQH 1qq7A 224 :AEAPDFVVPALGDLPRLVRGM Number of specific fragments extracted= 13 number of extra gaps= 0 total=1677 Number of alignments=131 # 1qq7A read from 1qq7A/merged-good-all-a2m # found chain 1qq7A in template set Warning: unaligning (T0341)V12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0341)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0341 7 :LKAVL 1qq7A 2 :IKAVV T0341 15 :NGTLHIEDAAVPGAQEA 1qq7A 10 :YGTLFDVQSVADATERA T0341 32 :LKRLRAT 1qq7A 35 :TQVWRQK T0341 52 :TKKDLLERLKKLEFE 1qq7A 42 :QLEYSWLRALMGRYA T0341 74 :TSLTAARNLIEQ 1qq7A 57 :DFWSVTREALAY T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAFR 1qq7A 78 :DESFLADMAQAYNRLTPYPDAAQCLAEL T0341 135 :LDGAPLIAIHKARYYKRKDGLALGPGPFVTAL 1qq7A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAV T0341 170 :TDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1qq7A 138 :ISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGF T0341 209 :DVDGAQNIGMLGILVKT 1qq7A 176 :DVGGAKNFGFSVARVAR T0341 228 :YKAADEE 1qq7A 193 :LSQEALA T0341 235 :KINPPPYLTCESFPHAVDHIL 1qq7A 222 :TYAEAPDFVVPALGDLPRLVR Number of specific fragments extracted= 11 number of extra gaps= 0 total=1688 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rloA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rloA expands to /projects/compbio/data/pdb/1rlo.pdb.gz 1rloA: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 # T0341 read from 1rloA/merged-good-all-a2m # 1rloA read from 1rloA/merged-good-all-a2m # adding 1rloA to template set # found chain 1rloA in template set Warning: unaligning (T0341)L7 because first residue in template chain is (1rloA)V3 Warning: unaligning (T0341)V12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rloA)M10 Warning: unaligning (T0341)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rloA)M10 T0341 8 :KAVL 1rloA 4 :KVIV T0341 15 :NGTLHI 1rloA 11 :DGTFLN T0341 21 :EDAAVPGAQEALKRLRATSVMVRFVTNTT 1rloA 19 :KTYNQPRFMAQYQELKKRGIKFVVASGNQ T0341 57 :LERLKKLEFEISED 1rloA 48 :YYQLISFFPELKDE T0341 72 :IFTSLTAARNLIEQK 1rloA 82 :GELTRHESRIVIGEL T0341 87 :QVR 1rloA 117 :NAP T0341 96 :DRALPEFTGVQT 1rloA 120 :EAFVALMAKHYH T0341 108 :QDP 1rloA 137 :KDY T0341 119 :PEHFHYQLLNQAFRLLLDGAPLIAIHKARYY 1rloA 153 :LPDEQIPLVIDKLHVALDGIMKPVTSGFGFI T0341 169 :AT 1rloA 185 :LI T0341 176 :VVGKPEKTFFLEALRDADCAPEEAVMIGDD 1rloA 187 :IPGLHKANGISRLLKRWDLSPQNVVAIGDS T0341 207 :RDDVDGAQN 1rloA 217 :GNDAEMLKM T0341 218 :MLGILVK 1rloA 226 :ARYSFAM T0341 226 :GK 1rloA 233 :GN T0341 229 :KAADEEKI 1rloA 235 :AAENIKQI T0341 240 :PYLTCESFPH 1rloA 243 :ARYATDDNNH T0341 250 :AVDHILQ 1rloA 258 :VIQAVLD Number of specific fragments extracted= 17 number of extra gaps= 0 total=1705 Number of alignments=133 # 1rloA read from 1rloA/merged-good-all-a2m # found chain 1rloA in template set Warning: unaligning (T0341)L7 because first residue in template chain is (1rloA)V3 Warning: unaligning (T0341)V12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rloA)M10 Warning: unaligning (T0341)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rloA)M10 T0341 8 :KAVL 1rloA 4 :KVIV T0341 15 :NGTLHIEDAAV 1rloA 11 :DGTFLNDAKTY T0341 26 :PGAQEALKRLRATSVMVRFVTNTTK 1rloA 24 :PRFMAQYQELKKRGIKFVVASGNQY T0341 96 :DRALPEFTGVQ 1rloA 49 :YQLISFFPELK T0341 119 :PEHFHYQLLNQAFRLLLD 1rloA 81 :HGELTRHESRIVIGELLK T0341 137 :GAP 1rloA 101 :QLN T0341 140 :LIAIHKARYYKRKDGLAL 1rloA 112 :AYVSENAPEAFVALMAKH T0341 158 :GPGPFVTALE 1rloA 141 :EIDDVLFKFS T0341 176 :VVG 1rloA 177 :TSG T0341 179 :K 1rloA 192 :K T0341 182 :KTFFLEALRDADCAPEEAVMIGDDCR 1rloA 193 :ANGISRLLKRWDLSPQNVVAIGDSGN T0341 209 :DVDGAQNIGM 1rloA 219 :DAEMLKMARY T0341 220 :GILV 1rloA 229 :SFAM T0341 226 :GKYKAADEEK 1rloA 233 :GNAAENIKQI T0341 240 :PYLTCESFPH 1rloA 243 :ARYATDDNNH T0341 250 :AVDHIL 1rloA 258 :VIQAVL Number of specific fragments extracted= 16 number of extra gaps= 0 total=1721 Number of alignments=134 # 1rloA read from 1rloA/merged-good-all-a2m # found chain 1rloA in template set Warning: unaligning (T0341)L7 because first residue in template chain is (1rloA)V3 Warning: unaligning (T0341)V12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rloA)M10 Warning: unaligning (T0341)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rloA)M10 T0341 8 :KAVL 1rloA 4 :KVIV T0341 15 :NGTLHIEDA 1rloA 11 :DGTFLNDAK T0341 24 :AVPGAQEALKRLRATSVMVRFVTNTTKET 1rloA 22 :NQPRFMAQYQELKKRGIKFVVASGNQYYQ T0341 61 :KKLE 1rloA 51 :LISF T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAFRL 1rloA 141 :EIDDVLFKFSLNLPDEQIPLVIDKLHVAL T0341 135 :LDGAPLIAIHKA 1rloA 170 :DGIMKPVTSGFG T0341 156 :ALGP 1rloA 187 :IPGL T0341 161 :PFVTA 1rloA 191 :HKANG T0341 185 :FLEALRDADCAPEEAVMIGDDCR 1rloA 196 :ISRLLKRWDLSPQNVVAIGDSGN T0341 209 :DVDGAQNIGML 1rloA 219 :DAEMLKMARYS T0341 223 :VKTGKYKAADEEK 1rloA 230 :FAMGNAAENIKQI T0341 240 :PYLTCESFP 1rloA 243 :ARYATDDNN Number of specific fragments extracted= 12 number of extra gaps= 0 total=1733 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aq6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aq6A expands to /projects/compbio/data/pdb/1aq6.pdb.gz 1aq6A:# T0341 read from 1aq6A/merged-good-all-a2m # 1aq6A read from 1aq6A/merged-good-all-a2m # adding 1aq6A to template set # found chain 1aq6A in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1aq6A)M1 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEA 1aq6A 2 :IKAVVFDAYGTLFDVQSVADATERA T0341 32 :LKRLRAT 1aq6A 35 :TQVWRQK T0341 52 :TKKDLLERLK 1aq6A 42 :QLEYSWLRAL T0341 69 :EDEIFTSLTAARNLIEQK 1aq6A 52 :MGRYADFWGVTREALAYT T0341 87 :QVRPM 1aq6A 74 :GLEPD T0341 96 :DRALPEFTGVQ 1aq6A 79 :ESFLADMAQAY T0341 119 :PEHFHYQLLNQAFRLLL 1aq6A 90 :NRLTPYPDAAQCLAELA T0341 137 :GAPL 1aq6A 107 :PLKR T0341 141 :IAIHKARYYKRKDGLALG 1aq6A 112 :ILSNGAPDMLQALVANAG T0341 162 :FVTALEYATDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDD 1aq6A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSN T0341 207 :RDDVDGAQNIGMLGILVKT 1aq6A 174 :GFDVGGAKNFGFSVARVAR T0341 228 :YKAADEEKI 1aq6A 193 :LSQEALARE T0341 237 :N 1aq6A 226 :A T0341 240 :PYLTCESFPHAVDHILQ 1aq6A 227 :PDFVVPALGDLPRLVRG Number of specific fragments extracted= 14 number of extra gaps= 0 total=1747 Number of alignments=136 # 1aq6A read from 1aq6A/merged-good-all-a2m # found chain 1aq6A in template set Warning: unaligning (T0341)A6 because first residue in template chain is (1aq6A)M1 T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEA 1aq6A 2 :IKAVVFDAYGTLFDVQSVADATERA T0341 33 :KRLR 1aq6A 36 :QVWR T0341 50 :KETKKDLLERLKKLEFE 1aq6A 40 :QKQLEYSWLRALMGRYA T0341 70 :DEIFTSLTAARNLIEQKQVRPM 1aq6A 57 :DFWGVTREALAYTLGTLGLEPD T0341 96 :DRALPEFTGVQ 1aq6A 79 :ESFLADMAQAY T0341 119 :PEHFHYQLLNQAFRLLL 1aq6A 90 :NRLTPYPDAAQCLAELA T0341 137 :GAPL 1aq6A 107 :PLKR T0341 141 :IAIHKARYYKRKDGLALGPGPFVTALEYA 1aq6A 112 :ILSNGAPDMLQALVANAGLTDSFDAVISV T0341 173 :KAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1aq6A 141 :DAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGF T0341 209 :DVDGAQNIGMLGILVKT 1aq6A 176 :DVGGAKNFGFSVARVAR T0341 228 :YKAADEEKI 1aq6A 193 :LSQEALARE T0341 237 :NPPPYLTCESFPHAVDHIL 1aq6A 224 :AEAPDFVVPALGDLPRLVR Number of specific fragments extracted= 12 number of extra gaps= 0 total=1759 Number of alignments=137 # 1aq6A read from 1aq6A/merged-good-all-a2m # found chain 1aq6A in template set T0341 7 :LKAVLVDLNGTLHIEDAAVPGAQEA 1aq6A 2 :IKAVVFDAYGTLFDVQSVADATERA T0341 49 :TKETKKDLLERL 1aq6A 27 :YPGRGEYITQVW T0341 76 :LTAARNLIEQKQVRPMLLLDDRALPEFTG 1aq6A 39 :RQKQLEYSWLRALMGRYADFWGVTREALA T0341 105 :VQTQDPNAVVIGLAPEHFHYQLLNQAFR 1aq6A 78 :DESFLADMAQAYNRLTPYPDAAQCLAEL T0341 135 :LDGAPLIAIHKARYYKRKDGLALGPGPFVTAL 1aq6A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAV T0341 170 :TDTKAMVVGKPEKTFFLEALRDADCAPEEAVMIGDDCR 1aq6A 138 :ISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGF T0341 209 :DVDGAQNIGMLGILVKT 1aq6A 176 :DVGGAKNFGFSVARVAR T0341 228 :YKAADEE 1aq6A 193 :LSQEALA T0341 235 :KINPPPYLTCESFPHAVDHIL 1aq6A 222 :TYAEAPDFVVPALGDLPRLVR Number of specific fragments extracted= 9 number of extra gaps= 0 total=1768 Number of alignments=138 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 138 Done printing distance constraints # command: