# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0341//projects/compbio/experiments/protein-predict/casp7/T0341/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0341//projects/compbio/experiments/protein-predict/casp7/T0341/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0341/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0341/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)I202.CB) [> 4.2669 = 7.1115 < 9.2449] w=1.0000 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)M201.CB) [> 2.8519 = 4.7531 < 6.1791] w=1.0000 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)V200.CB) [> 4.1769 = 6.9615 < 9.0499] w=1.0000 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)A199.CB) [> 3.6829 = 6.1382 < 7.9797] w=1.0000 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)V200.CB) [> 2.9955 = 4.9925 < 6.4903] w=1.0000 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)A199.CB) [> 4.4618 = 7.4363 < 9.6672] w=1.0000 to align # Constraint # added constraint: constraint((T0341)A9.CB, (T0341)V200.CB) [> 4.3611 = 7.2685 < 9.4490] w=1.0000 to align # Constraint # added constraint: constraint((T0341)A9.CB, (T0341)A199.CB) [> 2.8293 = 4.7155 < 6.1301] w=1.0000 to align # Constraint # added constraint: constraint((T0341)G16.CA, (T0341)D204.CB) [> 2.8506 = 4.7511 < 6.1764] w=0.9925 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)I202.CB) [> 3.5871 = 5.9785 < 7.7721] w=0.9925 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)G203.CA) [> 2.8718 = 4.7863 < 6.2222] w=0.9925 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)D204.CB) [> 3.0715 = 5.1192 < 6.6549] w=0.9925 to align # Constraint # added constraint: constraint((T0341)A9.CB, (T0341)E198.CB) [> 3.8628 = 6.4380 < 8.3695] w=0.9925 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)I202.CB) [> 4.0977 = 6.8295 < 8.8783] w=0.9867 to align # Constraint # added constraint: constraint((T0341)M201.CB, (T0341)A213.CB) [> 2.6659 = 4.4431 < 5.7761] w=0.9774 to align # Constraint # added constraint: constraint((T0341)F185.CB, (T0341)G212.CA) [> 3.7550 = 6.2583 < 8.1358] w=0.9473 to align # Constraint # added constraint: constraint((T0341)M201.CB, (T0341)G220.CA) [> 3.0081 = 5.0135 < 6.5175] w=0.9397 to align # Constraint # added constraint: constraint((T0341)V200.CB, (T0341)G220.CA) [> 3.7031 = 6.1719 < 8.0234] w=0.9397 to align # Constraint # added constraint: constraint((T0341)A9.CB, (T0341)A192.CB) [> 3.4401 = 5.7334 < 7.4535] w=0.9322 to align # Constraint # added constraint: constraint((T0341)I202.CB, (T0341)G220.CA) [> 4.1767 = 6.9612 < 9.0495] w=0.9021 to align # Constraint # added constraint: constraint((T0341)V200.CB, (T0341)L219.CB) [> 2.8571 = 4.7619 < 6.1905] w=0.9020 to align # Constraint # added constraint: constraint((T0341)L189.CB, (T0341)A199.CB) [> 3.7892 = 6.3154 < 8.2100] w=0.8945 to align # Constraint # added constraint: constraint((T0341)K8.CB, (T0341)E198.CB) [> 2.7108 = 4.5179 < 5.8733] w=0.8843 to align # Constraint # added constraint: constraint((T0341)F185.CB, (T0341)I216.CB) [> 2.9622 = 4.9370 < 6.4181] w=0.8723 to align # Constraint # added constraint: constraint((T0341)A199.CB, (T0341)L219.CB) [> 4.1237 = 6.8729 < 8.9348] w=0.8710 to align # Constraint # added constraint: constraint((T0341)G203.CA, (T0341)L222.CB) [> 3.7062 = 6.1770 < 8.0301] w=0.8661 to align # Constraint # added constraint: constraint((T0341)M201.CB, (T0341)L219.CB) [> 4.1557 = 6.9262 < 9.0041] w=0.8644 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)A188.CB) [> 3.6561 = 6.0935 < 7.9216] w=0.8643 to align # Constraint # added constraint: constraint((T0341)G203.CA, (T0341)I221.CB) [> 4.2239 = 7.0398 < 9.1517] w=0.8585 to align # Constraint # added constraint: constraint((T0341)G203.CA, (T0341)V223.CB) [> 3.4191 = 5.6985 < 7.4080] w=0.8578 to align # Constraint # added constraint: constraint((T0341)M201.CB, (T0341)I221.CB) [> 4.1647 = 6.9412 < 9.0236] w=0.8578 to align # Constraint # added constraint: constraint((T0341)I202.CB, (T0341)I221.CB) [> 2.8233 = 4.7054 < 6.1171] w=0.8434 to align # Constraint # added constraint: constraint((T0341)V200.CB, (T0341)I221.CB) [> 3.7112 = 6.1854 < 8.0410] w=0.8427 to align # Constraint # added constraint: constraint((T0341)A199.CB, (T0341)M218.CB) [> 2.9896 = 4.9827 < 6.4775] w=0.8404 to align # Constraint # added constraint: constraint((T0341)V200.CB, (T0341)M218.CB) [> 3.9000 = 6.4999 < 8.4499] w=0.8404 to align # Constraint # added constraint: constraint((T0341)K8.CB, (T0341)A199.CB) [> 4.3844 = 7.3073 < 9.4995] w=0.8391 to align # Constraint # added constraint: constraint((T0341)P196.CB, (T0341)G217.CA) [> 3.0112 = 5.0187 < 6.5243] w=0.8346 to align # Constraint # added constraint: constraint((T0341)M201.CB, (T0341)M218.CB) [> 3.0708 = 5.1181 < 6.6535] w=0.8329 to align # Constraint # added constraint: constraint((T0341)F185.CB, (T0341)M201.CB) [> 4.2105 = 7.0176 < 9.1229] w=0.8167 to align # Constraint # added constraint: constraint((T0341)K182.CB, (T0341)N215.CB) [> 3.0141 = 5.0235 < 6.5306] w=0.8166 to align # Constraint # added constraint: constraint((T0341)D204.CB, (T0341)L222.CB) [> 4.1327 = 6.8878 < 8.9541] w=0.8135 to align # Constraint # added constraint: constraint((T0341)D204.CB, (T0341)V223.CB) [> 2.9711 = 4.9519 < 6.4374] w=0.8126 to align # Constraint # added constraint: constraint((T0341)G220.CA, (T0341)L242.CB) [> 3.8904 = 6.4840 < 8.4292] w=0.8088 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)I202.CB) [> 3.1422 = 5.2370 < 6.8080] w=0.7968 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)G203.CA) [> 4.3167 = 7.1945 < 9.3528] w=0.7968 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)I202.CB) [> 3.9216 = 6.5360 < 8.4969] w=0.7968 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)G203.CA) [> 2.4128 = 4.0213 < 5.2277] w=0.7968 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)D204.CB) [> 3.7983 = 6.3305 < 8.2296] w=0.7968 to align # Constraint # added constraint: constraint((T0341)V223.CB, (T0341)C244.CB) [> 3.4662 = 5.7769 < 7.5100] w=0.7919 to align # Constraint # added constraint: constraint((T0341)I202.CB, (T0341)V223.CB) [> 3.6429 = 6.0715 < 7.8929] w=0.7901 to align # Constraint # added constraint: constraint((T0341)G16.CA, (T0341)G203.CA) [> 4.5599 = 7.5998 < 9.8797] w=0.7866 to align # Constraint # added constraint: constraint((T0341)P196.CB, (T0341)I216.CB) [> 3.4257 = 5.7095 < 7.4224] w=0.7818 to align # Constraint # added constraint: constraint((T0341)L222.CB, (T0341)C244.CB) [> 4.2613 = 7.1021 < 9.2327] w=0.7785 to align # Constraint # added constraint: constraint((T0341)I221.CB, (T0341)L242.CB) [> 2.9288 = 4.8814 < 6.3458] w=0.7778 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)D209.CB) [> 3.5004 = 5.8340 < 7.5842] w=0.7742 to align # Constraint # added constraint: constraint((T0341)L7.CB, (T0341)E198.CB) [> 3.6057 = 6.0095 < 7.8123] w=0.7712 to align # Constraint # added constraint: constraint((T0341)K8.CB, (T0341)C194.CB) [> 3.2655 = 5.4425 < 7.0752] w=0.7712 to align # Constraint # added constraint: constraint((T0341)L222.CB, (T0341)T243.CB) [> 2.8821 = 4.8035 < 6.2445] w=0.7702 to align # Constraint # added constraint: constraint((T0341)L222.CB, (T0341)L242.CB) [> 4.2164 = 7.0274 < 9.1356] w=0.7695 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)V223.CB) [> 3.4041 = 5.6735 < 7.3756] w=0.7675 to align # Constraint # added constraint: constraint((T0341)I202.CB, (T0341)A250.CB) [> 3.8041 = 6.3401 < 8.2421] w=0.7574 to align # Constraint # added constraint: constraint((T0341)I221.CB, (T0341)C244.CB) [> 3.8321 = 6.3868 < 8.3028] w=0.7560 to align # Constraint # added constraint: constraint((T0341)E197.CB, (T0341)G217.CA) [> 3.7806 = 6.3010 < 8.1913] w=0.7516 to align # Constraint # added constraint: constraint((T0341)I221.CB, (T0341)T243.CB) [> 4.3043 = 7.1738 < 9.3259] w=0.7409 to align # Constraint # added constraint: constraint((T0341)G220.CA, (T0341)Y241.CB) [> 2.9993 = 4.9988 < 6.4985] w=0.7335 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)L140.CB) [> 3.6194 = 6.0324 < 7.8421] w=0.7285 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)P139.CB) [> 3.9975 = 6.6625 < 8.6612] w=0.7285 to align # Constraint # added constraint: constraint((T0341)A9.CB, (T0341)A138.CB) [> 3.4170 = 5.6950 < 7.4035] w=0.7285 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)D205.CB) [> 4.2529 = 7.0881 < 9.2145] w=0.7284 to align # Constraint # added constraint: constraint((T0341)K179.CB, (T0341)D209.CB) [> 3.5322 = 5.8870 < 7.6530] w=0.7274 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)A138.CB) [> 3.6546 = 6.0910 < 7.9183] w=0.7218 to align # Constraint # added constraint: constraint((T0341)A9.CB, (T0341)P139.CB) [> 3.1650 = 5.2751 < 6.8576] w=0.7210 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)I141.CB) [> 4.1343 = 6.8905 < 8.9576] w=0.7209 to align # Constraint # added constraint: constraint((T0341)L7.CB, (T0341)V200.CB) [> 3.0782 = 5.1302 < 6.6693] w=0.7162 to align # Constraint # added constraint: constraint((T0341)P180.CB, (T0341)G212.CA) [> 3.0894 = 5.1490 < 6.6937] w=0.7041 to align # Constraint # added constraint: constraint((T0341)D204.CB, (T0341)K224.CB) [> 4.0251 = 6.7085 < 8.7210] w=0.6995 to align # Constraint # added constraint: constraint((T0341)I221.CB, (T0341)Y241.CB) [> 3.9323 = 6.5538 < 8.5199] w=0.6941 to align # Constraint # added constraint: constraint((T0341)A9.CB, (T0341)L140.CB) [> 4.2158 = 7.0264 < 9.1343] w=0.6909 to align # Constraint # added constraint: constraint((T0341)V210.CB, (T0341)G220.CA) [> 3.6720 = 6.1200 < 7.9561] w=0.6891 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)A142.CB) [> 3.2890 = 5.4817 < 7.1263] w=0.6834 to align # Constraint # added constraint: constraint((T0341)P180.CB, (T0341)D211.CB) [> 3.1271 = 5.2118 < 6.7754] w=0.6822 to align # Constraint # added constraint: constraint((T0341)G220.CA, (T0341)P240.CB) [> 3.3270 = 5.5451 < 7.2086] w=0.6798 to align # Constraint # added constraint: constraint((T0341)L7.CB, (T0341)A199.CB) [> 4.1320 = 6.8866 < 8.9526] w=0.6786 to align # Constraint # added constraint: constraint((T0341)I202.CB, (T0341)L222.CB) [> 4.4206 = 7.3677 < 9.5781] w=0.6753 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)F185.CB) [> 3.7166 = 6.1943 < 8.0526] w=0.6730 to align # Constraint # added constraint: constraint((T0341)H19.CB, (T0341)F122.CB) [> 3.9299 = 6.5497 < 8.5147] w=0.6700 to align # Constraint # added constraint: constraint((T0341)I221.CB, (T0341)A250.CB) [> 3.8786 = 6.4643 < 8.4035] w=0.6671 to align # Constraint # added constraint: constraint((T0341)P196.CB, (T0341)M218.CB) [> 3.0685 = 5.1142 < 6.6484] w=0.6664 to align # Constraint # added constraint: constraint((T0341)I221.CB, (T0341)P240.CB) [> 3.7999 = 6.3331 < 8.2330] w=0.6648 to align # Constraint # added constraint: constraint((T0341)L222.CB, (T0341)P240.CB) [> 2.4866 = 4.1443 < 5.3875] w=0.6566 to align # Constraint # added constraint: constraint((T0341)H19.CB, (T0341)H121.CB) [> 3.2540 = 5.4233 < 7.0503] w=0.6549 to align # Constraint # added constraint: constraint((T0341)V223.CB, (T0341)F247.CB) [> 3.8668 = 6.4447 < 8.3781] w=0.6523 to align # Constraint # added constraint: constraint((T0341)F185.CB, (T0341)A213.CB) [> 3.7420 = 6.2367 < 8.1078] w=0.6513 to align # Constraint # added constraint: constraint((T0341)F185.CB, (T0341)M218.CB) [> 3.9533 = 6.5888 < 8.5654] w=0.6491 to align # Constraint # added constraint: constraint((T0341)L186.CB, (T0341)I216.CB) [> 3.9488 = 6.5813 < 8.5556] w=0.6438 to align # Constraint # added constraint: constraint((T0341)K8.CB, (T0341)A138.CB) [> 3.7840 = 6.3066 < 8.1986] w=0.6354 to align # Constraint # added constraint: constraint((T0341)I20.CB, (T0341)F122.CB) [> 3.5505 = 5.9174 < 7.6927] w=0.6323 to align # Constraint # added constraint: constraint((T0341)L219.CB, (T0341)Y241.CB) [> 3.2443 = 5.4071 < 7.0293] w=0.6281 to align # Constraint # added constraint: constraint((T0341)L7.CB, (T0341)L219.CB) [> 4.0728 = 6.7880 < 8.8244] w=0.6258 to align # Constraint # added constraint: constraint((T0341)V223.CB, (T0341)T243.CB) [> 4.4935 = 7.4891 < 9.7359] w=0.6170 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)M218.CB) [> 4.3804 = 7.3007 < 9.4909] w=0.6107 to align # Constraint # added constraint: constraint((T0341)V210.CB, (T0341)L222.CB) [> 3.4284 = 5.7139 < 7.4281] w=0.6079 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)D204.CB) [> 4.5396 = 7.5660 < 9.8358] w=0.6057 to align # Constraint # added constraint: constraint((T0341)K179.CB, (T0341)G212.CA) [> 3.5724 = 5.9541 < 7.7403] w=0.6039 to align # Constraint # added constraint: constraint((T0341)K224.CB, (T0341)T243.CB) [> 3.6840 = 6.1400 < 7.9820] w=0.6022 to align # Constraint # added constraint: constraint((T0341)Y124.CB, (T0341)F247.CB) [> 3.3818 = 5.6363 < 7.3272] w=0.5992 to align # Constraint # added constraint: constraint((T0341)A142.CB, (T0341)A188.CB) [> 3.4526 = 5.7543 < 7.4806] w=0.5982 to align # Constraint # added constraint: constraint((T0341)H144.CB, (T0341)K179.CB) [> 3.6857 = 6.1428 < 7.9857] w=0.5843 to align # Constraint # added constraint: constraint((T0341)K224.CB, (T0341)C244.CB) [> 4.2630 = 7.1049 < 9.2364] w=0.5812 to align # Constraint # added constraint: constraint((T0341)K224.CB, (T0341)E245.CB) [> 3.4985 = 5.8307 < 7.5800] w=0.5784 to align # Constraint # added constraint: constraint((T0341)A142.CB, (T0341)F184.CB) [> 3.5499 = 5.9166 < 7.6915] w=0.5779 to align # Constraint # added constraint: constraint((T0341)L14.CB, (T0341)I141.CB) [> 3.4776 = 5.7959 < 7.5347] w=0.5778 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)L166.CB) [> 3.3609 = 5.6015 < 7.2820] w=0.5764 to align # Constraint # added constraint: constraint((T0341)L14.CB, (T0341)I143.CB) [> 2.5306 = 4.2177 < 5.4830] w=0.5704 to align # Constraint # added constraint: constraint((T0341)M201.CB, (T0341)V210.CB) [> 4.4912 = 7.4853 < 9.7309] w=0.5685 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)I141.CB) [> 3.2576 = 5.4293 < 7.0581] w=0.5479 to align # Constraint # added constraint: constraint((T0341)F185.CB, (T0341)A199.CB) [> 4.2307 = 7.0512 < 9.1666] w=0.5451 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)M201.CB) [> 4.6609 = 7.7681 < 10.0986] w=0.5426 to align # Constraint # added constraint: constraint((T0341)F185.CB, (T0341)P196.CB) [> 4.3395 = 7.2324 < 9.4022] w=0.5400 to align # Constraint # added constraint: constraint((T0341)G203.CA, (T0341)G220.CA) [> 4.6011 = 7.6685 < 9.9690] w=0.5358 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)I143.CB) [> 4.2234 = 7.0390 < 9.1508] w=0.5326 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)L140.CB) [> 4.2673 = 7.1121 < 9.2458] w=0.5296 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)I143.CB) [> 3.9003 = 6.5006 < 8.4507] w=0.5254 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)A142.CB) [> 3.9317 = 6.5528 < 8.5187] w=0.5254 to align # Constraint # added constraint: constraint((T0341)L18.CB, (T0341)I141.CB) [> 4.2467 = 7.0778 < 9.2011] w=0.5250 to align # Constraint # added constraint: constraint((T0341)M175.CB, (T0341)F184.CB) [> 3.5623 = 5.9372 < 7.7184] w=0.5246 to align # Constraint # added constraint: constraint((T0341)L219.CB, (T0341)L242.CB) [> 4.4426 = 7.4043 < 9.6256] w=0.5226 to align # Constraint # added constraint: constraint((T0341)F131.CB, (T0341)L140.CB) [> 3.6376 = 6.0627 < 7.8815] w=0.5211 to align # Constraint # added constraint: constraint((T0341)G16.CA, (T0341)V223.CB) [> 4.3030 = 7.1716 < 9.3231] w=0.5171 to align # Constraint # added constraint: constraint((T0341)M201.CB, (T0341)I216.CB) [> 3.3905 = 5.6508 < 7.3460] w=0.5147 to align # Constraint # added constraint: constraint((T0341)P180.CB, (T0341)R207.CB) [> 3.5881 = 5.9802 < 7.7742] w=0.5132 to align # Constraint # added constraint: constraint((T0341)T225.CB, (T0341)E245.CB) [> 3.8157 = 6.3595 < 8.2674] w=0.5129 to align # Constraint # added constraint: constraint((T0341)E181.CB, (T0341)G212.CA) [> 4.0996 = 6.8327 < 8.8825] w=0.5060 to align # Constraint # added constraint: constraint((T0341)L242.CB, (T0341)H253.CB) [> 3.3670 = 5.6117 < 7.2952] w=0.5041 to align # Constraint # added constraint: constraint((T0341)L127.CB, (T0341)F247.CB) [> 3.4747 = 5.7912 < 7.5286] w=0.5027 to align # Constraint # added constraint: constraint((T0341)E197.CB, (T0341)M218.CB) [> 4.3334 = 7.2223 < 9.3890] w=0.5005 to align # Constraint # added constraint: constraint((T0341)V200.CB, (T0341)I254.CB) [> 3.8484 = 6.4140 < 8.3382] w=0.4994 to align # Constraint # added constraint: constraint((T0341)H19.CB, (T0341)D153.CB) [> 3.8603 = 6.4338 < 8.3639] w=0.4986 to align # Constraint # added constraint: constraint((T0341)T225.CB, (T0341)S246.CB) [> 3.7195 = 6.1992 < 8.0589] w=0.4952 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)F247.CB) [> 4.0109 = 6.6848 < 8.6903] w=0.4939 to align # Constraint # added constraint: constraint((T0341)E197.CB, (T0341)L219.CB) [> 4.3017 = 7.1694 < 9.3203] w=0.4931 to align # Constraint # added constraint: constraint((T0341)F185.CB, (T0341)N215.CB) [> 4.0756 = 6.7927 < 8.8305] w=0.4924 to align # Constraint # added constraint: constraint((T0341)A9.CB, (T0341)L189.CB) [> 4.0664 = 6.7773 < 8.8105] w=0.4924 to align # Constraint # added constraint: constraint((T0341)G203.CA, (T0341)A213.CB) [> 4.3687 = 7.2811 < 9.4654] w=0.4919 to align # Constraint # added constraint: constraint((T0341)I20.CB, (T0341)H121.CB) [> 4.1258 = 6.8763 < 8.9392] w=0.4919 to align # Constraint # added constraint: constraint((T0341)M175.CB, (T0341)E187.CB) [> 3.7059 = 6.1765 < 8.0295] w=0.4854 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)L134.CB) [> 3.4785 = 5.7974 < 7.5367] w=0.4834 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)A142.CB) [> 4.3095 = 7.1825 < 9.3372] w=0.4819 to align # Constraint # added constraint: constraint((T0341)C244.CB, (T0341)H253.CB) [> 3.9259 = 6.5432 < 8.5061] w=0.4813 to align # Constraint # added constraint: constraint((T0341)P180.CB, (T0341)D209.CB) [> 4.0028 = 6.6713 < 8.6727] w=0.4780 to align # Constraint # added constraint: constraint((T0341)L18.CB, (T0341)L127.CB) [> 3.2269 = 5.3782 < 6.9916] w=0.4759 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)L140.CB) [> 3.7233 = 6.2055 < 8.0671] w=0.4756 to align # Constraint # added constraint: constraint((T0341)A142.CB, (T0341)F185.CB) [> 3.8192 = 6.3653 < 8.2748] w=0.4718 to align # Constraint # added constraint: constraint((T0341)L14.CB, (T0341)K145.CB) [> 3.8363 = 6.3938 < 8.3119] w=0.4694 to align # Constraint # added constraint: constraint((T0341)A199.CB, (T0341)I216.CB) [> 3.7383 = 6.2305 < 8.0997] w=0.4620 to align # Constraint # added constraint: constraint((T0341)P180.CB, (T0341)N215.CB) [> 4.0068 = 6.6781 < 8.6815] w=0.4600 to align # Constraint # added constraint: constraint((T0341)L18.CB, (T0341)H123.CB) [> 3.7886 = 6.3144 < 8.2087] w=0.4550 to align # Constraint # added constraint: constraint((T0341)H19.CB, (T0341)H123.CB) [> 3.5006 = 5.8344 < 7.5847] w=0.4550 to align # Constraint # added constraint: constraint((T0341)D204.CB, (T0341)T225.CB) [> 3.6746 = 6.1243 < 7.9616] w=0.4531 to align # Constraint # added constraint: constraint((T0341)V210.CB, (T0341)P240.CB) [> 3.0644 = 5.1074 < 6.6396] w=0.4526 to align # Constraint # added constraint: constraint((T0341)I221.CB, (T0341)H253.CB) [> 3.5731 = 5.9551 < 7.7417] w=0.4469 to align # Constraint # added constraint: constraint((T0341)P139.CB, (T0341)A192.CB) [> 3.4480 = 5.7467 < 7.4707] w=0.4460 to align # Constraint # added constraint: constraint((T0341)H19.CB, (T0341)Y124.CB) [> 3.9365 = 6.5607 < 8.5290] w=0.4458 to align # Constraint # added constraint: constraint((T0341)L18.CB, (T0341)Y124.CB) [> 3.7486 = 6.2476 < 8.1219] w=0.4458 to align # Constraint # added constraint: constraint((T0341)A142.CB, (T0341)M201.CB) [> 4.4324 = 7.3873 < 9.6035] w=0.4399 to align # Constraint # added constraint: constraint((T0341)L18.CB, (T0341)F247.CB) [> 4.2966 = 7.1611 < 9.3094] w=0.4389 to align # Constraint # added constraint: constraint((T0341)L189.CB, (T0341)I216.CB) [> 4.2699 = 7.1165 < 9.2514] w=0.4375 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)I141.CB) [> 4.4997 = 7.4996 < 9.7494] w=0.4347 to align # Constraint # added constraint: constraint((T0341)K8.CB, (T0341)P139.CB) [> 3.8468 = 6.4113 < 8.3347] w=0.4311 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)D209.CB) [> 4.6579 = 7.7632 < 10.0921] w=0.4299 to align # Constraint # added constraint: constraint((T0341)L7.CB, (T0341)I254.CB) [> 3.6613 = 6.1022 < 7.9329] w=0.4297 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)I254.CB) [> 4.2839 = 7.1398 < 9.2818] w=0.4293 to align # Constraint # added constraint: constraint((T0341)G16.CA, (T0341)D205.CB) [> 4.4740 = 7.4567 < 9.6937] w=0.4219 to align # Constraint # added constraint: constraint((T0341)L126.CB, (T0341)P248.CB) [> 3.1325 = 5.2208 < 6.7870] w=0.4201 to align # Constraint # added constraint: constraint((T0341)L126.CB, (T0341)F247.CB) [> 2.7109 = 4.5181 < 5.8736] w=0.4199 to align # Constraint # added constraint: constraint((T0341)H123.CB, (T0341)L157.CB) [> 3.4518 = 5.7529 < 7.4788] w=0.4125 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)V163.CB) [> 3.4562 = 5.7604 < 7.4885] w=0.4124 to align # Constraint # added constraint: constraint((T0341)I20.CB, (T0341)Y124.CB) [> 3.5299 = 5.8832 < 7.6482] w=0.4081 to align # Constraint # added constraint: constraint((T0341)D204.CB, (T0341)G226.CA) [> 3.6883 = 6.1472 < 7.9914] w=0.4073 to align # Constraint # added constraint: constraint((T0341)A130.CB, (T0341)A250.CB) [> 3.6011 = 6.0019 < 7.8024] w=0.4008 to align # Constraint # added constraint: constraint((T0341)A142.CB, (T0341)K179.CB) [> 4.2685 = 7.1143 < 9.2485] w=0.3882 to align # Constraint # added constraint: constraint((T0341)G16.CA, (T0341)K227.CB) [> 3.9981 = 6.6636 < 8.6626] w=0.3854 to align # Constraint # added constraint: constraint((T0341)A130.CB, (T0341)F247.CB) [> 2.8212 = 4.7020 < 6.1125] w=0.3823 to align # Constraint # added constraint: constraint((T0341)A130.CB, (T0341)V251.CB) [> 3.7888 = 6.3147 < 8.2091] w=0.3822 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)K145.CB) [> 4.1433 = 6.9055 < 8.9771] w=0.3789 to align # Constraint # added constraint: constraint((T0341)K179.CB, (T0341)D211.CB) [> 4.2718 = 7.1197 < 9.2556] w=0.3785 to align # Constraint # added constraint: constraint((T0341)D204.CB, (T0341)Y228.CB) [> 3.0307 = 5.0511 < 6.5665] w=0.3777 to align # Constraint # added constraint: constraint((T0341)L140.CB, (T0341)A165.CB) [> 3.6440 = 6.0733 < 7.8953] w=0.3775 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)M201.CB) [> 4.6167 = 7.6945 < 10.0029] w=0.3700 to align # Constraint # added constraint: constraint((T0341)H19.CB, (T0341)L157.CB) [> 4.0384 = 6.7306 < 8.7498] w=0.3694 to align # Constraint # added constraint: constraint((T0341)D209.CB, (T0341)L222.CB) [> 4.3804 = 7.3007 < 9.4909] w=0.3693 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)T170.CB) [> 3.9851 = 6.6418 < 8.6344] w=0.3622 to align # Constraint # added constraint: constraint((T0341)I202.CB, (T0341)F247.CB) [> 4.4015 = 7.3358 < 9.5365] w=0.3620 to align # Constraint # added constraint: constraint((T0341)L126.CB, (T0341)S246.CB) [> 3.4077 = 5.6795 < 7.3833] w=0.3596 to align # Constraint # added constraint: constraint((T0341)L140.CB, (T0341)V163.CB) [> 3.3824 = 5.6374 < 7.3286] w=0.3583 to align # Constraint # added constraint: constraint((T0341)A199.CB, (T0341)G217.CA) [> 3.7845 = 6.3075 < 8.1998] w=0.3563 to align # Constraint # added constraint: constraint((T0341)A213.CB, (T0341)P240.CB) [> 4.0291 = 6.7152 < 8.7298] w=0.3492 to align # Constraint # added constraint: constraint((T0341)L14.CB, (T0341)D153.CB) [> 4.0689 = 6.7815 < 8.8160] w=0.3482 to align # Constraint # added constraint: constraint((T0341)D205.CB, (T0341)Y228.CB) [> 4.0349 = 6.7248 < 8.7422] w=0.3475 to align # Constraint # added constraint: constraint((T0341)K8.CB, (T0341)G137.CA) [> 3.9352 = 6.5586 < 8.5262] w=0.3400 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)A165.CB) [> 4.1734 = 6.9558 < 9.0425] w=0.3365 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)A250.CB) [> 4.4452 = 7.4087 < 9.6313] w=0.3318 to align # Constraint # added constraint: constraint((T0341)L133.CB, (T0341)V251.CB) [> 3.2500 = 5.4167 < 7.0417] w=0.3254 to align # Constraint # added constraint: constraint((T0341)K179.CB, (T0341)R207.CB) [> 3.4436 = 5.7393 < 7.4611] w=0.3250 to align # Constraint # added constraint: constraint((T0341)G16.CA, (T0341)Y124.CB) [> 4.3093 = 7.1822 < 9.3369] w=0.3177 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)H144.CB) [> 4.2862 = 7.1437 < 9.2868] w=0.3171 to align # Constraint # added constraint: constraint((T0341)L140.CB, (T0341)T164.CB) [> 3.4740 = 5.7900 < 7.5270] w=0.3055 to align # Constraint # added constraint: constraint((T0341)H19.CB, (T0341)E120.CB) [> 3.9716 = 6.6194 < 8.6052] w=0.3054 to align # Constraint # added constraint: constraint((T0341)T170.CB, (T0341)A188.CB) [> 3.4351 = 5.7251 < 7.4426] w=0.3048 to align # Constraint # added constraint: constraint((T0341)K182.CB, (T0341)A213.CB) [> 4.5043 = 7.5072 < 9.7593] w=0.3038 to align # Constraint # added constraint: constraint((T0341)E181.CB, (T0341)N215.CB) [> 4.2151 = 7.0251 < 9.1326] w=0.3016 to align # Constraint # added constraint: constraint((T0341)I143.CB, (T0341)T170.CB) [> 4.2597 = 7.0996 < 9.2295] w=0.2990 to align # Constraint # added constraint: constraint((T0341)F131.CB, (T0341)F162.CB) [> 3.3500 = 5.5834 < 7.2584] w=0.2980 to align # Constraint # added constraint: constraint((T0341)T170.CB, (T0341)E187.CB) [> 3.4316 = 5.7193 < 7.4351] w=0.2972 to align # Constraint # added constraint: constraint((T0341)K179.CB, (T0341)D205.CB) [> 4.5086 = 7.5142 < 9.7685] w=0.2954 to align # Constraint # added constraint: constraint((T0341)L18.CB, (T0341)L157.CB) [> 4.3321 = 7.2202 < 9.3863] w=0.2918 to align # Constraint # added constraint: constraint((T0341)A165.CB, (T0341)A192.CB) [> 3.8059 = 6.3432 < 8.2462] w=0.2906 to align # Constraint # added constraint: constraint((T0341)A165.CB, (T0341)D191.CB) [> 3.2831 = 5.4719 < 7.1134] w=0.2906 to align # Constraint # added constraint: constraint((T0341)A6.CB, (T0341)E198.CB) [> 3.8053 = 6.3421 < 8.2448] w=0.2887 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)A192.CB) [> 4.5053 = 7.5089 < 9.7615] w=0.2886 to align # Constraint # added constraint: constraint((T0341)L18.CB, (T0341)P159.CB) [> 4.2738 = 7.1231 < 9.2600] w=0.2866 to align # Constraint # added constraint: constraint((T0341)A9.CB, (T0341)V40.CB) [> 4.1583 = 6.9305 < 9.0096] w=0.2782 to align # Constraint # added constraint: constraint((T0341)A9.CB, (T0341)M41.CB) [> 2.6893 = 4.4822 < 5.8269] w=0.2782 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)L35.CB) [> 3.8442 = 6.4071 < 8.3292] w=0.2782 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)V40.CB) [> 3.7139 = 6.1899 < 8.0469] w=0.2782 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)M41.CB) [> 4.3222 = 7.2037 < 9.3648] w=0.2782 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)V42.CB) [> 3.0750 = 5.1250 < 6.6625] w=0.2782 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)R43.CB) [> 4.3016 = 7.1693 < 9.3201] w=0.2782 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)R43.CB) [> 2.9395 = 4.8992 < 6.3690] w=0.2782 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)V45.CB) [> 3.2114 = 5.3523 < 6.9580] w=0.2782 to align # Constraint # added constraint: constraint((T0341)L32.CB, (T0341)V42.CB) [> 3.7216 = 6.2027 < 8.0635] w=0.2782 to align # Constraint # added constraint: constraint((T0341)I20.CB, (T0341)H123.CB) [> 4.4239 = 7.3731 < 9.5850] w=0.2752 to align # Constraint # added constraint: constraint((T0341)G154.CA, (T0341)V163.CB) [> 3.6280 = 6.0466 < 7.8606] w=0.2736 to align # Constraint # added constraint: constraint((T0341)L219.CB, (T0341)H257.CB) [> 3.6932 = 6.1554 < 8.0020] w=0.2735 to align # Constraint # added constraint: constraint((T0341)K145.CB, (T0341)T172.CB) [> 3.7216 = 6.2027 < 8.0635] w=0.2702 to align # Constraint # added constraint: constraint((T0341)Q129.CB, (T0341)P139.CB) [> 3.6618 = 6.1030 < 7.9339] w=0.2677 to align # Constraint # added constraint: constraint((T0341)V223.CB, (T0341)A250.CB) [> 4.0661 = 6.7768 < 8.8099] w=0.2665 to align # Constraint # added constraint: constraint((T0341)G16.CA, (T0341)G226.CA) [> 2.9847 = 4.9745 < 6.4668] w=0.2640 to align # Constraint # added constraint: constraint((T0341)K8.CB, (T0341)A192.CB) [> 4.5948 = 7.6580 < 9.9554] w=0.2640 to align # Constraint # added constraint: constraint((T0341)R43.CB, (T0341)A188.CB) [> 3.5854 = 5.9756 < 7.7682] w=0.2640 to align # Constraint # added constraint: constraint((T0341)M41.CB, (T0341)A192.CB) [> 3.6780 = 6.1300 < 7.9689] w=0.2640 to align # Constraint # added constraint: constraint((T0341)I143.CB, (T0341)A169.CB) [> 4.3593 = 7.2655 < 9.4451] w=0.2605 to align # Constraint # added constraint: constraint((T0341)V45.CB, (T0341)F184.CB) [> 3.9182 = 6.5304 < 8.4895] w=0.2564 to align # Constraint # added constraint: constraint((T0341)K8.CB, (T0341)M41.CB) [> 3.9862 = 6.6436 < 8.6367] w=0.2564 to align # Constraint # added constraint: constraint((T0341)T164.CB, (T0341)A192.CB) [> 4.0519 = 6.7532 < 8.7791] w=0.2564 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)A213.CB) [> 4.5148 = 7.5246 < 9.7820] w=0.2563 to align # Constraint # added constraint: constraint((T0341)L14.CB, (T0341)T46.CB) [> 2.8171 = 4.6951 < 6.1036] w=0.2555 to align # Constraint # added constraint: constraint((T0341)L14.CB, (T0341)F44.CB) [> 3.4296 = 5.7160 < 7.4308] w=0.2555 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)T46.CB) [> 4.0445 = 6.7408 < 8.7631] w=0.2555 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)V45.CB) [> 3.5798 = 5.9664 < 7.7563] w=0.2555 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)F44.CB) [> 3.4636 = 5.7727 < 7.5045] w=0.2555 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)R43.CB) [> 4.3378 = 7.2297 < 9.3986] w=0.2555 to align # Constraint # added constraint: constraint((T0341)L18.CB, (T0341)F44.CB) [> 4.3292 = 7.2153 < 9.3799] w=0.2555 to align # Constraint # added constraint: constraint((T0341)A9.CB, (T0341)R43.CB) [> 4.0368 = 6.7281 < 8.7465] w=0.2555 to align # Constraint # added constraint: constraint((T0341)G226.CA, (T0341)E245.CB) [> 4.0228 = 6.7047 < 8.7161] w=0.2555 to align # Constraint # added constraint: constraint((T0341)L18.CB, (T0341)H121.CB) [> 3.7904 = 6.3173 < 8.2125] w=0.2526 to align # Constraint # added constraint: constraint((T0341)K145.CB, (T0341)D171.CB) [> 3.5879 = 5.9799 < 7.7739] w=0.2520 to align # Constraint # added constraint: constraint((T0341)L140.CB, (T0341)A192.CB) [> 3.9139 = 6.5231 < 8.4800] w=0.2518 to align # Constraint # added constraint: constraint((T0341)A199.CB, (T0341)N215.CB) [> 4.4166 = 7.3611 < 9.5694] w=0.2507 to align # Constraint # added constraint: constraint((T0341)I143.CB, (T0341)L166.CB) [> 4.4594 = 7.4323 < 9.6620] w=0.2496 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)V45.CB) [> 4.1041 = 6.8403 < 8.8923] w=0.2489 to align # Constraint # added constraint: constraint((T0341)L134.CB, (T0341)V251.CB) [> 3.9177 = 6.5295 < 8.4884] w=0.2486 to align # Constraint # added constraint: constraint((T0341)T170.CB, (T0341)D191.CB) [> 3.7375 = 6.2291 < 8.0978] w=0.2444 to align # Constraint # added constraint: constraint((T0341)A28.CB, (T0341)F102.CB) [> 3.7195 = 6.1991 < 8.0589] w=0.2412 to align # Constraint # added constraint: constraint((T0341)K150.CB, (T0341)L166.CB) [> 3.4963 = 5.8272 < 7.5754] w=0.2412 to align # Constraint # added constraint: constraint((T0341)L18.CB, (T0341)A28.CB) [> 3.1519 = 5.2533 < 6.8292] w=0.2404 to align # Constraint # added constraint: constraint((T0341)E21.CB, (T0341)H121.CB) [> 3.4285 = 5.7141 < 7.4283] w=0.2392 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)R132.CB) [> 3.4508 = 5.7513 < 7.4768] w=0.2375 to align # Constraint # added constraint: constraint((T0341)V200.CB, (T0341)H257.CB) [> 4.0948 = 6.8246 < 8.8721] w=0.2358 to align # Constraint # added constraint: constraint((T0341)V200.CB, (T0341)G217.CA) [> 4.1507 = 6.9177 < 8.9931] w=0.2357 to align # Constraint # added constraint: constraint((T0341)N128.CB, (T0341)F162.CB) [> 4.0539 = 6.7565 < 8.7834] w=0.2326 to align # Constraint # added constraint: constraint((T0341)T170.CB, (T0341)F184.CB) [> 3.4780 = 5.7967 < 7.5358] w=0.2294 to align # Constraint # added constraint: constraint((T0341)C206.CB, (T0341)L222.CB) [> 3.7895 = 6.3159 < 8.2107] w=0.2269 to align # Constraint # added constraint: constraint((T0341)G16.CA, (T0341)T225.CB) [> 3.5932 = 5.9887 < 7.7853] w=0.2263 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)V42.CB) [> 4.0000 = 6.6666 < 8.6666] w=0.2263 to align # Constraint # added constraint: constraint((T0341)V210.CB, (T0341)I236.CB) [> 3.7592 = 6.2653 < 8.1450] w=0.2199 to align # Constraint # added constraint: constraint((T0341)G203.CA, (T0341)Y228.CB) [> 4.0522 = 6.7537 < 8.7798] w=0.2193 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)T225.CB) [> 3.9636 = 6.6059 < 8.5877] w=0.2187 to align # Constraint # added constraint: constraint((T0341)Q106.CB, (T0341)Y149.CB) [> 3.8193 = 6.3654 < 8.2750] w=0.2183 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)T46.CB) [> 4.3016 = 7.1694 < 9.3202] w=0.2178 to align # Constraint # added constraint: constraint((T0341)R34.CB, (T0341)E101.CB) [> 3.5049 = 5.8415 < 7.5940] w=0.2169 to align # Constraint # added constraint: constraint((T0341)A28.CB, (T0341)V105.CB) [> 3.5358 = 5.8930 < 7.6609] w=0.2169 to align # Constraint # added constraint: constraint((T0341)K224.CB, (T0341)E233.CB) [> 3.4857 = 5.8096 < 7.5524] w=0.2160 to align # Constraint # added constraint: constraint((T0341)N128.CB, (T0341)L157.CB) [> 3.9472 = 6.5787 < 8.5523] w=0.2155 to align # Constraint # added constraint: constraint((T0341)H144.CB, (T0341)A169.CB) [> 3.5611 = 5.9352 < 7.7158] w=0.2152 to align # Constraint # added constraint: constraint((T0341)L7.CB, (T0341)H257.CB) [> 3.9256 = 6.5427 < 8.5055] w=0.2111 to align # Constraint # added constraint: constraint((T0341)A9.CB, (T0341)V42.CB) [> 4.4187 = 7.3646 < 9.5739] w=0.2103 to align # Constraint # added constraint: constraint((T0341)L14.CB, (T0341)A142.CB) [> 4.3106 = 7.1843 < 9.3396] w=0.2056 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)Y168.CB) [> 4.1810 = 6.9683 < 9.0588] w=0.2050 to align # Constraint # added constraint: constraint((T0341)F131.CB, (T0341)P159.CB) [> 4.1918 = 6.9864 < 9.0823] w=0.2043 to align # Constraint # added constraint: constraint((T0341)C206.CB, (T0341)K229.CB) [> 3.9576 = 6.5960 < 8.5748] w=0.2041 to align # Constraint # added constraint: constraint((T0341)V200.CB, (T0341)A213.CB) [> 4.6426 = 7.7376 < 10.0589] w=0.2036 to align # Constraint # added constraint: constraint((T0341)L134.CB, (T0341)A250.CB) [> 4.3497 = 7.2495 < 9.4244] w=0.2036 to align # Constraint # added constraint: constraint((T0341)F185.CB, (T0341)G217.CA) [> 4.6776 = 7.7960 < 10.1348] w=0.2036 to align # Constraint # added constraint: constraint((T0341)M41.CB, (T0341)C194.CB) [> 4.3178 = 7.1963 < 9.3551] w=0.2036 to align # Constraint # added constraint: constraint((T0341)R34.CB, (T0341)V105.CB) [> 3.6196 = 6.0327 < 7.8425] w=0.2033 to align # Constraint # added constraint: constraint((T0341)G226.CA, (T0341)T243.CB) [> 3.5534 = 5.9224 < 7.6991] w=0.2027 to align # Constraint # added constraint: constraint((T0341)I143.CB, (T0341)E167.CB) [> 4.2325 = 7.0542 < 9.1705] w=0.2018 to align # Constraint # added constraint: constraint((T0341)A142.CB, (T0341)E167.CB) [> 3.2119 = 5.3531 < 6.9591] w=0.1992 to align # Constraint # added constraint: constraint((T0341)E198.CB, (T0341)G217.CA) [> 4.2927 = 7.1545 < 9.3008] w=0.1980 to align # Constraint # added constraint: constraint((T0341)S75.CB, (T0341)H144.CB) [> 3.1499 = 5.2498 < 6.8247] w=0.1975 to align # Constraint # added constraint: constraint((T0341)Q214.CB, (T0341)P240.CB) [> 4.1765 = 6.9609 < 9.0491] w=0.1961 to align # Constraint # added constraint: constraint((T0341)F44.CB, (T0341)L56.CB) [> 3.9297 = 6.5495 < 8.5144] w=0.1961 to align # Constraint # added constraint: constraint((T0341)L14.CB, (T0341)L56.CB) [> 4.2827 = 7.1378 < 9.2792] w=0.1961 to align # Constraint # added constraint: constraint((T0341)T46.CB, (T0341)L56.CB) [> 3.7508 = 6.2513 < 8.1266] w=0.1960 to align # Constraint # added constraint: constraint((T0341)K145.CB, (T0341)G178.CA) [> 4.1135 = 6.8558 < 8.9126] w=0.1951 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)A169.CB) [> 3.2109 = 5.3516 < 6.9570] w=0.1917 to align # Constraint # added constraint: constraint((T0341)L140.CB, (T0341)E167.CB) [> 3.6724 = 6.1207 < 7.9569] w=0.1908 to align # Constraint # added constraint: constraint((T0341)R36.CB, (T0341)K53.CB) [> 3.4527 = 5.7545 < 7.4809] w=0.1900 to align # Constraint # added constraint: constraint((T0341)L127.CB, (T0341)L157.CB) [> 4.2570 = 7.0950 < 9.2235] w=0.1898 to align # Constraint # added constraint: constraint((T0341)L32.CB, (T0341)F65.CB) [> 3.7498 = 6.2496 < 8.1245] w=0.1885 to align # Constraint # added constraint: constraint((T0341)Q214.CB, (T0341)P239.CB) [> 3.9330 = 6.5550 < 8.5215] w=0.1885 to align # Constraint # added constraint: constraint((T0341)A79.CB, (T0341)F102.CB) [> 3.9027 = 6.5045 < 8.4559] w=0.1877 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)F44.CB) [> 4.6769 = 7.7948 < 10.1332] w=0.1877 to align # Constraint # added constraint: constraint((T0341)F131.CB, (T0341)A165.CB) [> 2.9276 = 4.8794 < 6.3432] w=0.1841 to align # Constraint # added constraint: constraint((T0341)K8.CB, (T0341)A195.CB) [> 4.6610 = 7.7682 < 10.0987] w=0.1810 to align # Constraint # added constraint: constraint((T0341)Q29.CB, (T0341)L56.CB) [> 3.6318 = 6.0530 < 7.8689] w=0.1809 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)L127.CB) [> 4.2831 = 7.1385 < 9.2801] w=0.1804 to align # Constraint # added constraint: constraint((T0341)L242.CB, (T0341)H257.CB) [> 4.2464 = 7.0774 < 9.2006] w=0.1800 to align # Constraint # added constraint: constraint((T0341)L140.CB, (T0341)F162.CB) [> 3.6081 = 6.0135 < 7.8175] w=0.1782 to align # Constraint # added constraint: constraint((T0341)A169.CB, (T0341)G178.CA) [> 3.0585 = 5.0975 < 6.6268] w=0.1775 to align # Constraint # added constraint: constraint((T0341)I221.CB, (T0341)I254.CB) [> 4.1899 = 6.9832 < 9.0782] w=0.1754 to align # Constraint # added constraint: constraint((T0341)V45.CB, (T0341)F185.CB) [> 4.0882 = 6.8136 < 8.8577] w=0.1735 to align # Constraint # added constraint: constraint((T0341)Q29.CB, (T0341)F65.CB) [> 3.7341 = 6.2234 < 8.0905] w=0.1734 to align # Constraint # added constraint: constraint((T0341)L57.CB, (T0341)I67.CB) [> 3.7459 = 6.2432 < 8.1161] w=0.1734 to align # Constraint # added constraint: constraint((T0341)R147.CB, (T0341)Y168.CB) [> 3.0990 = 5.1649 < 6.7144] w=0.1734 to align # Constraint # added constraint: constraint((T0341)A213.CB, (T0341)Y241.CB) [> 4.3236 = 7.2059 < 9.3677] w=0.1732 to align # Constraint # added constraint: constraint((T0341)F44.CB, (T0341)L60.CB) [> 4.1722 = 6.9536 < 9.0397] w=0.1726 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)P139.CB) [> 4.3345 = 7.2242 < 9.3915] w=0.1724 to align # Constraint # added constraint: constraint((T0341)I143.CB, (T0341)Y168.CB) [> 3.6538 = 6.0897 < 7.9166] w=0.1700 to align # Constraint # added constraint: constraint((T0341)E167.CB, (T0341)D191.CB) [> 3.9618 = 6.6030 < 8.5840] w=0.1699 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)V25.CB) [> 3.8638 = 6.4397 < 8.3716] w=0.1699 to align # Constraint # added constraint: constraint((T0341)L32.CB, (T0341)L60.CB) [> 3.9701 = 6.6167 < 8.6018] w=0.1674 to align # Constraint # added constraint: constraint((T0341)A213.CB, (T0341)K235.CB) [> 3.1619 = 5.2698 < 6.8507] w=0.1667 to align # Constraint # added constraint: constraint((T0341)A24.CB, (T0341)L63.CB) [> 3.2080 = 5.3467 < 6.9506] w=0.1667 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)F44.CB) [> 4.6442 = 7.7404 < 10.0625] w=0.1650 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)L32.CB) [> 4.6529 = 7.7548 < 10.0812] w=0.1650 to align # Constraint # added constraint: constraint((T0341)E21.CB, (T0341)E120.CB) [> 4.2544 = 7.0907 < 9.2179] w=0.1645 to align # Constraint # added constraint: constraint((T0341)G27.CA, (T0341)V105.CB) [> 3.8014 = 6.3357 < 8.2364] w=0.1641 to align # Constraint # added constraint: constraint((T0341)A169.CB, (T0341)F184.CB) [> 3.6545 = 6.0908 < 7.9181] w=0.1624 to align # Constraint # added constraint: constraint((T0341)G16.CA, (T0341)V25.CB) [> 4.0901 = 6.8169 < 8.8620] w=0.1615 to align # Constraint # added constraint: constraint((T0341)K224.CB, (T0341)S246.CB) [> 4.1971 = 6.9951 < 9.0936] w=0.1584 to align # Constraint # added constraint: constraint((T0341)D209.CB, (T0341)G220.CA) [> 4.4566 = 7.4277 < 9.6560] w=0.1584 to align # Constraint # added constraint: constraint((T0341)L14.CB, (T0341)V45.CB) [> 4.3623 = 7.2705 < 9.4516] w=0.1584 to align # Constraint # added constraint: constraint((T0341)H123.CB, (T0341)P159.CB) [> 3.7449 = 6.2414 < 8.1139] w=0.1584 to align # Constraint # added constraint: constraint((T0341)L127.CB, (T0341)F162.CB) [> 4.4636 = 7.4394 < 9.6712] w=0.1584 to align # Constraint # added constraint: constraint((T0341)L35.CB, (T0341)L82.CB) [> 3.4353 = 5.7254 < 7.4430] w=0.1583 to align # Constraint # added constraint: constraint((T0341)P139.CB, (T0341)V163.CB) [> 3.3153 = 5.5255 < 7.1831] w=0.1582 to align # Constraint # added constraint: constraint((T0341)H123.CB, (T0341)F162.CB) [> 4.1172 = 6.8620 < 8.9206] w=0.1557 to align # Constraint # added constraint: constraint((T0341)K145.CB, (T0341)Y168.CB) [> 3.6372 = 6.0619 < 7.8805] w=0.1549 to align # Constraint # added constraint: constraint((T0341)H123.CB, (T0341)A156.CB) [> 3.9749 = 6.6249 < 8.6124] w=0.1544 to align # Constraint # added constraint: constraint((T0341)P119.CB, (T0341)Y149.CB) [> 3.4054 = 5.6757 < 7.3784] w=0.1540 to align # Constraint # added constraint: constraint((T0341)F131.CB, (T0341)L166.CB) [> 4.0926 = 6.8209 < 8.8672] w=0.1540 to align # Constraint # added constraint: constraint((T0341)Y168.CB, (T0341)A192.CB) [> 3.8709 = 6.4516 < 8.3870] w=0.1540 to align # Constraint # added constraint: constraint((T0341)P139.CB, (T0341)E167.CB) [> 3.1252 = 5.2087 < 6.7713] w=0.1540 to align # Constraint # added constraint: constraint((T0341)R43.CB, (T0341)F185.CB) [> 4.3163 = 7.1938 < 9.3520] w=0.1508 to align # Constraint # added constraint: constraint((T0341)L57.CB, (T0341)I72.CB) [> 3.6042 = 6.0071 < 7.8092] w=0.1508 to align # Constraint # added constraint: constraint((T0341)A146.CB, (T0341)Y168.CB) [> 3.5826 = 5.9711 < 7.7624] w=0.1508 to align # Constraint # added constraint: constraint((T0341)L35.CB, (T0341)A78.CB) [> 3.7478 = 6.2463 < 8.1202] w=0.1508 to align # Constraint # added constraint: constraint((T0341)T38.CB, (T0341)L82.CB) [> 3.7626 = 6.2709 < 8.1522] w=0.1508 to align # Constraint # added constraint: constraint((T0341)T225.CB, (T0341)C244.CB) [> 3.9597 = 6.5995 < 8.5794] w=0.1507 to align # Constraint # added constraint: constraint((T0341)L18.CB, (T0341)F131.CB) [> 4.5457 = 7.5761 < 9.8489] w=0.1503 to align # Constraint # added constraint: constraint((T0341)G154.CA, (T0341)L166.CB) [> 4.4465 = 7.4109 < 9.6342] w=0.1499 to align # Constraint # added constraint: constraint((T0341)A79.CB, (T0341)A98.CB) [> 3.5987 = 5.9978 < 7.7971] w=0.1491 to align # Constraint # added constraint: constraint((T0341)E167.CB, (T0341)F184.CB) [> 3.4080 = 5.6800 < 7.3840] w=0.1473 to align # Constraint # added constraint: constraint((T0341)C206.CB, (T0341)I236.CB) [> 3.5719 = 5.9532 < 7.7391] w=0.1441 to align # Constraint # added constraint: constraint((T0341)L63.CB, (T0341)A78.CB) [> 3.0538 = 5.0896 < 6.6165] w=0.1440 to align # Constraint # added constraint: constraint((T0341)I143.CB, (T0341)V176.CB) [> 4.4051 = 7.3418 < 9.5444] w=0.1440 to align # Constraint # added constraint: constraint((T0341)E21.CB, (T0341)P119.CB) [> 3.5485 = 5.9142 < 7.6885] w=0.1440 to align # Constraint # added constraint: constraint((T0341)L57.CB, (T0341)E69.CB) [> 3.3704 = 5.6173 < 7.3025] w=0.1433 to align # Constraint # added constraint: constraint((T0341)P110.CB, (T0341)P119.CB) [> 4.0596 = 6.7660 < 8.7958] w=0.1433 to align # Constraint # added constraint: constraint((T0341)D22.CB, (T0341)K227.CB) [> 3.5994 = 5.9989 < 7.7986] w=0.1433 to align # Constraint # added constraint: constraint((T0341)A31.CB, (T0341)F102.CB) [> 3.5918 = 5.9863 < 7.7822] w=0.1432 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)D205.CB) [> 4.4396 = 7.3994 < 9.6192] w=0.1432 to align # Constraint # added constraint: constraint((T0341)E198.CB, (T0341)L219.CB) [> 4.0256 = 6.7093 < 8.7221] w=0.1431 to align # Constraint # added constraint: constraint((T0341)A28.CB, (T0341)Q106.CB) [> 3.1722 = 5.2870 < 6.8731] w=0.1431 to align # Constraint # added constraint: constraint((T0341)L222.CB, (T0341)Y241.CB) [> 3.6860 = 6.1433 < 7.9863] w=0.1421 to align # Constraint # added constraint: constraint((T0341)N47.CB, (T0341)H144.CB) [> 2.6372 = 4.3954 < 5.7140] w=0.1416 to align # Constraint # added constraint: constraint((T0341)R80.CB, (T0341)L99.CB) [> 3.7328 = 6.2213 < 8.0878] w=0.1415 to align # Constraint # added constraint: constraint((T0341)L135.CB, (T0341)A165.CB) [> 3.8695 = 6.4492 < 8.3840] w=0.1389 to align # Constraint # added constraint: constraint((T0341)V210.CB, (T0341)P239.CB) [> 3.5926 = 5.9876 < 7.7839] w=0.1365 to align # Constraint # added constraint: constraint((T0341)A142.CB, (T0341)V176.CB) [> 3.2176 = 5.3626 < 6.9714] w=0.1365 to align # Constraint # added constraint: constraint((T0341)L35.CB, (T0341)L60.CB) [> 3.8274 = 6.3790 < 8.2927] w=0.1363 to align # Constraint # added constraint: constraint((T0341)L56.CB, (T0341)I72.CB) [> 3.0039 = 5.0065 < 6.5084] w=0.1358 to align # Constraint # added constraint: constraint((T0341)C206.CB, (T0341)Y228.CB) [> 3.0791 = 5.1318 < 6.6714] w=0.1358 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)G226.CA) [> 4.2856 = 7.1427 < 9.2855] w=0.1358 to align # Constraint # added constraint: constraint((T0341)L127.CB, (T0341)P159.CB) [> 4.3364 = 7.2274 < 9.3956] w=0.1358 to align # Constraint # added constraint: constraint((T0341)V45.CB, (T0341)D209.CB) [> 4.7059 = 7.8432 < 10.1961] w=0.1358 to align # Constraint # added constraint: constraint((T0341)A31.CB, (T0341)V251.CB) [> 2.6634 = 4.4390 < 5.7707] w=0.1358 to align # Constraint # added constraint: constraint((T0341)L7.CB, (T0341)V40.CB) [> 4.2138 = 7.0229 < 9.1298] w=0.1357 to align # Constraint # added constraint: constraint((T0341)K150.CB, (T0341)A169.CB) [> 3.4990 = 5.8317 < 7.5813] w=0.1357 to align # Constraint # added constraint: constraint((T0341)A199.CB, (T0341)A213.CB) [> 4.7100 = 7.8500 < 10.2050] w=0.1357 to align # Constraint # added constraint: constraint((T0341)L134.CB, (T0341)I254.CB) [> 4.3078 = 7.1797 < 9.3337] w=0.1355 to align # Constraint # added constraint: constraint((T0341)A213.CB, (T0341)L222.CB) [> 3.7528 = 6.2547 < 8.1311] w=0.1354 to align # Constraint # added constraint: constraint((T0341)V210.CB, (T0341)I221.CB) [> 4.6792 = 7.7987 < 10.1383] w=0.1305 to align # Constraint # added constraint: constraint((T0341)V223.CB, (T0341)H249.CB) [> 4.5189 = 7.5315 < 9.7909] w=0.1296 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)P159.CB) [> 3.6936 = 6.1560 < 8.0028] w=0.1289 to align # Constraint # added constraint: constraint((T0341)K145.CB, (T0341)V163.CB) [> 3.4563 = 5.7605 < 7.4886] w=0.1289 to align # Constraint # added constraint: constraint((T0341)V40.CB, (T0341)K86.CB) [> 3.8178 = 6.3631 < 8.2720] w=0.1288 to align # Constraint # added constraint: constraint((T0341)H144.CB, (T0341)V176.CB) [> 3.8437 = 6.4061 < 8.3280] w=0.1221 to align # Constraint # added constraint: constraint((T0341)K145.CB, (T0341)V176.CB) [> 3.2888 = 5.4814 < 7.1258] w=0.1214 to align # Constraint # added constraint: constraint((T0341)R147.CB, (T0341)L166.CB) [> 3.5111 = 5.8518 < 7.6074] w=0.1213 to align # Constraint # added constraint: constraint((T0341)L140.CB, (T0341)G160.CA) [> 3.8723 = 6.4538 < 8.3899] w=0.1212 to align # Constraint # added constraint: constraint((T0341)L222.CB, (T0341)I236.CB) [> 3.6411 = 6.0684 < 7.8889] w=0.1211 to align # Constraint # added constraint: constraint((T0341)V25.CB, (T0341)F247.CB) [> 4.0374 = 6.7291 < 8.7478] w=0.1207 to align # Constraint # added constraint: constraint((T0341)G27.CA, (T0341)F102.CB) [> 4.2525 = 7.0876 < 9.2138] w=0.1207 to align # Constraint # added constraint: constraint((T0341)D204.CB, (T0341)F247.CB) [> 4.1410 = 6.9016 < 8.9721] w=0.1207 to align # Constraint # added constraint: constraint((T0341)E167.CB, (T0341)A192.CB) [> 4.1256 = 6.8760 < 8.9389] w=0.1206 to align # Constraint # added constraint: constraint((T0341)T38.CB, (T0341)A98.CB) [> 4.2955 = 7.1592 < 9.3069] w=0.1206 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)M175.CB) [> 3.1748 = 5.2914 < 6.8788] w=0.1206 to align # Constraint # added constraint: constraint((T0341)P90.CB, (T0341)L99.CB) [> 3.4239 = 5.7064 < 7.4184] w=0.1205 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)L127.CB) [> 4.3554 = 7.2589 < 9.4366] w=0.1203 to align # Constraint # added constraint: constraint((T0341)L76.CB, (T0341)L99.CB) [> 3.4531 = 5.7552 < 7.4818] w=0.1189 to align # Constraint # added constraint: constraint((T0341)P139.CB, (T0341)A165.CB) [> 4.6192 = 7.6987 < 10.0083] w=0.1172 to align # Constraint # added constraint: constraint((T0341)L135.CB, (T0341)F162.CB) [> 3.7775 = 6.2959 < 8.1847] w=0.1172 to align # Constraint # added constraint: constraint((T0341)L14.CB, (T0341)L166.CB) [> 4.3345 = 7.2242 < 9.3915] w=0.1169 to align # Constraint # added constraint: constraint((T0341)L60.CB, (T0341)L82.CB) [> 3.8642 = 6.4404 < 8.3725] w=0.1145 to align # Constraint # added constraint: constraint((T0341)A142.CB, (T0341)M175.CB) [> 4.1959 = 6.9932 < 9.0911] w=0.1139 to align # Constraint # added constraint: constraint((T0341)S75.CB, (T0341)V177.CB) [> 3.5444 = 5.9073 < 7.6795] w=0.1139 to align # Constraint # added constraint: constraint((T0341)R43.CB, (T0341)A192.CB) [> 3.9784 = 6.6307 < 8.6199] w=0.1131 to align # Constraint # added constraint: constraint((T0341)A31.CB, (T0341)F247.CB) [> 2.9488 = 4.9148 < 6.3892] w=0.1131 to align # Constraint # added constraint: constraint((T0341)A28.CB, (T0341)F247.CB) [> 3.1401 = 5.2335 < 6.8035] w=0.1131 to align # Constraint # added constraint: constraint((T0341)V45.CB, (T0341)G212.CA) [> 4.5887 = 7.6479 < 9.9422] w=0.1131 to align # Constraint # added constraint: constraint((T0341)L140.CB, (T0341)M175.CB) [> 4.1427 = 6.9045 < 8.9759] w=0.1131 to align # Constraint # added constraint: constraint((T0341)I143.CB, (T0341)V177.CB) [> 3.3627 = 5.6045 < 7.2859] w=0.1131 to align # Constraint # added constraint: constraint((T0341)L35.CB, (T0341)A98.CB) [> 4.2637 = 7.1062 < 9.2381] w=0.1131 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)F247.CB) [> 4.3832 = 7.3054 < 9.4970] w=0.1131 to align # Constraint # added constraint: constraint((T0341)E198.CB, (T0341)M218.CB) [> 4.5988 = 7.6647 < 9.9641] w=0.1131 to align # Constraint # added constraint: constraint((T0341)A142.CB, (T0341)L166.CB) [> 3.5444 = 5.9073 < 7.6795] w=0.1129 to align # Constraint # added constraint: constraint((T0341)V200.CB, (T0341)L258.CB) [> 4.3103 = 7.1839 < 9.3391] w=0.1078 to align # Constraint # added constraint: constraint((T0341)I202.CB, (T0341)I254.CB) [> 4.3384 = 7.2306 < 9.3998] w=0.1076 to align # Constraint # added constraint: constraint((T0341)L32.CB, (T0341)A79.CB) [> 4.1242 = 6.8737 < 8.9358] w=0.1070 to align # Constraint # added constraint: constraint((T0341)L140.CB, (T0341)P159.CB) [> 3.2416 = 5.4026 < 7.0234] w=0.1063 to align # Constraint # added constraint: constraint((T0341)T38.CB, (T0341)K86.CB) [> 4.1062 = 6.8437 < 8.8968] w=0.1056 to align # Constraint # added constraint: constraint((T0341)L32.CB, (T0341)I67.CB) [> 3.9375 = 6.5624 < 8.5312] w=0.1056 to align # Constraint # added constraint: constraint((T0341)L63.CB, (T0341)T77.CB) [> 3.2348 = 5.3913 < 7.0088] w=0.1056 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)T48.CB) [> 4.5435 = 7.5725 < 9.8443] w=0.1056 to align # Constraint # added constraint: constraint((T0341)I143.CB, (T0341)G178.CA) [> 3.6871 = 6.1452 < 7.9887] w=0.1056 to align # Constraint # added constraint: constraint((T0341)K33.CB, (T0341)V105.CB) [> 3.5953 = 5.9921 < 7.7898] w=0.1056 to align # Constraint # added constraint: constraint((T0341)L35.CB, (T0341)A79.CB) [> 3.3999 = 5.6665 < 7.3665] w=0.1055 to align # Constraint # added constraint: constraint((T0341)G203.CA, (T0341)K224.CB) [> 3.8743 = 6.4571 < 8.3943] w=0.1053 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)P119.CB) [> 4.1961 = 6.9935 < 9.0915] w=0.1045 to align # Constraint # added constraint: constraint((T0341)G220.CA, (T0341)P239.CB) [> 3.9896 = 6.6493 < 8.6440] w=0.1043 to align # Constraint # added constraint: constraint((T0341)M41.CB, (T0341)T52.CB) [> 3.6777 = 6.1295 < 7.9684] w=0.1038 to align # Constraint # added constraint: constraint((T0341)R59.CB, (T0341)L82.CB) [> 3.5363 = 5.8938 < 7.6620] w=0.0994 to align # Constraint # added constraint: constraint((T0341)A146.CB, (T0341)G160.CA) [> 3.2822 = 5.4704 < 7.1115] w=0.0987 to align # Constraint # added constraint: constraint((T0341)H144.CB, (T0341)D208.CB) [> 3.7674 = 6.2790 < 8.1627] w=0.0987 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)D205.CB) [> 4.1578 = 6.9296 < 9.0085] w=0.0985 to align # Constraint # added constraint: constraint((T0341)A142.CB, (T0341)V177.CB) [> 4.2422 = 7.0703 < 9.1914] w=0.0981 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)V177.CB) [> 3.9468 = 6.5779 < 8.5513] w=0.0981 to align # Constraint # added constraint: constraint((T0341)L92.CB, (T0341)V113.CB) [> 3.2292 = 5.3820 < 6.9966] w=0.0981 to align # Constraint # added constraint: constraint((T0341)G226.CA, (T0341)F247.CB) [> 4.6329 = 7.7215 < 10.0380] w=0.0980 to align # Constraint # added constraint: constraint((T0341)D205.CB, (T0341)G226.CA) [> 4.2666 = 7.1111 < 9.2444] w=0.0980 to align # Constraint # added constraint: constraint((T0341)T46.CB, (T0341)T74.CB) [> 3.2894 = 5.4824 < 7.1271] w=0.0972 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)V42.CB) [> 4.4840 = 7.4733 < 9.7153] w=0.0972 to align # Constraint # added constraint: constraint((T0341)L18.CB, (T0341)L60.CB) [> 4.5270 = 7.5450 < 9.8085] w=0.0972 to align # Constraint # added constraint: constraint((T0341)L76.CB, (T0341)A98.CB) [> 3.0206 = 5.0344 < 6.5447] w=0.0963 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)T164.CB) [> 4.0718 = 6.7863 < 8.8223] w=0.0918 to align # Constraint # added constraint: constraint((T0341)M218.CB, (T0341)Y241.CB) [> 3.7237 = 6.2062 < 8.0681] w=0.0912 to align # Constraint # added constraint: constraint((T0341)G220.CA, (T0341)T243.CB) [> 4.3421 = 7.2368 < 9.4079] w=0.0912 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)P161.CB) [> 3.9408 = 6.5679 < 8.5383] w=0.0911 to align # Constraint # added constraint: constraint((T0341)A213.CB, (T0341)P239.CB) [> 3.7218 = 6.2030 < 8.0638] w=0.0910 to align # Constraint # added constraint: constraint((T0341)T46.CB, (T0341)I72.CB) [> 4.5645 = 7.6075 < 9.8897] w=0.0905 to align # Constraint # added constraint: constraint((T0341)V45.CB, (T0341)A188.CB) [> 3.7688 = 6.2813 < 8.1657] w=0.0905 to align # Constraint # added constraint: constraint((T0341)V45.CB, (T0341)F73.CB) [> 3.1651 = 5.2752 < 6.8577] w=0.0905 to align # Constraint # added constraint: constraint((T0341)F44.CB, (T0341)F73.CB) [> 4.1674 = 6.9457 < 9.0294] w=0.0905 to align # Constraint # added constraint: constraint((T0341)F44.CB, (T0341)I72.CB) [> 3.0251 = 5.0419 < 6.5545] w=0.0905 to align # Constraint # added constraint: constraint((T0341)R43.CB, (T0341)F73.CB) [> 3.3478 = 5.5797 < 7.2537] w=0.0905 to align # Constraint # added constraint: constraint((T0341)R43.CB, (T0341)I72.CB) [> 4.5418 = 7.5697 < 9.8406] w=0.0905 to align # Constraint # added constraint: constraint((T0341)V25.CB, (T0341)T225.CB) [> 3.3608 = 5.6014 < 7.2818] w=0.0905 to align # Constraint # added constraint: constraint((T0341)L76.CB, (T0341)I143.CB) [> 3.5427 = 5.9046 < 7.6760] w=0.0905 to align # Constraint # added constraint: constraint((T0341)F73.CB, (T0341)A188.CB) [> 3.6673 = 6.1122 < 7.9458] w=0.0905 to align # Constraint # added constraint: constraint((T0341)T49.CB, (T0341)S75.CB) [> 2.9116 = 4.8526 < 6.3084] w=0.0905 to align # Constraint # added constraint: constraint((T0341)T49.CB, (T0341)T74.CB) [> 3.5008 = 5.8346 < 7.5850] w=0.0905 to align # Constraint # added constraint: constraint((T0341)T48.CB, (T0341)S75.CB) [> 4.1297 = 6.8828 < 8.9476] w=0.0905 to align # Constraint # added constraint: constraint((T0341)N47.CB, (T0341)S75.CB) [> 2.9361 = 4.8935 < 6.3616] w=0.0905 to align # Constraint # added constraint: constraint((T0341)T46.CB, (T0341)S75.CB) [> 4.2708 = 7.1179 < 9.2533] w=0.0905 to align # Constraint # added constraint: constraint((T0341)T46.CB, (T0341)F73.CB) [> 4.6341 = 7.7235 < 10.0405] w=0.0905 to align # Constraint # added constraint: constraint((T0341)L133.CB, (T0341)F162.CB) [> 3.6710 = 6.1184 < 7.9539] w=0.0905 to align # Constraint # added constraint: constraint((T0341)V200.CB, (T0341)L242.CB) [> 4.1001 = 6.8335 < 8.8836] w=0.0905 to align # Constraint # added constraint: constraint((T0341)K8.CB, (T0341)E197.CB) [> 3.6932 = 6.1554 < 8.0020] w=0.0905 to align # Constraint # added constraint: constraint((T0341)V88.CB, (T0341)A98.CB) [> 3.5265 = 5.8775 < 7.6408] w=0.0904 to align # Constraint # added constraint: constraint((T0341)I143.CB, (T0341)F185.CB) [> 3.7230 = 6.2049 < 8.0664] w=0.0902 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)P139.CB) [> 4.6709 = 7.7848 < 10.1202] w=0.0896 to align # Constraint # added constraint: constraint((T0341)V223.CB, (T0341)L242.CB) [> 3.5066 = 5.8444 < 7.5977] w=0.0894 to align # Constraint # added constraint: constraint((T0341)P139.CB, (T0341)Y168.CB) [> 4.5239 = 7.5399 < 9.8019] w=0.0861 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)K224.CB) [> 4.2239 = 7.0398 < 9.1518] w=0.0840 to align # Constraint # added constraint: constraint((T0341)G203.CA, (T0341)T225.CB) [> 3.8562 = 6.4270 < 8.3551] w=0.0836 to align # Constraint # added constraint: constraint((T0341)D95.CB, (T0341)L117.CB) [> 3.5978 = 5.9964 < 7.7953] w=0.0830 to align # Constraint # added constraint: constraint((T0341)D95.CB, (T0341)G116.CA) [> 2.7871 = 4.6453 < 6.0388] w=0.0830 to align # Constraint # added constraint: constraint((T0341)L94.CB, (T0341)I115.CB) [> 2.9212 = 4.8687 < 6.3293] w=0.0830 to align # Constraint # added constraint: constraint((T0341)L92.CB, (T0341)V114.CB) [> 4.1830 = 6.9717 < 9.0632] w=0.0830 to align # Constraint # added constraint: constraint((T0341)I115.CB, (T0341)I141.CB) [> 3.9644 = 6.6073 < 8.5894] w=0.0830 to align # Constraint # added constraint: constraint((T0341)A78.CB, (T0341)T183.CB) [> 3.9713 = 6.6189 < 8.6046] w=0.0830 to align # Constraint # added constraint: constraint((T0341)G116.CA, (T0341)I143.CB) [> 3.1525 = 5.2542 < 6.8305] w=0.0830 to align # Constraint # added constraint: constraint((T0341)I115.CB, (T0341)A142.CB) [> 3.5987 = 5.9978 < 7.7971] w=0.0830 to align # Constraint # added constraint: constraint((T0341)V114.CB, (T0341)I141.CB) [> 3.3841 = 5.6402 < 7.3322] w=0.0830 to align # Constraint # added constraint: constraint((T0341)A142.CB, (T0341)P159.CB) [> 3.3737 = 5.6228 < 7.3097] w=0.0830 to align # Constraint # added constraint: constraint((T0341)F65.CB, (T0341)V177.CB) [> 3.8620 = 6.4367 < 8.3677] w=0.0830 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)I141.CB) [> 4.1867 = 6.9779 < 9.0713] w=0.0829 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)C244.CB) [> 4.3352 = 7.2254 < 9.3930] w=0.0829 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)C244.CB) [> 3.0682 = 5.1136 < 6.6477] w=0.0829 to align # Constraint # added constraint: constraint((T0341)A6.CB, (T0341)E197.CB) [> 3.8762 = 6.4603 < 8.3984] w=0.0829 to align # Constraint # added constraint: constraint((T0341)L219.CB, (T0341)P240.CB) [> 3.2591 = 5.4319 < 7.0614] w=0.0827 to align # Constraint # added constraint: constraint((T0341)A28.CB, (T0341)L63.CB) [> 4.4119 = 7.3531 < 9.5591] w=0.0762 to align # Constraint # added constraint: constraint((T0341)A146.CB, (T0341)V163.CB) [> 4.0497 = 6.7495 < 8.7743] w=0.0761 to align # Constraint # added constraint: constraint((T0341)M91.CB, (T0341)P110.CB) [> 3.4004 = 5.6672 < 7.3674] w=0.0754 to align # Constraint # added constraint: constraint((T0341)M91.CB, (T0341)A112.CB) [> 3.0213 = 5.0355 < 6.5462] w=0.0754 to align # Constraint # added constraint: constraint((T0341)L93.CB, (T0341)V114.CB) [> 3.0876 = 5.1460 < 6.6899] w=0.0754 to align # Constraint # added constraint: constraint((T0341)L94.CB, (T0341)V114.CB) [> 4.3209 = 7.2015 < 9.3619] w=0.0754 to align # Constraint # added constraint: constraint((T0341)V113.CB, (T0341)P139.CB) [> 3.8077 = 6.3461 < 8.2499] w=0.0754 to align # Constraint # added constraint: constraint((T0341)C206.CB, (T0341)N237.CB) [> 3.6300 = 6.0500 < 7.8650] w=0.0754 to align # Constraint # added constraint: constraint((T0341)L134.CB, (T0341)L166.CB) [> 3.9990 = 6.6649 < 8.6644] w=0.0754 to align # Constraint # added constraint: constraint((T0341)V114.CB, (T0341)I143.CB) [> 4.3580 = 7.2633 < 9.4422] w=0.0754 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)F247.CB) [> 4.4387 = 7.3978 < 9.6171] w=0.0754 to align # Constraint # added constraint: constraint((T0341)F44.CB, (T0341)R59.CB) [> 3.8396 = 6.3993 < 8.3191] w=0.0754 to align # Constraint # added constraint: constraint((T0341)Q214.CB, (T0341)I236.CB) [> 4.2193 = 7.0321 < 9.1418] w=0.0753 to align # Constraint # added constraint: constraint((T0341)V45.CB, (T0341)T74.CB) [> 4.5647 = 7.6079 < 9.8902] w=0.0745 to align # Constraint # added constraint: constraint((T0341)R43.CB, (T0341)F65.CB) [> 3.6272 = 6.0453 < 7.8588] w=0.0745 to align # Constraint # added constraint: constraint((T0341)V42.CB, (T0341)F65.CB) [> 3.4967 = 5.8278 < 7.5762] w=0.0745 to align # Constraint # added constraint: constraint((T0341)H144.CB, (T0341)Y168.CB) [> 4.2959 = 7.1599 < 9.3078] w=0.0737 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)V163.CB) [> 4.3063 = 7.1771 < 9.3303] w=0.0737 to align # Constraint # added constraint: constraint((T0341)L140.CB, (T0341)Y168.CB) [> 4.4943 = 7.4906 < 9.7377] w=0.0728 to align # Constraint # added constraint: constraint((T0341)L140.CB, (T0341)P161.CB) [> 4.3882 = 7.3136 < 9.5077] w=0.0684 to align # Constraint # added constraint: constraint((T0341)C206.CB, (T0341)K227.CB) [> 4.4705 = 7.4509 < 9.6861] w=0.0679 to align # Constraint # added constraint: constraint((T0341)A146.CB, (T0341)D208.CB) [> 4.3019 = 7.1698 < 9.3208] w=0.0679 to align # Constraint # added constraint: constraint((T0341)I143.CB, (T0341)P159.CB) [> 3.6204 = 6.0341 < 7.8443] w=0.0679 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)G226.CA) [> 4.5652 = 7.6087 < 9.8913] w=0.0679 to align # Constraint # added constraint: constraint((T0341)M91.CB, (T0341)V113.CB) [> 4.1174 = 6.8623 < 8.9211] w=0.0679 to align # Constraint # added constraint: constraint((T0341)L92.CB, (T0341)A130.CB) [> 3.7313 = 6.2189 < 8.0845] w=0.0679 to align # Constraint # added constraint: constraint((T0341)Y148.CB, (T0341)P161.CB) [> 4.0069 = 6.6781 < 8.6816] w=0.0679 to align # Constraint # added constraint: constraint((T0341)L117.CB, (T0341)H144.CB) [> 4.5352 = 7.5586 < 9.8262] w=0.0679 to align # Constraint # added constraint: constraint((T0341)R36.CB, (T0341)I67.CB) [> 4.6284 = 7.7140 < 10.0282] w=0.0679 to align # Constraint # added constraint: constraint((T0341)A31.CB, (T0341)L255.CB) [> 4.0591 = 6.7652 < 8.7948] w=0.0679 to align # Constraint # added constraint: constraint((T0341)G203.CA, (T0341)L242.CB) [> 4.3052 = 7.1753 < 9.3278] w=0.0678 to align # Constraint # added constraint: constraint((T0341)L11.CB, (T0341)I143.CB) [> 3.3205 = 5.5342 < 7.1944] w=0.0678 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)A192.CB) [> 3.3771 = 5.6285 < 7.3170] w=0.0678 to align # Constraint # added constraint: constraint((T0341)P119.CB, (T0341)L166.CB) [> 3.2708 = 5.4513 < 7.0866] w=0.0677 to align # Constraint # added constraint: constraint((T0341)V200.CB, (T0341)L222.CB) [> 4.4341 = 7.3902 < 9.6073] w=0.0677 to align # Constraint # added constraint: constraint((T0341)P90.CB, (T0341)P110.CB) [> 3.2836 = 5.4726 < 7.1144] w=0.0603 to align # Constraint # added constraint: constraint((T0341)V114.CB, (T0341)A142.CB) [> 4.3761 = 7.2935 < 9.4815] w=0.0603 to align # Constraint # added constraint: constraint((T0341)L94.CB, (T0341)V113.CB) [> 4.3520 = 7.2533 < 9.4293] w=0.0603 to align # Constraint # added constraint: constraint((T0341)L93.CB, (T0341)I115.CB) [> 4.2781 = 7.1302 < 9.2692] w=0.0603 to align # Constraint # added constraint: constraint((T0341)H144.CB, (T0341)P159.CB) [> 3.0198 = 5.0330 < 6.5429] w=0.0603 to align # Constraint # added constraint: constraint((T0341)L134.CB, (T0341)T172.CB) [> 3.2381 = 5.3968 < 7.0158] w=0.0603 to align # Constraint # added constraint: constraint((T0341)L94.CB, (T0341)A130.CB) [> 3.4028 = 5.6713 < 7.3727] w=0.0603 to align # Constraint # added constraint: constraint((T0341)L94.CB, (T0341)P119.CB) [> 3.3736 = 5.6226 < 7.3094] w=0.0603 to align # Constraint # added constraint: constraint((T0341)I20.CB, (T0341)A118.CB) [> 3.3838 = 5.6397 < 7.3316] w=0.0603 to align # Constraint # added constraint: constraint((T0341)I115.CB, (T0341)L166.CB) [> 3.7670 = 6.2783 < 8.1618] w=0.0603 to align # Constraint # added constraint: constraint((T0341)P139.CB, (T0341)M175.CB) [> 3.9696 = 6.6160 < 8.6008] w=0.0603 to align # Constraint # added constraint: constraint((T0341)E64.CB, (T0341)L76.CB) [> 3.8373 = 6.3955 < 8.3141] w=0.0603 to align # Constraint # added constraint: constraint((T0341)V42.CB, (T0341)I67.CB) [> 3.1845 = 5.3075 < 6.8998] w=0.0603 to align # Constraint # added constraint: constraint((T0341)R4.CB, (T0341)V200.CB) [> 4.5188 = 7.5313 < 9.7907] w=0.0603 to align # Constraint # added constraint: constraint((T0341)L7.CB, (T0341)G217.CA) [> 4.5493 = 7.5822 < 9.8568] w=0.0603 to align # Constraint # added constraint: constraint((T0341)A142.CB, (T0341)A165.CB) [> 4.3473 = 7.2454 < 9.4191] w=0.0603 to align # Constraint # added constraint: constraint((T0341)A31.CB, (T0341)I83.CB) [> 3.5993 = 5.9988 < 7.7984] w=0.0603 to align # Constraint # added constraint: constraint((T0341)P119.CB, (T0341)A165.CB) [> 4.4274 = 7.3790 < 9.5927] w=0.0602 to align # Constraint # added constraint: constraint((T0341)L76.CB, (T0341)R97.CB) [> 3.6382 = 6.0636 < 7.8827] w=0.0586 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)L258.CB) [> 4.3672 = 7.2786 < 9.4622] w=0.0551 to align # Constraint # added constraint: constraint((T0341)V163.CB, (T0341)M175.CB) [> 3.7744 = 6.2907 < 8.1779] w=0.0535 to align # Constraint # added constraint: constraint((T0341)H144.CB, (T0341)A165.CB) [> 3.9641 = 6.6068 < 8.5888] w=0.0534 to align # Constraint # added constraint: constraint((T0341)V113.CB, (T0341)A130.CB) [> 3.1784 = 5.2973 < 6.8865] w=0.0528 to align # Constraint # added constraint: constraint((T0341)V88.CB, (T0341)A112.CB) [> 3.4313 = 5.7188 < 7.4344] w=0.0528 to align # Constraint # added constraint: constraint((T0341)T74.CB, (T0341)P119.CB) [> 4.0377 = 6.7295 < 8.7483] w=0.0528 to align # Constraint # added constraint: constraint((T0341)R43.CB, (T0341)S68.CB) [> 3.2163 = 5.3605 < 6.9686] w=0.0528 to align # Constraint # added constraint: constraint((T0341)I83.CB, (T0341)V114.CB) [> 4.2732 = 7.1220 < 9.2586] w=0.0528 to align # Constraint # added constraint: constraint((T0341)R4.CB, (T0341)L219.CB) [> 4.1728 = 6.9546 < 9.0410] w=0.0528 to align # Constraint # added constraint: constraint((T0341)R5.CB, (T0341)E198.CB) [> 3.5678 = 5.9463 < 7.7302] w=0.0527 to align # Constraint # added constraint: constraint((T0341)V163.CB, (T0341)V177.CB) [> 3.8973 = 6.4955 < 8.4441] w=0.0526 to align # Constraint # added constraint: constraint((T0341)K224.CB, (T0341)L242.CB) [> 4.4111 = 7.3518 < 9.5573] w=0.0519 to align # Constraint # added constraint: constraint((T0341)T46.CB, (T0341)I67.CB) [> 4.2132 = 7.0219 < 9.1285] w=0.0519 to align # Constraint # added constraint: constraint((T0341)T46.CB, (T0341)S68.CB) [> 3.2233 = 5.3721 < 6.9837] w=0.0519 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)N47.CB) [> 4.0160 = 6.6933 < 8.7013] w=0.0519 to align # Constraint # added constraint: constraint((T0341)A24.CB, (T0341)D204.CB) [> 3.6695 = 6.1159 < 7.9506] w=0.0516 to align # Constraint # added constraint: constraint((T0341)V25.CB, (T0341)F102.CB) [> 3.8590 = 6.4317 < 8.3612] w=0.0511 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)H144.CB) [> 4.3515 = 7.2525 < 9.4282] w=0.0510 to align # Constraint # added constraint: constraint((T0341)A6.CB, (T0341)C194.CB) [> 4.5084 = 7.5140 < 9.7682] w=0.0475 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)A31.CB) [> 3.5079 = 5.8465 < 7.6005] w=0.0467 to align # Constraint # added constraint: constraint((T0341)A142.CB, (T0341)T164.CB) [> 4.3679 = 7.2799 < 9.4638] w=0.0466 to align # Constraint # added constraint: constraint((T0341)D205.CB, (T0341)T225.CB) [> 4.1866 = 6.9777 < 9.0711] w=0.0459 to align # Constraint # added constraint: constraint((T0341)I143.CB, (T0341)A165.CB) [> 4.1779 = 6.9631 < 9.0521] w=0.0459 to align # Constraint # added constraint: constraint((T0341)I143.CB, (T0341)T164.CB) [> 3.4967 = 5.8279 < 7.5762] w=0.0459 to align # Constraint # added constraint: constraint((T0341)E30.CB, (T0341)F247.CB) [> 4.3288 = 7.2146 < 9.3790] w=0.0453 to align # Constraint # added constraint: constraint((T0341)V88.CB, (T0341)P139.CB) [> 3.9596 = 6.5993 < 8.5791] w=0.0453 to align # Constraint # added constraint: constraint((T0341)V42.CB, (T0341)A192.CB) [> 4.5313 = 7.5521 < 9.8177] w=0.0453 to align # Constraint # added constraint: constraint((T0341)M41.CB, (T0341)D193.CB) [> 3.9629 = 6.6049 < 8.5863] w=0.0453 to align # Constraint # added constraint: constraint((T0341)V42.CB, (T0341)L60.CB) [> 4.4082 = 7.3470 < 9.5510] w=0.0453 to align # Constraint # added constraint: constraint((T0341)I202.CB, (T0341)K224.CB) [> 4.5662 = 7.6103 < 9.8934] w=0.0453 to align # Constraint # added constraint: constraint((T0341)L219.CB, (T0341)L258.CB) [> 4.2449 = 7.0748 < 9.1972] w=0.0452 to align # Constraint # added constraint: constraint((T0341)F44.CB, (T0341)S68.CB) [> 4.2371 = 7.0619 < 9.1805] w=0.0444 to align # Constraint # added constraint: constraint((T0341)A138.CB, (T0341)L258.CB) [> 4.5149 = 7.5249 < 9.7824] w=0.0417 to align # Constraint # added constraint: constraint((T0341)H144.CB, (T0341)T164.CB) [> 4.2363 = 7.0605 < 9.1786] w=0.0384 to align # Constraint # added constraint: constraint((T0341)Y148.CB, (T0341)L166.CB) [> 4.1131 = 6.8552 < 8.9118] w=0.0383 to align # Constraint # added constraint: constraint((T0341)L140.CB, (T0341)A199.CB) [> 4.4650 = 7.4417 < 9.6742] w=0.0377 to align # Constraint # added constraint: constraint((T0341)A3.CB, (T0341)L219.CB) [> 4.0146 = 6.6910 < 8.6983] w=0.0377 to align # Constraint # added constraint: constraint((T0341)A118.CB, (T0341)G158.CA) [> 3.2681 = 5.4468 < 7.0808] w=0.0377 to align # Constraint # added constraint: constraint((T0341)E167.CB, (T0341)F185.CB) [> 4.5858 = 7.6430 < 9.9359] w=0.0377 to align # Constraint # added constraint: constraint((T0341)H144.CB, (T0341)E167.CB) [> 4.2577 = 7.0962 < 9.2251] w=0.0377 to align # Constraint # added constraint: constraint((T0341)I83.CB, (T0341)V177.CB) [> 3.4680 = 5.7800 < 7.5140] w=0.0377 to align # Constraint # added constraint: constraint((T0341)A199.CB, (T0341)G220.CA) [> 4.2106 = 7.0176 < 9.1229] w=0.0375 to align # Constraint # added constraint: constraint((T0341)F44.CB, (T0341)E66.CB) [> 3.0665 = 5.1108 < 6.6441] w=0.0368 to align # Constraint # added constraint: constraint((T0341)F44.CB, (T0341)E64.CB) [> 4.2868 = 7.1446 < 9.2880] w=0.0368 to align # Constraint # added constraint: constraint((T0341)D204.CB, (T0341)I221.CB) [> 4.1693 = 6.9488 < 9.0334] w=0.0309 to align # Constraint # added constraint: constraint((T0341)N15.CB, (T0341)G203.CA) [> 4.4817 = 7.4694 < 9.7103] w=0.0307 to align # Constraint # added constraint: constraint((T0341)F122.CB, (T0341)A142.CB) [> 4.0138 = 6.6897 < 8.6966] w=0.0302 to align # Constraint # added constraint: constraint((T0341)N47.CB, (T0341)A142.CB) [> 4.5956 = 7.6593 < 9.9571] w=0.0302 to align # Constraint # added constraint: constraint((T0341)L127.CB, (T0341)V163.CB) [> 3.3093 = 5.5155 < 7.1701] w=0.0302 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)L222.CB) [> 3.2339 = 5.3898 < 7.0068] w=0.0234 to align # Constraint # added constraint: constraint((T0341)K53.CB, (T0341)Y228.CB) [> 3.7353 = 6.2255 < 8.0931] w=0.0226 to align # Constraint # added constraint: constraint((T0341)R43.CB, (T0341)D70.CB) [> 4.6493 = 7.7488 < 10.0735] w=0.0226 to align # Constraint # added constraint: constraint((T0341)V10.CB, (T0341)A192.CB) [> 4.6241 = 7.7069 < 10.0189] w=0.0226 to align # Constraint # added constraint: constraint((T0341)V45.CB, (T0341)G203.CA) [> 4.7616 = 7.9360 < 10.3168] w=0.0226 to align # Constraint # added constraint: constraint((T0341)R43.CB, (T0341)A199.CB) [> 4.6036 = 7.6727 < 9.9745] w=0.0226 to align # Constraint # added constraint: constraint((T0341)V12.CB, (T0341)I143.CB) [> 4.7275 = 7.8791 < 10.2429] w=0.0226 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)A199.CB) [> 4.4755 = 7.4591 < 9.6969] w=0.0226 to align # Constraint # added constraint: constraint((T0341)T74.CB, (T0341)M91.CB) [> 2.6240 = 4.3733 < 5.6852] w=0.0226 to align # Constraint # added constraint: constraint((T0341)N47.CB, (T0341)I141.CB) [> 4.5304 = 7.5507 < 9.8159] w=0.0226 to align # Constraint # added constraint: constraint((T0341)V40.CB, (T0341)P119.CB) [> 3.6814 = 6.1356 < 7.9763] w=0.0226 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)F185.CB) [> 4.1929 = 6.9881 < 9.0845] w=0.0226 to align # Constraint # added constraint: constraint((T0341)H144.CB, (T0341)F185.CB) [> 4.3455 = 7.2425 < 9.4152] w=0.0223 to align # Constraint # added constraint: constraint((T0341)L140.CB, (T0341)F185.CB) [> 4.6219 = 7.7031 < 10.0140] w=0.0151 to align # Constraint # added constraint: constraint((T0341)M91.CB, (T0341)H144.CB) [> 2.3892 = 3.9820 < 5.1765] w=0.0151 to align # Constraint # added constraint: constraint((T0341)A199.CB, (T0341)I221.CB) [> 4.4561 = 7.4268 < 9.6549] w=0.0151 to align # Constraint # added constraint: constraint((T0341)P119.CB, (T0341)I143.CB) [> 3.7405 = 6.2342 < 8.1045] w=0.0151 to align # Constraint # added constraint: constraint((T0341)H144.CB, (T0341)D204.CB) [> 4.5147 = 7.5245 < 9.7818] w=0.0151 to align # Constraint # added constraint: constraint((T0341)H121.CB, (T0341)T164.CB) [> 3.3990 = 5.6650 < 7.3645] w=0.0151 to align # Constraint # added constraint: constraint((T0341)E198.CB, (T0341)G220.CA) [> 4.7150 = 7.8584 < 10.2159] w=0.0150 to align # Constraint # added constraint: constraint((T0341)P139.CB, (T0341)A199.CB) [> 4.6057 = 7.6762 < 9.9790] w=0.0116 to align # Constraint # added constraint: constraint((T0341)P119.CB, (T0341)F247.CB) [> 4.1518 = 6.9197 < 8.9957] w=0.0075 to align # Constraint # added constraint: constraint((T0341)T17.CB, (T0341)P119.CB) [> 4.1877 = 6.9794 < 9.0732] w=0.0075 to align # Constraint # added constraint: constraint((T0341)I141.CB, (T0341)F185.CB) [> 4.5932 = 7.6553 < 9.9519] w=0.0075 to align # Constraint # added constraint: constraint((T0341)N47.CB, (T0341)L140.CB) [> 4.6262 = 7.7103 < 10.0234] w=0.0075 to align # Constraint # added constraint: constraint((T0341)L222.CB, (T0341)F247.CB) [> 3.1553 = 5.2589 < 6.8366] w=0.0075 to align # Constraint # added constraint: constraint((T0341)P119.CB, (T0341)A142.CB) [> 2.4681 = 4.1134 < 5.3475] w=0.0075 to align # Constraint # added constraint: constraint((T0341)P119.CB, (T0341)T164.CB) [> 3.8913 = 6.4855 < 8.4311] w=0.0075 to align # Constraint # added constraint: constraint((T0341)A3.CB, (T0341)E198.CB) [> 4.2008 = 7.0013 < 9.1017] w=0.0075 to align # Constraint # added constraint: constraint((T0341)D13.CB, (T0341)L222.CB) [> 4.5411 = 7.5685 < 9.8390] w=0.0008 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0341/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0341/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 21 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 200 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 241 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 246 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 242 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 203 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 203 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 257 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 26 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 31, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 396, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 Skipped atom 86, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 87, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 133, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 790, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 795, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 928, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 953, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 506, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 508, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 510, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 512, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 31, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 396, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 Skipped atom 86, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 87, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 133, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 775, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 908, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 933, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 506, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 508, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 510, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 512, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 219 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 239 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 247 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 247 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 256 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 26 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # Found a chain break before 26 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 26 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 256 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 223 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 256 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 241 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 257 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # Found a chain break before 247 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 234 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 181 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 239 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 256 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 14 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 Skipped atom 75, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 109, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 771, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 776, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 909, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 934, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 247 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 181 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 248 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 148 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 211 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 197 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 257 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 Skipped atom 79, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 80, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 113, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 771, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 776, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 901, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 926, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 Skipped atom 75, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 109, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 751, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 889, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 914, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 172 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 211 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 197 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/panther3_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0341)A118.CA and (T0341)E181.CA only 0.000 apart, marking (T0341)E181.CA as missing WARNING: atoms too close: (T0341)A118.O and (T0341)E181.O only 0.000 apart, marking (T0341)E181.O as missing WARNING: atoms too close: (T0341)A118.C and (T0341)E181.C only 0.000 apart, marking (T0341)E181.C as missing # WARNING: incomplete conformation T0341 can't currently be optimized by undertaker # naming current conformation panther3_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 0.4422 model score 0.3879 model score 0.3796 model score 0.3791 model score 0.4384 model score 0.5715 model score 0.5771 model score 0.5511 model score 0.5694 model score 0.5783 model score 0.5717 model score 0.3785 model score 0.4267 model score 0.4739 model score 0.3854 model score 0.2981 model score 0.2945 model score 0.3115 model score 0.3293 model score 0.3119 model score 2.1103 model score 1.7380 model score 1.8906 model score 1.9679 model score 1.9176 model score 0.2557 model score 0.3020 model score 0.3092 model score 0.3061 model score 0.2973 model score 0.3085 model score 0.2975 model score 0.3186 model score 0.3067 model score 0.2717 model score 0.3084 model score 0.4339 model score 0.2577 model score 0.3821 model score 0.3125 model score 0.3170 model score 0.2973 model score 1.2648 model score 1.2651 model score 1.2616 model score 1.2674 model score 1.2631 model score 0.2564 model score 0.3022 model score 0.2972 model score 0.3186 model score 0.4227 model score 0.2619 model score 0.2717 model score 0.3067 model score 0.2975 model score 0.2972 model score 0.2974 model score 0.3128 model score 0.3137 model score 0.3141 model score 0.3356 model score 1.2659 model score 1.2590 model score 1.2632 model score 1.2620 model score 1.2586 model score 1.2659 model score 1.2590 model score 1.2620 model score 1.2632 model score 1.2586 model score 2.5225 model score 2.3931 model score 2.3695 model score 2.3095 model score 2.0267 model score 0.6042 model score 0.0274 model score 0.1382 model score 0.4299 model score 0.9642 model score 1.2585 model score 1.2586 model score 1.2602 model score 1.2617 model score 0.3213 model score 0.3196 model score 0.3499 model score 0.6329 model score 0.2911 model score 0.3113 model score 0.3250 model score 0.4205 model score 0.3114 model score 0.2974 model score 0.3059 model score 0.3091 model score 0.2978 model score 0.3305 model score 0.2680 model score 0.2736 model score 0.4647 model score 0.5125 model score 0.5702 model score 0.4717 model score 0.5810 model score 0.3850 model score 0.3271 model score 0.3255 model score 0.3220 model score 0.3339 model score 0.2627 model score 0.3145 model score 0.3079 model score 0.3120 model score 0.3150 model score 0.3057 model score 0.2791 model score 0.3079 model score 0.3182 model score 0.3150 model score 0.2192 model score 0.1373 model score 0.0076 model score 0.0263 model score 0.3850 model score 0.2926 model score 0.3267 model score 0.3193 model score 0.3214 model score 0.3189 model score 0.2906 model score 0.3045 model score 0.2945 model score 0.3026 model score 0.2926 model score 0.2938 model score 0.3095 model score 0.3182 model score 0.3124 model score 0.2882 model score 0.3274 model score 0.3262 model score 0.3262 model score 0.3280 model score 0.3155 model score 0.3255 model score 0.3098 model score 0.2838 model score 0.2677 model score 0.2885 model score 0.2610 model score 0.3284 model score 0.3255 model score 0.2477 model score 0.3776 model score 0.6091 model score 0.3327 model score 0.2892 model score 0.3049 model score 0.3186 model score 0.2943 model score 0.3166 model score 0.3196 model score 0.3245 model score 0.3172 model score 0.3091 model score 0.2838 model score 0.3002 model score 0.2677 model score 0.2885 model score 0.3098 model score 0.3468 model score 0.3751 model score 0.3099 model score 0.2779 model score 0.3154 model score 1.2590 model score 1.2588 model score 1.2591 model score 1.2590 model score 1.2587 model score 1.2592 model score 1.2585 model score 1.2587 model score 1.2587 model score 1.2588 model score 0.3230 model score 0.4333 model score 0.3176 model score 0.3152 model score 0.2300 model score 0.3255 model score 0.2477 model score 0.3776 model score 0.6347 model score 0.1517 model score 0.3142 model score 0.2477 model score 0.3643 model score 0.6379 model score 0.1751 model score 0.3255 model score 0.2747 model score 0.6715 model score 0.3596 model score 0.0894 model score 1.2587 model score 1.2586 model score 1.2588 model score 1.2588 model score 1.2585 model score 0.3084 model score 1.2587 model score 1.2586 model score 1.2588 model score 1.2588 model score 1.2591 model score 0.2344 model score 0.2309 model score 0.2402 model score 0.2536 model score 0.2842 model score 0.2445 model score 0.2772 model score 1.2590 model score 1.2632 model score 1.2611 model score 1.2623 model score 1.2626 model score 1.2590 model score 1.2592 model score 1.2586 model score 1.2665 model score 1.2610 model score 0.3058 model score 0.3061 model score 0.3088 model score 0.5576 model score 0.5502 model score 0.0244 model score -0.1087 model score 0.2222 model score -0.0202 model score 0.3184 model score 0.3244 model score 0.3348 model score 0.3102 model score 0.3080 model score 0.3217 model score 0.3166 model score 0.5582 model score 0.1797 model score 0.0816 model score -0.0955 model score 0.3724 model score 0.7478 model score 0.4126 USE_META, weight: 0.8115 cost: 0.4422 min: -0.1087 max: 2.5225 USE_META, weight: 0.8301 cost: 0.3879 min: -0.1087 max: 2.5225 USE_META, weight: 0.8330 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max: 2.5225 USE_META, weight: 0.8354 cost: 0.3724 min: -0.1087 max: 2.5225 USE_META, weight: 0.7070 cost: 0.7478 min: -0.1087 max: 2.5225 USE_META, weight: 0.8217 cost: 0.4126 min: -0.1087 max: 2.5225 USE_EVALUE, weight: 0.9984 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9984 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9984 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 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USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.7687 eval: 0.0001 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.7687 eval: 0.0001 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.7687 eval: 0.0001 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9958 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9958 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9958 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.1003 eval: 0.0003 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.1003 eval: 0.0003 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.1003 eval: 0.0003 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9975 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9975 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, 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USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.7696 eval: 0.0001 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.7696 eval: 0.0001 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.7696 eval: 0.0001 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9926 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9926 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9926 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0003 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0003 Number of contacts in models: 259 Number of contacts in alignments: 138 NUMB_ALIGNS: 138 Adding 10655 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -451.6569, CN propb: -451.6569 weights: 0.3493 constraints: 758 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 758 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 758 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 9897 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 9897 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 10655 # command: