# 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/T0374/ # command:# Making conformation for sequence T0374 numbered 1 through 160 Created new target T0374 from T0374.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0374/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0374//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0374/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0374//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0374/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0374/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0374/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p0hA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0374 read from 1p0hA/merged-good-all-a2m # 1p0hA read from 1p0hA/merged-good-all-a2m # found chain 1p0hA in training set Warning: unaligning (T0374)D58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0hA)G215 Warning: unaligning (T0374)Y108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0hA)V275 T0374 3 :LSHRPAE 1p0hA 152 :VVIRTYA # choosing archetypes in rotamer library T0374 10 :TGDLETVAGFPQDRDELF 1p0hA 160 :TSDDAELLRVNNAAFAGH T0374 32 :KAIWPFSVAQLAAAIA 1p0hA 178 :PEQGGWTAVQLAERRG T0374 52 :STVAVH 1p0hA 202 :LILAFG T0374 61 :VLGFANFYQWQHGD 1p0hA 217 :LLGFHWTKVHPDHP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1p0hA 232 :LGEVYVLGVDPAAQRRGLGQMLTSIGIVSLARR T0374 111 :RLMKISCFNANAAGLLLYTQLGYQPRAIAERHD 1p0hA 277 :PAVLLYVESDNVAAVRTYQSLGFTTYSVDTAYA Number of specific fragments extracted= 7 number of extra gaps= 0 total=7 Number of alignments=1 # 1p0hA read from 1p0hA/merged-good-all-a2m # found chain 1p0hA in training set Warning: unaligning (T0374)G59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p0hA)G215 Warning: unaligning (T0374)Y108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0hA)V275 T0374 2 :QLSHRPAE 1p0hA 151 :GVVIRTYA T0374 10 :TGDLETVAGFPQDRDELFYCYPK 1p0hA 160 :TSDDAELLRVNNAAFAGHPEQGG T0374 37 :FSVAQLAAAI 1p0hA 183 :WTAVQLAERR T0374 47 :AERRGSTVAV 1p0hA 197 :FDPDGLILAF T0374 60 :QVLGFANFYQWQH 1p0hA 216 :RLLGFHWTKVHPD T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1p0hA 230 :PGLGEVYVLGVDPAAQRRGLGQMLTSIGIVSLARR T0374 110 :ARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1p0hA 276 :EPAVLLYVESDNVAAVRTYQSLGFTTYSVDTAY Number of specific fragments extracted= 7 number of extra gaps= 0 total=14 Number of alignments=2 # 1p0hA read from 1p0hA/merged-good-all-a2m # found chain 1p0hA in training set Warning: unaligning (T0374)D58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0hA)G215 Warning: unaligning (T0374)G59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p0hA)G215 Warning: unaligning (T0374)Y108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0hA)V275 Warning: unaligning (T0374)P144 because last residue in template chain is (1p0hA)L310 T0374 3 :LSHRPAE 1p0hA 152 :VVIRTYA T0374 10 :TGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAAIAERRGSTVAVH 1p0hA 160 :TSDDAELLRVNNAAFAGHPEQGGWTAVQLAERRGEAWFDPDGLILAFG T0374 60 :QVLGFANFYQ 1p0hA 216 :RLLGFHWTKV T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1p0hA 227 :PDHPGLGEVYVLGVDPAAQRRGLGQMLTSIGIVSLARR T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHD 1p0hA 279 :VLLYVESDNVAAVRTYQSLGFTTYSVDTAYA Number of specific fragments extracted= 5 number of extra gaps= 0 total=19 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bl1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bl1A expands to /projects/compbio/data/pdb/2bl1.pdb.gz 2bl1A:Skipped atom 603, because occupancy 0.5 <= existing 0.500 in 2bl1A Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 804, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 806, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 808, because occupancy 0.500 <= existing 0.500 in 2bl1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1037, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1041, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1043, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1045, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1047, because occupancy 0.500 <= existing 0.500 in 2bl1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2bl1A/merged-good-all-a2m # 2bl1A read from 2bl1A/merged-good-all-a2m # adding 2bl1A to template set # found chain 2bl1A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2bl1A)A3 Warning: unaligning (T0374)L13 because of BadResidue code BAD_PEPTIDE in next template residue (2bl1A)P14 Warning: unaligning (T0374)E14 because of BadResidue code BAD_PEPTIDE at template residue (2bl1A)P14 T0374 4 :SHRPAETGD 2bl1A 4 :SIRDAGVAD T0374 15 :TVAGFPQDRDELFYCYPK 2bl1A 15 :GILAIYNDAVGNTTAIWN T0374 34 :IWPFSVAQLAAAIA 2bl1A 33 :ETPVDLANRQAWFD T0374 48 :ERRGSTVAVHD 2bl1A 51 :QGYPILVASDA T0374 59 :GQVLGFANFYQWQHGD 2bl1A 63 :GEVLGYASYGDWRPFE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2bl1A 82 :GTVEHSVYVRDDQRGKGLGVQLLQALIERARAQ T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 2bl1A 115 :GLHVMVAAIESGNAASIGLHRRLGFEISG T0374 138 :IAERHDPDGRRVALIQMDKPLE 2bl1A 145 :MPQVGQKFGRWLDLTFMQLNLD Number of specific fragments extracted= 8 number of extra gaps= 1 total=27 Number of alignments=4 # 2bl1A read from 2bl1A/merged-good-all-a2m # found chain 2bl1A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2bl1A)A3 Warning: unaligning (T0374)L13 because of BadResidue code BAD_PEPTIDE in next template residue (2bl1A)P14 Warning: unaligning (T0374)E14 because of BadResidue code BAD_PEPTIDE at template residue (2bl1A)P14 T0374 4 :SHRPAETGD 2bl1A 4 :SIRDAGVAD T0374 15 :TVAGFPQDRDELFY 2bl1A 15 :GILAIYNDAVGNTT T0374 29 :CYPKAIWPFSVAQLAAAIAERRGSTVAVHD 2bl1A 32 :NETPVDLANRQAWFDARARQGYPILVASDA T0374 59 :GQVLGFANFYQWQH 2bl1A 63 :GEVLGYASYGDWRP T0374 73 :GDFCAL 2bl1A 81 :RGTVEH T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQ 2bl1A 87 :SVYVRDDQRGKGLGVQLLQALIERARAQ T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 2bl1A 115 :GLHVMVAAIESGNAASIGLHRRLGFEISGQMPQV T0374 143 :DPDGRRVALIQMDKPLE 2bl1A 150 :QKFGRWLDLTFMQLNLD Number of specific fragments extracted= 8 number of extra gaps= 1 total=35 Number of alignments=5 # 2bl1A read from 2bl1A/merged-good-all-a2m # found chain 2bl1A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2bl1A)A3 Warning: unaligning (T0374)L13 because of BadResidue code BAD_PEPTIDE in next template residue (2bl1A)P14 Warning: unaligning (T0374)E14 because of BadResidue code BAD_PEPTIDE at template residue (2bl1A)P14 T0374 4 :SHRPAETGD 2bl1A 4 :SIRDAGVAD T0374 15 :TVAGFPQDRDELFYCY 2bl1A 15 :GILAIYNDAVGNTTAI T0374 31 :PKAIWPFS 2bl1A 32 :NETPVDLA T0374 39 :VAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGD 2bl1A 43 :AWFDARARQGYPILVASDAAGEVLGYASYGDWRPFE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2bl1A 82 :GTVEHSVYVRDDQRGKGLGVQLLQALIERARAQGLHV T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRVALIQMD 2bl1A 119 :MVAAIESGNAASIGLHRRLGFEISGQMPQVGQKFGRWLDLTFM Number of specific fragments extracted= 6 number of extra gaps= 1 total=41 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ae6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ae6A expands to /projects/compbio/data/pdb/2ae6.pdb.gz 2ae6A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1072, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1074, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1076, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1078, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1080, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1082, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1084, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1086, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1088, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1090, because occupancy 0.300 <= existing 0.700 in 2ae6A # T0374 read from 2ae6A/merged-good-all-a2m # 2ae6A read from 2ae6A/merged-good-all-a2m # adding 2ae6A to template set # found chain 2ae6A in template set Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ae6A)S39 Warning: unaligning (T0374)I34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ae6A)S39 Warning: unaligning (T0374)H57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ae6A)G58 Warning: unaligning (T0374)D58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ae6A)G58 Warning: unaligning (T0374)I152 because of BadResidue code BAD_PEPTIDE in next template residue (2ae6A)Q156 Warning: unaligning (T0374)Q153 because of BadResidue code BAD_PEPTIDE at template residue (2ae6A)Q156 Warning: unaligning (T0374)L158 because last residue in template chain is (2ae6A)I161 T0374 1 :MQ 2ae6A 1 :MS T0374 3 :LSHRPAETGDLETVAGFPQD 2ae6A 5 :LTIRLVAEADWPALHALDQI T0374 35 :WP 2ae6A 40 :LA T0374 44 :AAIA 2ae6A 42 :AYQE T0374 48 :ERRGSTVAV 2ae6A 48 :KDETIFVAI T0374 59 :GQVLGFANFYQWQHGD 2ae6A 59 :QQLAGFIEVHPPTSLA T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2ae6A 78 :KQWLLSIGVSPDFQDQGIGGSLLSYIKDMAEIS T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 2ae6A 111 :GIHKLSLRVMATNQEAIRFYEKHGFVQEA T0374 138 :IAERHDPDGRRVAL 2ae6A 141 :FKEEFYINGHYCDD T0374 154 :MDKP 2ae6A 157 :YAYF Number of specific fragments extracted= 10 number of extra gaps= 2 total=51 Number of alignments=7 # 2ae6A read from 2ae6A/merged-good-all-a2m # found chain 2ae6A in template set Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ae6A)S39 Warning: unaligning (T0374)I34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ae6A)S39 Warning: unaligning (T0374)H57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ae6A)G58 Warning: unaligning (T0374)D58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ae6A)G58 Warning: unaligning (T0374)I152 because of BadResidue code BAD_PEPTIDE in next template residue (2ae6A)Q156 Warning: unaligning (T0374)Q153 because of BadResidue code BAD_PEPTIDE at template residue (2ae6A)Q156 Warning: unaligning (T0374)L158 because last residue in template chain is (2ae6A)I161 T0374 1 :M 2ae6A 1 :M T0374 2 :QLSHRPAETGDLETVAGFPQD 2ae6A 4 :SLTIRLVAEADWPALHALDQI T0374 35 :WPFSVAQ 2ae6A 40 :LAAYQEK T0374 47 :AERRGSTVAV 2ae6A 47 :MKDETIFVAI T0374 59 :GQVLGFANFYQWQH 2ae6A 59 :QQLAGFIEVHPPTS T0374 73 :GDFCAL 2ae6A 77 :QKQWLL T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQ 2ae6A 83 :SIGVSPDFQDQGIGGSLLSYIKDMAEIS T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 2ae6A 111 :GIHKLSLRVMATNQEAIRFYEKHGFVQEAHFKEE T0374 143 :DPDGRRVAL 2ae6A 146 :YINGHYCDD T0374 154 :MDKP 2ae6A 157 :YAYF Number of specific fragments extracted= 10 number of extra gaps= 2 total=61 Number of alignments=8 # 2ae6A read from 2ae6A/merged-good-all-a2m # found chain 2ae6A in template set Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ae6A)S39 Warning: unaligning (T0374)K32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ae6A)S39 Warning: unaligning (T0374)H57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ae6A)G58 Warning: unaligning (T0374)D58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ae6A)G58 T0374 1 :MQLSHRPAETGDLETVAGFPQD 2ae6A 3 :TSLTIRLVAEADWPALHALDQI T0374 33 :AIWPFSV 2ae6A 40 :LAAYQEK T0374 47 :AERRGSTVAV 2ae6A 47 :MKDETIFVAI T0374 59 :GQVLGFANFYQ 2ae6A 59 :QQLAGFIEVHP T0374 71 :QHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2ae6A 74 :AAHQKQWLLSIGVSPDFQDQGIGGSLLSYIKDMAEISGIHK T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGR 2ae6A 115 :LSLRVMATNQEAIRFYEKHGFVQEAHFKEEFYING Number of specific fragments extracted= 6 number of extra gaps= 1 total=67 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qsmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qsmA expands to /projects/compbio/data/pdb/1qsm.pdb.gz 1qsmA:# T0374 read from 1qsmA/merged-good-all-a2m # 1qsmA read from 1qsmA/merged-good-all-a2m # adding 1qsmA to template set # found chain 1qsmA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELF 1qsmA 8 :NITVRFVTENDKEGWQRLWKSYQDFY T0374 34 :IWPFSVAQLAAAIA 1qsmA 34 :EVSFPDDLDDFNFG T0374 48 :ERRG 1qsmA 52 :PNIK T0374 52 :STVAVH 1qsmA 58 :AAVAVE T0374 58 :DGQVLGFANFYQWQHGD 1qsmA 66 :SEKIIGMINFFNHMTTW T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1qsmA 87 :KIYINDLYVDENSRVKGAGGKLIQFVYDEADKL T0374 109 :KARLMKISCFNANAAGLLLYTQLG 1qsmA 120 :GTPSVYWCTDESNHRAQLLYVKVG T0374 134 :QPRAIAERHDPD 1qsmA 144 :YKAPKILYKRKG Number of specific fragments extracted= 8 number of extra gaps= 0 total=75 Number of alignments=10 # 1qsmA read from 1qsmA/merged-good-all-a2m # found chain 1qsmA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFY 1qsmA 8 :NITVRFVTENDKEGWQRLWKSYQDFYE T0374 32 :KAIWPFSVAQLAAAI 1qsmA 35 :VSFPDDLDDFNFGRF T0374 47 :AERRGSTVAVHD 1qsmA 53 :NIKMWAAVAVES T0374 59 :GQVLGFANFYQWQH 1qsmA 67 :EKIIGMINFFNHMT T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1qsmA 85 :KDKIYINDLYVDENSRVKGAGGKLIQFVYDEADKL T0374 109 :KARLMKISCFNANAAGLLLYTQLG 1qsmA 120 :GTPSVYWCTDESNHRAQLLYVKVG T0374 134 :QPRAIAERHDPD 1qsmA 144 :YKAPKILYKRKG Number of specific fragments extracted= 7 number of extra gaps= 0 total=82 Number of alignments=11 # 1qsmA read from 1qsmA/merged-good-all-a2m # found chain 1qsmA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAAIAERRGSTVAVH 1qsmA 8 :NITVRFVTENDKEGWQRLWKSYQDFYEVSFPDDLDDFNFGRFLDPNIKMWAAVAVE T0374 58 :DGQVLGFANFYQ 1qsmA 66 :SEKIIGMINFFN T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1qsmA 82 :WDFKDKIYINDLYVDENSRVKGAGGKLIQFVYDEADKLGTPS T0374 113 :MKISCFNANAAGLLLYTQLG 1qsmA 124 :VYWCTDESNHRAQLLYVKVG T0374 134 :QPRAIA 1qsmA 144 :YKAPKI T0374 142 :HDP 1qsmA 150 :LYK Number of specific fragments extracted= 6 number of extra gaps= 0 total=88 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vkcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vkcA expands to /projects/compbio/data/pdb/1vkc.pdb.gz 1vkcA:Skipped atom 421, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 423, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 425, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 427, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 429, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 431, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 988, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 990, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 992, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 1137, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 1139, because occupancy 0.350 <= existing 0.650 in 1vkcA # T0374 read from 1vkcA/merged-good-all-a2m # 1vkcA read from 1vkcA/merged-good-all-a2m # adding 1vkcA to template set # found chain 1vkcA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1vkcA)E2 Warning: unaligning (T0374)L112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vkcA)I120 Warning: unaligning (T0374)M113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vkcA)I120 Warning: unaligning (T0374)F118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vkcA)I126 Warning: unaligning (T0374)N119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vkcA)I126 T0374 3 :LSHRPA 1vkcA 3 :YTIVDG T0374 10 :TGDLETVAGFPQDRDELF 1vkcA 9 :EEYIEEIKKLDREISYSF T0374 33 :AIWPFSVAQLAAAIA 1vkcA 27 :VRFPISYEEYEERHE T0374 48 :ERRGSTVAVHDG 1vkcA 51 :GEHKFFVALNER T0374 60 :QVLGFANFYQWQHGD 1vkcA 64 :ELLGHVWICITLDTV T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1vkcA 83 :IAYIYDIEVVKWARGLGIGSALLRKAEEWAKER T0374 109 :KAR 1vkcA 116 :GAK T0374 114 :KISC 1vkcA 121 :VLRV T0374 120 :ANAA 1vkcA 127 :DNPA T0374 125 :LLLYTQLGYQPRAIA 1vkcA 131 :VKWYEERGYKARALI Number of specific fragments extracted= 10 number of extra gaps= 2 total=98 Number of alignments=13 # 1vkcA read from 1vkcA/merged-good-all-a2m # found chain 1vkcA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1vkcA)E2 Warning: unaligning (T0374)L112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vkcA)I120 Warning: unaligning (T0374)M113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vkcA)I120 Warning: unaligning (T0374)F118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vkcA)I126 Warning: unaligning (T0374)N119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vkcA)I126 T0374 3 :LSHRPA 1vkcA 3 :YTIVDG T0374 10 :TGDLETVAGFPQDRDELF 1vkcA 9 :EEYIEEIKKLDREISYSF T0374 29 :CYPKAIWPFSVAQLAAAI 1vkcA 27 :VRFPISYEEYEERHEELF T0374 47 :AERRGSTVAVHD 1vkcA 50 :QGEHKFFVALNE T0374 59 :GQVLGFANFYQWQH 1vkcA 63 :SELLGHVWICITLD T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1vkcA 81 :VKIAYIYDIEVVKWARGLGIGSALLRKAEEWAKER T0374 109 :KAR 1vkcA 116 :GAK T0374 114 :KISC 1vkcA 121 :VLRV T0374 120 :ANA 1vkcA 127 :DNP T0374 124 :GLLLYTQLGYQPR 1vkcA 130 :AVKWYEERGYKAR Number of specific fragments extracted= 10 number of extra gaps= 2 total=108 Number of alignments=14 # 1vkcA read from 1vkcA/merged-good-all-a2m # found chain 1vkcA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1vkcA)E2 Warning: unaligning (T0374)R111 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vkcA)I120 Warning: unaligning (T0374)M113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vkcA)I120 Warning: unaligning (T0374)F118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vkcA)I126 Warning: unaligning (T0374)N119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vkcA)I126 T0374 3 :LSHRPA 1vkcA 3 :YTIVDG T0374 10 :TGDLETVAGFPQDRDE 1vkcA 9 :EEYIEEIKKLDREISY T0374 28 :YCYPKAIWPFSVAQ 1vkcA 25 :SFVRFPISYEEYEE T0374 42 :LAAAIAERRGSTVAVHDG 1vkcA 45 :ESLLSQGEHKFFVALNER T0374 60 :QVLGFANFYQWQHGD 1vkcA 64 :ELLGHVWICITLDTV T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKA 1vkcA 83 :IAYIYDIEVVKWARGLGIGSALLRKAEEWAKERGAK T0374 114 :KISC 1vkcA 121 :VLRV T0374 120 :ANAA 1vkcA 127 :DNPA T0374 125 :LLLYTQLGYQPRAIAER 1vkcA 131 :VKWYEERGYKARALIME Number of specific fragments extracted= 9 number of extra gaps= 2 total=117 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qsoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qsoA expands to /projects/compbio/data/pdb/1qso.pdb.gz 1qsoA:# T0374 read from 1qsoA/merged-good-all-a2m # 1qsoA read from 1qsoA/merged-good-all-a2m # adding 1qsoA to template set # found chain 1qsoA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1qsoA)N8 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPK 1qsoA 9 :ITVRFVTENDKEGWQRLWKSYQDFYEVSFP T0374 36 :PFSVAQLAAAIA 1qsoA 39 :DDLDDFNFGRFL T0374 48 :ERRG 1qsoA 52 :PNIK T0374 52 :STVAVHDG 1qsoA 58 :AAVAVESS T0374 60 :QVLGFANFYQWQHGD 1qsoA 68 :KIIGMINFFNHMTTW T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1qsoA 87 :KIYINDLYVDENSRVKGAGGKLIQFVYDEADKL T0374 109 :KARLMKISCFNANAAGLLLYTQLG 1qsoA 120 :GTPSVYWCTDESNHRAQLLYVKVG T0374 134 :QPRAIAERHDP 1qsoA 144 :YKAPKILYKRK Number of specific fragments extracted= 8 number of extra gaps= 0 total=125 Number of alignments=16 # 1qsoA read from 1qsoA/merged-good-all-a2m # found chain 1qsoA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1qsoA)N8 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1qsoA 9 :ITVRFVTENDKEGWQRLWKSYQDFYE T0374 29 :CYPKAIWPFSVAQLA 1qsoA 36 :SFPDDLDDFNFGRFL T0374 47 :AERRGSTVAVHDG 1qsoA 53 :NIKMWAAVAVESS T0374 60 :QVLGFANFYQWQH 1qsoA 68 :KIIGMINFFNHMT T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1qsoA 85 :KDKIYINDLYVDENSRVKGAGGKLIQFVYDEADKL T0374 109 :KARLMKISCFNANAAGLLLYTQLG 1qsoA 120 :GTPSVYWCTDESNHRAQLLYVKVG T0374 134 :QPRAIAERHDP 1qsoA 144 :YKAPKILYKRK Number of specific fragments extracted= 7 number of extra gaps= 0 total=132 Number of alignments=17 # 1qsoA read from 1qsoA/merged-good-all-a2m # found chain 1qsoA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1qsoA)N8 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAAIAERRGSTVAVHDG 1qsoA 9 :ITVRFVTENDKEGWQRLWKSYQDFYEVSFPDDLDDFNFGRFLDPNIKMWAAVAVESS T0374 60 :QVLGFANFYQ 1qsoA 68 :KIIGMINFFN T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1qsoA 82 :WDFKDKIYINDLYVDENSRVKGAGGKLIQFVYDEADKLGTPS T0374 113 :MKISCFNANAAGLLLYTQLG 1qsoA 124 :VYWCTDESNHRAQLLYVKVG T0374 134 :QPRAIAERHDPD 1qsoA 144 :YKAPKILYKRKG Number of specific fragments extracted= 5 number of extra gaps= 0 total=137 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2beiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2beiA expands to /projects/compbio/data/pdb/2bei.pdb.gz 2beiA:Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 2beiA Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 2beiA Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 2beiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2beiA/merged-good-all-a2m # 2beiA read from 2beiA/merged-good-all-a2m # adding 2beiA to template set # found chain 2beiA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (2beiA)S3 Warning: unaligning (T0374)C29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2beiA)K35 Warning: unaligning (T0374)P36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2beiA)K35 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 2beiA 4 :VRIREAKEGDCGDILRLIRELAEFEK T0374 37 :FSVAQLAAAIA 2beiA 36 :ISEEALRADGF T0374 48 :ERRGSTVAVH 2beiA 50 :PFYHCLVAEI T0374 61 :VLGFANFYQWQHGD 2beiA 71 :VVGYGIYYFIYSTW T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2beiA 88 :TIYLEDIYVMPEYRGQGIGSKIIKKVAEVALDK T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQP 2beiA 121 :GCSQFRLAVLDWNQRAMDLYKALGAQD T0374 136 :RAIAERHDPD 2beiA 152 :EGWHFFCFQG Number of specific fragments extracted= 7 number of extra gaps= 0 total=144 Number of alignments=19 # 2beiA read from 2beiA/merged-good-all-a2m # found chain 2beiA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (2beiA)S3 Warning: unaligning (T0374)C29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2beiA)K35 Warning: unaligning (T0374)P36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2beiA)K35 Warning: unaligning (T0374)A47 because of BadResidue code BAD_PEPTIDE at template residue (2beiA)N49 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 2beiA 4 :VRIREAKEGDCGDILRLIRELAEFEK T0374 37 :FSVAQLAAAI 2beiA 36 :ISEEALRADG T0374 48 :ERRGSTVAV 2beiA 50 :PFYHCLVAE T0374 60 :QVLGFANFYQWQH 2beiA 70 :CVVGYGIYYFIYS T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2beiA 86 :GRTIYLEDIYVMPEYRGQGIGSKIIKKVAEVALDK T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPR 2beiA 121 :GCSQFRLAVLDWNQRAMDLYKALGAQDL T0374 137 :AIAERH 2beiA 153 :GWHFFC Number of specific fragments extracted= 7 number of extra gaps= 1 total=151 Number of alignments=20 # 2beiA read from 2beiA/merged-good-all-a2m # found chain 2beiA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (2beiA)S3 Warning: unaligning (T0374)C29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2beiA)K35 Warning: unaligning (T0374)I34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2beiA)K35 Warning: unaligning (T0374)A47 because of BadResidue code BAD_PEPTIDE in next template residue (2beiA)N49 Warning: unaligning (T0374)E48 because of BadResidue code BAD_PEPTIDE at template residue (2beiA)N49 Warning: unaligning (T0374)D58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2beiA)G68 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 2beiA 4 :VRIREAKEGDCGDILRLIRELAEFEK T0374 35 :WPFSVAQLAAAI 2beiA 36 :ISEEALRADGFG T0374 49 :RRGSTVAVH 2beiA 51 :FYHCLVAEI T0374 59 :GQVLGFANFYQWQHGD 2beiA 69 :PCVVGYGIYYFIYSTW T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2beiA 88 :TIYLEDIYVMPEYRGQGIGSKIIKKVAEVALDKGCSQ T0374 113 :MKISCFNANAAGLLLYTQLGYQP 2beiA 125 :FRLAVLDWNQRAMDLYKALGAQD Number of specific fragments extracted= 6 number of extra gaps= 1 total=157 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s3zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1s3zA expands to /projects/compbio/data/pdb/1s3z.pdb.gz 1s3zA:# T0374 read from 1s3zA/merged-good-all-a2m # 1s3zA read from 1s3zA/merged-good-all-a2m # adding 1s3zA to template set # found chain 1s3zA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDR 1s3zA 0 :HMDIRQMNKTHLEHWRGLRKQL T0374 34 :IWPFSVAQLAAAIA 1s3zA 22 :WPGHPDDAHLADGE T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHG 1s3zA 41 :DHLASFIAMADGVAIGFADASIRHDY T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1s3zA 75 :VVFLEGIFVLPSFRQRGVAKQLIAAVQRWGTNK T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1s3zA 108 :GCREMASDTSPENTISQKVHQALGFEETERVIFY Number of specific fragments extracted= 5 number of extra gaps= 0 total=162 Number of alignments=22 # 1s3zA read from 1s3zA/merged-good-all-a2m # found chain 1s3zA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDE 1s3zA 0 :HMDIRQMNKTHLEHWRGLRKQLWP T0374 32 :KAIWPFSVAQLAAAI 1s3zA 24 :GHPDDAHLADGEEIL T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1s3zA 40 :ADHLASFIAMADGVAIGFADASIRHD T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1s3zA 73 :SPVVFLEGIFVLPSFRQRGVAKQLIAAVQRWGTNK T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1s3zA 108 :GCREMASDTSPENTISQKVHQALGFEETERVIFY T0374 155 :DKP 1s3zA 142 :RKR Number of specific fragments extracted= 6 number of extra gaps= 0 total=168 Number of alignments=23 # 1s3zA read from 1s3zA/merged-good-all-a2m # found chain 1s3zA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRD 1s3zA 0 :HMDIRQMNKTHLEHWRGLRKQLW T0374 32 :KAIWPFSVAQ 1s3zA 23 :PGHPDDAHLA T0374 42 :LAAAIAERRGSTVAVHDGQVLGFANFYQ 1s3zA 35 :EEILQADHLASFIAMADGVAIGFADASI T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1s3zA 70 :CDSSPVVFLEGIFVLPSFRQRGVAKQLIAAVQRWGTNKGCRE T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDP 1s3zA 112 :MASDTSPENTISQKVHQALGFEETERVIFYRK Number of specific fragments extracted= 5 number of extra gaps= 0 total=173 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i21A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i21A expands to /projects/compbio/data/pdb/1i21.pdb.gz 1i21A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1i21A/merged-good-all-a2m # 1i21A read from 1i21A/merged-good-all-a2m # adding 1i21A to template set # found chain 1i21A in template set Warning: unaligning (T0374)P157 because last residue in template chain is (1i21A)R158 T0374 1 :MQ 1i21A 1 :MS T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i21A 7 :FYIRRMEEGDLEQVTETLKVLT T0374 33 :AIWPFSVAQLAAAIA 1i21A 29 :TVGTITPESFCKLIK T0374 49 :RRGSTVAVH 1i21A 61 :QYNPMVIVD T0374 58 :DGQVLGFANFYQWQHGD 1i21A 72 :TETVAATGNIIIERKII T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1i21A 94 :CGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDY T0374 109 :KARLMKISCFNAN 1i21A 127 :GCYKIILDCDEKN T0374 125 :LLLYTQLGYQPRA 1i21A 140 :VKFYEKCGFSNAG T0374 152 :IQMDK 1i21A 153 :VEMQI Number of specific fragments extracted= 9 number of extra gaps= 0 total=182 Number of alignments=25 # 1i21A read from 1i21A/merged-good-all-a2m # found chain 1i21A in template set Warning: unaligning (T0374)P157 because last residue in template chain is (1i21A)R158 T0374 3 :LSHRPAETGDLETVAGFPQDRDE 1i21A 7 :FYIRRMEEGDLEQVTETLKVLTT T0374 30 :YPKAIWPFSVAQLAAAI 1i21A 30 :VGTITPESFCKLIKYWN T0374 47 :AERRGSTVAVHD 1i21A 60 :MQYNPMVIVDKR T0374 59 :GQVLGFANFYQWQH 1i21A 73 :ETVAATGNIIIERK T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1i21A 92 :GLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDY T0374 109 :KARLMKISCFNANAA 1i21A 127 :GCYKIILDCDEKNVK T0374 127 :LYTQLGYQPRAIAE 1i21A 142 :FYEKCGFSNAGVEM T0374 155 :DK 1i21A 156 :QI Number of specific fragments extracted= 8 number of extra gaps= 0 total=190 Number of alignments=26 # 1i21A read from 1i21A/merged-good-all-a2m # found chain 1i21A in template set T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i21A 7 :FYIRRMEEGDLEQVTETLKVLT T0374 29 :CYPKAIWPFSVAQLAAA 1i21A 29 :TVGTITPESFCKLIKYW T0374 46 :IAERRGSTVAVH 1i21A 59 :IMQYNPMVIVDK T0374 58 :DGQVLGFANFYQWQHG 1i21A 72 :TETVAATGNIIIERKI T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1i21A 94 :CGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYK T0374 113 :MKISCFNAN 1i21A 131 :IILDCDEKN T0374 125 :LLLYTQLGYQPRAIAERH 1i21A 140 :VKFYEKCGFSNAGVEMQI Number of specific fragments extracted= 7 number of extra gaps= 0 total=197 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yreA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yreA expands to /projects/compbio/data/pdb/1yre.pdb.gz 1yreA:# T0374 read from 1yreA/merged-good-all-a2m # 1yreA read from 1yreA/merged-good-all-a2m # adding 1yreA to template set # found chain 1yreA in template set Warning: unaligning (T0374)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yreA)F85 Warning: unaligning (T0374)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yreA)F85 Warning: unaligning (T0374)M81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yreA)W101 Warning: unaligning (T0374)M82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yreA)W101 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYC 1yreA 20 :LRLEPLVEADIPELVSLAEANREALQY T0374 33 :AIWPFSVAQLAAAIA 1yreA 47 :MDGPTRPDWYRQSLA T0374 48 :ERRGSTVAVHDGQVLGFA 1yreA 66 :GRALPLAVRLGVQLVGTT T0374 68 :YQWQHGD 1yreA 86 :AEFLPAL T0374 75 :FCALGN 1yreA 94 :ACEIGW T0374 83 :VAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRA 1yreA 102 :LDQAQHGSGLNRMIKYLMLKHAFDNLRMVRVQLSTAASNLRAQGAIDKLGAQREG T0374 138 :IAERHD 1yreA 158 :LRNHRR T0374 144 :PDGRRVALIQMDKP 1yreA 165 :AGGRLDDTFVYSIT Number of specific fragments extracted= 8 number of extra gaps= 2 total=205 Number of alignments=28 # 1yreA read from 1yreA/merged-good-all-a2m # found chain 1yreA in template set Warning: unaligning (T0374)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yreA)F85 Warning: unaligning (T0374)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yreA)F85 Warning: unaligning (T0374)M81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yreA)W101 Warning: unaligning (T0374)M82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yreA)W101 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAAI 1yreA 20 :LRLEPLVEADIPELVSLAEANREALQYMDGPTRPDWYRQSLAEQ T0374 47 :AERRGSTVAVHDGQVLGFA 1yreA 65 :EGRALPLAVRLGVQLVGTT T0374 68 :YQWQH 1yreA 86 :AEFLP T0374 73 :GDFCALGN 1yreA 92 :LPACEIGW T0374 83 :VAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1yreA 102 :LDQAQHGSGLNRMIKYLMLKHAFDNLRMVRVQLSTAASNLRAQGAIDKLGAQREGVLRNH T0374 143 :DPDGRRVALIQMDKP 1yreA 164 :LAGGRLDDTFVYSIT Number of specific fragments extracted= 6 number of extra gaps= 2 total=211 Number of alignments=29 # 1yreA read from 1yreA/merged-good-all-a2m # found chain 1yreA in template set Warning: unaligning (T0374)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yreA)F85 Warning: unaligning (T0374)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yreA)F85 Warning: unaligning (T0374)M81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yreA)W101 Warning: unaligning (T0374)M82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yreA)W101 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAA 1yreA 20 :LRLEPLVEADIPELVSLAEANREALQYMDGPTRPDWYRQSLAE T0374 46 :IAERRGSTVAVHDGQVLGFA 1yreA 64 :REGRALPLAVRLGVQLVGTT T0374 68 :YQ 1yreA 86 :AE T0374 70 :WQHGDFCALGN 1yreA 89 :LPALPACEIGW T0374 83 :VAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDP 1yreA 102 :LDQAQHGSGLNRMIKYLMLKHAFDNLRMVRVQLSTAASNLRAQGAIDKLGAQREGVLRNHRR Number of specific fragments extracted= 5 number of extra gaps= 2 total=216 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yr0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yr0A expands to /projects/compbio/data/pdb/1yr0.pdb.gz 1yr0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1yr0A/merged-good-all-a2m # 1yr0A read from 1yr0A/merged-good-all-a2m # adding 1yr0A to template set # found chain 1yr0A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1yr0A)S4 Warning: unaligning (T0374)L158 because last residue in template chain is (1yr0A)L166 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPK 1yr0A 5 :VELRDATVDDLSGIMEIYNDAVVNTTAIWN T0374 34 :IWPFSVAQLAAAIA 1yr0A 35 :EVVVDLENRKDWFA T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1yr0A 53 :RGFPVIVAILDGKVAGYASYGDWRAFD T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1yr0A 83 :HTREHSVYVHKDARGHGIGKRLMQALIDHAGGN T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 1yr0A 116 :DVHVLIAAIEAENTASIRLHESLGFRVVG T0374 138 :IAERHDPDGRRVALIQMDKP 1yr0A 146 :FSEVGTKFGRWLDLTCMELK Number of specific fragments extracted= 6 number of extra gaps= 0 total=222 Number of alignments=31 # 1yr0A read from 1yr0A/merged-good-all-a2m # found chain 1yr0A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1yr0A)S4 Warning: unaligning (T0374)L158 because last residue in template chain is (1yr0A)L166 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1yr0A 5 :VELRDATVDDLSGIMEIYNDAVVNTT T0374 29 :CYPKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQH 1yr0A 34 :NEVVVDLENRKDWFAARTSRGFPVIVAILDGKVAGYASYGDWRA T0374 73 :GDFCAL 1yr0A 82 :RHTREH T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQ 1yr0A 88 :SVYVHKDARGHGIGKRLMQALIDHAGGN T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1yr0A 116 :DVHVLIAAIEAENTASIRLHESLGFRVVGRFSEV T0374 143 :DPDGRRVALIQMDKP 1yr0A 151 :TKFGRWLDLTCMELK Number of specific fragments extracted= 6 number of extra gaps= 0 total=228 Number of alignments=32 # 1yr0A read from 1yr0A/merged-good-all-a2m # found chain 1yr0A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1yr0A)S4 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQ 1yr0A 5 :VELRDATVDDLSGIMEIYNDAVVNTTAIWNEVVVDLENR T0374 42 :LAAAIAERRGSTVAVHDGQVLGFANFYQWQHGD 1yr0A 47 :FAARTSRGFPVIVAILDGKVAGYASYGDWRAFD T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1yr0A 83 :HTREHSVYVHKDARGHGIGKRLMQALIDHAGGNDVHV T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRVALIQMD 1yr0A 120 :LIAAIEAENTASIRLHESLGFRVVGRFSEVGTKFGRWLDLTCM Number of specific fragments extracted= 4 number of extra gaps= 0 total=232 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cjwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0374 read from 1cjwA/merged-good-all-a2m # 1cjwA read from 1cjwA/merged-good-all-a2m # found chain 1cjwA in training set T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 1cjwA 36 :EFRCLTPEDAAGVFEIEREAFISVS T0374 33 :AIWPFSVAQLAAAIA 1cjwA 61 :GNCPLNLDEVQHFLT T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1cjwA 77 :CPELSLGWFVEGRLVAFIIGSLWDEER T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNAN 1cjwA 118 :SAHLHALAVHRSFRQQGKGSVLLWRYLHHVGAQPAVRRAVLMCEDAL T0374 125 :LLLYTQLGYQPRAIAERHDPDGRRVA 1cjwA 165 :VPFYQRFGFHPAGPCAIVVGSLTFTE T0374 152 :IQM 1cjwA 191 :MHC Number of specific fragments extracted= 6 number of extra gaps= 0 total=238 Number of alignments=34 # 1cjwA read from 1cjwA/merged-good-all-a2m # found chain 1cjwA in training set Warning: unaligning (T0374)L158 because last residue in template chain is (1cjwA)L195 T0374 4 :SHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAA 1cjwA 36 :EFRCLTPEDAAGVFEIEREAFISVSGNCPLNLDEVQHFLTLC T0374 49 :RRGSTVAVHDGQVLGFANFYQWQH 1cjwA 78 :PELSLGWFVEGRLVAFIIGSLWDE T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNA 1cjwA 116 :GHSAHLHALAVHRSFRQQGKGSVLLWRYLHHVGAQPAVRRAVLMCEDA T0374 124 :GLLLYTQLGYQPRAIAERHDPD 1cjwA 164 :LVPFYQRFGFHPAGPCAIVVGS T0374 149 :VALIQMDKP 1cjwA 186 :LTFTEMHCS Number of specific fragments extracted= 5 number of extra gaps= 0 total=243 Number of alignments=35 # 1cjwA read from 1cjwA/merged-good-all-a2m # found chain 1cjwA in training set T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 1cjwA 36 :EFRCLTPEDAAGVFEIEREAFISVS T0374 31 :PKAIWPFSVAQLAAAIAER 1cjwA 61 :GNCPLNLDEVQHFLTLCPE T0374 51 :GSTVAVHDGQVLGFANFYQWQHGD 1cjwA 80 :LSLGWFVEGRLVAFIIGSLWDEER T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNAN 1cjwA 118 :SAHLHALAVHRSFRQQGKGSVLLWRYLHHVGAQPAVRRAVLMCEDAL T0374 125 :LLLYTQLGYQPRAIAERHD 1cjwA 165 :VPFYQRFGFHPAGPCAIVV Number of specific fragments extracted= 5 number of extra gaps= 0 total=248 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cy2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cy2A expands to /projects/compbio/data/pdb/2cy2.pdb.gz 2cy2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2cy2A/merged-good-all-a2m # 2cy2A read from 2cy2A/merged-good-all-a2m # adding 2cy2A to template set # found chain 2cy2A in template set T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 2cy2A 2 :RIRRAGLEDLPGVARVLVDTWRATY T0374 29 :CYPKAIWPFSVAQLAAAIA 2cy2A 30 :VPEAFLEGLSYEGQAERWA T0374 48 :E 2cy2A 54 :P T0374 49 :RRGSTVAVHD 2cy2A 57 :PGRLFVAESE T0374 59 :GQVLGFANFYQWQHGD 2cy2A 68 :GEVVGFAAFGPDRASG T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2cy2A 88 :TAELWAIYVLPTWQRKGLGRALFHEGARLLQAE T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDP 2cy2A 121 :GYGRMLVWVLKENPKGRGFYEHLGGVLLGEREIELG T0374 146 :GRRVALIQMDKPLEP 2cy2A 157 :GAKLWEVAYGFDLGG Number of specific fragments extracted= 8 number of extra gaps= 0 total=256 Number of alignments=37 # 2cy2A read from 2cy2A/merged-good-all-a2m # found chain 2cy2A in template set T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 2cy2A 2 :RIRRAGLEDLPGVARVLVDTWRATY T0374 29 :CYPKAIWPFSVAQLAAAI 2cy2A 34 :FLEGLSYEGQAERWAQRL T0374 47 :AERRGSTVAVHD 2cy2A 55 :TWPGRLFVAESE T0374 59 :GQVLGFANFYQWQH 2cy2A 68 :GEVVGFAAFGPDRA T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2cy2A 86 :GYTAELWAIYVLPTWQRKGLGRALFHEGARLLQAE T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDP 2cy2A 121 :GYGRMLVWVLKENPKGRGFYEHLGGVLLGEREIELG T0374 146 :GRRVALIQMDKPLE 2cy2A 157 :GAKLWEVAYGFDLG Number of specific fragments extracted= 7 number of extra gaps= 0 total=263 Number of alignments=38 # 2cy2A read from 2cy2A/merged-good-all-a2m # found chain 2cy2A in template set T0374 5 :HRPAETGDLETVAGFPQDRDELFYCY 2cy2A 3 :IRRAGLEDLPGVARVLVDTWRATYRG T0374 31 :PKAIWPFSVAQLAAAIAE 2cy2A 38 :LSYEGQAERWAQRLKTPT T0374 49 :RRGSTVAVH 2cy2A 57 :PGRLFVAES T0374 58 :DGQVLGFANFYQ 2cy2A 67 :SGEVVGFAAFGP T0374 70 :WQHGD 2cy2A 82 :SGFPG T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2cy2A 88 :TAELWAIYVLPTWQRKGLGRALFHEGARLLQAEGYGR T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPD 2cy2A 125 :MLVWVLKENPKGRGFYEHLGGVLLGEREIELGG Number of specific fragments extracted= 7 number of extra gaps= 0 total=270 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kuxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kuxA expands to /projects/compbio/data/pdb/1kux.pdb.gz 1kuxA:# T0374 read from 1kuxA/merged-good-all-a2m # 1kuxA read from 1kuxA/merged-good-all-a2m # adding 1kuxA to template set # found chain 1kuxA in template set Warning: unaligning (T0374)Q107 because of BadResidue code BAD_PEPTIDE in next template residue (1kuxA)P151 Warning: unaligning (T0374)Y108 because of BadResidue code BAD_PEPTIDE at template residue (1kuxA)P151 Warning: unaligning (T0374)L158 because last residue in template chain is (1kuxA)L195 T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 1kuxA 36 :EFRCLTPEDAAGVFEIEREAFISVS T0374 33 :AIWPFSVAQLAAAIA 1kuxA 61 :GNCPLNLDEVQHFLT T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1kuxA 77 :CPELSLGWFVEGRLVAFIIGSLWDEER T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLARE 1kuxA 118 :SAHLHALAVHRSFRQQGKGSVLLWRYLHHVGA T0374 109 :KARLMKISCFNAN 1kuxA 152 :AVRRAVLMCEDAL T0374 125 :LLLYTQLGYQPRAIAERHDPDGRRV 1kuxA 165 :VPFYQRFGFHPAGPCAIVVGSLTFT T0374 153 :QMDKP 1kuxA 190 :EMHCS Number of specific fragments extracted= 7 number of extra gaps= 1 total=277 Number of alignments=40 # 1kuxA read from 1kuxA/merged-good-all-a2m # found chain 1kuxA in template set Warning: unaligning (T0374)Q107 because of BadResidue code BAD_PEPTIDE in next template residue (1kuxA)P151 Warning: unaligning (T0374)Y108 because of BadResidue code BAD_PEPTIDE at template residue (1kuxA)P151 Warning: unaligning (T0374)L158 because last residue in template chain is (1kuxA)L195 T0374 4 :SHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAA 1kuxA 36 :EFRCLTPEDAAGVFEIEREAFISVSGNCPLNLDEVQHFLTLC T0374 49 :RRGSTVAVHDGQVLGFANFYQWQH 1kuxA 78 :PELSLGWFVEGRLVAFIIGSLWDE T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLARE 1kuxA 116 :GHSAHLHALAVHRSFRQQGKGSVLLWRYLHHVGA T0374 109 :KARLMKISCFNA 1kuxA 152 :AVRRAVLMCEDA T0374 124 :GLLLYTQLGYQPRAIAERHDPD 1kuxA 164 :LVPFYQRFGFHPAGPCAIVVGS T0374 149 :VALIQMDKP 1kuxA 186 :LTFTEMHCS Number of specific fragments extracted= 6 number of extra gaps= 1 total=283 Number of alignments=41 # 1kuxA read from 1kuxA/merged-good-all-a2m # found chain 1kuxA in template set Warning: unaligning (T0374)Q107 because of BadResidue code BAD_PEPTIDE in next template residue (1kuxA)P151 Warning: unaligning (T0374)Y108 because of BadResidue code BAD_PEPTIDE at template residue (1kuxA)P151 T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 1kuxA 36 :EFRCLTPEDAAGVFEIEREAFISVS T0374 31 :PKAIWPFSVAQLAAAIAER 1kuxA 61 :GNCPLNLDEVQHFLTLCPE T0374 51 :GSTVAVHDGQVLGFANFYQWQHGD 1kuxA 80 :LSLGWFVEGRLVAFIIGSLWDEER T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLARE 1kuxA 118 :SAHLHALAVHRSFRQQGKGSVLLWRYLHHVGA T0374 109 :KARLMKISCFNAN 1kuxA 152 :AVRRAVLMCEDAL T0374 125 :LLLYTQLGYQPRAIAER 1kuxA 165 :VPFYQRFGFHPAGPCAI Number of specific fragments extracted= 6 number of extra gaps= 1 total=289 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c27A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c27A expands to /projects/compbio/data/pdb/2c27.pdb.gz 2c27A:# T0374 read from 2c27A/merged-good-all-a2m # 2c27A read from 2c27A/merged-good-all-a2m # adding 2c27A to template set # found chain 2c27A in template set Warning: unaligning (T0374)Y108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c27A)K269 Warning: unaligning (T0374)K156 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c27A)G312 T0374 3 :LSHRPA 2c27A 152 :VVIRTY T0374 9 :ETGDLETVAGFPQDRDELFY 2c27A 159 :GTSDDAELLRVNNAAFAGHP T0374 33 :AIWPFSVAQLAAAIA 2c27A 179 :EQGGWTAVQLAERRG T0374 48 :ERRGSTVAVHD 2c27A 199 :PDGLILAFGDS T0374 59 :GQVLGFANFYQWQHGD 2c27A 215 :GRLLGFHWTKVHPDHP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2c27A 232 :LGEVYVLGVDPAAQRRGLGQMLTSIGIVSLARR T0374 112 :LMKISCFNANAAGLLLYTQLGYQPRAI 2c27A 278 :AVLLYVESDNVAAVRTYQSLGFTTYSV T0374 150 :ALIQMD 2c27A 305 :DTAYAL Number of specific fragments extracted= 8 number of extra gaps= 1 total=297 Number of alignments=43 # 2c27A read from 2c27A/merged-good-all-a2m # found chain 2c27A in template set Warning: unaligning (T0374)Y108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c27A)K269 T0374 2 :QLSHRPAE 2c27A 151 :GVVIRTYA T0374 10 :TGDLETVAGFPQDRDELFYCYPKAI 2c27A 160 :TSDDAELLRVNNAAFAGHPEQGGWT T0374 39 :VAQLAAAI 2c27A 185 :AVQLAERR T0374 47 :AERRGSTVAVHD 2c27A 198 :DPDGLILAFGDS T0374 59 :GQVLGFANFYQWQH 2c27A 215 :GRLLGFHWTKVHPD T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2c27A 230 :PGLGEVYVLGVDPAAQRRGLGQMLTSIGIVSLARR T0374 111 :RLMKISCFNANAAGLLLYTQLGYQPRAIAE 2c27A 277 :PAVLLYVESDNVAAVRTYQSLGFTTYSVDT T0374 153 :QMDK 2c27A 307 :AYAL Number of specific fragments extracted= 8 number of extra gaps= 0 total=305 Number of alignments=44 # 2c27A read from 2c27A/merged-good-all-a2m # found chain 2c27A in template set Warning: unaligning (T0374)Y108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c27A)K269 Warning: unaligning (T0374)D145 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c27A)G312 Warning: unaligning (T0374)G146 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c27A)G312 T0374 3 :LSHRPA 2c27A 152 :VVIRTY T0374 9 :ETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAA 2c27A 159 :GTSDDAELLRVNNAAFAGHPEQGGWTAVQLAERRGE T0374 45 :AIAERRGSTVAVHD 2c27A 196 :WFDPDGLILAFGDS T0374 59 :GQVLGFANFYQ 2c27A 215 :GRLLGFHWTKV T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2c27A 227 :PDHPGLGEVYVLGVDPAAQRRGLGQMLTSIGIVSLARR T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDP 2c27A 275 :VEPAVLLYVESDNVAAVRTYQSLGFTTYSVDTAYAL Number of specific fragments extracted= 6 number of extra gaps= 1 total=311 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yx0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yx0A expands to /projects/compbio/data/pdb/1yx0.pdb.gz 1yx0A:# T0374 read from 1yx0A/merged-good-all-a2m # 1yx0A read from 1yx0A/merged-good-all-a2m # adding 1yx0A to template set # found chain 1yx0A in template set T0374 1 :MQLSHRPAE 1yx0A 1 :MHIKIDDLT T0374 14 :ETVAGFPQDRDELFY 1yx0A 11 :RQVVSLVNEHLHSMT T0374 29 :CYPKAIWPFSVAQL 1yx0A 28 :SPPESIHALGLEKL T0374 47 :A 1yx0A 42 :R T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHG 1yx0A 44 :PEITFWSAWEGDELAGCGALKELDTR T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1yx0A 70 :HGEIKSMRTSASHLRKGVAKQVLQHIIEEAEKR T0374 109 :KARLMKISC 1yx0A 103 :GYERLSLET T0374 118 :FNANAAGLLLYTQLGYQPRA 1yx0A 114 :MASFEPARKLYESFGFQYCE T0374 138 :IAERHD 1yx0A 135 :FADYGE T0374 144 :PDGRRVA 1yx0A 142 :PNSVFMT T0374 152 :I 1yx0A 149 :K Number of specific fragments extracted= 11 number of extra gaps= 0 total=322 Number of alignments=46 # 1yx0A read from 1yx0A/merged-good-all-a2m # found chain 1yx0A in template set T0374 1 :MQLSHRPAE 1yx0A 1 :MHIKIDDLT T0374 14 :ETVAGFPQDRDELFY 1yx0A 11 :RQVVSLVNEHLHSMT T0374 29 :CYPKAIWPF 1yx0A 27 :MSPPESIHA T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQ 1yx0A 43 :GPEITFWSAWEGDELAGCGALKELD T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1yx0A 68 :TRHGEIKSMRTSASHLRKGVAKQVLQHIIEEAEKR T0374 109 :KARLMKISC 1yx0A 103 :GYERLSLET T0374 118 :FNANAAGLLLYTQLGYQPRAIAERH 1yx0A 114 :MASFEPARKLYESFGFQYCEPFADY T0374 143 :DPDGRR 1yx0A 141 :DPNSVF T0374 150 :AL 1yx0A 147 :MT Number of specific fragments extracted= 9 number of extra gaps= 0 total=331 Number of alignments=47 # 1yx0A read from 1yx0A/merged-good-all-a2m # found chain 1yx0A in template set T0374 14 :ETVAGFPQDRDELFYCYPKAIWPFS 1yx0A 11 :RQVVSLVNEHLHSMTLMSPPESIHA T0374 44 :AAIAERRGSTVAVHDGQVLGFANFYQW 1yx0A 40 :KLRGPEITFWSAWEGDELAGCGALKEL T0374 72 :HGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1yx0A 67 :DTRHGEIKSMRTSASHLRKGVAKQVLQHIIEEAEKRGYER T0374 113 :MKISCFN 1yx0A 107 :LSLETGS T0374 120 :ANAAGLLLYTQLGYQPRAIAERHDPDGRR 1yx0A 116 :SFEPARKLYESFGFQYCEPFADYGEDPNS Number of specific fragments extracted= 5 number of extra gaps= 0 total=336 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tiqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tiqA expands to /projects/compbio/data/pdb/1tiq.pdb.gz 1tiqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1tiqA/merged-good-all-a2m # 1tiqA read from 1tiqA/merged-good-all-a2m # adding 1tiqA to template set # found chain 1tiqA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1tiqA)S2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELF 1tiqA 3 :VKMKKCSREDLQTLQQLSIETFNDT T0374 33 :AIWPFSVAQLAAAIA 1tiqA 28 :FKEQNSPENMKAYLE T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1tiqA 57 :MSSQFFFIYFDHEIAGYVKVNIDDAQS T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1tiqA 90 :SLEIERIYIKNSFQKHGLGKHLLNKAIEIALER T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGR 1tiqA 123 :NKKNIWLGVWEKNENAIAFYKKMGFVQTGAHSFYMGDEE T0374 149 :VALIQMDKPLE 1tiqA 162 :QTDLIMAKTLI Number of specific fragments extracted= 6 number of extra gaps= 0 total=342 Number of alignments=49 # 1tiqA read from 1tiqA/merged-good-all-a2m # found chain 1tiqA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1tiqA)S2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCY 1tiqA 3 :VKMKKCSREDLQTLQQLSIETFNDTFKE T0374 32 :KAIWPFSVAQLAAAI 1tiqA 31 :QNSPENMKAYLESAF T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1tiqA 56 :NMSSQFFFIYFDHEIAGYVKVNIDDA T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1tiqA 88 :AESLEIERIYIKNSFQKHGLGKHLLNKAIEIALER T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDPD 1tiqA 123 :NKKNIWLGVWEKNENAIAFYKKMGFVQTGAHSFYMGD T0374 147 :RRVALIQMDKPLE 1tiqA 160 :EEQTDLIMAKTLI Number of specific fragments extracted= 6 number of extra gaps= 0 total=348 Number of alignments=50 # 1tiqA read from 1tiqA/merged-good-all-a2m # found chain 1tiqA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1tiqA)S2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAA 1tiqA 3 :VKMKKCSREDLQTLQQLSIETFNDTFKEQNSPENMKAYLESA T0374 45 :AIAERRGSTVAVHDGQVLGFANFYQ 1tiqA 54 :LSNMSSQFFFIYFDHEIAGYVKVNI T0374 70 :W 1tiqA 86 :M T0374 72 :HGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1tiqA 87 :GAESLEIERIYIKNSFQKHGLGKHLLNKAIEIALERNKKN T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRR 1tiqA 127 :IWLGVWEKNENAIAFYKKMGFVQTGAHSFYMGDEEQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=353 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fckA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fckA expands to /projects/compbio/data/pdb/2fck.pdb.gz 2fckA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 189, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 666, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 668, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 670, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 672, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 674, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 676, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 678, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 680, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1043, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1045, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1047, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1049, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1051, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1053, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1055, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1057, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1059, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1199, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 1201, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 1203, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 1205, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 1207, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 1209, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 1291, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1293, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1295, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1305, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1307, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1309, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1311, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1313, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1315, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1321, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1325, because occupancy 0.500 <= existing 0.500 in 2fckA # T0374 read from 2fckA/merged-good-all-a2m # 2fckA read from 2fckA/merged-good-all-a2m # adding 2fckA to template set # found chain 2fckA in template set Warning: unaligning (T0374)K32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fckA)F46 Warning: unaligning (T0374)F37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fckA)F46 Warning: unaligning (T0374)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fckA)I86 Warning: unaligning (T0374)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fckA)I86 Warning: unaligning (T0374)A137 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fckA)L157 Warning: unaligning (T0374)I138 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fckA)L157 Warning: unaligning (T0374)L158 because last residue in template chain is (2fckA)P178 T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYP 2fckA 11 :RLQLRLITADEAEELVQCIRQSQTLHQWVD T0374 38 :SVAQLAAAIA 2fckA 47 :SQQEAEQFIQ T0374 48 :ERRGSTVAVHDG 2fckA 65 :AEAYGFGVFERQ T0374 60 :QVLGFA 2fckA 79 :TLVGMV T0374 68 :YQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPR 2fckA 87 :NEFYHTFNMASLGYWIGDRYQRQGYGKEALTALILFCFERLELTRLEIVCDPENVPSQALALRCGANRE T0374 139 :AERHDP 2fckA 158 :APNRFL T0374 145 :DGRRVALIQMDKP 2fckA 165 :AGEPKAGIVFSLI Number of specific fragments extracted= 7 number of extra gaps= 2 total=360 Number of alignments=52 # 2fckA read from 2fckA/merged-good-all-a2m # found chain 2fckA in template set Warning: unaligning (T0374)A33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fckA)F46 Warning: unaligning (T0374)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fckA)I86 Warning: unaligning (T0374)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fckA)I86 Warning: unaligning (T0374)A137 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fckA)L157 Warning: unaligning (T0374)I138 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fckA)L157 Warning: unaligning (T0374)L158 because last residue in template chain is (2fckA)P178 T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYP 2fckA 11 :RLQLRLITADEAEELVQCIRQSQTLHQWVD T0374 34 :IWPFSVAQLAAAI 2fckA 47 :SQQEAEQFIQATR T0374 47 :AERRGSTVAVHDG 2fckA 64 :KAEAYGFGVFERQ T0374 60 :QVLGFA 2fckA 79 :TLVGMV T0374 68 :YQWQH 2fckA 87 :NEFYH T0374 73 :GDFCAL 2fckA 93 :FNMASL T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPR 2fckA 99 :GYWIGDRYQRQGYGKEALTALILFCFERLELTRLEIVCDPENVPSQALALRCGANRE T0374 139 :AERH 2fckA 158 :APNR T0374 143 :DPDGRRVALIQMDKP 2fckA 163 :LYAGEPKAGIVFSLI Number of specific fragments extracted= 9 number of extra gaps= 2 total=369 Number of alignments=53 # 2fckA read from 2fckA/merged-good-all-a2m # found chain 2fckA in template set Warning: unaligning (T0374)K32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fckA)F46 Warning: unaligning (T0374)F37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fckA)F46 Warning: unaligning (T0374)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fckA)I86 Warning: unaligning (T0374)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fckA)I86 Warning: unaligning (T0374)A137 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fckA)L157 Warning: unaligning (T0374)I138 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fckA)L157 T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYP 2fckA 11 :RLQLRLITADEAEELVQCIRQSQTLHQWVD T0374 38 :SVAQLAAA 2fckA 47 :SQQEAEQF T0374 46 :IAERRGSTVAVHDG 2fckA 64 :KAEAYGFGVFERQT T0374 60 :QVLGFA 2fckA 79 :TLVGMV T0374 68 :YQ 2fckA 87 :NE T0374 70 :WQHGDFCAL 2fckA 90 :YHTFNMASL T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPR 2fckA 99 :GYWIGDRYQRQGYGKEALTALILFCFERLELTRLEIVCDPENVPSQALALRCGANRE T0374 139 :AERHDPDG 2fckA 158 :APNRFLYA Number of specific fragments extracted= 8 number of extra gaps= 2 total=377 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i12A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0374 read from 1i12A/merged-good-all-a2m # 1i12A read from 1i12A/merged-good-all-a2m # found chain 1i12A in training set T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i12A 7 :FYIRRMEEGDLEQVTETLKVLT T0374 33 :AIWPFSVAQLAAAIA 1i12A 29 :TVGTITPESFCKLIK T0374 48 :ERRGSTVAVH 1i12A 61 :QYNPMVIVDK T0374 59 :GQVLGFANFYQWQHG 1i12A 73 :ETVAATGNIIIERKI T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1i12A 94 :CGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDY T0374 109 :KARLMKISCFNAN 1i12A 127 :GCYKIILDCDEKN T0374 125 :LLLYTQLGYQPRA 1i12A 140 :VKFYEKCGFSNAG T0374 138 :I 1i12A 154 :E T0374 154 :MDKP 1i12A 155 :MQIR Number of specific fragments extracted= 9 number of extra gaps= 0 total=386 Number of alignments=55 # 1i12A read from 1i12A/merged-good-all-a2m # found chain 1i12A in training set T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i12A 7 :FYIRRMEEGDLEQVTETLKVLT T0374 29 :CYPKAIWPFSVAQLAAAI 1i12A 29 :TVGTITPESFCKLIKYWN T0374 47 :A 1i12A 60 :M T0374 49 :RRGSTVAVHD 1i12A 61 :QYNPMVIVDK T0374 59 :GQVLGFANFYQWQH 1i12A 73 :ETVAATGNIIIERK T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1i12A 92 :GLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDY T0374 109 :KARLMKISCFNANAA 1i12A 127 :GCYKIILDCDEKNVK T0374 127 :LYTQLGYQPRAI 1i12A 142 :FYEKCGFSNAGV T0374 153 :QMDKP 1i12A 154 :EMQIR Number of specific fragments extracted= 9 number of extra gaps= 0 total=395 Number of alignments=56 # 1i12A read from 1i12A/merged-good-all-a2m # found chain 1i12A in training set Warning: unaligning (T0374)P144 because last residue in template chain is (1i12A)K159 T0374 3 :LSHRPAETGDLETVAGFPQDR 1i12A 7 :FYIRRMEEGDLEQVTETLKVL T0374 28 :YCYPKAIWPFSVAQLAA 1i12A 28 :TTVGTITPESFCKLIKY T0374 46 :IAERRGSTVAVHDGQVLGFANFYQWQHG 1i12A 60 :MQYNPMVIVDKRTETVAATGNIIIERKI T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1i12A 94 :CGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYK T0374 113 :MKISCFNAN 1i12A 131 :IILDCDEKN T0374 125 :LLLYTQLGYQPRAIAERHD 1i12A 140 :VKFYEKCGFSNAGVEMQIR Number of specific fragments extracted= 6 number of extra gaps= 0 total=401 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mk4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0374 read from 1mk4A/merged-good-all-a2m # 1mk4A read from 1mk4A/merged-good-all-a2m # found chain 1mk4A in training set Warning: unaligning (T0374)L158 because last residue in template chain is (1mk4A)I156 T0374 3 :LSHRPAETGDLETVAGFPQD 1mk4A 1 :MDIRTITSSDYEMVTSVLNE T0374 29 :CYPK 1mk4A 21 :WWGG T0374 33 :AIWPFSVAQLAAA 1mk4A 27 :LKEKLPRLFFEHF T0374 49 :RRGSTVAVHDGQVLGFANFYQWQHGD 1mk4A 40 :QDTSFITSEHNSMTGFLIGFQSQSDP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1mk4A 67 :TAYIHFSGVHPDFRKMQIGKQLYDVFIETVKQR T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 1mk4A 100 :GCTRVKCVTSPVNKVSIAYHTKLGFDIEK T0374 138 :IAER 1mk4A 130 :TKTV T0374 142 :HDPDGR 1mk4A 142 :YDGPGQ T0374 150 :ALIQMDKP 1mk4A 148 :DRVLFVKN Number of specific fragments extracted= 9 number of extra gaps= 0 total=410 Number of alignments=58 # 1mk4A read from 1mk4A/merged-good-all-a2m # found chain 1mk4A in training set Warning: unaligning (T0374)Q2 because first residue in template chain is (1mk4A)H0 Warning: unaligning (T0374)L158 because last residue in template chain is (1mk4A)I156 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSV 1mk4A 1 :MDIRTITSSDYEMVTSVLNEWWGGRQLKEKLPRLFFE T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1mk4A 38 :HFQDTSFITSEHNSMTGFLIGFQSQS T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1mk4A 65 :PETAYIHFSGVHPDFRKMQIGKQLYDVFIETVKQR T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPR 1mk4A 100 :GCTRVKCVTSPVNKVSIAYHTKLGFDIE T0374 137 :AIA 1mk4A 131 :KTV T0374 140 :ERH 1mk4A 137 :SVF T0374 143 :DPDG 1mk4A 143 :DGPG T0374 149 :VALIQMDKP 1mk4A 147 :QDRVLFVKN Number of specific fragments extracted= 8 number of extra gaps= 0 total=418 Number of alignments=59 # 1mk4A read from 1mk4A/merged-good-all-a2m # found chain 1mk4A in training set T0374 3 :LSHRPAETGDLETVAGFPQDRD 1mk4A 1 :MDIRTITSSDYEMVTSVLNEWW T0374 29 :CYPKAIWPFSVAQLAAAIAE 1mk4A 23 :GGRQLKEKLPRLFFEHFQDT T0374 52 :STVAVHDGQVLGFANFYQWQHGD 1mk4A 43 :SFITSEHNSMTGFLIGFQSQSDP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1mk4A 67 :TAYIHFSGVHPDFRKMQIGKQLYDVFIETVKQRGCTR T0374 113 :MKISCFNANAAGLLLYTQLGYQPRA 1mk4A 104 :VKCVTSPVNKVSIAYHTKLGFDIEK T0374 138 :IAERHDPDGRRVA 1mk4A 138 :VFANYDGPGQDRV Number of specific fragments extracted= 6 number of extra gaps= 0 total=424 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bswA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bswA expands to /projects/compbio/data/pdb/2bsw.pdb.gz 2bswA:Skipped atom 137, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 2bswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 867, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1004, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1006, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1008, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1018, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1020, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1022, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1024, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1026, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1028, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1030, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1032, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1056, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1058, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1060, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1062, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1064, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1066, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1068, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1070, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1072, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1074, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 2bswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2bswA/merged-good-all-a2m # 2bswA read from 2bswA/merged-good-all-a2m # adding 2bswA to template set # found chain 2bswA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2bswA)I2 Warning: unaligning (T0374)I115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bswA)N109 Warning: unaligning (T0374)S116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bswA)N109 Warning: unaligning (T0374)E159 because last residue in template chain is (2bswA)T146 T0374 4 :SHRPAETGD 2bswA 3 :EVKPINAED T0374 13 :LETVAGFPQDR 2bswA 13 :YELRHRILRPN T0374 24 :DELFYCYPKAI 2bswA 25 :PIEACMFESDL T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 2bswA 37 :RGAFHLGGYYGGKLISIASFHQAEHSE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2bswA 69 :QYQLRGMATLEGYREQKAGSSLIKHAEEILRKR T0374 109 :KARLMK 2bswA 102 :GADLLW T0374 117 :CFNAN 2bswA 110 :ARTSA T0374 125 :LLLYTQLGYQPRA 2bswA 115 :SGYYKKLGFSEQG T0374 139 :AERHDPDGR 2bswA 128 :EVFDTPPVG T0374 150 :ALIQMDKPL 2bswA 137 :PHILMYKRI Number of specific fragments extracted= 10 number of extra gaps= 1 total=434 Number of alignments=61 # 2bswA read from 2bswA/merged-good-all-a2m # found chain 2bswA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2bswA)I2 Warning: unaligning (T0374)I115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bswA)N109 Warning: unaligning (T0374)S116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bswA)N109 Warning: unaligning (T0374)E159 because last residue in template chain is (2bswA)T146 T0374 4 :SHRPAETGD 2bswA 3 :EVKPINAED T0374 13 :LETVAGFPQDRDELFY 2bswA 13 :YELRHRILRPNQPIEA T0374 29 :CYPKAI 2bswA 30 :MFESDL T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 2bswA 36 :LRGAFHLGGYYGGKLISIASFHQAEH T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2bswA 67 :QKQYQLRGMATLEGYREQKAGSSLIKHAEEILRKR T0374 109 :KARLMK 2bswA 102 :GADLLW T0374 117 :CFNA 2bswA 110 :ARTS T0374 124 :GLLLYTQLGYQPRAIAER 2bswA 114 :ASGYYKKLGFSEQGEVFD T0374 143 :DPDGR 2bswA 132 :TPPVG T0374 150 :ALIQMDKPL 2bswA 137 :PHILMYKRI Number of specific fragments extracted= 10 number of extra gaps= 1 total=444 Number of alignments=62 # 2bswA read from 2bswA/merged-good-all-a2m # found chain 2bswA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2bswA)I2 Warning: unaligning (T0374)I115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bswA)N109 Warning: unaligning (T0374)S116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bswA)N109 T0374 4 :SHRPAETGDL 2bswA 3 :EVKPINAEDT T0374 14 :ETVAGFPQ 2bswA 14 :ELRHRILR T0374 28 :YCYPKAIWPFSV 2bswA 22 :PNQPIEACMFES T0374 45 :AIAERRGSTVAVHDGQVLGFANFYQ 2bswA 34 :DLLRGAFHLGGYYGGKLISIASFHQ T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2bswA 64 :LQGQKQYQLRGMATLEGYREQKAGSSLIKHAEEILRKRGADL T0374 113 :MK 2bswA 106 :LW T0374 117 :CFNAN 2bswA 110 :ARTSA T0374 125 :LLLYTQLGYQPRAIAERHDPDG 2bswA 115 :SGYYKKLGFSEQGEVFDTPPVG Number of specific fragments extracted= 8 number of extra gaps= 1 total=452 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bo4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bo4A expands to /projects/compbio/data/pdb/1bo4.pdb.gz 1bo4A:# T0374 read from 1bo4A/merged-good-all-a2m # 1bo4A read from 1bo4A/merged-good-all-a2m # adding 1bo4A to template set # found chain 1bo4A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1bo4A)G25 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPK 1bo4A 27 :IRTCRLGPDQVKSMRAALDLFGREFGDVAT T0374 33 :AIWPFSVAQLAAAIA 1bo4A 58 :SQHQPDSDYLGNLLR T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1bo4A 74 :KTFIALAAFDQEAVVGALAAYVLPKFE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1bo4A 105 :EIYIYDLAVSGEHRRQGIATALINLLKHEANAL T0374 109 :KARLMKI 1bo4A 138 :GAYVIYV Number of specific fragments extracted= 5 number of extra gaps= 0 total=457 Number of alignments=64 # 1bo4A read from 1bo4A/merged-good-all-a2m # found chain 1bo4A in template set T0374 2 :QLSHRPAETGDLETVAGFP 1bo4A 26 :IIRTCRLGPDQVKSMRAAL T0374 21 :QDRDELFYCYPK 1bo4A 52 :GDVATYSQHQPD T0374 39 :VAQLAAAI 1bo4A 64 :SDYLGNLL T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1bo4A 73 :SKTFIALAAFDQEAVVGALAAYVLPK T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1bo4A 103 :RSEIYIYDLAVSGEHRRQGIATALINLLKHEANAL T0374 109 :KARLMKISCFNA 1bo4A 138 :GAYVIYVQADYG T0374 144 :PDGRRVALI 1bo4A 150 :DDPAVALYT Number of specific fragments extracted= 7 number of extra gaps= 0 total=464 Number of alignments=65 # 1bo4A read from 1bo4A/merged-good-all-a2m # found chain 1bo4A in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCY 1bo4A 26 :IIRTCRLGPDQVKSMRAALDLFGREFGDV T0374 31 :PKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQ 1bo4A 57 :YSQHQPDSDYLGNLLRSKTFIALAAFDQEAVVGALAAYV T0374 70 :WQHGD 1bo4A 99 :FEQPR T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1bo4A 105 :EIYIYDLAVSGEHRRQGIATALINLLKHEANALGAYV T0374 113 :MKIS 1bo4A 142 :IYVQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=469 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fl4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fl4A expands to /projects/compbio/data/pdb/2fl4.pdb.gz 2fl4A:# T0374 read from 2fl4A/merged-good-all-a2m # 2fl4A read from 2fl4A/merged-good-all-a2m # adding 2fl4A to template set # found chain 2fl4A in template set Warning: unaligning (T0374)V56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fl4A)D52 Warning: unaligning (T0374)H57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fl4A)D52 Warning: unaligning (T0374)Q71 because of BadResidue code BAD_PEPTIDE in next template residue (2fl4A)D67 Warning: unaligning (T0374)H72 because of BadResidue code BAD_PEPTIDE at template residue (2fl4A)D67 Warning: unaligning (T0374)E159 because last residue in template chain is (2fl4A)Q146 T0374 1 :MQLSHRPAETGDLE 2fl4A 1 :MEIHFEKVTSDNRK T0374 25 :ELFYCYPKAIWPFSVAQLAAAIA 2fl4A 15 :AVENLQVFAEQQAFIESMAENLK T0374 48 :ERRGSTVA 2fl4A 43 :PEWESAGI T0374 58 :DGQVLGFANFYQW 2fl4A 53 :GNQLIGYAMYGRW T0374 73 :G 2fl4A 68 :G T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRA 2fl4A 69 :RVWLDRFLIDQRFQGQGYGKAACRLLMLKLIEKYQTNKLYLSVYDTNSSAIRLYQQLGFVFNG T0374 141 :RHDPDGR 2fl4A 132 :ELDTNGE T0374 152 :IQMDKPL 2fl4A 139 :RVMEWTH Number of specific fragments extracted= 8 number of extra gaps= 2 total=477 Number of alignments=67 # 2fl4A read from 2fl4A/merged-good-all-a2m # found chain 2fl4A in template set Warning: unaligning (T0374)V56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fl4A)D52 Warning: unaligning (T0374)H57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fl4A)D52 Warning: unaligning (T0374)Q71 because of BadResidue code BAD_PEPTIDE in next template residue (2fl4A)D67 Warning: unaligning (T0374)G73 because of BadResidue code BAD_PEPTIDE at template residue (2fl4A)D67 Warning: unaligning (T0374)E159 because last residue in template chain is (2fl4A)Q146 T0374 1 :MQLSHRPAETGDLETVAGFP 2fl4A 1 :MEIHFEKVTSDNRKAVENLQ T0374 31 :PKAIWPFSVAQLAAAI 2fl4A 21 :VFAEQQAFIESMAENL T0374 47 :AERRGSTVA 2fl4A 42 :FPEWESAGI T0374 58 :DGQVLGFANFYQW 2fl4A 53 :GNQLIGYAMYGRW T0374 74 :DFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRA 2fl4A 68 :GRVWLDRFLIDQRFQGQGYGKAACRLLMLKLIEKYQTNKLYLSVYDTNSSAIRLYQQLGFVFNG T0374 141 :RHDPDGR 2fl4A 132 :ELDTNGE T0374 152 :IQMDKPL 2fl4A 139 :RVMEWTH Number of specific fragments extracted= 7 number of extra gaps= 2 total=484 Number of alignments=68 # 2fl4A read from 2fl4A/merged-good-all-a2m # found chain 2fl4A in template set Warning: unaligning (T0374)V56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fl4A)D52 Warning: unaligning (T0374)H57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fl4A)D52 Warning: unaligning (T0374)H72 because of BadResidue code BAD_PEPTIDE in next template residue (2fl4A)D67 Warning: unaligning (T0374)G73 because of BadResidue code BAD_PEPTIDE at template residue (2fl4A)D67 T0374 1 :MQLSHRPAETGDLET 2fl4A 1 :MEIHFEKVTSDNRKA T0374 25 :ELFYCYPKAIWPFSVAQLAA 2fl4A 16 :VENLQVFAEQQAFIESMAEN T0374 45 :AIAERRGSTVA 2fl4A 40 :DQFPEWESAGI T0374 58 :DGQVLGFANFYQW 2fl4A 53 :GNQLIGYAMYGRW T0374 74 :DFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIA 2fl4A 68 :GRVWLDRFLIDQRFQGQGYGKAACRLLMLKLIEKYQTNKLYLSVYDTNSSAIRLYQQLGFVFNGEL T0374 143 :DPDGR 2fl4A 134 :DTNGE Number of specific fragments extracted= 6 number of extra gaps= 2 total=490 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b5gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b5gA expands to /projects/compbio/data/pdb/2b5g.pdb.gz 2b5gA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2b5gA/merged-good-all-a2m # 2b5gA read from 2b5gA/merged-good-all-a2m # adding 2b5gA to template set # found chain 2b5gA in template set Warning: unaligning (T0374)L26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b5gA)E32 Warning: unaligning (T0374)F27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b5gA)E32 T0374 2 :QLSHRPAETGDLETVAGFPQDRDE 2b5gA 3 :KFVIRPATAADCSDILRLIKELAK T0374 34 :IWPFSVAQLAAAIA 2b5gA 33 :QVILTEKDLLEDGF T0374 48 :ERRGSTVAVH 2b5gA 50 :PFYHCLVAEV T0374 58 :DG 2b5gA 66 :PE T0374 60 :QVLGFANFYQWQHGD 2b5gA 70 :SIVGFAMYYFTYDPW T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2b5gA 88 :LLYLEDFFVMSDYRGFGIGSEILKNLSQVAMRC T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQP 2b5gA 121 :RCSSMHFLVAEWNEPSINFYKRRGASD Number of specific fragments extracted= 7 number of extra gaps= 1 total=497 Number of alignments=70 # 2b5gA read from 2b5gA/merged-good-all-a2m # found chain 2b5gA in template set Warning: unaligning (T0374)L26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b5gA)E32 Warning: unaligning (T0374)F27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b5gA)E32 T0374 2 :QLSHRPAETGDLETVAGFPQDRDE 2b5gA 3 :KFVIRPATAADCSDILRLIKELAK T0374 32 :KAIWP 2b5gA 33 :QVILT T0374 39 :VAQLAAAI 2b5gA 38 :EKDLLEDG T0374 47 :AERRGSTVAV 2b5gA 49 :HPFYHCLVAE T0374 58 :DG 2b5gA 66 :PE T0374 60 :QVLGFANFYQWQH 2b5gA 70 :SIVGFAMYYFTYD T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2b5gA 86 :GKLLYLEDFFVMSDYRGFGIGSEILKNLSQVAMRC T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQP 2b5gA 121 :RCSSMHFLVAEWNEPSINFYKRRGASD Number of specific fragments extracted= 8 number of extra gaps= 1 total=505 Number of alignments=71 # 2b5gA read from 2b5gA/merged-good-all-a2m # found chain 2b5gA in template set Warning: unaligning (T0374)L26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b5gA)E32 Warning: unaligning (T0374)F27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b5gA)E32 T0374 2 :QLSHRPAETGDLETVAGFPQDRDE 2b5gA 3 :KFVIRPATAADCSDILRLIKELAK T0374 32 :KAIWPFSVAQLAAA 2b5gA 33 :QVILTEKDLLEDGF T0374 46 :IAERRGSTVAVH 2b5gA 48 :EHPFYHCLVAEV T0374 58 :DGQVLGFANFYQWQHGD 2b5gA 68 :GHSIVGFAMYYFTYDPW T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2b5gA 88 :LLYLEDFFVMSDYRGFGIGSEILKNLSQVAMRCRCSS T0374 113 :MKISCFNANAAGLLLYTQLGYQP 2b5gA 125 :MHFLVAEWNEPSINFYKRRGASD Number of specific fragments extracted= 6 number of extra gaps= 1 total=511 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vhsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0374 read from 1vhsA/merged-good-all-a2m # 1vhsA read from 1vhsA/merged-good-all-a2m # found chain 1vhsA in training set Warning: unaligning (T0374)Q2 because first residue in template chain is (1vhsA)S0 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYP 1vhsA 1 :LTLRLAEHRDLEAVVAIYNSTIASRMVTA T0374 33 :AIWPFSVAQLAAAIA 1vhsA 30 :DTEPVTPEDRMEWFS T0374 48 :ERRGSTVAVHD 1vhsA 48 :ESRPLYVAEDE T0374 59 :GQVLGFANFYQWQHGD 1vhsA 60 :GNVAAWISFETFYGRP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1vhsA 79 :KTAEVSIYIDEACRGKGVGSYLLQEALRIAPNL T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 1vhsA 112 :GIRSLMAFIFGHNKPSLKLFEKHGFAEWG T0374 138 :IAERHDPDGRRVALIQMDKPLEP 1vhsA 142 :FPGIAEMDGKRYDLKILGRELSE Number of specific fragments extracted= 7 number of extra gaps= 0 total=518 Number of alignments=73 # 1vhsA read from 1vhsA/merged-good-all-a2m # found chain 1vhsA in training set Warning: unaligning (T0374)Q2 because first residue in template chain is (1vhsA)S0 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1vhsA 1 :LTLRLAEHRDLEAVVAIYNSTIASRM T0374 29 :CYPKAIWPFSVAQLAAA 1vhsA 30 :DTEPVTPEDRMEWFSGH T0374 47 :AERRGSTVAVHD 1vhsA 47 :TESRPLYVAEDE T0374 59 :GQVLGFANFYQWQH 1vhsA 60 :GNVAAWISFETFYG T0374 73 :GDFCAL 1vhsA 78 :NKTAEV T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQ 1vhsA 84 :SIYIDEACRGKGVGSYLLQEALRIAPNL T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1vhsA 112 :GIRSLMAFIFGHNKPSLKLFEKHGFAEWGLFPGI T0374 143 :DPDGRRVALIQMDKPLEP 1vhsA 147 :EMDGKRYDLKILGRELSE Number of specific fragments extracted= 8 number of extra gaps= 0 total=526 Number of alignments=74 # 1vhsA read from 1vhsA/merged-good-all-a2m # found chain 1vhsA in training set Warning: unaligning (T0374)Q2 because first residue in template chain is (1vhsA)S0 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCY 1vhsA 1 :LTLRLAEHRDLEAVVAIYNSTIASRMVT T0374 31 :PKAIWPFSVAQLAAA 1vhsA 30 :DTEPVTPEDRMEWFS T0374 46 :IAERRGSTVAVH 1vhsA 46 :HTESRPLYVAED T0374 58 :DGQVLGFANFYQWQHGD 1vhsA 59 :NGNVAAWISFETFYGRP T0374 75 :FCAL 1vhsA 80 :TAEV T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQYKAR 1vhsA 84 :SIYIDEACRGKGVGSYLLQEALRIAPNLGIRS T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGR 1vhsA 116 :LMAFIFGHNKPSLKLFEKHGFAEWGLFPGIAEMDG Number of specific fragments extracted= 7 number of extra gaps= 0 total=533 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wwzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0374 read from 1wwzA/merged-good-all-a2m # 1wwzA read from 1wwzA/merged-good-all-a2m # found chain 1wwzA in training set Warning: unaligning (T0374)L158 because last residue in template chain is (1wwzA)Q157 T0374 1 :MQ 1wwzA 1 :MD T0374 3 :LSHRPAE 1wwzA 4 :IKIEKLK T0374 10 :TGDLETVAGFPQDRDELF 1wwzA 14 :KKALNELIDVYMSGYEGL T0374 31 :P 1wwzA 32 :E T0374 33 :AIWPFSVAQLAAAIA 1wwzA 33 :EYGGEGRDYARNYIK T0374 49 :RRGSTVAVHDGQVLGFANF 1wwzA 54 :SDGFFVAKVGDKIVGFIVC T0374 68 :YQWQHGD 1wwzA 76 :WFSKYEG T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1wwzA 85 :VGAIHEFVVDKKFQGKGIGRKLLITCLDFLGKY T0374 110 :ARLMKISCFNANAAGLLLYTQLGYQPRAIAER 1wwzA 118 :NDTIELWVGEKNYGAMNLYEKFGFKKVGKSGI T0374 151 :LIQMDKP 1wwzA 150 :WVRMIKR Number of specific fragments extracted= 10 number of extra gaps= 0 total=543 Number of alignments=76 # 1wwzA read from 1wwzA/merged-good-all-a2m # found chain 1wwzA in training set Warning: unaligning (T0374)L158 because last residue in template chain is (1wwzA)Q157 T0374 1 :M 1wwzA 1 :M T0374 2 :QLSHRPAE 1wwzA 3 :EIKIEKLK T0374 10 :TGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAAI 1wwzA 14 :KKALNELIDVYMSGYEGLEEYGGEGRDYARNYIKWCW T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1wwzA 52 :KASDGFFVAKVGDKIVGFIVCDKDWF T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1wwzA 83 :RIVGAIHEFVVDKKFQGKGIGRKLLITCLDFLGKY T0374 110 :ARLMKISCFNANAAGLLLYTQLGYQPRAIAER 1wwzA 118 :NDTIELWVGEKNYGAMNLYEKFGFKKVGKSGI T0374 151 :LIQMDKP 1wwzA 150 :WVRMIKR Number of specific fragments extracted= 7 number of extra gaps= 0 total=550 Number of alignments=77 # 1wwzA read from 1wwzA/merged-good-all-a2m # found chain 1wwzA in training set T0374 2 :QLSHRPAE 1wwzA 3 :EIKIEKLK T0374 10 :TGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAA 1wwzA 14 :KKALNELIDVYMSGYEGLEEYGGEGRDYARNYIKWC T0374 46 :IAE 1wwzA 53 :ASD T0374 51 :GSTVAVHDGQVLGFANFYQ 1wwzA 56 :GFFVAKVGDKIVGFIVCDK T0374 70 :WQHGD 1wwzA 78 :SKYEG T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKA 1wwzA 85 :VGAIHEFVVDKKFQGKGIGRKLLITCLDFLGKYNDT T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERH 1wwzA 121 :IELWVGEKNYGAMNLYEKFGFKKVGKSGIW Number of specific fragments extracted= 7 number of extra gaps= 0 total=557 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fsrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fsrA expands to /projects/compbio/data/pdb/2fsr.pdb.gz 2fsrA:Skipped atom 26, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 28, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 30, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 32, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 34, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 36, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 38, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 40, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 138, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 140, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 142, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 144, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 146, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 148, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 150, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 152, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 154, because occupancy 0.400 <= existing 0.600 in 2fsrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 333, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 341, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 343, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 345, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 347, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 349, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 351, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 353, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 436, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 438, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 440, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 442, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 444, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 446, because occupancy 0.400 <= existing 0.600 in 2fsrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 897, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 907, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 911, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1057, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1059, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1061, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1063, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1065, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1067, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1069, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1071, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1135, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1141, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1143, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1145, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1154, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1156, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1158, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1160, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1162, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1230, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1232, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1234, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1238, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1254, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1260, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1262, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1266, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1284, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1286, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1288, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1290, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1292, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1294, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1296, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1352, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1354, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1356, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1358, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1360, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1362, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1379, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1381, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1383, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1385, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1387, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1389, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1391, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1393, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1395, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1455, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1457, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1459, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1463, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1469, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1485, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1487, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1489, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1491, because occupancy 0.500 <= existing 0.500 in 2fsrA # T0374 read from 2fsrA/merged-good-all-a2m # 2fsrA read from 2fsrA/merged-good-all-a2m # adding 2fsrA to template set # found chain 2fsrA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELF 2fsrA 12 :RLTLRPLAMADFPAYRDFMASPRSTG T0374 33 :AIWPFSVAQLAAAIA 2fsrA 38 :VGGPYDLPSTWGVFC T0374 48 :ERRGSTVAVHD 2fsrA 61 :FGHGALMIDLG T0374 59 :GQVLGFANFYQWQHGDFC 2fsrA 74 :GECIGQIGINHGPLFPEK T0374 78 :LGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRVA 2fsrA 92 :ELGWLLYEGHEGRGYAAEAAVALRDWAFETLNLPTLVSYVSPQNRKSAAVAERIGGTLDPLAPRSDPEDLVYR T0374 155 :D 2fsrA 165 :Y Number of specific fragments extracted= 6 number of extra gaps= 0 total=563 Number of alignments=79 # 2fsrA read from 2fsrA/merged-good-all-a2m # found chain 2fsrA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFY 2fsrA 12 :RLTLRPLAMADFPAYRDFMASPRSTGV T0374 29 :CYPKAIWPFSVAQLAAAI 2fsrA 41 :PYDLPSTWGVFCHDLANW T0374 47 :AERRGSTVAVHD 2fsrA 60 :FFGHGALMIDLG T0374 59 :GQVLGFANFYQWQHGDFCAL 2fsrA 74 :GECIGQIGINHGPLFPEKEL T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRR 2fsrA 94 :GWLLYEGHEGRGYAAEAAVALRDWAFETLNLPTLVSYVSPQNRKSAAVAERIGGTLDPLAPRSDPEDLV T0374 152 :IQ 2fsrA 163 :YR Number of specific fragments extracted= 6 number of extra gaps= 0 total=569 Number of alignments=80 # 2fsrA read from 2fsrA/merged-good-all-a2m # found chain 2fsrA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQ 2fsrA 12 :RLTLRPLAMADFPAYRDFMASPRSTGVGGPYDLPSTWGVF T0374 42 :LAAAIAERRGSTVAVHD 2fsrA 55 :LANWHFFGHGALMIDLG T0374 59 :GQVLGFANFYQWQHGDFCALG 2fsrA 74 :GECIGQIGINHGPLFPEKELG T0374 81 :MMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAE 2fsrA 95 :WLLYEGHEGRGYAAEAAVALRDWAFETLNLPTLVSYVSPQNRKSAAVAERIGGTLDPLAP Number of specific fragments extracted= 4 number of extra gaps= 0 total=573 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a4nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a4nA expands to /projects/compbio/data/pdb/2a4n.pdb.gz 2a4nA:# T0374 read from 2a4nA/merged-good-all-a2m # 2a4nA read from 2a4nA/merged-good-all-a2m # adding 2a4nA to template set # found chain 2a4nA in template set T0374 4 :SHRPAETGD 2a4nA 2 :IISEFDRNN T0374 13 :LETVAGFP 2a4nA 14 :KDQLSDLL T0374 27 :FYCYPKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2a4nA 22 :RLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASR T0374 109 :KARLMKISC 2a4nA 103 :GGITIYLGT T0374 118 :F 2a4nA 114 :L T0374 125 :LLLYTQLGYQPRAIAERHDPDGR 2a4nA 144 :YEFYEKLGYKIVGVLPNANGWDK T0374 150 :ALIQMDKPLEP 2a4nA 167 :PDIWMAKTIIP Number of specific fragments extracted= 7 number of extra gaps= 0 total=580 Number of alignments=82 # 2a4nA read from 2a4nA/merged-good-all-a2m # found chain 2a4nA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2a4nA)M1 T0374 4 :SHRPAETGD 2a4nA 2 :IISEFDRNN T0374 13 :LETVAGFPQDR 2a4nA 14 :KDQLSDLLRLT T0374 30 :YPKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2a4nA 25 :WPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASR T0374 109 :KARLMKISC 2a4nA 103 :GGITIYLGT T0374 118 :FNANA 2a4nA 139 :LREHP T0374 125 :LLLYTQLGYQPRAIAERH 2a4nA 144 :YEFYEKLGYKIVGVLPNA T0374 143 :DPD 2a4nA 163 :GWD T0374 149 :VALIQMDKPL 2a4nA 166 :KPDIWMAKTI T0374 159 :E 2a4nA 179 :P Number of specific fragments extracted= 9 number of extra gaps= 0 total=589 Number of alignments=83 # 2a4nA read from 2a4nA/merged-good-all-a2m # found chain 2a4nA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2a4nA)M1 T0374 4 :SHRPAETGD 2a4nA 2 :IISEFDRNN T0374 13 :LETVAGFPQDRD 2a4nA 14 :KDQLSDLLRLTW T0374 31 :PKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2a4nA 26 :PEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGIT T0374 113 :MKISCFNA 2a4nA 107 :IYLGTDDL T0374 125 :LLLYTQLGYQPRAIAERHDPDGRRVALIQMDKPLEP 2a4nA 144 :YEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRP Number of specific fragments extracted= 5 number of extra gaps= 0 total=594 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fe7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fe7A expands to /projects/compbio/data/pdb/2fe7.pdb.gz 2fe7A:# T0374 read from 2fe7A/merged-good-all-a2m # 2fe7A read from 2fe7A/merged-good-all-a2m # adding 2fe7A to template set # found chain 2fe7A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2fe7A)L3 Warning: unaligning (T0374)R88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fe7A)G96 Warning: unaligning (T0374)G89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fe7A)G96 T0374 4 :SHRPAETGDLETVAGFPQDRDELFYCY 2fe7A 4 :EIRPAVPADAEQILAFIIELADYERAR T0374 33 :AIWPFSVAQLAAAIA 2fe7A 31 :HEVVTDVEGIRRSLF T0374 48 :ERRG 2fe7A 47 :EGSP T0374 52 :STVAVHDGQVLGFANFYQWQHGD 2fe7A 53 :ALMCLSEGRPIGYAVFFYSYSTW T0374 75 :FCALGNMMVAPAA 2fe7A 80 :GIYLEDLYVTPEY T0374 92 :VARYLIGVMENLAREQ 2fe7A 97 :AGRRLLRELAREAVAN T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 2fe7A 113 :DCGRLEWSVLDWNQPAIDFYRSIGALPQD T0374 138 :IAERH 2fe7A 143 :WVRYR Number of specific fragments extracted= 8 number of extra gaps= 1 total=602 Number of alignments=85 # 2fe7A read from 2fe7A/merged-good-all-a2m # found chain 2fe7A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2fe7A)L3 Warning: unaligning (T0374)R88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fe7A)G96 Warning: unaligning (T0374)G89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fe7A)G96 T0374 4 :SHRPAETGDLETVAGFPQDRDELFYCYPKAIWP 2fe7A 4 :EIRPAVPADAEQILAFIIELADYERARHEVVTD T0374 39 :VAQLAAAI 2fe7A 37 :VEGIRRSL T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 2fe7A 48 :GSPTRALMCLSEGRPIGYAVFFYSYS T0374 73 :GDFCALGNMMVAPAA 2fe7A 78 :RNGIYLEDLYVTPEY T0374 92 :VARYLIGVMENLAREQ 2fe7A 97 :AGRRLLRELAREAVAN T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPR 2fe7A 113 :DCGRLEWSVLDWNQPAIDFYRSIGALPQ T0374 137 :AIAER 2fe7A 142 :EWVRY Number of specific fragments extracted= 7 number of extra gaps= 1 total=609 Number of alignments=86 # 2fe7A read from 2fe7A/merged-good-all-a2m # found chain 2fe7A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2fe7A)L3 Warning: unaligning (T0374)R88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fe7A)G96 Warning: unaligning (T0374)G89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fe7A)G96 T0374 4 :SHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAAIAE 2fe7A 4 :EIRPAVPADAEQILAFIIELADYERARHEVVTDVEGIRRSLFAEG T0374 49 :RRGSTVAVHDGQVLGFANFYQ 2fe7A 50 :PTRALMCLSEGRPIGYAVFFY T0374 74 :D 2fe7A 75 :W T0374 75 :FCALGNMMVAPAA 2fe7A 80 :GIYLEDLYVTPEY T0374 92 :VARYLIGVMENLAREQYKAR 2fe7A 97 :AGRRLLRELAREAVANDCGR T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRVALI 2fe7A 117 :LEWSVLDWNQPAIDFYRSIGALPQDEWVRYRLDGEALRKM Number of specific fragments extracted= 6 number of extra gaps= 1 total=615 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y9kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y9kA expands to /projects/compbio/data/pdb/1y9k.pdb.gz 1y9kA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1099, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1115, because occupancy 0.500 <= existing 0.500 in 1y9kA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1y9kA/merged-good-all-a2m # 1y9kA read from 1y9kA/merged-good-all-a2m # adding 1y9kA to template set # found chain 1y9kA in template set Warning: unaligning (T0374)E159 because last residue in template chain is (1y9kA)N152 T0374 1 :MQLSHRPAETG 1y9kA 1 :MSVVIERIPKE T0374 18 :GFPQDRDELF 1y9kA 12 :AIPKSLLLLA T0374 36 :PFSVAQLAAAIA 1y9kA 22 :DPSERQIATYVQ T0374 49 :RRGSTVAVHDGQVLGFANFYQWQ 1y9kA 34 :RGLTYVAKQGGSVIGVYVLLETR T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1y9kA 57 :PKTMEIMNIAVAEHLQGKGIGKKLLRHAVETAKGY T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1y9kA 92 :GMSKLEVGTGNSSVSQLALYQKCGFRIFSIDFDY T0374 143 :DP 1y9kA 130 :YE T0374 145 :DG 1y9kA 137 :NG T0374 147 :RRVALIQMDKPL 1y9kA 140 :VCRDMIRLAMEL Number of specific fragments extracted= 9 number of extra gaps= 0 total=624 Number of alignments=88 # 1y9kA read from 1y9kA/merged-good-all-a2m # found chain 1y9kA in template set Warning: unaligning (T0374)E159 because last residue in template chain is (1y9kA)N152 T0374 1 :MQLSHRPAETG 1y9kA 1 :MSVVIERIPKE T0374 18 :GFPQDRDELF 1y9kA 12 :AIPKSLLLLA T0374 32 :KAIWPFSVAQLA 1y9kA 22 :DPSERQIATYVQ T0374 49 :RRGSTVAVHDGQVLGFANFYQWQ 1y9kA 34 :RGLTYVAKQGGSVIGVYVLLETR T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1y9kA 57 :PKTMEIMNIAVAEHLQGKGIGKKLLRHAVETAKGY T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1y9kA 92 :GMSKLEVGTGNSSVSQLALYQKCGFRIFSIDFDY T0374 143 :DPDGRRV 1y9kA 130 :YEEEIIE T0374 150 :ALIQMDKPL 1y9kA 143 :DMIRLAMEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=632 Number of alignments=89 # 1y9kA read from 1y9kA/merged-good-all-a2m # found chain 1y9kA in template set T0374 1 :MQLSHRPAETGD 1y9kA 1 :MSVVIERIPKEA T0374 17 :AGFPQDR 1y9kA 15 :KSLLLLA T0374 33 :AIWPFSVAQLA 1y9kA 22 :DPSERQIATYV T0374 48 :ERRGSTVAVHDGQVLGFANFYQ 1y9kA 33 :QRGLTYVAKQGGSVIGVYVLLE T0374 71 :QHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1y9kA 55 :TRPKTMEIMNIAVAEHLQGKGIGKKLLRHAVETAKGYGMSK T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERH 1y9kA 96 :LEVGTGNSSVSQLALYQKCGFRIFSIDFDY Number of specific fragments extracted= 6 number of extra gaps= 0 total=638 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s7kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0374 read from 1s7kA/merged-good-all-a2m # 1s7kA read from 1s7kA/merged-good-all-a2m # found chain 1s7kA in training set Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s7kA)T51 Warning: unaligning (T0374)S38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s7kA)T51 T0374 3 :LSHRPAETGDLETVAGFPQD 1s7kA 11 :LELRAADESHVPALHQLVLK T0374 39 :VAQLAAAIA 1s7kA 52 :RKHVQGNIL T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRA 1s7kA 65 :GYAKMYLIFCQNEMAGVLSFNAIEPINKAAYIGYWLDESFQGQGIMSQSLQALMTHYARRGDIRRFVIKCRVDNQASNAVARRNHFTLEG T0374 138 :IAERHDPDGRRVALIQMDKPLEP 1s7kA 156 :MKQAEYLNGDYHDVNMYARIIDA Number of specific fragments extracted= 4 number of extra gaps= 0 total=642 Number of alignments=91 # 1s7kA read from 1s7kA/merged-good-all-a2m # found chain 1s7kA in training set Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s7kA)T51 Warning: unaligning (T0374)S38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s7kA)T51 T0374 3 :LSHRPAETGDLETVAGFPQD 1s7kA 11 :LELRAADESHVPALHQLVLK T0374 39 :VAQLAAAI 1s7kA 52 :RKHVQGNI T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1s7kA 64 :RGYAKMYLIFCQNEMAGVLSFNAIEP T0374 73 :GDFCAL 1s7kA 91 :NKAAYI T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1s7kA 97 :GYWLDESFQGQGIMSQSLQALMTHYARRGDIRRFVIKCRVDNQASNAVARRNHFTLEGCMKQA T0374 143 :DPDGRRVALIQMDKPLEP 1s7kA 161 :YLNGDYHDVNMYARIIDA Number of specific fragments extracted= 6 number of extra gaps= 0 total=648 Number of alignments=92 # 1s7kA read from 1s7kA/merged-good-all-a2m # found chain 1s7kA in training set Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s7kA)T51 Warning: unaligning (T0374)I34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s7kA)T51 T0374 2 :QLSHRPAETGDLETVAGFPQD 1s7kA 10 :TLELRAADESHVPALHQLVLK T0374 35 :WPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQ 1s7kA 52 :RKHVQGNILLHQRGYAKMYLIFCQNEMAGVLSFNA T0374 70 :WQHGDFCALG 1s7kA 88 :EPINKAAYIG T0374 81 :MMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRV 1s7kA 98 :YWLDESFQGQGIMSQSLQALMTHYARRGDIRRFVIKCRVDNQASNAVARRNHFTLEGCMKQAEYLNGDY Number of specific fragments extracted= 4 number of extra gaps= 0 total=652 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ge3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ge3A expands to /projects/compbio/data/pdb/2ge3.pdb.gz 2ge3A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2ge3A/merged-good-all-a2m # 2ge3A read from 2ge3A/merged-good-all-a2m # adding 2ge3A to template set # found chain 2ge3A in template set Warning: unaligning (T0374)G79 because of BadResidue code BAD_PEPTIDE in next template residue (2ge3A)G90 Warning: unaligning (T0374)N80 because of BadResidue code BAD_PEPTIDE at template residue (2ge3A)G90 Warning: unaligning (T0374)E159 because last residue in template chain is (2ge3A)G169 T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYP 2ge3A 7 :TVTIKPIRAEHVESFHRALDAVSRERKYLS T0374 33 :AIWPFSVAQLAAAIA 2ge3A 37 :FLEAPPLEAVRAFVL T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 2ge3A 56 :NDHPQFVAIADGDVIGWCDIRRQDRAT T0374 75 :FCAL 2ge3A 85 :HCGT T0374 81 :MMVAPAARGLGVARYLIGVMENLAREQ 2ge3A 91 :MGILPAYRNKGLGARLMRRTLDAAHEF T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 2ge3A 118 :GLHRIELSVHADNARAIALYEKIGFAHEG T0374 138 :IAERHDPDGRRVALIQMDKPL 2ge3A 148 :ARDAVSIDGHYIDSLNMAIIF Number of specific fragments extracted= 7 number of extra gaps= 1 total=659 Number of alignments=94 # 2ge3A read from 2ge3A/merged-good-all-a2m # found chain 2ge3A in template set Warning: unaligning (T0374)L78 because of BadResidue code BAD_PEPTIDE in next template residue (2ge3A)G90 Warning: unaligning (T0374)N80 because of BadResidue code BAD_PEPTIDE at template residue (2ge3A)G90 Warning: unaligning (T0374)E159 because last residue in template chain is (2ge3A)G169 T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFY 2ge3A 7 :TVTIKPIRAEHVESFHRALDAVSRERK T0374 29 :CYPKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQH 2ge3A 37 :FLEAPPLEAVRAFVLDMIENDHPQFVAIADGDVIGWCDIRRQDR T0374 73 :GDFCA 2ge3A 84 :AHCGT T0374 81 :MMVAPAARGLGVARYLIGVMENLAREQ 2ge3A 91 :MGILPAYRNKGLGARLMRRTLDAAHEF T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 2ge3A 118 :GLHRIELSVHADNARAIALYEKIGFAHEGRARDA T0374 143 :DPDGRRVALIQMDKPL 2ge3A 153 :SIDGHYIDSLNMAIIF Number of specific fragments extracted= 6 number of extra gaps= 1 total=665 Number of alignments=95 # 2ge3A read from 2ge3A/merged-good-all-a2m # found chain 2ge3A in template set Warning: unaligning (T0374)L78 because of BadResidue code BAD_PEPTIDE in next template residue (2ge3A)G90 Warning: unaligning (T0374)N80 because of BadResidue code BAD_PEPTIDE at template residue (2ge3A)G90 T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQ 2ge3A 7 :TVTIKPIRAEHVESFHRALDAVSRERKYLSFLEAPPLEAV T0374 42 :LAAAIAERRGSTVAVHDGQVLGFANFYQWQHGD 2ge3A 50 :VLDMIENDHPQFVAIADGDVIGWCDIRRQDRAT T0374 75 :FCA 2ge3A 86 :CGT T0374 81 :MMVAPAARGLGVARYLIGVMENLAREQYKAR 2ge3A 91 :MGILPAYRNKGLGARLMRRTLDAAHEFGLHR T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRVALIQ 2ge3A 122 :IELSVHADNARAIALYEKIGFAHEGRARDAVSIDGHYIDSL Number of specific fragments extracted= 5 number of extra gaps= 1 total=670 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1on0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1on0A expands to /projects/compbio/data/pdb/1on0.pdb.gz 1on0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1on0A/merged-good-all-a2m # 1on0A read from 1on0A/merged-good-all-a2m # adding 1on0A to template set # found chain 1on0A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1on0A)T2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSV 1on0A 3 :IMLTPMQTEEFRSYLTYTTKHYAEEKVKAGTWLPEDA T0374 40 :AQLAAAIA 1on0A 45 :QVFTDLLP T0374 48 :ERRGSTVAVHD 1on0A 58 :PHHHLWSLKLN T0374 59 :GQVLGFANFYQWQHGD 1on0A 70 :KDIVGWLWIHAEPEHP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1on0A 88 :EAFIYDFGLYEPYRGKGYAKQALAALDQAARSM T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 1on0A 121 :GIRKLSLHVFAHNQTARKLYEQTGFQETD T0374 138 :IA 1on0A 151 :VM Number of specific fragments extracted= 7 number of extra gaps= 0 total=677 Number of alignments=97 # 1on0A read from 1on0A/merged-good-all-a2m # found chain 1on0A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1on0A)T2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1on0A 3 :IMLTPMQTEEFRSYLTYTTKHYAEEK T0374 29 :CYPKAIWP 1on0A 33 :TWLPEDAQ T0374 37 :FSVAQLAAAI 1on0A 42 :LSKQVFTDLL T0374 47 :AERRGSTVAVHD 1on0A 57 :TPHHHLWSLKLN T0374 59 :GQVLGFANFYQWQH 1on0A 70 :KDIVGWLWIHAEPE T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1on0A 86 :QQEAFIYDFGLYEPYRGKGYAKQALAALDQAARSM T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAE 1on0A 121 :GIRKLSLHVFAHNQTARKLYEQTGFQETDVVM Number of specific fragments extracted= 7 number of extra gaps= 0 total=684 Number of alignments=98 # 1on0A read from 1on0A/merged-good-all-a2m # found chain 1on0A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1on0A)T2 Warning: unaligning (T0374)D145 because last residue in template chain is (1on0A)L157 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCY 1on0A 3 :IMLTPMQTEEFRSYLTYTTKHYAEEKVK T0374 31 :PKAIWPFSVAQ 1on0A 35 :LPEDAQLLSKQ T0374 42 :LAA 1on0A 47 :FTD T0374 46 :IAERRGSTVAVH 1on0A 56 :ETPHHHLWSLKL T0374 58 :DGQVLGFANFYQ 1on0A 69 :EKDIVGWLWIHA T0374 72 :HGD 1on0A 83 :EHP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1on0A 88 :EAFIYDFGLYEPYRGKGYAKQALAALDQAARSMGIRK T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDP 1on0A 125 :LSLHVFAHNQTARKLYEQTGFQETDVVMSKKL Number of specific fragments extracted= 8 number of extra gaps= 0 total=692 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yvkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yvkA expands to /projects/compbio/data/pdb/1yvk.pdb.gz 1yvkA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1yvkA/merged-good-all-a2m # 1yvkA read from 1yvkA/merged-good-all-a2m # adding 1yvkA to template set # found chain 1yvkA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1yvkA)K5 Warning: unaligning (T0374)E159 because last residue in template chain is (1yvkA)L156 T0374 3 :LSHRPAET 1yvkA 6 :LRIELGEE T0374 14 :ETVAGFPQD 1yvkA 16 :DELYDLLLL T0374 35 :WPFSVAQLAAAIA 1yvkA 25 :ADPSKDIVDEYLE T0374 49 :RRGSTVAVHDGQVLGFANFYQWQH 1yvkA 38 :RGECYTAWAGDELAGVYVLLKTRP T0374 74 :DFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1yvkA 62 :QTVEIVNIAVKESLQKKGFGKQLVLDAIEKAKKL T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIA 1yvkA 96 :GADTIEIGTGNSSIHQLSLYQKCGFRIQAID T0374 140 :ERHDPDGRRVALIQMDKPL 1yvkA 137 :DIFENGIQCRDMVRLYLDL Number of specific fragments extracted= 7 number of extra gaps= 0 total=699 Number of alignments=100 # 1yvkA read from 1yvkA/merged-good-all-a2m # found chain 1yvkA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1yvkA)K5 Warning: unaligning (T0374)E159 because last residue in template chain is (1yvkA)L156 T0374 3 :LSHRPAE 1yvkA 6 :LRIELGE T0374 14 :ETVAGFPQDR 1yvkA 16 :DELYDLLLLA T0374 32 :KAIWPFSVAQLAA 1yvkA 26 :DPSKDIVDEYLER T0374 50 :RGSTVAVHDGQVLGFANFYQWQ 1yvkA 39 :GECYTAWAGDELAGVYVLLKTR T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1yvkA 61 :PQTVEIVNIAVKESLQKKGFGKQLVLDAIEKAKKL T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1yvkA 96 :GADTIEIGTGNSSIHQLSLYQKCGFRIQAIDHDF T0374 143 :DPDG 1yvkA 133 :HYDE T0374 147 :RRVALIQMDKPL 1yvkA 144 :QCRDMVRLYLDL Number of specific fragments extracted= 8 number of extra gaps= 0 total=707 Number of alignments=101 # 1yvkA read from 1yvkA/merged-good-all-a2m # found chain 1yvkA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1yvkA)K5 T0374 3 :LSHRPAET 1yvkA 6 :LRIELGEE T0374 14 :ETVAGFPQDRD 1yvkA 16 :DELYDLLLLAD T0374 33 :AIWPFSVAQLAA 1yvkA 27 :PSKDIVDEYLER T0374 50 :RGSTVAVHDGQVLGFANFYQ 1yvkA 39 :GECYTAWAGDELAGVYVLLK T0374 71 :QHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1yvkA 59 :TRPQTVEIVNIAVKESLQKKGFGKQLVLDAIEKAKKLGADT T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAER 1yvkA 100 :IEIGTGNSSIHQLSLYQKCGFRIQAIDHD Number of specific fragments extracted= 6 number of extra gaps= 0 total=713 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i1dA expands to /projects/compbio/data/pdb/1i1d.pdb.gz 1i1dA:Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 515, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 522, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 524, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 1i1dA # T0374 read from 1i1dA/merged-good-all-a2m # 1i1dA read from 1i1dA/merged-good-all-a2m # adding 1i1dA to template set # found chain 1i1dA in template set T0374 1 :MQ 1i1dA 1 :MS T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i1dA 7 :FYIRRMEEGDLEQVTETLKVLT T0374 33 :AIWPFSVAQLAAAIA 1i1dA 29 :TVGTITPESFCKLIK T0374 49 :RRGSTVAVHD 1i1dA 61 :QYNPMVIVDK T0374 59 :GQVLGFANFYQWQHG 1i1dA 73 :ETVAATGNIIIERKI T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1i1dA 94 :CGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDY T0374 109 :KARLMKISCFNAN 1i1dA 127 :GCYKIILDCDEKN T0374 125 :LLLYTQLGYQPRA 1i1dA 140 :VKFYEKCGFSNAG T0374 138 :I 1i1dA 154 :E T0374 154 :MDKP 1i1dA 155 :MQIR Number of specific fragments extracted= 10 number of extra gaps= 0 total=723 Number of alignments=103 # 1i1dA read from 1i1dA/merged-good-all-a2m # found chain 1i1dA in template set T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i1dA 7 :FYIRRMEEGDLEQVTETLKVLT T0374 29 :CYPKAIWPFSVAQLAAAI 1i1dA 29 :TVGTITPESFCKLIKYWN T0374 47 :AERR 1i1dA 60 :MQYN T0374 52 :STVAVHD 1i1dA 64 :PMVIVDK T0374 59 :GQVLGFANFYQWQH 1i1dA 73 :ETVAATGNIIIERK T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1i1dA 92 :GLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDY T0374 109 :KARLMKISCFNANAA 1i1dA 127 :GCYKIILDCDEKNVK T0374 127 :LYTQLGYQPRAIAER 1i1dA 142 :FYEKCGFSNAGVEMQ T0374 156 :KP 1i1dA 157 :IR Number of specific fragments extracted= 9 number of extra gaps= 0 total=732 Number of alignments=104 # 1i1dA read from 1i1dA/merged-good-all-a2m # found chain 1i1dA in template set Warning: unaligning (T0374)P144 because last residue in template chain is (1i1dA)K159 T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i1dA 7 :FYIRRMEEGDLEQVTETLKVLT T0374 29 :C 1i1dA 29 :T T0374 31 :PKAIWPFSVAQ 1i1dA 30 :VGTITPESFCK T0374 42 :LAA 1i1dA 42 :IKY T0374 46 :IAERRGSTVAVH 1i1dA 59 :IMQYNPMVIVDK T0374 58 :DGQVLGFANFYQWQHG 1i1dA 72 :TETVAATGNIIIERKI T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1i1dA 94 :CGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYK T0374 113 :MKISCFNAN 1i1dA 131 :IILDCDEKN T0374 125 :LLLYTQLGYQPRAIAERHD 1i1dA 140 :VKFYEKCGFSNAGVEMQIR Number of specific fragments extracted= 9 number of extra gaps= 0 total=741 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qstA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0374 read from 1qstA/merged-good-all-a2m # 1qstA read from 1qstA/merged-good-all-a2m # found chain 1qstA in training set T0374 13 :LETVAGFPQD 1qstA 66 :LIDLKNIFSR T0374 33 :AIWPFSVAQLAAAIA 1qstA 76 :QLPKMPKEYIVKLVF T0374 48 :ERRGSTVAVHD 1qstA 92 :RHHESMVILKN T0374 59 :GQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1qstA 104 :QKVIGGICFRQYKPQRFAEVAFLAVTANEQVRGYGTRLMNKFKDHMQKQ T0374 109 :KARLMKISCFNAN 1qstA 153 :NIEYLLTYADNFA T0374 125 :LLLYTQLGYQPRA 1qstA 166 :IGYFKKQGFTKEH T0374 138 :IA 1qstA 180 :MP T0374 140 :ERHDP 1qstA 186 :KGYIK T0374 145 :DGRR 1qstA 193 :DGGT T0374 153 :QMDKPLE 1qstA 197 :LMECYIH Number of specific fragments extracted= 10 number of extra gaps= 0 total=751 Number of alignments=106 # 1qstA read from 1qstA/merged-good-all-a2m # found chain 1qstA in training set T0374 2 :QLSHRPAE 1qstA 50 :DFDILTND T0374 10 :TGD 1qstA 60 :HRN T0374 13 :LETVAGFPQ 1qstA 66 :LIDLKNIFS T0374 32 :KAIWPFSVAQLAAAI 1qstA 75 :RQLPKMPKEYIVKLV T0374 47 :AERRGSTVAVHD 1qstA 91 :DRHHESMVILKN T0374 59 :GQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1qstA 104 :QKVIGGICFRQYKPQRFAEVAFLAVTANEQVRGYGTRLMNKFKDHMQKQ T0374 109 :KARLMKISCFNA 1qstA 153 :NIEYLLTYADNF T0374 124 :GLLLYTQLGYQPRAIAE 1qstA 165 :AIGYFKKQGFTKEHRMP T0374 141 :RH 1qstA 187 :GY T0374 143 :DPDGRRVAL 1qstA 192 :YDGGTLMEC T0374 157 :P 1qstA 201 :Y Number of specific fragments extracted= 11 number of extra gaps= 0 total=762 Number of alignments=107 # 1qstA read from 1qstA/merged-good-all-a2m # found chain 1qstA in training set T0374 13 :LETVAGFPQDRDELF 1qstA 66 :LIDLKNIFSRQLPKM T0374 36 :P 1qstA 81 :P T0374 38 :SVAQLAAAIAERRGSTVAVHD 1qstA 82 :KEYIVKLVFDRHHESMVILKN T0374 59 :GQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1qstA 104 :QKVIGGICFRQYKPQRFAEVAFLAVTANEQVRGYGTRLMNKFKDHMQKQNIEY T0374 113 :MKISCFNAN 1qstA 157 :LLTYADNFA T0374 125 :LLLYTQLGYQPRAIAE 1qstA 166 :IGYFKKQGFTKEHRMP Number of specific fragments extracted= 6 number of extra gaps= 0 total=768 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ufhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ufhA expands to /projects/compbio/data/pdb/1ufh.pdb.gz 1ufhA:# T0374 read from 1ufhA/merged-good-all-a2m # 1ufhA read from 1ufhA/merged-good-all-a2m # adding 1ufhA to template set # found chain 1ufhA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1ufhA)T2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1ufhA 3 :IMLTPMQTEEFRSYLTYTTKHYAEEK T0374 29 :CYPKAIWPFSVAQLAAAIA 1ufhA 34 :WLPEDAQLLSKQVFTDLLP T0374 48 :ERRGSTVAVHD 1ufhA 58 :PHHHLWSLKLN T0374 59 :GQVLGFANFYQWQHGD 1ufhA 70 :KDIVGWLWIHAEPEHP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1ufhA 88 :EAFIYDFGLYEPYRGKGYAKQALAALDQAARSM T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAE 1ufhA 121 :GIRKLSLHVFAHNQTARKLYEQTGFQETDVVM Number of specific fragments extracted= 6 number of extra gaps= 0 total=774 Number of alignments=109 # 1ufhA read from 1ufhA/merged-good-all-a2m # found chain 1ufhA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1ufhA)T2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1ufhA 3 :IMLTPMQTEEFRSYLTYTTKHYAEEK T0374 29 :CYPKAIWP 1ufhA 33 :TWLPEDAQ T0374 37 :FSVAQLAAAI 1ufhA 42 :LSKQVFTDLL T0374 47 :AERRGSTVAVHD 1ufhA 57 :TPHHHLWSLKLN T0374 59 :GQVLGFANFYQWQH 1ufhA 70 :KDIVGWLWIHAEPE T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1ufhA 86 :QQEAFIYDFGLYEPYRGKGYAKQALAALDQAARSM T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAI 1ufhA 121 :GIRKLSLHVFAHNQTARKLYEQTGFQETDV Number of specific fragments extracted= 7 number of extra gaps= 0 total=781 Number of alignments=110 # 1ufhA read from 1ufhA/merged-good-all-a2m # found chain 1ufhA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1ufhA)T2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCY 1ufhA 3 :IMLTPMQTEEFRSYLTYTTKHYAEEKVK T0374 31 :PKAIWPFSVAQLAA 1ufhA 35 :LPEDAQLLSKQVFT T0374 45 :AIAERRGSTVAVHDG 1ufhA 55 :LETPHHHLWSLKLNE T0374 60 :QVLGFANFYQ 1ufhA 71 :DIVGWLWIHA T0374 70 :WQHG 1ufhA 82 :PEHP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1ufhA 88 :EAFIYDFGLYEPYRGKGYAKQALAALDQAARSMGIRK T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAER 1ufhA 125 :LSLHVFAHNQTARKLYEQTGFQETDVVMS Number of specific fragments extracted= 7 number of extra gaps= 0 total=788 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u6mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u6mA expands to /projects/compbio/data/pdb/1u6m.pdb.gz 1u6mA:# T0374 read from 1u6mA/merged-good-all-a2m # 1u6mA read from 1u6mA/merged-good-all-a2m # adding 1u6mA to template set # found chain 1u6mA in template set Warning: unaligning (T0374)L26 because of BadResidue code BAD_PEPTIDE in next template residue (1u6mA)K24 Warning: unaligning (T0374)F27 because of BadResidue code BAD_PEPTIDE at template residue (1u6mA)K24 Warning: unaligning (T0374)Y28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u6mA)D25 Warning: unaligning (T0374)F75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u6mA)W113 Warning: unaligning (T0374)C76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u6mA)W113 Warning: unaligning (T0374)E159 because last residue in template chain is (1u6mA)E190 T0374 4 :SHRPAETGDLETVAGFPQ 1u6mA 3 :LIRSATKEDGQAIARLVL T0374 24 :DE 1u6mA 21 :VI T0374 29 :CYPKAIWPFSVAQLAAAIA 1u6mA 26 :MELPILEEVSEEQMIDLLA T0374 48 :ERRG 1u6mA 50 :PTYR T0374 52 :STVAVHDGQVLGFANF 1u6mA 59 :ILVYEHAGEVAGIAVG T0374 68 :YQWQHGD 1u6mA 105 :EEETLPN T0374 77 :ALGNMMVAPAARGLGVARYLIGVMENLAREQ 1u6mA 114 :YLDTISVDERFRGMGIGSKLLDALPEVAKAS T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAER 1u6mA 145 :GKQALGLNVDFDNPGARKLYASKGFKDVTTMTI T0374 145 :DGRR 1u6mA 178 :SGHL T0374 151 :LIQMDKPL 1u6mA 182 :YNHMQKEV Number of specific fragments extracted= 10 number of extra gaps= 2 total=798 Number of alignments=112 # 1u6mA read from 1u6mA/merged-good-all-a2m # found chain 1u6mA in template set Warning: unaligning (T0374)D24 because of BadResidue code BAD_PEPTIDE in next template residue (1u6mA)K24 Warning: unaligning (T0374)E25 because of BadResidue code BAD_PEPTIDE at template residue (1u6mA)K24 Warning: unaligning (T0374)L26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u6mA)D25 Warning: unaligning (T0374)F75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u6mA)W113 Warning: unaligning (T0374)C76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u6mA)W113 Warning: unaligning (T0374)E159 because last residue in template chain is (1u6mA)E190 T0374 4 :SHRPAETGDLETVAGFPQDR 1u6mA 3 :LIRSATKEDGQAIARLVLVI T0374 27 :FY 1u6mA 26 :ME T0374 29 :CYPKAIWPFSVAQLAAAI 1u6mA 30 :ILEEVSEEQMIDLLAEAT T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1u6mA 54 :YGYQRILVYEHAGEVAGIAVGYPAED T0374 73 :GD 1u6mA 110 :PN T0374 77 :ALGNMMVAPAARGLGVARYLIGVMENLAREQ 1u6mA 114 :YLDTISVDERFRGMGIGSKLLDALPEVAKAS T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1u6mA 145 :GKQALGLNVDFDNPGARKLYASKGFKDVTTMTIS T0374 146 :G 1u6mA 179 :G T0374 149 :VALIQMDKPL 1u6mA 180 :HLYNHMQKEV Number of specific fragments extracted= 9 number of extra gaps= 2 total=807 Number of alignments=113 # 1u6mA read from 1u6mA/merged-good-all-a2m # found chain 1u6mA in template set Warning: unaligning (T0374)D24 because of BadResidue code BAD_PEPTIDE in next template residue (1u6mA)K24 Warning: unaligning (T0374)E25 because of BadResidue code BAD_PEPTIDE at template residue (1u6mA)K24 Warning: unaligning (T0374)L26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u6mA)D25 Warning: unaligning (T0374)F75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u6mA)W113 Warning: unaligning (T0374)C76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u6mA)W113 T0374 4 :SHRPAETGDLETVAGFPQDR 1u6mA 3 :LIRSATKEDGQAIARLVLVI T0374 27 :FYCYPKAIWPFSVAQLAA 1u6mA 26 :MELPILEEVSEEQMIDLL T0374 45 :AIAERRGSTVAVHDGQVLGFANFYQ 1u6mA 52 :YRYGYQRILVYEHAGEVAGIAVGYP T0374 70 :WQHGD 1u6mA 107 :ETLPN T0374 77 :ALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1u6mA 114 :YLDTISVDERFRGMGIGSKLLDALPEVAKASGKQA T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAER 1u6mA 149 :LGLNVDFDNPGARKLYASKGFKDVTTMTI Number of specific fragments extracted= 6 number of extra gaps= 2 total=813 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z4rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z4rA expands to /projects/compbio/data/pdb/1z4r.pdb.gz 1z4rA:# T0374 read from 1z4rA/merged-good-all-a2m # 1z4rA read from 1z4rA/merged-good-all-a2m # adding 1z4rA to template set # found chain 1z4rA in template set T0374 13 :LETVAGFPQDR 1z4rA 520 :LVGLQNVFSHQ T0374 34 :IWPFSVAQLAAAIA 1z4rA 531 :LPRMPKEYIARLVF T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1z4rA 546 :PKHKTLALIKDGRVIGGICFRMFPTQGFTEIVFCAVTSNEQVKGYGTHLMNHLKEYHIKH T0374 109 :KARLMKISCFNA 1z4rA 606 :NILYFLTYADEY T0374 124 :GLLLYTQLGYQPR 1z4rA 618 :AIGYFKKQGFSKD T0374 137 :A 1z4rA 640 :G T0374 141 :RHD 1z4rA 641 :YIK T0374 145 :DGR 1z4rA 646 :EGA T0374 152 :IQMDKPLEP 1z4rA 649 :TLMECELNP Number of specific fragments extracted= 9 number of extra gaps= 0 total=822 Number of alignments=115 # 1z4rA read from 1z4rA/merged-good-all-a2m # found chain 1z4rA in template set T0374 9 :ETGDLETVAGFPQDRDELFYCYP 1z4rA 513 :NRRVLLWLVGLQNVFSHQLPRMP T0374 39 :VAQLAAAI 1z4rA 536 :KEYIARLV T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1z4rA 545 :DPKHKTLALIKDGRVIGGICFRMFPTQGFTEIVFCAVTSNEQVKGYGTHLMNHLKEYHIKH T0374 109 :KARLMKISCFNA 1z4rA 606 :NILYFLTYADEY T0374 124 :GLLLYTQLGYQPR 1z4rA 618 :AIGYFKKQGFSKD T0374 141 :RH 1z4rA 640 :GY T0374 143 :DPD 1z4rA 645 :YEG T0374 151 :LIQMDKPLEP 1z4rA 648 :ATLMECELNP Number of specific fragments extracted= 8 number of extra gaps= 0 total=830 Number of alignments=116 # 1z4rA read from 1z4rA/merged-good-all-a2m # found chain 1z4rA in template set T0374 13 :LETVAGFPQDRDELF 1z4rA 520 :LVGLQNVFSHQLPRM T0374 36 :PFS 1z4rA 535 :PKE T0374 40 :AQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1z4rA 538 :YIARLVFDPKHKTLALIKDGRVIGGICFRMFPTQGFTEIVFCAVTSNEQVKGYGTHLMNHLKEYHIKHNILY T0374 113 :MKISCFNA 1z4rA 610 :FLTYADEY T0374 124 :GLLLYTQLGYQP 1z4rA 618 :AIGYFKKQGFSK Number of specific fragments extracted= 5 number of extra gaps= 0 total=835 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yvoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yvoA expands to /projects/compbio/data/pdb/1yvo.pdb.gz 1yvoA:Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 422, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 764, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 766, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 778, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 1yvoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1yvoA/merged-good-all-a2m # 1yvoA read from 1yvoA/merged-good-all-a2m # adding 1yvoA to template set # found chain 1yvoA in template set Warning: unaligning (T0374)S4 because first residue in template chain is (1yvoA)S4 T0374 5 :HRPAETGDLETVAGFPQDRDELFYCYPK 1yvoA 5 :IRDAGVADLPGILAIYNDAVGNTTAIWN T0374 34 :IWPFSVAQLAAAIA 1yvoA 33 :ETPVDLANRQAWFD T0374 48 :ERRGSTVAVHD 1yvoA 51 :QGYPILVASDA T0374 59 :GQVLGFANFYQWQHGD 1yvoA 63 :GEVLGYASYGDWRPFE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1yvoA 82 :GTVEHSVYVRDDQRGKGLGVQLLQALIERARAQ T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 1yvoA 115 :GLHVMVAAIESGNAASIGLHRRLGFEISG T0374 138 :IAERHDPDGRRVALIQMDKPLE 1yvoA 145 :MPQVGQKFGRWLDLTFMQLNLD Number of specific fragments extracted= 7 number of extra gaps= 0 total=842 Number of alignments=118 # 1yvoA read from 1yvoA/merged-good-all-a2m # found chain 1yvoA in template set Warning: unaligning (T0374)S4 because first residue in template chain is (1yvoA)S4 T0374 5 :HRPAETGDLETVAGFPQDRDELFY 1yvoA 5 :IRDAGVADLPGILAIYNDAVGNTT T0374 29 :CYPKAIWPFSVAQLAAAIAERRGSTVAVHD 1yvoA 32 :NETPVDLANRQAWFDTRARQGYPILVASDA T0374 59 :GQVLGFANFYQWQH 1yvoA 63 :GEVLGYASYGDWRP T0374 73 :GDFCAL 1yvoA 81 :RGTVEH T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQ 1yvoA 87 :SVYVRDDQRGKGLGVQLLQALIERARAQ T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1yvoA 115 :GLHVMVAAIESGNAASIGLHRRLGFEISGQMPQV T0374 143 :DPDGRRVALIQMDKPLE 1yvoA 150 :QKFGRWLDLTFMQLNLD Number of specific fragments extracted= 7 number of extra gaps= 0 total=849 Number of alignments=119 # 1yvoA read from 1yvoA/merged-good-all-a2m # found chain 1yvoA in template set Warning: unaligning (T0374)S4 because first residue in template chain is (1yvoA)S4 T0374 5 :HRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAA 1yvoA 5 :IRDAGVADLPGILAIYNDAVGNTTAIWNETPVDLANRQAWF T0374 46 :IAERRGSTVAVH 1yvoA 49 :ARQGYPILVASD T0374 58 :DGQVLGFANFYQWQHGD 1yvoA 62 :AGEVLGYASYGDWRPFE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1yvoA 82 :GTVEHSVYVRDDQRGKGLGVQLLQALIERARAQGLHV T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRVALIQMD 1yvoA 119 :MVAAIESGNAASIGLHRRLGFEISGQMPQVGQKFGRWLDLTFM Number of specific fragments extracted= 5 number of extra gaps= 0 total=854 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2atrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2atrA expands to /projects/compbio/data/pdb/2atr.pdb.gz 2atrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2atrA/merged-good-all-a2m # 2atrA read from 2atrA/merged-good-all-a2m # adding 2atrA to template set # found chain 2atrA in template set Warning: unaligning (T0374)P20 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2atrA)G23 Warning: unaligning (T0374)A33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)G23 Warning: unaligning (T0374)I34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)W24 Warning: unaligning (T0374)W35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)T25 Warning: unaligning (T0374)P36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)N26 Warning: unaligning (T0374)M82 because of BadResidue code BAD_PEPTIDE in next template residue (2atrA)V74 Warning: unaligning (T0374)V83 because of BadResidue code BAD_PEPTIDE at template residue (2atrA)V74 T0374 1 :M 2atrA 1 :M T0374 3 :LSHRP 2atrA 2 :ITIKK T0374 8 :AETGDLETVAGF 2atrA 10 :VKLEDVLHLYQA T0374 42 :LAAAIAERRGSTVAVHDGQVLGFANFYQ 2atrA 34 :LEQALSHSLVIYLALDGDAVVGLIRLVG T0374 71 :QHGDFCALGNM 2atrA 62 :DGFSSVFVQDL T0374 84 :APAARGLGVARYLIGVMEN 2atrA 75 :LPSYQRQGIGSSLMKEALG T0374 106 :EQYKARLMKISCFNANAA 2atrA 94 :NFKEAYQVQLATEETEKN T0374 125 :LLLYTQLGYQPRAIAERHD 2atrA 112 :VGFYRSMGFEILSTYDCTG Number of specific fragments extracted= 8 number of extra gaps= 2 total=862 Number of alignments=121 # 2atrA read from 2atrA/merged-good-all-a2m # found chain 2atrA in template set Warning: unaligning (T0374)P20 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2atrA)G23 Warning: unaligning (T0374)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)G23 Warning: unaligning (T0374)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)W24 Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)T25 Warning: unaligning (T0374)D24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)N26 Warning: unaligning (T0374)Y30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)E32 Warning: unaligning (T0374)P31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)M33 Warning: unaligning (T0374)M82 because of BadResidue code BAD_PEPTIDE in next template residue (2atrA)V74 Warning: unaligning (T0374)V83 because of BadResidue code BAD_PEPTIDE at template residue (2atrA)V74 T0374 1 :M 2atrA 1 :M T0374 3 :LSHRP 2atrA 2 :ITIKK T0374 8 :AETGDLETVAGF 2atrA 10 :VKLEDVLHLYQA T0374 42 :LAAAIAERRGSTVAVHDGQVLGFANFYQWQ 2atrA 34 :LEQALSHSLVIYLALDGDAVVGLIRLVGDG T0374 73 :GDFCALGNM 2atrA 64 :FSSVFVQDL T0374 84 :APAARGLGVARYLIGVME 2atrA 75 :LPSYQRQGIGSSLMKEAL T0374 109 :KARLMKISCFNA 2atrA 97 :EAYQVQLATEET T0374 122 :AAGLLLYTQLGYQPRAI 2atrA 109 :EKNVGFYRSMGFEILST Number of specific fragments extracted= 8 number of extra gaps= 2 total=870 Number of alignments=122 # 2atrA read from 2atrA/merged-good-all-a2m # found chain 2atrA in template set Warning: unaligning (T0374)R23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2atrA)G23 Warning: unaligning (T0374)P31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)G23 Warning: unaligning (T0374)K32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)W24 Warning: unaligning (T0374)A33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)T25 Warning: unaligning (T0374)I34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)N26 Warning: unaligning (T0374)A40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)E32 Warning: unaligning (T0374)Q41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)M33 Warning: unaligning (T0374)M82 because of BadResidue code BAD_PEPTIDE in next template residue (2atrA)V74 Warning: unaligning (T0374)V83 because of BadResidue code BAD_PEPTIDE at template residue (2atrA)V74 T0374 3 :LSHRPAETGDLETVAGFPQD 2atrA 2 :ITIKKQEIVKLEDVLHLYQA T0374 42 :LAAAIAERRGSTVAVHDGQVLGFANFYQ 2atrA 34 :LEQALSHSLVIYLALDGDAVVGLIRLVG T0374 71 :QHGDFCALGNM 2atrA 62 :DGFSSVFVQDL T0374 84 :APAARGLGVARYLIGVME 2atrA 75 :LPSYQRQGIGSSLMKEAL T0374 108 :YKAR 2atrA 97 :EAYQ T0374 113 :MKISCFNA 2atrA 101 :VQLATEET T0374 122 :AAGLLLYTQLGYQPRAIAERHD 2atrA 109 :EKNVGFYRSMGFEILSTYDCTG Number of specific fragments extracted= 7 number of extra gaps= 2 total=877 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q2yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1q2yA expands to /projects/compbio/data/pdb/1q2y.pdb.gz 1q2yA:# T0374 read from 1q2yA/merged-good-all-a2m # 1q2yA read from 1q2yA/merged-good-all-a2m # adding 1q2yA to template set # found chain 1q2yA in template set Warning: unaligning (T0374)P157 because last residue in template chain is (1q2yA)D140 T0374 1 :MQ 1q2yA 1 :MK T0374 5 :HRPAE 1q2yA 3 :AVIAK T0374 10 :TGDLETVAGFPQDRDELFY 1q2yA 9 :EEQLKDAFYVREEVFVKEQ T0374 29 :CYPKAIWP 1q2yA 29 :VPAEEEID T0374 48 :ERRGSTVAVHDGQVLGFANF 1q2yA 40 :NESEHIVVYDGEKPVGAGRW T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1q2yA 60 :RMKDGYGKLERICVLKSHRSAGVGGIIMKALEKAAADG T0374 109 :KARLMKISCFNA 1q2yA 98 :GASGFILNAQTQ T0374 124 :GLLLYTQLGYQPRAIAERHDP 1q2yA 110 :AVPFYKKHGYRVLSEKEFLDA T0374 148 :RVALIQMDK 1q2yA 131 :GIPHLQMMK Number of specific fragments extracted= 9 number of extra gaps= 0 total=886 Number of alignments=124 # 1q2yA read from 1q2yA/merged-good-all-a2m # found chain 1q2yA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (1q2yA)M1 Warning: unaligning (T0374)P157 because last residue in template chain is (1q2yA)D140 T0374 4 :SHRPAE 1q2yA 2 :KAVIAK T0374 10 :TGDLETVAGFPQDRDELFY 1q2yA 9 :EEQLKDAFYVREEVFVKEQ T0374 29 :CYPKA 1q2yA 29 :VPAEE T0374 34 :IWPF 1q2yA 35 :IDEL T0374 47 :AERRGSTVAVHDGQVLGFANFYQW 1q2yA 39 :ENESEHIVVYDGEKPVGAGRWRMK T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1q2yA 63 :DGYGKLERICVLKSHRSAGVGGIIMKALEKAAADG T0374 109 :KARLMKISCFNA 1q2yA 98 :GASGFILNAQTQ T0374 124 :GLLLYTQLGYQP 1q2yA 110 :AVPFYKKHGYRV T0374 136 :RAIAERH 1q2yA 124 :EKEFLDA T0374 149 :VALIQMDK 1q2yA 132 :IPHLQMMK Number of specific fragments extracted= 10 number of extra gaps= 0 total=896 Number of alignments=125 # 1q2yA read from 1q2yA/merged-good-all-a2m # found chain 1q2yA in template set T0374 9 :ETGDLETVAGFPQDRDELFYCYPKAIWPFSV 1q2yA 8 :NEEQLKDAFYVREEVFVKEQNVPAEEEIDEL T0374 47 :AERRGSTVAVHDGQVLGFANFYQ 1q2yA 39 :ENESEHIVVYDGEKPVGAGRWRM T0374 72 :HGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1q2yA 62 :KDGYGKLERICVLKSHRSAGVGGIIMKALEKAAADGGASG T0374 113 :MKISCFNA 1q2yA 102 :FILNAQTQ T0374 124 :GLLLYTQLGYQPRAI 1q2yA 110 :AVPFYKKHGYRVLSE Number of specific fragments extracted= 5 number of extra gaps= 0 total=901 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nslA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nslA expands to /projects/compbio/data/pdb/1nsl.pdb.gz 1nslA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1nslA/merged-good-all-a2m # 1nslA read from 1nslA/merged-good-all-a2m # adding 1nslA to template set # found chain 1nslA in template set Warning: unaligning (T0374)D12 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)A20 Warning: unaligning (T0374)L13 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)A20 Warning: unaligning (T0374)K32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nslA)S45 Warning: unaligning (T0374)F37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nslA)S45 Warning: unaligning (T0374)E48 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)N66 Warning: unaligning (T0374)R49 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)N66 Warning: unaligning (T0374)M113 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)A131 Warning: unaligning (T0374)K114 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)A131 Warning: unaligning (T0374)T129 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)R147 Warning: unaligning (T0374)Q130 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)R147 T0374 3 :LSHRPAETG 1nslA 10 :ITIRLLEPK T0374 14 :ETVAGFPQDRDELFY 1nslA 21 :ERLAELIIQNQQRLG T0374 29 :CYP 1nslA 37 :WLF T0374 38 :SVAQLA 1nslA 46 :SADTYR T0374 44 :AAIA 1nslA 57 :DWRR T0374 50 :RGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARL 1nslA 67 :GIEAGLLYDGSLCGMISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNR T0374 115 :ISCFNANAAGLLLY 1nslA 132 :ICAAVGNEKSRAVP T0374 131 :LGYQPRA 1nslA 148 :IGFLEEG T0374 138 :IAERHDPDGRRVALIQMDKP 1nslA 156 :ARDGLYVNGMHHDLVYYSLL Number of specific fragments extracted= 9 number of extra gaps= 4 total=910 Number of alignments=127 # 1nslA read from 1nslA/merged-good-all-a2m # found chain 1nslA in template set Warning: unaligning (T0374)D12 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)A20 Warning: unaligning (T0374)L13 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)A20 Warning: unaligning (T0374)E48 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)N66 Warning: unaligning (T0374)R49 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)N66 Warning: unaligning (T0374)M113 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)A131 Warning: unaligning (T0374)K114 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)A131 Warning: unaligning (T0374)T129 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)R147 Warning: unaligning (T0374)Q130 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)R147 T0374 3 :LSHRPAETG 1nslA 10 :ITIRLLEPK T0374 14 :ETVAGFPQDRDELFY 1nslA 21 :ERLAELIIQNQQRLG T0374 31 :P 1nslA 39 :F T0374 32 :KAIWPFSVAQLAAAI 1nslA 48 :DTYRETIIPDWRRQY T0374 47 :A 1nslA 64 :D T0374 50 :RGSTVAVHDGQVLGFANFYQWQH 1nslA 67 :GIEAGLLYDGSLCGMISLHNLDQ T0374 73 :GDFCAL 1nslA 91 :NRKAEI T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQYKARL 1nslA 97 :GYWIAKEFEGKGIITAACRKLITYAFEELELNR T0374 115 :ISCFNANAAGLLLY 1nslA 132 :ICAAVGNEKSRAVP T0374 131 :LGYQPRAIAERH 1nslA 148 :IGFLEEGKARDG T0374 143 :DPDGRRVALIQMDKP 1nslA 161 :YVNGMHHDLVYYSLL Number of specific fragments extracted= 11 number of extra gaps= 4 total=921 Number of alignments=128 # 1nslA read from 1nslA/merged-good-all-a2m # found chain 1nslA in template set Warning: unaligning (T0374)D12 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)A20 Warning: unaligning (T0374)L13 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)A20 Warning: unaligning (T0374)E48 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)N66 Warning: unaligning (T0374)R49 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)N66 Warning: unaligning (T0374)M113 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)A131 Warning: unaligning (T0374)K114 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)A131 Warning: unaligning (T0374)T129 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)R147 Warning: unaligning (T0374)Q130 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)R147 T0374 2 :QLSHRPAETG 1nslA 9 :HITIRLLEPK T0374 14 :ETVAGFPQDRDELFYCY 1nslA 21 :ERLAELIIQNQQRLGKW T0374 31 :PKAIWPFSVAQLAAAIA 1nslA 48 :DTYRETIIPDWRRQYAD T0374 50 :RGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARL 1nslA 67 :GIEAGLLYDGSLCGMISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNR T0374 115 :ISCFNANAAGLLLY 1nslA 132 :ICAAVGNEKSRAVP T0374 131 :LGYQPRAIAERHDP 1nslA 148 :IGFLEEGKARDGLY Number of specific fragments extracted= 6 number of extra gaps= 4 total=927 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xebA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xebA expands to /projects/compbio/data/pdb/1xeb.pdb.gz 1xebA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1xebA/merged-good-all-a2m # 1xebA read from 1xebA/merged-good-all-a2m # adding 1xebA to template set # found chain 1xebA in template set T0374 3 :LSHRP 1xebA 5 :WTCKH T0374 8 :AETGDLETVAGFPQDRDELFY 1xebA 13 :LTLKELYALLQLRTEVFVVEQ T0374 29 :CYPKAIWPF 1xebA 35 :CPYQEVDGL T0374 45 :AIAERRGSTVAVHDGQVLGFANFYQWQHGD 1xebA 44 :DLVGDTHHLMAWRDGQLLAYLRLLDPVRHE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNAN 1xebA 75 :QVVIGRVVSSSAARGQGLGHQLMERALQAAERLWLDTPVYLSAQAHL T0374 125 :LLLYTQLGYQPRA 1xebA 122 :QAYYGRYGFVAVT T0374 138 :IAER 1xebA 136 :VYLE T0374 145 :DG 1xebA 140 :DD T0374 149 :VALIQMDK 1xebA 142 :IPHIGMRR Number of specific fragments extracted= 9 number of extra gaps= 0 total=936 Number of alignments=130 # 1xebA read from 1xebA/merged-good-all-a2m # found chain 1xebA in template set T0374 2 :QLSHRP 1xebA 4 :DWTCKH T0374 8 :AETGDLETVAGFPQDRDELFY 1xebA 13 :LTLKELYALLQLRTEVFVVEQ T0374 29 :CYPKAIWPF 1xebA 35 :CPYQEVDGL T0374 45 :AIAERRGSTVAVHDGQVLGFANFYQWQH 1xebA 44 :DLVGDTHHLMAWRDGQLLAYLRLLDPVR T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1xebA 73 :EGQVVIGRVVSSSAARGQGLGHQLMERALQAAERL T0374 108 :YKAR 1xebA 109 :LDTP T0374 113 :MKISCFNA 1xebA 113 :VYLSAQAH T0374 124 :GLLLYTQLGYQPRAIAERHDP 1xebA 121 :LQAYYGRYGFVAVTEVYLEDD T0374 149 :VALIQMDK 1xebA 142 :IPHIGMRR Number of specific fragments extracted= 9 number of extra gaps= 0 total=945 Number of alignments=131 # 1xebA read from 1xebA/merged-good-all-a2m # found chain 1xebA in template set T0374 8 :AETGDLETVAGFPQDRDELFYCYPKAIWPFS 1xebA 13 :LTLKELYALLQLRTEVFVVEQKCPYQEVDGL T0374 45 :AIAERRGSTVAVHDGQVLGFANFYQ 1xebA 44 :DLVGDTHHLMAWRDGQLLAYLRLLD T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNAN 1xebA 70 :VRHEGQVVIGRVVSSSAARGQGLGHQLMERALQAAERLWLDTPVYLSAQAHL T0374 125 :LLLYTQLGYQPRAIAE 1xebA 122 :QAYYGRYGFVAVTEVY Number of specific fragments extracted= 4 number of extra gaps= 0 total=949 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gheA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0374 read from 1gheA/merged-good-all-a2m # 1gheA read from 1gheA/merged-good-all-a2m # found chain 1gheA in training set Warning: unaligning (T0374)L3 because first residue in template chain is (1gheA)A4 Warning: unaligning (T0374)L158 because last residue in template chain is (1gheA)L173 T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 1gheA 5 :QLRRVTAESFAHYRHGLAQLLFETV T0374 29 :CYPKAIWPFSVAQLAAAIA 1gheA 33 :ASVGFMADLDMQQAYAWCD T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1gheA 60 :GSLLLWVVAEDDNVLASAQLSLCQKPN T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1gheA 90 :RAEVQKLMVLPSARGRGLGRQLMDEVEQVAVKH T0374 109 :KARLMKISCFNAN 1gheA 123 :KRGLLHLDTEAGS T0374 123 :AGLLLYTQLGYQPRAIAERHD 1gheA 136 :VAEAFYSALAYTRVGELPGYC T0374 144 :PDGRRVALIQMDKP 1gheA 159 :PDGRLHPTAIYFKT Number of specific fragments extracted= 7 number of extra gaps= 0 total=956 Number of alignments=133 # 1gheA read from 1gheA/merged-good-all-a2m # found chain 1gheA in training set Warning: unaligning (T0374)L3 because first residue in template chain is (1gheA)A4 Warning: unaligning (T0374)L158 because last residue in template chain is (1gheA)L173 T0374 4 :SHRPAETGDLET 1gheA 5 :QLRRVTAESFAH T0374 16 :VAGFPQDRDE 1gheA 21 :LAQLLFETVH T0374 29 :CYPKAIWPFSVAQLAAAI 1gheA 37 :FMADLDMQQAYAWCDGLK T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1gheA 59 :AGSLLLWVVAEDDNVLASAQLSLCQK T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1gheA 88 :LNRAEVQKLMVLPSARGRGLGRQLMDEVEQVAVKH T0374 109 :KARLMKISCFNANA 1gheA 123 :KRGLLHLDTEAGSV T0374 124 :GLLLYTQLGYQPRAIAERH 1gheA 137 :AEAFYSALAYTRVGELPGY T0374 143 :DPDGRRVALIQMDKP 1gheA 158 :TPDGRLHPTAIYFKT Number of specific fragments extracted= 8 number of extra gaps= 0 total=964 Number of alignments=134 # 1gheA read from 1gheA/merged-good-all-a2m # found chain 1gheA in training set Warning: unaligning (T0374)L3 because first residue in template chain is (1gheA)A4 T0374 4 :SHRPAETGDLETVAGFPQDRDELFYCY 1gheA 5 :QLRRVTAESFAHYRHGLAQLLFETVHG T0374 31 :PKAIWPFSVAQLAA 1gheA 37 :FMADLDMQQAYAWC T0374 46 :IAERRGSTVAVHDGQVLGFANFYQWQHGD 1gheA 58 :AAGSLLLWVVAEDDNVLASAQLSLCQKPN T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1gheA 90 :RAEVQKLMVLPSARGRGLGRQLMDEVEQVAVKHKRGL T0374 113 :MKISCFNANAA 1gheA 127 :LHLDTEAGSVA T0374 125 :LLLYTQLGYQPRAIAERHDPDGR 1gheA 138 :EAFYSALAYTRVGELPGYCATPD Number of specific fragments extracted= 6 number of extra gaps= 0 total=970 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z4eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z4eA expands to /projects/compbio/data/pdb/1z4e.pdb.gz 1z4eA:# T0374 read from 1z4eA/merged-good-all-a2m # 1z4eA read from 1z4eA/merged-good-all-a2m # adding 1z4eA to template set # found chain 1z4eA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1z4eA)H4 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYP 1z4eA 5 :VTIREATEGDLEQMVHMLADDVLGRKRER T0374 33 :AIWPFSVAQLAAAIA 1z4eA 34 :YEKPLPVSYVRAFKE T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1z4eA 53 :KNNELIVACNGEEIVGMLQVTFTPYLT T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1z4eA 85 :RATIEGVRTHSAARGQGIGSQLVCWAIERAKER T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 1z4eA 118 :GCHLIQLTTDKQRPDALRFYEQLGFKASH T0374 138 :IAERH 1z4eA 148 :GLKMH Number of specific fragments extracted= 6 number of extra gaps= 0 total=976 Number of alignments=136 # 1z4eA read from 1z4eA/merged-good-all-a2m # found chain 1z4eA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1z4eA)H4 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1z4eA 5 :VTIREATEGDLEQMVHMLADDVLGRK T0374 29 :CYPKAIWPFSVAQLAAAI 1z4eA 33 :RYEKPLPVSYVRAFKEIK T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1z4eA 52 :DKNNELIVACNGEEIVGMLQVTFTPY T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1z4eA 83 :SWRATIEGVRTHSAARGQGIGSQLVCWAIERAKER T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAER 1z4eA 118 :GCHLIQLTTDKQRPDALRFYEQLGFKASHEGLK Number of specific fragments extracted= 5 number of extra gaps= 0 total=981 Number of alignments=137 # 1z4eA read from 1z4eA/merged-good-all-a2m # found chain 1z4eA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1z4eA)H4 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCY 1z4eA 5 :VTIREATEGDLEQMVHMLADDVLGRKRE T0374 31 :PKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGD 1z4eA 36 :KPLPVSYVRAFKEIKKDKNNELIVACNGEEIVGMLQVTFTPYLT T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1z4eA 85 :RATIEGVRTHSAARGQGIGSQLVCWAIERAKERGCHL T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIA 1z4eA 122 :IQLTTDKQRPDALRFYEQLGFKASHEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=985 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b87A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b87A expands to /projects/compbio/data/pdb/1b87.pdb.gz 1b87A:# T0374 read from 1b87A/merged-good-all-a2m # 1b87A read from 1b87A/merged-good-all-a2m # adding 1b87A to template set # found chain 1b87A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (1b87A)M1 T0374 4 :SHRPAETGD 1b87A 2 :IISEFDRNN T0374 13 :LETVAGFPQDR 1b87A 14 :KDQLSDLLRLT T0374 30 :YPKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1b87A 25 :WPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASR T0374 109 :KARLMKIS 1b87A 103 :GGITIYLG T0374 118 :FNA 1b87A 114 :LDH T0374 125 :LLLYTQLGYQPRAIAERHDPDGR 1b87A 144 :YEFYEKLGYKIVGVLPNANGWDK T0374 150 :ALIQMDKPLEP 1b87A 167 :PDIWMAKTIIP Number of specific fragments extracted= 7 number of extra gaps= 0 total=992 Number of alignments=139 # 1b87A read from 1b87A/merged-good-all-a2m # found chain 1b87A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (1b87A)M1 T0374 4 :SHRPAETGD 1b87A 2 :IISEFDRNN T0374 13 :LETVAGFPQDRDE 1b87A 14 :KDQLSDLLRLTWP T0374 32 :KAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1b87A 27 :EEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASR T0374 109 :KARLMKISC 1b87A 103 :GGITIYLGT T0374 118 :FNANA 1b87A 139 :LREHP T0374 125 :LLLYTQLGYQPRAIAERH 1b87A 144 :YEFYEKLGYKIVGVLPNA T0374 143 :DPD 1b87A 163 :GWD T0374 149 :VALIQMDKPL 1b87A 166 :KPDIWMAKTI T0374 159 :EP 1b87A 178 :RP Number of specific fragments extracted= 9 number of extra gaps= 0 total=1001 Number of alignments=140 # 1b87A read from 1b87A/merged-good-all-a2m # found chain 1b87A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (1b87A)M1 T0374 4 :SHRPAETGD 1b87A 2 :IISEFDRNN T0374 13 :LETVAGFPQDRDE 1b87A 14 :KDQLSDLLRLTWP T0374 32 :KAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1b87A 27 :EEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGIT T0374 113 :MKISCFNA 1b87A 107 :IYLGTDDL T0374 125 :LLLYTQLGYQPRAIAERHDPDGRRVALIQMDKPLEP 1b87A 144 :YEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRP Number of specific fragments extracted= 5 number of extra gaps= 0 total=1006 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y9wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y9wA expands to /projects/compbio/data/pdb/1y9w.pdb.gz 1y9wA:# T0374 read from 1y9wA/merged-good-all-a2m # 1y9wA read from 1y9wA/merged-good-all-a2m # adding 1y9wA to template set # found chain 1y9wA in template set Warning: unaligning (T0374)L158 because last residue in template chain is (1y9wA)L140 T0374 1 :MQ 1y9wA 3 :MK T0374 4 :SHRPAETGDLETVAGFPQ 1y9wA 5 :HIENGTRIEGEYIKNKVI T0374 23 :RDELFYCYPKAIWPF 1y9wA 23 :QYNMSILTDEVKQPM T0374 49 :RRGSTVAVHD 1y9wA 38 :EEVSLVVKNE T0374 59 :GQVLGFANFYQWQ 1y9wA 49 :GKIFGGVTGTMYF T0374 74 :DFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1y9wA 62 :YHLHIDFLWVDESVRHDGYGSQLLHEIEGIAKEK T0374 109 :KARLMKISCFNA 1y9wA 96 :GCRLILLDSFSF T0374 121 :N 1y9wA 110 :P T0374 126 :LLYTQLGYQPRAIAERHDPDG 1y9wA 111 :EFYKKHGYREYGVVEDHPKGH T0374 150 :ALIQMDKP 1y9wA 132 :SQHFFEKR Number of specific fragments extracted= 10 number of extra gaps= 0 total=1016 Number of alignments=142 # 1y9wA read from 1y9wA/merged-good-all-a2m # found chain 1y9wA in template set Warning: unaligning (T0374)L158 because last residue in template chain is (1y9wA)L140 T0374 4 :SHRPAETGDLETVAG 1y9wA 5 :HIENGTRIEGEYIKN T0374 22 :DRDELFY 1y9wA 20 :KVIQYNM T0374 29 :CYPKAIWPF 1y9wA 29 :LTDEVKQPM T0374 49 :RRGSTVAVHD 1y9wA 38 :EEVSLVVKNE T0374 59 :GQVLGFANFYQW 1y9wA 49 :GKIFGGVTGTMY T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1y9wA 61 :FYHLHIDFLWVDESVRHDGYGSQLLHEIEGIAKEK T0374 109 :KARLMKISCFNAN 1y9wA 96 :GCRLILLDSFSFQ T0374 124 :GLLLYTQLGYQPRAIAER 1y9wA 109 :APEFYKKHGYREYGVVED T0374 143 :DPDG 1y9wA 127 :HPKG T0374 149 :VALIQMDKP 1y9wA 131 :HSQHFFEKR Number of specific fragments extracted= 10 number of extra gaps= 0 total=1026 Number of alignments=143 # 1y9wA read from 1y9wA/merged-good-all-a2m # found chain 1y9wA in template set T0374 4 :SHRPAETGDLETVAGFPQDRDEL 1y9wA 5 :HIENGTRIEGEYIKNKVIQYNMS T0374 46 :IAERRGSTVAVH 1y9wA 35 :QPMEEVSLVVKN T0374 58 :DGQVLGFANFYQ 1y9wA 48 :EGKIFGGVTGTM T0374 72 :HGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1y9wA 60 :YFYHLHIDFLWVDESVRHDGYGSQLLHEIEGIAKEKGCRL T0374 113 :MKISCFNA 1y9wA 100 :ILLDSFSF T0374 125 :LLLYTQLGYQPRAIAERHDPDGR 1y9wA 110 :PEFYKKHGYREYGVVEDHPKGHS Number of specific fragments extracted= 6 number of extra gaps= 0 total=1032 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n71A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0374 read from 1n71A/merged-good-all-a2m # 1n71A read from 1n71A/merged-good-all-a2m # found chain 1n71A in training set T0374 4 :SHRPAETGD 1n71A 2 :IISEFDRNN T0374 13 :LETVAGFPQDR 1n71A 14 :KDQLSDLLRLT T0374 30 :YPKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1n71A 25 :WPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASR T0374 109 :KARLMKISCF 1n71A 103 :GGITIYLGTD T0374 125 :LLLYTQLGYQPRAIAERHDPDGR 1n71A 144 :YEFYEKLGYKIVGVLPNANGWDK T0374 150 :ALIQMDKPLEP 1n71A 167 :PDIWMAKTIIP Number of specific fragments extracted= 6 number of extra gaps= 0 total=1038 Number of alignments=145 # 1n71A read from 1n71A/merged-good-all-a2m # found chain 1n71A in training set Warning: unaligning (T0374)L3 because first residue in template chain is (1n71A)M1 T0374 4 :SHRPAETGD 1n71A 2 :IISEFDRNN T0374 13 :LETVAGFPQDRDE 1n71A 14 :KDQLSDLLRLTWP T0374 32 :KAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1n71A 27 :EEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASR T0374 109 :KARLMKISC 1n71A 103 :GGITIYLGT T0374 118 :FNANA 1n71A 139 :LREHP T0374 125 :LLLYTQLGYQPRAIAERH 1n71A 144 :YEFYEKLGYKIVGVLPNA T0374 143 :DPD 1n71A 163 :GWD T0374 149 :VALIQMDKPL 1n71A 166 :KPDIWMAKTI T0374 159 :EP 1n71A 178 :RP Number of specific fragments extracted= 9 number of extra gaps= 0 total=1047 Number of alignments=146 # 1n71A read from 1n71A/merged-good-all-a2m # found chain 1n71A in training set Warning: unaligning (T0374)L3 because first residue in template chain is (1n71A)M1 T0374 4 :SHRPAETGD 1n71A 2 :IISEFDRNN T0374 13 :LETVAGFPQDRDE 1n71A 14 :KDQLSDLLRLTWP T0374 32 :KAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1n71A 27 :EEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGIT T0374 113 :MKISCFNA 1n71A 107 :IYLGTDDL T0374 125 :LLLYTQLGYQPRAIAERHDPDGRRVALIQMDKPLEP 1n71A 144 :YEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRP Number of specific fragments extracted= 5 number of extra gaps= 0 total=1052 Number of alignments=147 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0374//projects/compbio/experiments/protein-predict/casp7/T0374/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0374//projects/compbio/experiments/protein-predict/casp7/T0374/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0374/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0374/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((T0374)A65.CB, (T0374)M100.CB) [> 3.3137 = 5.5229 < 7.1797] w=1.0000 to align # Constraint # added constraint: constraint((T0374)A65.CB, (T0374)L96.CB) [> 2.8491 = 4.7485 < 6.1730] w=1.0000 to align # Constraint # added constraint: constraint((T0374)T53.CB, (T0374)F64.CB) [> 3.9806 = 6.6343 < 8.6246] w=1.0000 to align # Constraint # added constraint: constraint((T0374)S52.CB, (T0374)F64.CB) [> 3.9329 = 6.5548 < 8.5212] w=1.0000 to align # Constraint # added constraint: constraint((T0374)V54.CB, (T0374)F64.CB) [> 3.2505 = 5.4175 < 7.0427] w=0.9930 to align # Constraint # added constraint: constraint((T0374)V54.CB, (T0374)G63.CA) [> 3.7771 = 6.2951 < 8.1837] w=0.9930 to align # Constraint # added constraint: constraint((T0374)I97.CB, (T0374)L131.CB) [> 3.3241 = 5.5402 < 7.2023] w=0.9790 to align # Constraint # added constraint: constraint((T0374)V83.CB, (T0374)A93.CB) [> 3.1715 = 5.2859 < 6.8717] w=0.9790 to align # Constraint # added constraint: constraint((T0374)L62.CB, (T0374)V92.CB) [> 3.6158 = 6.0264 < 7.8343] w=0.9790 to align # Constraint # added constraint: constraint((T0374)A65.CB, (T0374)M81.CB) [> 2.8756 = 4.7927 < 6.2305] w=0.9790 to align # Constraint # added constraint: constraint((T0374)M81.CB, (T0374)I97.CB) [> 4.1655 = 6.9425 < 9.0253] w=0.9790 to align # Constraint # added constraint: constraint((T0374)L62.CB, (T0374)A84.CB) [> 3.2824 = 5.4706 < 7.1118] w=0.9790 to align # Constraint # added constraint: constraint((T0374)L62.CB, (T0374)A87.CB) [> 2.8279 = 4.7132 < 6.1272] w=0.9790 to align # Constraint # added constraint: constraint((T0374)G63.CA, (T0374)A84.CB) [> 3.5346 = 5.8910 < 7.6583] w=0.9790 to align # Constraint # added constraint: constraint((T0374)C117.CB, (T0374)Y128.CB) [> 3.9236 = 6.5393 < 8.5011] w=0.9720 to align # Constraint # added constraint: constraint((T0374)A77.CB, (T0374)K114.CB) [> 3.2448 = 5.4080 < 7.0304] w=0.9720 to align # Constraint # added constraint: constraint((T0374)Y68.CB, (T0374)A77.CB) [> 3.1312 = 5.2186 < 6.7842] w=0.9720 to align # Constraint # added constraint: constraint((T0374)L78.CB, (T0374)I115.CB) [> 2.8378 = 4.7297 < 6.1486] w=0.9650 to align # Constraint # added constraint: constraint((T0374)I115.CB, (T0374)Y128.CB) [> 3.8842 = 6.4737 < 8.4159] w=0.9580 to align # Constraint # added constraint: constraint((T0374)C76.CB, (T0374)K114.CB) [> 4.2359 = 7.0599 < 9.1779] w=0.9580 to align # Constraint # added constraint: constraint((T0374)G63.CA, (T0374)M82.CB) [> 3.5510 = 5.9183 < 7.6938] w=0.9580 to align # Constraint # added constraint: constraint((T0374)F64.CB, (T0374)M82.CB) [> 3.4453 = 5.7421 < 7.4647] w=0.9580 to align # Constraint # added constraint: constraint((T0374)L62.CB, (T0374)V83.CB) [> 4.0468 = 6.7447 < 8.7681] w=0.9580 to align # Constraint # added constraint: constraint((T0374)G63.CA, (T0374)V83.CB) [> 2.9633 = 4.9389 < 6.4205] w=0.9580 to align # Constraint # added constraint: constraint((T0374)F64.CB, (T0374)M81.CB) [> 4.4412 = 7.4019 < 9.6225] w=0.9580 to align # Constraint # added constraint: constraint((T0374)F67.CB, (T0374)A77.CB) [> 3.8456 = 6.4093 < 8.3321] w=0.9510 to align # Constraint # added constraint: constraint((T0374)A65.CB, (T0374)N80.CB) [> 4.0900 = 6.8166 < 8.8616] w=0.9510 to align # Constraint # added constraint: constraint((T0374)S52.CB, (T0374)N66.CB) [> 3.0027 = 5.0044 < 6.5057] w=0.9510 to align # Constraint # added constraint: constraint((T0374)L78.CB, (T0374)K114.CB) [> 4.2001 = 7.0002 < 9.1003] w=0.9440 to align # Constraint # added constraint: constraint((T0374)F67.CB, (T0374)L78.CB) [> 3.2971 = 5.4952 < 7.1438] w=0.9440 to align # Constraint # added constraint: constraint((T0374)G63.CA, (T0374)A87.CB) [> 4.2538 = 7.0897 < 9.2167] w=0.9370 to align # Constraint # added constraint: constraint((T0374)C76.CB, (T0374)M113.CB) [> 3.0359 = 5.0599 < 6.5778] w=0.9370 to align # Constraint # added constraint: constraint((T0374)E101.CB, (T0374)M113.CB) [> 3.8575 = 6.4292 < 8.3579] w=0.9370 to align # Constraint # added constraint: constraint((T0374)A104.CB, (T0374)M113.CB) [> 3.4342 = 5.7236 < 7.4407] w=0.9370 to align # Constraint # added constraint: constraint((T0374)M81.CB, (T0374)L96.CB) [> 3.8431 = 6.4052 < 8.3267] w=0.9370 to align # Constraint # added constraint: constraint((T0374)F67.CB, (T0374)M100.CB) [> 3.4920 = 5.8199 < 7.5659] w=0.9370 to align # Constraint # added constraint: constraint((T0374)A55.CB, (T0374)L96.CB) [> 3.4535 = 5.7559 < 7.4827] w=0.9336 to align # Constraint # added constraint: constraint((T0374)A55.CB, (T0374)V92.CB) [> 3.4075 = 5.6791 < 7.3829] w=0.9336 to align # Constraint # added constraint: constraint((T0374)A55.CB, (T0374)F64.CB) [> 4.0988 = 6.8313 < 8.8807] w=0.9336 to align # Constraint # added constraint: constraint((T0374)T53.CB, (T0374)A65.CB) [> 2.9972 = 4.9954 < 6.4940] w=0.9336 to align # Constraint # added constraint: constraint((T0374)L78.CB, (T0374)M113.CB) [> 3.8389 = 6.3981 < 8.3176] w=0.9300 to align # Constraint # added constraint: constraint((T0374)S52.CB, (T0374)A65.CB) [> 4.2449 = 7.0748 < 9.1973] w=0.9300 to align # Constraint # added constraint: constraint((T0374)N66.CB, (T0374)N80.CB) [> 2.7960 = 4.6600 < 6.0580] w=0.9230 to align # Constraint # added constraint: constraint((T0374)M81.CB, (T0374)A93.CB) [> 3.8362 = 6.3937 < 8.3118] w=0.9210 to align # Constraint # added constraint: constraint((T0374)G63.CA, (T0374)L96.CB) [> 4.0490 = 6.7483 < 8.7728] w=0.9160 to align # Constraint # added constraint: constraint((T0374)G51.CA, (T0374)N66.CB) [> 3.6648 = 6.1080 < 7.9404] w=0.9019 to align # Constraint # added constraint: constraint((T0374)H5.CB, (T0374)T53.CB) [> 3.4097 = 5.6829 < 7.3877] w=0.9019 to align # Constraint # added constraint: constraint((T0374)G63.CA, (T0374)V92.CB) [> 3.7387 = 6.2312 < 8.1005] w=0.9000 to align # Constraint # added constraint: constraint((T0374)G51.CA, (T0374)F67.CB) [> 3.3158 = 5.5264 < 7.1843] w=0.8949 to align # Constraint # added constraint: constraint((T0374)H5.CB, (T0374)V54.CB) [> 4.2820 = 7.1367 < 9.2777] w=0.8949 to align # Constraint # added constraint: constraint((T0374)A77.CB, (T0374)M113.CB) [> 4.3746 = 7.2910 < 9.4784] w=0.8858 to align # Constraint # added constraint: constraint((T0374)H5.CB, (T0374)V99.CB) [> 3.2106 = 5.3510 < 6.9563] w=0.8809 to align # Constraint # added constraint: constraint((T0374)A65.CB, (T0374)L78.CB) [> 3.9637 = 6.6061 < 8.5879] w=0.8809 to align # Constraint # added constraint: constraint((T0374)T15.CB, (T0374)V61.CB) [> 2.6968 = 4.4946 < 5.8430] w=0.8790 to align # Constraint # added constraint: constraint((T0374)I115.CB, (T0374)Y133.CB) [> 4.0978 = 6.8297 < 8.8786] w=0.8739 to align # Constraint # added constraint: constraint((T0374)F75.CB, (T0374)A110.CB) [> 3.8211 = 6.3685 < 8.2790] w=0.8739 to align # Constraint # added constraint: constraint((T0374)N66.CB, (T0374)G79.CA) [> 3.1760 = 5.2933 < 6.8813] w=0.8739 to align # Constraint # added constraint: constraint((T0374)A93.CB, (T0374)L127.CB) [> 3.5991 = 5.9985 < 7.7980] w=0.8718 to align # Constraint # added constraint: constraint((T0374)P7.CB, (T0374)T53.CB) [> 3.7262 = 6.2102 < 8.0733] w=0.8599 to align # Constraint # added constraint: constraint((T0374)H5.CB, (T0374)A55.CB) [> 3.4294 = 5.7157 < 7.4304] w=0.8599 to align # Constraint # added constraint: constraint((T0374)R6.CB, (T0374)T53.CB) [> 4.0236 = 6.7060 < 8.7177] w=0.8599 to align # Constraint # added constraint: constraint((T0374)A8.CB, (T0374)S52.CB) [> 2.7474 = 4.5790 < 5.9528] w=0.8599 to align # Constraint # added constraint: constraint((T0374)G79.CA, (T0374)I115.CB) [> 3.8700 = 6.4500 < 8.3850] w=0.8599 to align # Constraint # added constraint: constraint((T0374)C76.CB, (T0374)A104.CB) [> 2.8696 = 4.7827 < 6.2175] w=0.8599 to align # Constraint # added constraint: constraint((T0374)V16.CB, (T0374)F64.CB) [> 3.4405 = 5.7342 < 7.4545] w=0.8529 to align # Constraint # added constraint: constraint((T0374)F75.CB, (T0374)R111.CB) [> 3.6943 = 6.1571 < 8.0043] w=0.8529 to align # Constraint # added constraint: constraint((T0374)A77.CB, (T0374)I115.CB) [> 4.0450 = 6.7417 < 8.7642] w=0.8529 to align # Constraint # added constraint: constraint((T0374)F75.CB, (T0374)K114.CB) [> 3.6651 = 6.1085 < 7.9411] w=0.8529 to align # Constraint # added constraint: constraint((T0374)F19.CB, (T0374)V61.CB) [> 3.7286 = 6.2143 < 8.0786] w=0.8510 to align # Constraint # added constraint: constraint((T0374)L78.CB, (T0374)M100.CB) [> 3.7394 = 6.2324 < 8.1021] w=0.8459 to align # Constraint # added constraint: constraint((T0374)F67.CB, (T0374)C76.CB) [> 3.3161 = 5.5268 < 7.1848] w=0.8459 to align # Constraint # added constraint: constraint((T0374)F64.CB, (T0374)N80.CB) [> 4.2647 = 7.1078 < 9.2401] w=0.8459 to align # Constraint # added constraint: constraint((T0374)F19.CB, (T0374)A84.CB) [> 3.6867 = 6.1444 < 7.9878] w=0.8440 to align # Constraint # added constraint: constraint((T0374)R6.CB, (T0374)V54.CB) [> 3.5631 = 5.9385 < 7.7201] w=0.8426 to align # Constraint # added constraint: constraint((T0374)S4.CB, (T0374)A55.CB) [> 4.3357 = 7.2262 < 9.3940] w=0.8389 to align # Constraint # added constraint: constraint((T0374)F19.CB, (T0374)G63.CA) [> 3.6333 = 6.0556 < 7.8723] w=0.8370 to align # Constraint # added constraint: constraint((T0374)A8.CB, (T0374)T53.CB) [> 3.8932 = 6.4887 < 8.4354] w=0.8319 to align # Constraint # added constraint: constraint((T0374)F75.CB, (T0374)M113.CB) [> 4.3987 = 7.3312 < 9.5305] w=0.8319 to align # Constraint # added constraint: constraint((T0374)R50.CB, (T0374)Y68.CB) [> 3.1882 = 5.3136 < 6.9077] w=0.8298 to align # Constraint # added constraint: constraint((T0374)S4.CB, (T0374)V56.CB) [> 3.0879 = 5.1465 < 6.6904] w=0.8286 to align # Constraint # added constraint: constraint((T0374)A65.CB, (T0374)I97.CB) [> 4.1259 = 6.8765 < 8.9394] w=0.8160 to align # Constraint # added constraint: constraint((T0374)T53.CB, (T0374)M100.CB) [> 3.8578 = 6.4297 < 8.3586] w=0.8126 to align # Constraint # added constraint: constraint((T0374)P7.CB, (T0374)S52.CB) [> 4.2470 = 7.0783 < 9.2017] w=0.8039 to align # Constraint # added constraint: constraint((T0374)N66.CB, (T0374)L78.CB) [> 4.3965 = 7.3275 < 9.5258] w=0.8039 to align # Constraint # added constraint: constraint((T0374)A8.CB, (T0374)V54.CB) [> 3.0538 = 5.0896 < 6.6165] w=0.8006 to align # Constraint # added constraint: constraint((T0374)T53.CB, (T0374)L96.CB) [> 3.7402 = 6.2337 < 8.1038] w=0.7986 to align # Constraint # added constraint: constraint((T0374)V16.CB, (T0374)V61.CB) [> 3.8676 = 6.4459 < 8.3797] w=0.7880 to align # Constraint # added constraint: constraint((T0374)R50.CB, (T0374)N66.CB) [> 3.8419 = 6.4033 < 8.3242] w=0.7878 to align # Constraint # added constraint: constraint((T0374)Y68.CB, (T0374)G79.CA) [> 4.0124 = 6.6873 < 8.6935] w=0.7829 to align # Constraint # added constraint: constraint((T0374)R6.CB, (T0374)V56.CB) [> 4.0215 = 6.7025 < 8.7133] w=0.7796 to align # Constraint # added constraint: constraint((T0374)T53.CB, (T0374)V99.CB) [> 3.4825 = 5.8041 < 7.5453] w=0.7776 to align # Constraint # added constraint: constraint((T0374)V83.CB, (T0374)L96.CB) [> 4.4872 = 7.4787 < 9.7223] w=0.7689 to align # Constraint # added constraint: constraint((T0374)H5.CB, (T0374)L96.CB) [> 3.9319 = 6.5532 < 8.5191] w=0.7669 to align # Constraint # added constraint: constraint((T0374)R50.CB, (T0374)F67.CB) [> 3.8338 = 6.3897 < 8.3066] w=0.7668 to align # Constraint # added constraint: constraint((T0374)F19.CB, (T0374)M82.CB) [> 3.3388 = 5.5647 < 7.2340] w=0.7599 to align # Constraint # added constraint: constraint((T0374)A55.CB, (T0374)Y95.CB) [> 4.0564 = 6.7607 < 8.7890] w=0.7566 to align # Constraint # added constraint: constraint((T0374)G98.CA, (T0374)L131.CB) [> 4.1241 = 6.8735 < 8.9356] w=0.7479 to align # Constraint # added constraint: constraint((T0374)V16.CB, (T0374)V54.CB) [> 4.1476 = 6.9126 < 8.9864] w=0.7335 to align # Constraint # added constraint: constraint((T0374)C76.CB, (T0374)A110.CB) [> 3.1379 = 5.2298 < 6.7988] w=0.7234 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)M82.CB) [> 3.8739 = 6.4566 < 8.3935] w=0.7179 to align # Constraint # added constraint: constraint((T0374)G51.CA, (T0374)Y68.CB) [> 4.2126 = 7.0210 < 9.1272] w=0.7165 to align # Constraint # added constraint: constraint((T0374)F67.CB, (T0374)A104.CB) [> 3.8141 = 6.3569 < 8.2639] w=0.7058 to align # Constraint # added constraint: constraint((T0374)P7.CB, (T0374)G51.CA) [> 4.2734 = 7.1224 < 9.2591] w=0.7039 to align # Constraint # added constraint: constraint((T0374)R23.CB, (T0374)M82.CB) [> 2.8461 = 4.7436 < 6.1667] w=0.7039 to align # Constraint # added constraint: constraint((T0374)C76.CB, (T0374)L112.CB) [> 4.1401 = 6.9001 < 8.9702] w=0.6954 to align # Constraint # added constraint: constraint((T0374)F75.CB, (T0374)L112.CB) [> 3.1398 = 5.2330 < 6.8029] w=0.6954 to align # Constraint # added constraint: constraint((T0374)N66.CB, (T0374)M81.CB) [> 4.5436 = 7.5727 < 9.8444] w=0.6882 to align # Constraint # added constraint: constraint((T0374)A55.CB, (T0374)V83.CB) [> 4.3538 = 7.2563 < 9.4332] w=0.6743 to align # Constraint # added constraint: constraint((T0374)M100.CB, (T0374)M113.CB) [> 4.2944 = 7.1573 < 9.3044] w=0.6617 to align # Constraint # added constraint: constraint((T0374)H5.CB, (T0374)V56.CB) [> 4.5633 = 7.6055 < 9.8872] w=0.6586 to align # Constraint # added constraint: constraint((T0374)D12.CB, (T0374)V61.CB) [> 3.8854 = 6.4756 < 8.4183] w=0.6569 to align # Constraint # added constraint: constraint((T0374)L3.CB, (T0374)V56.CB) [> 4.1333 = 6.8888 < 8.9554] w=0.6548 to align # Constraint # added constraint: constraint((T0374)L3.CB, (T0374)A55.CB) [> 3.4798 = 5.7997 < 7.5396] w=0.6548 to align # Constraint # added constraint: constraint((T0374)L78.CB, (T0374)I97.CB) [> 4.3546 = 7.2577 < 9.4350] w=0.6528 to align # Constraint # added constraint: constraint((T0374)H57.CB, (T0374)A87.CB) [> 4.2688 = 7.1148 < 9.2492] w=0.6465 to align # Constraint # added constraint: constraint((T0374)D12.CB, (T0374)V54.CB) [> 3.4616 = 5.7693 < 7.5001] w=0.6395 to align # Constraint # added constraint: constraint((T0374)M81.CB, (T0374)I115.CB) [> 4.5475 = 7.5792 < 9.8530] w=0.6218 to align # Constraint # added constraint: constraint((T0374)R49.CB, (T0374)Y68.CB) [> 3.8233 = 6.3721 < 8.2838] w=0.6127 to align # Constraint # added constraint: constraint((T0374)L3.CB, (T0374)V92.CB) [> 3.8053 = 6.3421 < 8.2447] w=0.5987 to align # Constraint # added constraint: constraint((T0374)P7.CB, (T0374)V54.CB) [> 4.5338 = 7.5563 < 9.8231] w=0.5975 to align # Constraint # added constraint: constraint((T0374)K114.CB, (T0374)R136.CB) [> 4.3679 = 7.2798 < 9.4637] w=0.5938 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)N80.CB) [> 4.0389 = 6.7315 < 8.7509] w=0.5868 to align # Constraint # added constraint: constraint((T0374)T53.CB, (T0374)N66.CB) [> 4.4513 = 7.4188 < 9.6444] w=0.5813 to align # Constraint # added constraint: constraint((T0374)L3.CB, (T0374)Y95.CB) [> 3.8620 = 6.4367 < 8.3677] w=0.5777 to align # Constraint # added constraint: constraint((T0374)Q69.CB, (T0374)Q107.CB) [> 3.8751 = 6.4585 < 8.3960] w=0.5777 to align # Constraint # added constraint: constraint((T0374)L3.CB, (T0374)H57.CB) [> 3.4195 = 5.6991 < 7.4088] w=0.5707 to align # Constraint # added constraint: constraint((T0374)A65.CB, (T0374)G79.CA) [> 4.3029 = 7.1715 < 9.3229] w=0.5638 to align # Constraint # added constraint: constraint((T0374)T53.CB, (T0374)L103.CB) [> 4.2936 = 7.1560 < 9.3028] w=0.5623 to align # Constraint # added constraint: constraint((T0374)V61.CB, (T0374)A84.CB) [> 4.3395 = 7.2325 < 9.4023] w=0.5588 to align # Constraint # added constraint: constraint((T0374)L3.CB, (T0374)L62.CB) [> 4.0402 = 6.7337 < 8.7539] w=0.5567 to align # Constraint # added constraint: constraint((T0374)A8.CB, (T0374)G51.CA) [> 4.3283 = 7.2139 < 9.3780] w=0.5547 to align # Constraint # added constraint: constraint((T0374)T15.CB, (T0374)Q60.CB) [> 4.2076 = 7.0127 < 9.1166] w=0.5498 to align # Constraint # added constraint: constraint((T0374)R49.CB, (T0374)Q69.CB) [> 3.4418 = 5.7362 < 7.4571] w=0.5357 to align # Constraint # added constraint: constraint((T0374)R50.CB, (T0374)Q69.CB) [> 4.2551 = 7.0918 < 9.2194] w=0.5337 to align # Constraint # added constraint: constraint((T0374)D74.CB, (T0374)R111.CB) [> 3.2590 = 5.4317 < 7.0612] w=0.5224 to align # Constraint # added constraint: constraint((T0374)M113.CB, (T0374)Y133.CB) [> 4.5820 = 7.6367 < 9.9277] w=0.5223 to align # Constraint # added constraint: constraint((T0374)A65.CB, (T0374)M82.CB) [> 4.5111 = 7.5185 < 9.7740] w=0.5197 to align # Constraint # added constraint: constraint((T0374)F67.CB, (T0374)L103.CB) [> 3.9393 = 6.5655 < 8.5351] w=0.5197 to align # Constraint # added constraint: constraint((T0374)S4.CB, (T0374)H57.CB) [> 4.4001 = 7.3336 < 9.5336] w=0.5186 to align # Constraint # added constraint: constraint((T0374)R94.CB, (T0374)Q130.CB) [> 4.0790 = 6.7983 < 8.8378] w=0.5168 to align # Constraint # added constraint: constraint((T0374)C76.CB, (T0374)Q107.CB) [> 4.3257 = 7.2094 < 9.3722] w=0.5077 to align # Constraint # added constraint: constraint((T0374)E101.CB, (T0374)L131.CB) [> 4.2610 = 7.1016 < 9.2321] w=0.4798 to align # Constraint # added constraint: constraint((T0374)I97.CB, (T0374)L127.CB) [> 4.2001 = 7.0001 < 9.1001] w=0.4782 to align # Constraint # added constraint: constraint((T0374)V16.CB, (T0374)S52.CB) [> 3.9599 = 6.5998 < 8.5798] w=0.4712 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)F64.CB) [> 4.1116 = 6.8526 < 8.9084] w=0.4637 to align # Constraint # added constraint: constraint((T0374)G79.CA, (T0374)S116.CB) [> 4.3284 = 7.2140 < 9.3781] w=0.4572 to align # Constraint # added constraint: constraint((T0374)I97.CB, (T0374)Y128.CB) [> 4.4970 = 7.4949 < 9.7434] w=0.4567 to align # Constraint # added constraint: constraint((T0374)C117.CB, (T0374)I152.CB) [> 3.4388 = 5.7314 < 7.4508] w=0.4349 to align # Constraint # added constraint: constraint((T0374)K114.CB, (T0374)M154.CB) [> 4.1242 = 6.8737 < 8.9358] w=0.4286 to align # Constraint # added constraint: constraint((T0374)A55.CB, (T0374)A65.CB) [> 4.2309 = 7.0515 < 9.1670] w=0.4221 to align # Constraint # added constraint: constraint((T0374)Q134.CB, (T0374)M154.CB) [> 3.9014 = 6.5023 < 8.4531] w=0.4216 to align # Constraint # added constraint: constraint((T0374)S116.CB, (T0374)I152.CB) [> 4.1784 = 6.9640 < 9.0532] w=0.4209 to align # Constraint # added constraint: constraint((T0374)P135.CB, (T0374)M154.CB) [> 3.4477 = 5.7462 < 7.4700] w=0.4146 to align # Constraint # added constraint: constraint((T0374)F67.CB, (T0374)M113.CB) [> 4.3287 = 7.2144 < 9.3788] w=0.4096 to align # Constraint # added constraint: constraint((T0374)C76.CB, (T0374)M100.CB) [> 4.2371 = 7.0618 < 9.1803] w=0.4007 to align # Constraint # added constraint: constraint((T0374)I115.CB, (T0374)M154.CB) [> 3.0165 = 5.0275 < 6.5358] w=0.4006 to align # Constraint # added constraint: constraint((T0374)M113.CB, (T0374)K156.CB) [> 2.8911 = 4.8185 < 6.2641] w=0.4006 to align # Constraint # added constraint: constraint((T0374)K114.CB, (T0374)Q153.CB) [> 3.8175 = 6.3625 < 8.2712] w=0.4006 to align # Constraint # added constraint: constraint((T0374)G51.CA, (T0374)L103.CB) [> 3.9937 = 6.6562 < 8.6530] w=0.3994 to align # Constraint # added constraint: constraint((T0374)S116.CB, (T0374)Q153.CB) [> 3.2937 = 5.4896 < 7.1364] w=0.3987 to align # Constraint # added constraint: constraint((T0374)A17.CB, (T0374)L42.CB) [> 3.5120 = 5.8534 < 7.6094] w=0.3965 to align # Constraint # added constraint: constraint((T0374)L112.CB, (T0374)D155.CB) [> 3.5944 = 5.9906 < 7.7878] w=0.3936 to align # Constraint # added constraint: constraint((T0374)R136.CB, (T0374)Q153.CB) [> 2.9288 = 4.8813 < 6.3457] w=0.3936 to align # Constraint # added constraint: constraint((T0374)L125.CB, (T0374)I152.CB) [> 3.7964 = 6.3274 < 8.2256] w=0.3859 to align # Constraint # added constraint: constraint((T0374)C117.CB, (T0374)M154.CB) [> 3.9308 = 6.5513 < 8.5167] w=0.3796 to align # Constraint # added constraint: constraint((T0374)S116.CB, (T0374)L151.CB) [> 3.0759 = 5.1265 < 6.6644] w=0.3788 to align # Constraint # added constraint: constraint((T0374)L13.CB, (T0374)L42.CB) [> 3.2199 = 5.3664 < 6.9764] w=0.3777 to align # Constraint # added constraint: constraint((T0374)L13.CB, (T0374)V39.CB) [> 3.6011 = 6.0019 < 7.8025] w=0.3777 to align # Constraint # added constraint: constraint((T0374)C76.CB, (T0374)R111.CB) [> 4.1099 = 6.8499 < 8.9048] w=0.3747 to align # Constraint # added constraint: constraint((T0374)N119.CB, (T0374)I138.CB) [> 4.0751 = 6.7918 < 8.8294] w=0.3731 to align # Constraint # added constraint: constraint((T0374)L112.CB, (T0374)P157.CB) [> 3.2809 = 5.4682 < 7.1086] w=0.3726 to align # Constraint # added constraint: constraint((T0374)R111.CB, (T0374)P157.CB) [> 4.0402 = 6.7337 < 8.7538] w=0.3726 to align # Constraint # added constraint: constraint((T0374)E101.CB, (T0374)K156.CB) [> 4.2508 = 7.0847 < 9.2101] w=0.3725 to align # Constraint # added constraint: constraint((T0374)C117.CB, (T0374)L151.CB) [> 4.1618 = 6.9364 < 9.0173] w=0.3649 to align # Constraint # added constraint: constraint((T0374)D74.CB, (T0374)L112.CB) [> 4.0181 = 6.6968 < 8.7058] w=0.3632 to align # Constraint # added constraint: constraint((T0374)Y68.CB, (T0374)L78.CB) [> 4.1888 = 6.9813 < 9.0757] w=0.3591 to align # Constraint # added constraint: constraint((T0374)N119.CB, (T0374)I152.CB) [> 3.3209 = 5.5348 < 7.1952] w=0.3579 to align # Constraint # added constraint: constraint((T0374)V16.CB, (T0374)L42.CB) [> 3.7492 = 6.2486 < 8.1232] w=0.3578 to align # Constraint # added constraint: constraint((T0374)A17.CB, (T0374)V39.CB) [> 3.4796 = 5.7993 < 7.5390] w=0.3578 to align # Constraint # added constraint: constraint((T0374)W70.CB, (T0374)K114.CB) [> 3.9086 = 6.5143 < 8.4686] w=0.3523 to align # Constraint # added constraint: constraint((T0374)I115.CB, (T0374)Q153.CB) [> 4.4115 = 7.3525 < 9.5582] w=0.3516 to align # Constraint # added constraint: constraint((T0374)N119.CB, (T0374)A150.CB) [> 2.8612 = 4.7686 < 6.1992] w=0.3502 to align # Constraint # added constraint: constraint((T0374)S116.CB, (T0374)A139.CB) [> 3.9951 = 6.6585 < 8.6560] w=0.3485 to align # Constraint # added constraint: constraint((T0374)S116.CB, (T0374)M154.CB) [> 4.3270 = 7.2116 < 9.3751] w=0.3445 to align # Constraint # added constraint: constraint((T0374)N119.CB, (T0374)L151.CB) [> 3.9607 = 6.6012 < 8.5815] w=0.3432 to align # Constraint # added constraint: constraint((T0374)A17.CB, (T0374)S38.CB) [> 3.6664 = 6.1107 < 7.9439] w=0.3375 to align # Constraint # added constraint: constraint((T0374)M81.CB, (T0374)M100.CB) [> 4.5496 = 7.5827 < 9.8576] w=0.3362 to align # Constraint # added constraint: constraint((T0374)R23.CB, (T0374)P85.CB) [> 3.7850 = 6.3083 < 8.2008] w=0.3312 to align # Constraint # added constraint: constraint((T0374)I138.CB, (T0374)I152.CB) [> 3.7067 = 6.1778 < 8.0312] w=0.3298 to align # Constraint # added constraint: constraint((T0374)I138.CB, (T0374)A150.CB) [> 3.5054 = 5.8423 < 7.5950] w=0.3298 to align # Constraint # added constraint: constraint((T0374)A45.CB, (T0374)N66.CB) [> 3.7845 = 6.3075 < 8.1998] w=0.3228 to align # Constraint # added constraint: constraint((T0374)L13.CB, (T0374)I46.CB) [> 3.9530 = 6.5883 < 8.5647] w=0.3158 to align # Constraint # added constraint: constraint((T0374)A139.CB, (T0374)L151.CB) [> 2.9969 = 4.9948 < 6.4933] w=0.3158 to align # Constraint # added constraint: constraint((T0374)I138.CB, (T0374)Q153.CB) [> 4.0916 = 6.8194 < 8.8652] w=0.3095 to align # Constraint # added constraint: constraint((T0374)F118.CB, (T0374)I152.CB) [> 4.4624 = 7.4373 < 9.6686] w=0.3089 to align # Constraint # added constraint: constraint((T0374)A8.CB, (T0374)I46.CB) [> 4.1081 = 6.8468 < 8.9008] w=0.3070 to align # Constraint # added constraint: constraint((T0374)F118.CB, (T0374)V149.CB) [> 3.5808 = 5.9680 < 7.7584] w=0.3025 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)L42.CB) [> 4.0401 = 6.7335 < 8.7535] w=0.2977 to align # Constraint # added constraint: constraint((T0374)E48.CB, (T0374)Q69.CB) [> 3.9998 = 6.6663 < 8.6662] w=0.2912 to align # Constraint # added constraint: constraint((T0374)A139.CB, (T0374)Q153.CB) [> 4.1354 = 6.8924 < 8.9601] w=0.2885 to align # Constraint # added constraint: constraint((T0374)H142.CB, (T0374)L151.CB) [> 2.9930 = 4.9883 < 6.4848] w=0.2871 to align # Constraint # added constraint: constraint((T0374)T10.CB, (T0374)I46.CB) [> 3.6666 = 6.1109 < 7.9442] w=0.2860 to align # Constraint # added constraint: constraint((T0374)Q69.CB, (T0374)A104.CB) [> 4.1951 = 6.9918 < 9.0894] w=0.2836 to align # Constraint # added constraint: constraint((T0374)H57.CB, (T0374)V92.CB) [> 4.1646 = 6.9411 < 9.0234] w=0.2821 to align # Constraint # added constraint: constraint((T0374)F19.CB, (T0374)L62.CB) [> 4.4913 = 7.4855 < 9.7311] w=0.2746 to align # Constraint # added constraint: constraint((T0374)L125.CB, (T0374)M154.CB) [> 4.3414 = 7.2357 < 9.4063] w=0.2745 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)A33.CB) [> 3.9647 = 6.6078 < 8.5901] w=0.2745 to align # Constraint # added constraint: constraint((T0374)L13.CB, (T0374)A43.CB) [> 3.7664 = 6.2773 < 8.1604] w=0.2738 to align # Constraint # added constraint: constraint((T0374)A93.CB, (T0374)G124.CA) [> 4.4200 = 7.3667 < 9.5767] w=0.2732 to align # Constraint # added constraint: constraint((T0374)N66.CB, (T0374)M100.CB) [> 4.5584 = 7.5973 < 9.8765] w=0.2676 to align # Constraint # added constraint: constraint((T0374)A17.CB, (T0374)W35.CB) [> 3.8023 = 6.3372 < 8.2384] w=0.2612 to align # Constraint # added constraint: constraint((T0374)R23.CB, (T0374)V83.CB) [> 4.1817 = 6.9695 < 9.0603] w=0.2542 to align # Constraint # added constraint: constraint((T0374)G63.CA, (T0374)A93.CB) [> 4.5821 = 7.6368 < 9.9278] w=0.2542 to align # Constraint # added constraint: constraint((T0374)D12.CB, (T0374)F64.CB) [> 4.5806 = 7.6344 < 9.9247] w=0.2492 to align # Constraint # added constraint: constraint((T0374)K114.CB, (T0374)K156.CB) [> 4.6405 = 7.7342 < 10.0545] w=0.2465 to align # Constraint # added constraint: constraint((T0374)A17.CB, (T0374)F37.CB) [> 3.8188 = 6.3646 < 8.2740] w=0.2447 to align # Constraint # added constraint: constraint((T0374)G51.CA, (T0374)M100.CB) [> 4.3708 = 7.2846 < 9.4700] w=0.2432 to align # Constraint # added constraint: constraint((T0374)R23.CB, (T0374)N80.CB) [> 3.6483 = 6.0806 < 7.9047] w=0.2396 to align # Constraint # added constraint: constraint((T0374)Q2.CB, (T0374)H57.CB) [> 4.0886 = 6.8143 < 8.8586] w=0.2311 to align # Constraint # added constraint: constraint((T0374)M113.CB, (T0374)L158.CB) [> 3.7836 = 6.3060 < 8.1978] w=0.2311 to align # Constraint # added constraint: constraint((T0374)R105.CB, (T0374)L158.CB) [> 3.1301 = 5.2168 < 6.7818] w=0.2311 to align # Constraint # added constraint: constraint((T0374)A17.CB, (T0374)I34.CB) [> 4.1855 = 6.9759 < 9.0686] w=0.2299 to align # Constraint # added constraint: constraint((T0374)G63.CA, (T0374)M81.CB) [> 4.6439 = 7.7398 < 10.0618] w=0.2241 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)Y30.CB) [> 3.8696 = 6.4493 < 8.3841] w=0.2204 to align # Constraint # added constraint: constraint((T0374)E9.CB, (T0374)V54.CB) [> 4.5482 = 7.5803 < 9.8544] w=0.2190 to align # Constraint # added constraint: constraint((T0374)L78.CB, (T0374)A104.CB) [> 4.5385 = 7.5642 < 9.8335] w=0.2186 to align # Constraint # added constraint: constraint((T0374)L112.CB, (T0374)L158.CB) [> 3.9116 = 6.5194 < 8.4752] w=0.2171 to align # Constraint # added constraint: constraint((T0374)C76.CB, (T0374)L103.CB) [> 4.3616 = 7.2693 < 9.4500] w=0.2101 to align # Constraint # added constraint: constraint((T0374)V54.CB, (T0374)A65.CB) [> 4.6464 = 7.7440 < 10.0672] w=0.2031 to align # Constraint # added constraint: constraint((T0374)A8.CB, (T0374)L42.CB) [> 3.8421 = 6.4035 < 8.3246] w=0.2001 to align # Constraint # added constraint: constraint((T0374)Q60.CB, (T0374)A84.CB) [> 4.6007 = 7.6678 < 9.9682] w=0.1975 to align # Constraint # added constraint: constraint((T0374)G51.CA, (T0374)Q69.CB) [> 4.4138 = 7.3563 < 9.5632] w=0.1962 to align # Constraint # added constraint: constraint((T0374)A120.CB, (T0374)V149.CB) [> 4.1075 = 6.8457 < 8.8995] w=0.1961 to align # Constraint # added constraint: constraint((T0374)S4.CB, (T0374)G59.CA) [> 4.2906 = 7.1511 < 9.2964] w=0.1912 to align # Constraint # added constraint: constraint((T0374)A65.CB, (T0374)A93.CB) [> 4.5328 = 7.5547 < 9.8211] w=0.1891 to align # Constraint # added constraint: constraint((T0374)H5.CB, (T0374)A65.CB) [> 4.0610 = 6.7684 < 8.7989] w=0.1840 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)I34.CB) [> 3.3342 = 5.5569 < 7.2240] w=0.1809 to align # Constraint # added constraint: constraint((T0374)G18.CA, (T0374)V61.CB) [> 4.2691 = 7.1152 < 9.2498] w=0.1751 to align # Constraint # added constraint: constraint((T0374)A17.CB, (T0374)A33.CB) [> 3.9608 = 6.6013 < 8.5816] w=0.1728 to align # Constraint # added constraint: constraint((T0374)A45.CB, (T0374)Y68.CB) [> 3.9992 = 6.6653 < 8.6649] w=0.1695 to align # Constraint # added constraint: constraint((T0374)E14.CB, (T0374)V39.CB) [> 3.9100 = 6.5166 < 8.4716] w=0.1687 to align # Constraint # added constraint: constraint((T0374)C29.CB, (T0374)F118.CB) [> 4.0160 = 6.6934 < 8.7014] w=0.1681 to align # Constraint # added constraint: constraint((T0374)R88.CB, (T0374)A123.CB) [> 4.5127 = 7.5211 < 9.7774] w=0.1681 to align # Constraint # added constraint: constraint((T0374)S116.CB, (T0374)H142.CB) [> 4.2309 = 7.0515 < 9.1670] w=0.1681 to align # Constraint # added constraint: constraint((T0374)L3.CB, (T0374)L90.CB) [> 4.1919 = 6.9865 < 9.0824] w=0.1681 to align # Constraint # added constraint: constraint((T0374)A45.CB, (T0374)N80.CB) [> 4.2425 = 7.0709 < 9.1922] w=0.1680 to align # Constraint # added constraint: constraint((T0374)F27.CB, (T0374)N121.CB) [> 4.1891 = 6.9819 < 9.0765] w=0.1630 to align # Constraint # added constraint: constraint((T0374)L78.CB, (T0374)S116.CB) [> 4.0967 = 6.8278 < 8.8762] w=0.1611 to align # Constraint # added constraint: constraint((T0374)L13.CB, (T0374)S38.CB) [> 3.3895 = 5.6491 < 7.3439] w=0.1581 to align # Constraint # added constraint: constraint((T0374)Q60.CB, (T0374)A87.CB) [> 4.5731 = 7.6218 < 9.9083] w=0.1560 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)F37.CB) [> 3.9200 = 6.5333 < 8.4933] w=0.1548 to align # Constraint # added constraint: constraint((T0374)V16.CB, (T0374)G63.CA) [> 4.3293 = 7.2154 < 9.3801] w=0.1541 to align # Constraint # added constraint: constraint((T0374)Y28.CB, (T0374)F118.CB) [> 3.6103 = 6.0172 < 7.8224] w=0.1471 to align # Constraint # added constraint: constraint((T0374)A120.CB, (T0374)A150.CB) [> 4.4630 = 7.4383 < 9.6698] w=0.1471 to align # Constraint # added constraint: constraint((T0374)S52.CB, (T0374)N80.CB) [> 4.6322 = 7.7204 < 10.0365] w=0.1452 to align # Constraint # added constraint: constraint((T0374)S4.CB, (T0374)V54.CB) [> 4.0683 = 6.7806 < 8.8147] w=0.1434 to align # Constraint # added constraint: constraint((T0374)H5.CB, (T0374)M100.CB) [> 4.2488 = 7.0813 < 9.2057] w=0.1420 to align # Constraint # added constraint: constraint((T0374)L26.CB, (T0374)M82.CB) [> 3.7359 = 6.2266 < 8.0945] w=0.1401 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)W35.CB) [> 3.6941 = 6.1568 < 8.0039] w=0.1345 to align # Constraint # added constraint: constraint((T0374)S116.CB, (T0374)R141.CB) [> 4.1518 = 6.9197 < 8.9956] w=0.1282 to align # Constraint # added constraint: constraint((T0374)F27.CB, (T0374)F118.CB) [> 3.6906 = 6.1510 < 7.9963] w=0.1280 to align # Constraint # added constraint: constraint((T0374)R136.CB, (T0374)I152.CB) [> 4.3992 = 7.3320 < 9.5317] w=0.1268 to align # Constraint # added constraint: constraint((T0374)S4.CB, (T0374)D58.CB) [> 3.9740 = 6.6234 < 8.6104] w=0.1261 to align # Constraint # added constraint: constraint((T0374)C117.CB, (T0374)L127.CB) [> 4.6579 = 7.7632 < 10.0921] w=0.1226 to align # Constraint # added constraint: constraint((T0374)V16.CB, (T0374)N66.CB) [> 4.4359 = 7.3932 < 9.6112] w=0.1212 to align # Constraint # added constraint: constraint((T0374)L62.CB, (T0374)L90.CB) [> 4.4857 = 7.4762 < 9.7190] w=0.1205 to align # Constraint # added constraint: constraint((T0374)C117.CB, (T0374)Q153.CB) [> 4.2815 = 7.1359 < 9.2767] w=0.1191 to align # Constraint # added constraint: constraint((T0374)N80.CB, (T0374)S116.CB) [> 4.5824 = 7.6374 < 9.9286] w=0.1191 to align # Constraint # added constraint: constraint((T0374)C29.CB, (T0374)M82.CB) [> 3.8299 = 6.3831 < 8.2980] w=0.1191 to align # Constraint # added constraint: constraint((T0374)A17.CB, (T0374)Q41.CB) [> 3.9637 = 6.6062 < 8.5880] w=0.1190 to align # Constraint # added constraint: constraint((T0374)F27.CB, (T0374)M82.CB) [> 3.5694 = 5.9490 < 7.7337] w=0.1121 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)Q41.CB) [> 4.1328 = 6.8881 < 8.9545] w=0.1120 to align # Constraint # added constraint: constraint((T0374)G51.CA, (T0374)A65.CB) [> 4.3078 = 7.1796 < 9.3335] w=0.1105 to align # Constraint # added constraint: constraint((T0374)H72.CB, (T0374)K114.CB) [> 4.1394 = 6.8990 < 8.9686] w=0.1051 to align # Constraint # added constraint: constraint((T0374)M81.CB, (T0374)G124.CA) [> 4.6167 = 7.6945 < 10.0028] w=0.1051 to align # Constraint # added constraint: constraint((T0374)L3.CB, (T0374)A87.CB) [> 4.5189 = 7.5315 < 9.7910] w=0.1051 to align # Constraint # added constraint: constraint((T0374)C117.CB, (T0374)Y133.CB) [> 4.4495 = 7.4158 < 9.6405] w=0.1051 to align # Constraint # added constraint: constraint((T0374)L62.CB, (T0374)A86.CB) [> 4.5761 = 7.6268 < 9.9148] w=0.1051 to align # Constraint # added constraint: constraint((T0374)G79.CA, (T0374)K114.CB) [> 4.3793 = 7.2989 < 9.4885] w=0.1050 to align # Constraint # added constraint: constraint((T0374)G73.CA, (T0374)L112.CB) [> 4.2215 = 7.0358 < 9.1466] w=0.1034 to align # Constraint # added constraint: constraint((T0374)S52.CB, (T0374)M100.CB) [> 4.1689 = 6.9482 < 9.0326] w=0.1014 to align # Constraint # added constraint: constraint((T0374)R6.CB, (T0374)S52.CB) [> 3.9054 = 6.5090 < 8.4618] w=0.1014 to align # Constraint # added constraint: constraint((T0374)H5.CB, (T0374)S52.CB) [> 3.7865 = 6.3108 < 8.2040] w=0.1014 to align # Constraint # added constraint: constraint((T0374)A77.CB, (T0374)A104.CB) [> 3.7861 = 6.3101 < 8.2031] w=0.0981 to align # Constraint # added constraint: constraint((T0374)R50.CB, (T0374)C76.CB) [> 4.2920 = 7.1533 < 9.2993] w=0.0981 to align # Constraint # added constraint: constraint((T0374)Y30.CB, (T0374)N80.CB) [> 4.3503 = 7.2506 < 9.4258] w=0.0980 to align # Constraint # added constraint: constraint((T0374)D74.CB, (T0374)Y108.CB) [> 4.0415 = 6.7358 < 8.7566] w=0.0980 to align # Constraint # added constraint: constraint((T0374)G79.CA, (T0374)M100.CB) [> 4.1815 = 6.9692 < 9.0599] w=0.0911 to align # Constraint # added constraint: constraint((T0374)I115.CB, (T0374)I152.CB) [> 3.9025 = 6.5042 < 8.4554] w=0.0910 to align # Constraint # added constraint: constraint((T0374)C76.CB, (T0374)Y108.CB) [> 3.7793 = 6.2989 < 8.1885] w=0.0840 to align # Constraint # added constraint: constraint((T0374)H72.CB, (T0374)R111.CB) [> 4.0739 = 6.7899 < 8.8268] w=0.0840 to align # Constraint # added constraint: constraint((T0374)Y128.CB, (T0374)I152.CB) [> 3.8623 = 6.4371 < 8.3682] w=0.0840 to align # Constraint # added constraint: constraint((T0374)E9.CB, (T0374)L42.CB) [> 4.1458 = 6.9097 < 8.9825] w=0.0811 to align # Constraint # added constraint: constraint((T0374)Y30.CB, (T0374)M82.CB) [> 4.0429 = 6.7381 < 8.7596] w=0.0770 to align # Constraint # added constraint: constraint((T0374)T10.CB, (T0374)W35.CB) [> 4.4380 = 7.3967 < 9.6157] w=0.0734 to align # Constraint # added constraint: constraint((T0374)A77.CB, (T0374)A110.CB) [> 3.2192 = 5.3653 < 6.9748] w=0.0700 to align # Constraint # added constraint: constraint((T0374)Y30.CB, (T0374)F118.CB) [> 3.7906 = 6.3177 < 8.2130] w=0.0683 to align # Constraint # added constraint: constraint((T0374)G51.CA, (T0374)F64.CB) [> 4.0651 = 6.7752 < 8.8077] w=0.0664 to align # Constraint # added constraint: constraint((T0374)A17.CB, (T0374)Y30.CB) [> 3.4970 = 5.8283 < 7.5767] w=0.0664 to align # Constraint # added constraint: constraint((T0374)Y28.CB, (T0374)V149.CB) [> 3.8232 = 6.3719 < 8.2835] w=0.0637 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)P31.CB) [> 3.7981 = 6.3301 < 8.2291] w=0.0637 to align # Constraint # added constraint: constraint((T0374)A77.CB, (T0374)L112.CB) [> 4.4858 = 7.4764 < 9.7193] w=0.0630 to align # Constraint # added constraint: constraint((T0374)A45.CB, (T0374)G79.CA) [> 3.9612 = 6.6021 < 8.5827] w=0.0630 to align # Constraint # added constraint: constraint((T0374)F37.CB, (T0374)N80.CB) [> 4.0678 = 6.7796 < 8.8135] w=0.0567 to align # Constraint # added constraint: constraint((T0374)C117.CB, (T0374)R148.CB) [> 3.7293 = 6.2155 < 8.0802] w=0.0567 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)K32.CB) [> 3.7471 = 6.2452 < 8.1187] w=0.0567 to align # Constraint # added constraint: constraint((T0374)Q71.CB, (T0374)A110.CB) [> 4.2907 = 7.1512 < 9.2966] w=0.0560 to align # Constraint # added constraint: constraint((T0374)I34.CB, (T0374)N80.CB) [> 3.8844 = 6.4741 < 8.4163] w=0.0497 to align # Constraint # added constraint: constraint((T0374)Q2.CB, (T0374)V56.CB) [> 3.2063 = 5.3438 < 6.9470] w=0.0490 to align # Constraint # added constraint: constraint((T0374)Q2.CB, (T0374)Y95.CB) [> 3.7926 = 6.3209 < 8.2172] w=0.0490 to align # Constraint # added constraint: constraint((T0374)F27.CB, (T0374)N80.CB) [> 4.0520 = 6.7533 < 8.7793] w=0.0490 to align # Constraint # added constraint: constraint((T0374)S116.CB, (T0374)A150.CB) [> 3.9890 = 6.6483 < 8.6428] w=0.0490 to align # Constraint # added constraint: constraint((T0374)K114.CB, (T0374)I152.CB) [> 4.0045 = 6.6741 < 8.6764] w=0.0490 to align # Constraint # added constraint: constraint((T0374)S116.CB, (T0374)V149.CB) [> 3.2959 = 5.4931 < 7.1411] w=0.0427 to align # Constraint # added constraint: constraint((T0374)H142.CB, (T0374)Q153.CB) [> 3.9579 = 6.5965 < 8.5754] w=0.0420 to align # Constraint # added constraint: constraint((T0374)V83.CB, (T0374)L127.CB) [> 4.4558 = 7.4263 < 9.6542] w=0.0420 to align # Constraint # added constraint: constraint((T0374)I115.CB, (T0374)L127.CB) [> 4.1309 = 6.8848 < 8.9503] w=0.0420 to align # Constraint # added constraint: constraint((T0374)F27.CB, (T0374)A123.CB) [> 3.7817 = 6.3028 < 8.1936] w=0.0420 to align # Constraint # added constraint: constraint((T0374)I115.CB, (T0374)G124.CA) [> 4.4879 = 7.4798 < 9.7237] w=0.0420 to align # Constraint # added constraint: constraint((T0374)S4.CB, (T0374)T53.CB) [> 4.3531 = 7.2551 < 9.4316] w=0.0420 to align # Constraint # added constraint: constraint((T0374)E9.CB, (T0374)S52.CB) [> 4.4105 = 7.3509 < 9.5562] w=0.0420 to align # Constraint # added constraint: constraint((T0374)G132.CA, (T0374)M154.CB) [> 3.7401 = 6.2334 < 8.1035] w=0.0420 to align # Constraint # added constraint: constraint((T0374)Y28.CB, (T0374)S38.CB) [> 4.2718 = 7.1196 < 9.2555] w=0.0370 to align # Constraint # added constraint: constraint((T0374)K32.CB, (T0374)G79.CA) [> 4.2205 = 7.0342 < 9.1445] w=0.0357 to align # Constraint # added constraint: constraint((T0374)C29.CB, (T0374)C117.CB) [> 4.3602 = 7.2671 < 9.4472] w=0.0350 to align # Constraint # added constraint: constraint((T0374)C29.CB, (T0374)V149.CB) [> 4.3144 = 7.1907 < 9.3479] w=0.0350 to align # Constraint # added constraint: constraint((T0374)P31.CB, (T0374)M82.CB) [> 3.9907 = 6.6511 < 8.6465] w=0.0350 to align # Constraint # added constraint: constraint((T0374)Q2.CB, (T0374)A55.CB) [> 4.4206 = 7.3677 < 9.5780] w=0.0350 to align # Constraint # added constraint: constraint((T0374)L26.CB, (T0374)V83.CB) [> 4.4492 = 7.4153 < 9.6399] w=0.0350 to align # Constraint # added constraint: constraint((T0374)F118.CB, (T0374)R141.CB) [> 4.0522 = 6.7537 < 8.7797] w=0.0350 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)C29.CB) [> 3.9481 = 6.5802 < 8.5542] w=0.0350 to align # Constraint # added constraint: constraint((T0374)W70.CB, (T0374)Y108.CB) [> 4.3044 = 7.1740 < 9.3262] w=0.0333 to align # Constraint # added constraint: constraint((T0374)T53.CB, (T0374)L62.CB) [> 4.2259 = 7.0432 < 9.1561] w=0.0313 to align # Constraint # added constraint: constraint((T0374)D74.CB, (T0374)R136.CB) [> 4.5298 = 7.5496 < 9.8145] w=0.0294 to align # Constraint # added constraint: constraint((T0374)A77.CB, (T0374)R111.CB) [> 4.5330 = 7.5549 < 9.8214] w=0.0280 to align # Constraint # added constraint: constraint((T0374)Y30.CB, (T0374)N121.CB) [> 4.1277 = 6.8796 < 8.9435] w=0.0280 to align # Constraint # added constraint: constraint((T0374)Y30.CB, (T0374)C117.CB) [> 4.5996 = 7.6660 < 9.9658] w=0.0280 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)V54.CB) [> 3.8467 = 6.4112 < 8.3346] w=0.0280 to align # Constraint # added constraint: constraint((T0374)P20.CB, (T0374)V61.CB) [> 3.1563 = 5.2605 < 6.8386] w=0.0280 to align # Constraint # added constraint: constraint((T0374)L131.CB, (T0374)M154.CB) [> 4.3925 = 7.3209 < 9.5171] w=0.0280 to align # Constraint # added constraint: constraint((T0374)A17.CB, (T0374)P31.CB) [> 4.2873 = 7.1455 < 9.2892] w=0.0250 to align # Constraint # added constraint: constraint((T0374)Q69.CB, (T0374)K114.CB) [> 4.5957 = 7.6595 < 9.9574] w=0.0210 to align # Constraint # added constraint: constraint((T0374)L125.CB, (T0374)D155.CB) [> 4.2868 = 7.1446 < 9.2880] w=0.0210 to align # Constraint # added constraint: constraint((T0374)Q60.CB, (T0374)A86.CB) [> 4.6511 = 7.7519 < 10.0774] w=0.0210 to align # Constraint # added constraint: constraint((T0374)L26.CB, (T0374)N80.CB) [> 4.7635 = 7.9391 < 10.3209] w=0.0210 to align # Constraint # added constraint: constraint((T0374)M82.CB, (T0374)G124.CA) [> 4.7580 = 7.9300 < 10.3089] w=0.0210 to align # Constraint # added constraint: constraint((T0374)A17.CB, (T0374)Y28.CB) [> 3.7681 = 6.2802 < 8.1643] w=0.0210 to align # Constraint # added constraint: constraint((T0374)V83.CB, (T0374)G124.CA) [> 4.5047 = 7.5078 < 9.7601] w=0.0210 to align # Constraint # added constraint: constraint((T0374)M1.CB, (T0374)A55.CB) [> 4.0339 = 6.7232 < 8.7401] w=0.0210 to align # Constraint # added constraint: constraint((T0374)M1.CB, (T0374)V56.CB) [> 4.3221 = 7.2034 < 9.3645] w=0.0210 to align # Constraint # added constraint: constraint((T0374)M1.CB, (T0374)L62.CB) [> 4.0241 = 6.7069 < 8.7189] w=0.0210 to align # Constraint # added constraint: constraint((T0374)M1.CB, (T0374)L90.CB) [> 4.6391 = 7.7319 < 10.0514] w=0.0210 to align # Constraint # added constraint: constraint((T0374)A17.CB, (T0374)F64.CB) [> 4.6456 = 7.7428 < 10.0656] w=0.0210 to align # Constraint # added constraint: constraint((T0374)C29.CB, (T0374)S38.CB) [> 4.0048 = 6.6746 < 8.6770] w=0.0210 to align # Constraint # added constraint: constraint((T0374)R6.CB, (T0374)F64.CB) [> 4.2986 = 7.1643 < 9.3136] w=0.0210 to align # Constraint # added constraint: constraint((T0374)Q69.CB, (T0374)G79.CA) [> 4.5769 = 7.6282 < 9.9167] w=0.0210 to align # Constraint # added constraint: constraint((T0374)A122.CB, (T0374)P135.CB) [> 3.9894 = 6.6490 < 8.6437] w=0.0192 to align # Constraint # added constraint: constraint((T0374)A33.CB, (T0374)G79.CA) [> 4.4061 = 7.3434 < 9.5465] w=0.0147 to align # Constraint # added constraint: constraint((T0374)V54.CB, (T0374)V83.CB) [> 4.5018 = 7.5030 < 9.7539] w=0.0140 to align # Constraint # added constraint: constraint((T0374)W70.CB, (T0374)L112.CB) [> 4.1805 = 6.9675 < 9.0578] w=0.0140 to align # Constraint # added constraint: constraint((T0374)G11.CA, (T0374)C29.CB) [> 4.5856 = 7.6427 < 9.9356] w=0.0140 to align # Constraint # added constraint: constraint((T0374)L26.CB, (T0374)F118.CB) [> 4.3257 = 7.2096 < 9.3724] w=0.0140 to align # Constraint # added constraint: constraint((T0374)Y28.CB, (T0374)M82.CB) [> 3.1744 = 5.2908 < 6.8780] w=0.0140 to align # Constraint # added constraint: constraint((T0374)F75.CB, (T0374)R148.CB) [> 4.7661 = 7.9435 < 10.3266] w=0.0140 to align # Constraint # added constraint: constraint((T0374)A17.CB, (T0374)N80.CB) [> 4.6634 = 7.7723 < 10.1039] w=0.0140 to align # Constraint # added constraint: constraint((T0374)H5.CB, (T0374)F67.CB) [> 4.7699 = 7.9499 < 10.3348] w=0.0140 to align # Constraint # added constraint: constraint((T0374)M81.CB, (T0374)S116.CB) [> 4.0924 = 6.8207 < 8.8668] w=0.0140 to align # Constraint # added constraint: constraint((T0374)F27.CB, (T0374)F64.CB) [> 4.6094 = 7.6824 < 9.9871] w=0.0140 to align # Constraint # added constraint: constraint((T0374)F27.CB, (T0374)M81.CB) [> 3.5831 = 5.9719 < 7.7634] w=0.0140 to align # Constraint # added constraint: constraint((T0374)M1.CB, (T0374)V99.CB) [> 4.4465 = 7.4109 < 9.6342] w=0.0122 to align # Constraint # added constraint: constraint((T0374)S52.CB, (T0374)L62.CB) [> 4.5872 = 7.6453 < 9.9389] w=0.0070 to align # Constraint # added constraint: constraint((T0374)F64.CB, (T0374)G79.CA) [> 4.7779 = 7.9631 < 10.3520] w=0.0070 to align # Constraint # added constraint: constraint((T0374)L3.CB, (T0374)M100.CB) [> 4.7000 = 7.8333 < 10.1833] w=0.0070 to align # Constraint # added constraint: constraint((T0374)G132.CA, (T0374)L151.CB) [> 3.2920 = 5.4867 < 7.1327] w=0.0070 to align # Constraint # added constraint: constraint((T0374)L131.CB, (T0374)D155.CB) [> 4.2986 = 7.1643 < 9.3136] w=0.0070 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0374/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0374/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 30 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 147 # 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 64 # 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 151 # 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 151 # 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 121 # 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 159 # 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 156 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # 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 10 # 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 # 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 80 # 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 108 # 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 158 # 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 T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 143 # 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 T0374 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 T0374 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 T0374 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 T0374 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 159 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 156 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 159 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 144 # 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 154 # 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 80 # 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 123 # 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 64 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 115 # 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 138 # 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 158 # 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 138 # 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 78 # 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 T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 T0374 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 # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 394, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 396, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz # WARNING: incomplete conformation T0374 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 156 # 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 159 # 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 159 # 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 159 # 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 159 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 61 # 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 97 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 # Found a chain break before 33 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 T0374 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 42 # 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 26 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 114 # 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 155 # 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 35 # 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 # Found a chain break before 158 # copying to AlignedFragments data structure # 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 111 # 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 155 # 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 112 # 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 142 # 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 # 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 70 # 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 159 # 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 159 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 28 # 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 151 # 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 152 # 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 143 # 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 151 # 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 146 # 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 137 # 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 156 # 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 73 # 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 T0374 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 142 # 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 109 # 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 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # 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 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # 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 114 # 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 143 # 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 29 # 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 159 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 143 # 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 144 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # 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 73 # 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 71 # 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 137 # 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 146 # 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 111 # 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 30 # 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 86 # 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 25 # 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 49 # 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 86 # 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 Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 370, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 372, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 374, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 376, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz # WARNING: incomplete conformation T0374 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 T0374 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 T0374 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 385, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 387, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 513, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 515, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 516, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz # WARNING: incomplete conformation T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 Skipped atom 34, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 36, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 154 # 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 T0374 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 T0374 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 T0374 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 T0374 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 109 # 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 114 # 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 86 # 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 153 # 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 153 # 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 147 # 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 153 # 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 144 # 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 33 # 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 48 # 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 142 # 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 114 # 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 49 # 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 153 # 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 153 # 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 T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 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 T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0374 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 T0374 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 Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 366, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 368, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 370, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 372, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz # WARNING: incomplete conformation T0374 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 T0374 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 143 # 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 143 # 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 148 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # 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 T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 T0374 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 374, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 376, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz # WARNING: incomplete conformation T0374 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 T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 50 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 86 # 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 50 # 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 50 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0374)Q153.O and (T0374)M154.N only 0.000 apart, marking (T0374)M154.N as missing # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0374)Q134.O and (T0374)P135.N only 0.000 apart, marking (T0374)P135.N as missing # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 T0374 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 T0374 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 T0374 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # 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 T0374 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 T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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 T0374 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 T0374 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0374 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: atoms too close: (T0374)L26.N and (T0374)F27.N only 0.000 apart, marking (T0374)F27.N as missing WARNING: atoms too close: (T0374)L26.CA and (T0374)F27.CA only 0.000 apart, marking (T0374)F27.CA as missing WARNING: atoms too close: (T0374)L26.CB and (T0374)F27.CB only 0.000 apart, marking (T0374)F27.CB as missing WARNING: atoms too close: (T0374)L26.O and (T0374)F27.O only 0.000 apart, marking (T0374)F27.O as missing WARNING: atoms too close: (T0374)L26.C and (T0374)F27.C only 0.000 apart, marking (T0374)F27.C as missing WARNING: atoms too close: (T0374)F27.N and (T0374)S52.N only 0.000 apart, marking (T0374)F27.N as missing WARNING: atoms too close: (T0374)L26.N and (T0374)S52.N only 0.000 apart, marking (T0374)S52.N as missing WARNING: atoms too close: (T0374)F27.CA and (T0374)S52.CA only 0.000 apart, marking (T0374)S52.CA as missing WARNING: atoms too close: (T0374)L26.CA and (T0374)S52.CA only 0.000 apart, marking (T0374)S52.CA as missing WARNING: atoms too close: (T0374)F27.CB and (T0374)S52.CB only 0.000 apart, marking (T0374)S52.CB as missing WARNING: atoms too close: (T0374)L26.CB and (T0374)S52.CB only 0.000 apart, marking (T0374)S52.CB as missing WARNING: atoms too close: (T0374)F27.O and (T0374)S52.O only 0.000 apart, marking (T0374)S52.O as missing WARNING: atoms too close: (T0374)L26.O and (T0374)S52.O only 0.000 apart, marking (T0374)S52.O as missing WARNING: atoms too close: (T0374)F27.C and (T0374)S52.C only 0.000 apart, marking (T0374)S52.C as missing WARNING: atoms too close: (T0374)L26.C and (T0374)S52.C only 0.000 apart, marking (T0374)S52.C as missing WARNING: atoms too close: (T0374)S52.N and (T0374)T53.N only 0.000 apart, marking (T0374)S52.N as missing WARNING: atoms too close: (T0374)F27.N and (T0374)T53.N only 0.000 apart, marking (T0374)F27.N as missing WARNING: atoms too close: (T0374)L26.N and (T0374)T53.N only 0.000 apart, marking (T0374)T53.N as missing WARNING: atoms too close: (T0374)S52.CA and (T0374)T53.CA only 0.000 apart, marking (T0374)T53.CA as missing WARNING: atoms too close: (T0374)F27.CA and (T0374)T53.CA only 0.000 apart, marking (T0374)T53.CA as missing WARNING: atoms too close: (T0374)L26.CA and (T0374)T53.CA only 0.000 apart, marking (T0374)T53.CA as missing WARNING: atoms too close: (T0374)S52.CB and (T0374)T53.CB only 0.000 apart, marking (T0374)T53.CB as missing WARNING: atoms too close: (T0374)F27.CB and (T0374)T53.CB only 0.000 apart, marking (T0374)T53.CB as missing WARNING: atoms too close: (T0374)L26.CB and (T0374)T53.CB only 0.000 apart, marking (T0374)T53.CB as missing WARNING: atoms too close: (T0374)S52.OG and (T0374)T53.OG1 only 0.000 apart, marking (T0374)T53.OG1 as missing WARNING: atoms too close: (T0374)S52.O and (T0374)T53.O only 0.000 apart, marking (T0374)T53.O as missing WARNING: atoms too close: (T0374)F27.O and (T0374)T53.O only 0.000 apart, marking (T0374)T53.O as missing WARNING: atoms too close: (T0374)L26.O and (T0374)T53.O only 0.000 apart, marking (T0374)T53.O as missing WARNING: atoms too close: (T0374)S52.C and (T0374)T53.C only 0.000 apart, marking (T0374)T53.C as missing WARNING: atoms too close: (T0374)F27.C and (T0374)T53.C only 0.000 apart, marking (T0374)T53.C as missing WARNING: atoms too close: (T0374)L26.C and (T0374)T53.C only 0.000 apart, marking (T0374)T53.C as missing WARNING: atoms too close: (T0374)T53.N and (T0374)V54.N only 0.000 apart, marking (T0374)T53.N as missing WARNING: atoms too close: (T0374)S52.N and (T0374)V54.N only 0.000 apart, marking (T0374)S52.N as missing WARNING: atoms too close: (T0374)F27.N and (T0374)V54.N only 0.000 apart, marking (T0374)F27.N as missing WARNING: atoms too close: (T0374)L26.N and (T0374)V54.N only 0.000 apart, marking (T0374)V54.N as missing WARNING: atoms too close: (T0374)T53.CA and (T0374)V54.CA only 0.000 apart, marking (T0374)V54.CA as missing WARNING: atoms too close: (T0374)S52.CA and (T0374)V54.CA only 0.000 apart, marking (T0374)V54.CA as missing WARNING: atoms too close: (T0374)F27.CA and (T0374)V54.CA only 0.000 apart, marking (T0374)V54.CA as missing WARNING: atoms too close: (T0374)L26.CA and (T0374)V54.CA only 0.000 apart, marking (T0374)V54.CA as missing WARNING: atoms too close: (T0374)T53.CB and (T0374)V54.CB only 0.000 apart, marking (T0374)V54.CB as missing WARNING: atoms too close: (T0374)S52.CB and (T0374)V54.CB only 0.000 apart, marking (T0374)V54.CB as missing WARNING: atoms too close: (T0374)F27.CB and (T0374)V54.CB only 0.000 apart, marking (T0374)V54.CB as missing WARNING: atoms too close: (T0374)L26.CB and (T0374)V54.CB only 0.000 apart, marking (T0374)V54.CB as missing WARNING: atoms too close: (T0374)T53.O and (T0374)V54.O only 0.000 apart, marking (T0374)V54.O as missing WARNING: atoms too close: (T0374)S52.O and (T0374)V54.O only 0.000 apart, marking (T0374)V54.O as missing WARNING: atoms too close: (T0374)F27.O and (T0374)V54.O only 0.000 apart, marking (T0374)V54.O as missing WARNING: atoms too close: (T0374)L26.O and (T0374)V54.O only 0.000 apart, marking (T0374)V54.O as missing WARNING: atoms too close: (T0374)T53.C and (T0374)V54.C only 0.000 apart, marking (T0374)V54.C as missing WARNING: atoms too close: (T0374)S52.C and (T0374)V54.C only 0.000 apart, marking (T0374)V54.C as missing WARNING: atoms too close: (T0374)F27.C and (T0374)V54.C only 0.000 apart, marking (T0374)V54.C as missing WARNING: atoms too close: (T0374)L26.C and (T0374)V54.C only 0.000 apart, marking (T0374)V54.C as missing WARNING: atoms too close: (T0374)V54.N and (T0374)A55.N only 0.000 apart, marking (T0374)V54.N as missing WARNING: atoms too close: (T0374)T53.N and (T0374)A55.N only 0.000 apart, marking (T0374)T53.N as missing WARNING: atoms too close: (T0374)S52.N and (T0374)A55.N only 0.000 apart, marking (T0374)S52.N as missing WARNING: atoms too close: (T0374)F27.N and (T0374)A55.N only 0.000 apart, marking (T0374)F27.N as missing WARNING: atoms too close: (T0374)L26.N and (T0374)A55.N only 0.000 apart, marking (T0374)A55.N as missing WARNING: atoms too close: (T0374)V54.CA and (T0374)A55.CA only 0.000 apart, marking (T0374)A55.CA as missing WARNING: atoms too close: (T0374)T53.CA and (T0374)A55.CA only 0.000 apart, marking (T0374)A55.CA as missing WARNING: atoms too close: (T0374)S52.CA and (T0374)A55.CA only 0.000 apart, marking (T0374)A55.CA as missing WARNING: atoms too close: (T0374)F27.CA and (T0374)A55.CA only 0.000 apart, marking (T0374)A55.CA as missing WARNING: atoms too close: (T0374)L26.CA and (T0374)A55.CA only 0.000 apart, marking (T0374)A55.CA as missing WARNING: atoms too close: (T0374)V54.CB and (T0374)A55.CB only 0.000 apart, marking (T0374)A55.CB as missing WARNING: atoms too close: (T0374)T53.CB and (T0374)A55.CB only 0.000 apart, marking (T0374)A55.CB as missing WARNING: atoms too close: (T0374)S52.CB and (T0374)A55.CB only 0.000 apart, marking (T0374)A55.CB as missing WARNING: atoms too close: (T0374)F27.CB and (T0374)A55.CB only 0.000 apart, marking (T0374)A55.CB as missing WARNING: atoms too close: (T0374)L26.CB and (T0374)A55.CB only 0.000 apart, marking (T0374)A55.CB as missing WARNING: atoms too close: (T0374)V54.O and (T0374)A55.O only 0.000 apart, marking (T0374)A55.O as missing WARNING: atoms too close: (T0374)T53.O and (T0374)A55.O only 0.000 apart, marking (T0374)A55.O as missing WARNING: atoms too close: (T0374)S52.O and (T0374)A55.O only 0.000 apart, marking (T0374)A55.O as missing WARNING: atoms too close: (T0374)F27.O and (T0374)A55.O only 0.000 apart, marking (T0374)A55.O as missing WARNING: atoms too close: (T0374)L26.O and (T0374)A55.O only 0.000 apart, marking (T0374)A55.O as missing WARNING: atoms too close: (T0374)V54.C and (T0374)A55.C only 0.000 apart, marking (T0374)A55.C as missing WARNING: atoms too close: (T0374)T53.C and (T0374)A55.C only 0.000 apart, marking (T0374)A55.C as missing WARNING: atoms too close: (T0374)S52.C and (T0374)A55.C only 0.000 apart, marking (T0374)A55.C as missing WARNING: atoms too close: (T0374)F27.C and (T0374)A55.C only 0.000 apart, marking (T0374)A55.C as missing WARNING: atoms too close: (T0374)L26.C and (T0374)A55.C only 0.000 apart, marking (T0374)A55.C as missing WARNING: atoms too close: (T0374)A55.N and (T0374)V56.N only 0.000 apart, marking (T0374)A55.N as missing WARNING: atoms too close: (T0374)V54.N and (T0374)V56.N only 0.000 apart, marking (T0374)V54.N as missing WARNING: atoms too close: (T0374)T53.N and (T0374)V56.N only 0.000 apart, marking (T0374)T53.N as missing WARNING: atoms too close: (T0374)S52.N and (T0374)V56.N only 0.000 apart, marking (T0374)S52.N as missing WARNING: atoms too close: (T0374)F27.N and (T0374)V56.N only 0.000 apart, marking (T0374)F27.N as missing WARNING: atoms too close: (T0374)L26.N and (T0374)V56.N only 0.000 apart, marking (T0374)V56.N as missing WARNING: atoms too close: (T0374)A55.CA and (T0374)V56.CA only 0.000 apart, marking (T0374)V56.CA as missing WARNING: atoms too close: (T0374)V54.CA and (T0374)V56.CA only 0.000 apart, marking (T0374)V56.CA as missing WARNING: atoms too close: (T0374)T53.CA and (T0374)V56.CA only 0.000 apart, marking (T0374)V56.CA as missing WARNING: atoms too close: (T0374)S52.CA and (T0374)V56.CA only 0.000 apart, marking (T0374)V56.CA as missing WARNING: atoms too close: (T0374)F27.CA and (T0374)V56.CA only 0.000 apart, marking (T0374)V56.CA as missing WARNING: atoms too close: (T0374)L26.CA and (T0374)V56.CA only 0.000 apart, marking (T0374)V56.CA as missing WARNING: atoms too close: (T0374)A55.CB and (T0374)V56.CB only 0.000 apart, marking (T0374)V56.CB as missing WARNING: atoms too close: (T0374)V54.CB and (T0374)V56.CB only 0.000 apart, marking (T0374)V56.CB as missing WARNING: atoms too close: (T0374)T53.CB and (T0374)V56.CB only 0.000 apart, marking (T0374)V56.CB as missing WARNING: atoms too close: (T0374)S52.CB and (T0374)V56.CB only 0.000 apart, marking (T0374)V56.CB as missing WARNING: atoms too close: (T0374)F27.CB and (T0374)V56.CB only 0.000 apart, marking (T0374)V56.CB as missing WARNING: atoms too close: (T0374)L26.CB and (T0374)V56.CB only 0.000 apart, marking (T0374)V56.CB as missing WARNING: atoms too close: (T0374)A55.O and (T0374)V56.O only 0.000 apart, marking (T0374)V56.O as missing WARNING: atoms too close: (T0374)V54.O and (T0374)V56.O only 0.000 apart, marking (T0374)V56.O as missing WARNING: atoms too close: (T0374)T53.O and (T0374)V56.O only 0.000 apart, marking (T0374)V56.O as missing WARNING: atoms too close: (T0374)S52.O and (T0374)V56.O only 0.000 apart, marking (T0374)V56.O as missing WARNING: atoms too close: (T0374)F27.O and (T0374)V56.O only 0.000 apart, marking (T0374)V56.O as missing WARNING: atoms too close: (T0374)L26.O and (T0374)V56.O only 0.000 apart, marking (T0374)V56.O as missing WARNING: atoms too close: (T0374)A55.C and (T0374)V56.C only 0.000 apart, marking (T0374)V56.C as missing WARNING: atoms too close: (T0374)V54.C and (T0374)V56.C only 0.000 apart, marking (T0374)V56.C as missing WARNING: atoms too close: (T0374)T53.C and (T0374)V56.C only 0.000 apart, marking (T0374)V56.C as missing WARNING: atoms too close: (T0374)S52.C and (T0374)V56.C only 0.000 apart, marking (T0374)V56.C as missing WARNING: atoms too close: (T0374)F27.C and (T0374)V56.C only 0.000 apart, marking (T0374)V56.C as missing WARNING: atoms too close: (T0374)L26.C and (T0374)V56.C only 0.000 apart, marking (T0374)V56.C as missing WARNING: atoms too close: (T0374)V56.N and (T0374)H57.N only 0.000 apart, marking (T0374)V56.N as missing WARNING: atoms too close: (T0374)A55.N and (T0374)H57.N only 0.000 apart, marking (T0374)A55.N as missing WARNING: atoms too close: (T0374)V54.N and (T0374)H57.N only 0.000 apart, marking (T0374)V54.N as missing WARNING: atoms too close: (T0374)T53.N and (T0374)H57.N only 0.000 apart, marking (T0374)T53.N as missing WARNING: atoms too close: (T0374)S52.N and (T0374)H57.N only 0.000 apart, marking (T0374)S52.N as missing WARNING: atoms too close: (T0374)F27.N and (T0374)H57.N only 0.000 apart, marking (T0374)F27.N as missing WARNING: atoms too close: (T0374)L26.N and (T0374)H57.N only 0.000 apart, marking (T0374)H57.N as missing WARNING: atoms too close: (T0374)V56.CA and (T0374)H57.CA only 0.000 apart, marking (T0374)H57.CA as missing WARNING: atoms too close: (T0374)A55.CA and (T0374)H57.CA only 0.000 apart, marking (T0374)H57.CA as missing WARNING: atoms too close: (T0374)V54.CA and (T0374)H57.CA only 0.000 apart, marking (T0374)H57.CA as missing WARNING: atoms too close: (T0374)T53.CA and (T0374)H57.CA only 0.000 apart, marking (T0374)H57.CA as missing WARNING: atoms too close: (T0374)S52.CA and (T0374)H57.CA only 0.000 apart, marking (T0374)H57.CA as missing WARNING: atoms too close: (T0374)F27.CA and (T0374)H57.CA only 0.000 apart, marking (T0374)H57.CA as missing WARNING: atoms too close: (T0374)L26.CA and (T0374)H57.CA only 0.000 apart, marking (T0374)H57.CA as missing WARNING: atoms too close: (T0374)V56.CB and (T0374)H57.CB only 0.000 apart, marking (T0374)H57.CB as missing WARNING: atoms too close: (T0374)A55.CB and (T0374)H57.CB only 0.000 apart, marking (T0374)H57.CB as missing WARNING: atoms too close: (T0374)V54.CB and (T0374)H57.CB only 0.000 apart, marking (T0374)H57.CB as missing WARNING: atoms too close: (T0374)T53.CB and (T0374)H57.CB only 0.000 apart, marking (T0374)H57.CB as missing WARNING: atoms too close: (T0374)S52.CB and (T0374)H57.CB only 0.000 apart, marking (T0374)H57.CB as missing WARNING: atoms too close: (T0374)F27.CB and (T0374)H57.CB only 0.000 apart, marking (T0374)H57.CB as missing WARNING: atoms too close: (T0374)L26.CB and (T0374)H57.CB only 0.000 apart, marking (T0374)H57.CB as missing WARNING: atoms too close: (T0374)V56.O and (T0374)H57.O only 0.000 apart, marking (T0374)H57.O as missing WARNING: atoms too close: (T0374)A55.O and (T0374)H57.O only 0.000 apart, marking (T0374)H57.O as missing WARNING: atoms too close: (T0374)V54.O and (T0374)H57.O only 0.000 apart, marking (T0374)H57.O as missing WARNING: atoms too close: (T0374)T53.O and (T0374)H57.O only 0.000 apart, marking (T0374)H57.O as missing WARNING: atoms too close: (T0374)S52.O and (T0374)H57.O only 0.000 apart, marking (T0374)H57.O as missing WARNING: atoms too close: (T0374)F27.O and (T0374)H57.O only 0.000 apart, marking (T0374)H57.O as missing WARNING: atoms too close: (T0374)L26.O and (T0374)H57.O only 0.000 apart, marking (T0374)H57.O as missing WARNING: atoms too close: (T0374)V56.C and (T0374)H57.C only 0.000 apart, marking (T0374)H57.C as missing WARNING: atoms too close: (T0374)A55.C and (T0374)H57.C only 0.000 apart, marking (T0374)H57.C as missing WARNING: atoms too close: (T0374)V54.C and (T0374)H57.C only 0.000 apart, marking (T0374)H57.C as missing WARNING: atoms too close: (T0374)T53.C and (T0374)H57.C only 0.000 apart, marking (T0374)H57.C as missing WARNING: atoms too close: (T0374)S52.C and (T0374)H57.C only 0.000 apart, marking (T0374)H57.C as missing WARNING: atoms too close: (T0374)F27.C and (T0374)H57.C only 0.000 apart, marking (T0374)H57.C as missing WARNING: atoms too close: (T0374)L26.C and (T0374)H57.C only 0.000 apart, marking (T0374)H57.C as missing WARNING: atoms too close: (T0374)H57.N and (T0374)D58.N only 0.000 apart, marking (T0374)H57.N as missing WARNING: atoms too close: (T0374)V56.N and (T0374)D58.N only 0.000 apart, marking (T0374)V56.N as missing WARNING: atoms too close: (T0374)A55.N and (T0374)D58.N only 0.000 apart, marking (T0374)A55.N as missing WARNING: atoms too close: (T0374)V54.N and (T0374)D58.N only 0.000 apart, marking (T0374)V54.N as missing WARNING: atoms too close: (T0374)T53.N and (T0374)D58.N only 0.000 apart, marking (T0374)T53.N as missing WARNING: atoms too close: (T0374)S52.N and (T0374)D58.N only 0.000 apart, marking (T0374)S52.N as missing WARNING: atoms too close: (T0374)F27.N and (T0374)D58.N only 0.000 apart, marking (T0374)F27.N as missing WARNING: atoms too close: (T0374)L26.N and (T0374)D58.N only 0.000 apart, marking (T0374)D58.N as missing WARNING: atoms too close: (T0374)H57.CA and (T0374)D58.CA only 0.000 apart, marking (T0374)D58.CA as missing WARNING: atoms too close: (T0374)V56.CA and (T0374)D58.CA only 0.000 apart, marking (T0374)D58.CA as missing WARNING: atoms too close: (T0374)A55.CA and (T0374)D58.CA only 0.000 apart, marking (T0374)D58.CA as missing WARNING: atoms too close: (T0374)V54.CA and (T0374)D58.CA only 0.000 apart, marking (T0374)D58.CA as missing WARNING: atoms too close: (T0374)T53.CA and (T0374)D58.CA only 0.000 apart, marking (T0374)D58.CA as missing WARNING: atoms too close: (T0374)S52.CA and (T0374)D58.CA only 0.000 apart, marking (T0374)D58.CA as missing WARNING: atoms too close: (T0374)F27.CA and (T0374)D58.CA only 0.000 apart, marking (T0374)D58.CA as missing WARNING: atoms too close: (T0374)L26.CA and (T0374)D58.CA only 0.000 apart, marking (T0374)D58.CA as missing WARNING: atoms too close: (T0374)H57.CB and (T0374)D58.CB only 0.000 apart, marking (T0374)D58.CB as missing WARNING: atoms too close: (T0374)V56.CB and (T0374)D58.CB only 0.000 apart, marking (T0374)D58.CB as missing WARNING: atoms too close: (T0374)A55.CB and (T0374)D58.CB only 0.000 apart, marking (T0374)D58.CB as missing WARNING: atoms too close: (T0374)V54.CB and (T0374)D58.CB only 0.000 apart, marking (T0374)D58.CB as missing WARNING: atoms too close: (T0374)T53.CB and (T0374)D58.CB only 0.000 apart, marking (T0374)D58.CB as missing WARNING: atoms too close: (T0374)S52.CB and (T0374)D58.CB only 0.000 apart, marking (T0374)D58.CB as missing WARNING: atoms too close: (T0374)F27.CB and (T0374)D58.CB only 0.000 apart, marking (T0374)D58.CB as missing WARNING: atoms too close: (T0374)L26.CB and (T0374)D58.CB only 0.000 apart, marking (T0374)D58.CB as missing WARNING: atoms too close: (T0374)H57.O and (T0374)D58.O only 0.000 apart, marking (T0374)D58.O as missing WARNING: atoms too close: (T0374)V56.O and (T0374)D58.O only 0.000 apart, marking (T0374)D58.O as missing WARNING: atoms too close: (T0374)A55.O and (T0374)D58.O only 0.000 apart, marking (T0374)D58.O as missing WARNING: atoms too close: (T0374)V54.O and (T0374)D58.O only 0.000 apart, marking (T0374)D58.O as missing WARNING: atoms too close: (T0374)T53.O and (T0374)D58.O only 0.000 apart, marking (T0374)D58.O as missing WARNING: atoms too close: (T0374)S52.O and (T0374)D58.O only 0.000 apart, marking (T0374)D58.O as missing WARNING: atoms too close: (T0374)F27.O and (T0374)D58.O only 0.000 apart, marking (T0374)D58.O as missing WARNING: atoms too close: (T0374)L26.O and (T0374)D58.O only 0.000 apart, marking (T0374)D58.O as missing WARNING: atoms too close: (T0374)H57.C and (T0374)D58.C only 0.000 apart, marking (T0374)D58.C as missing WARNING: atoms too close: (T0374)V56.C and (T0374)D58.C only 0.000 apart, marking (T0374)D58.C as missing WARNING: atoms too close: (T0374)A55.C and (T0374)D58.C only 0.000 apart, marking (T0374)D58.C as missing WARNING: atoms too close: (T0374)V54.C and (T0374)D58.C only 0.000 apart, marking (T0374)D58.C as missing WARNING: atoms too close: (T0374)T53.C and (T0374)D58.C only 0.000 apart, marking (T0374)D58.C as missing WARNING: atoms too close: (T0374)S52.C and (T0374)D58.C only 0.000 apart, marking (T0374)D58.C as missing WARNING: atoms too close: (T0374)F27.C and (T0374)D58.C only 0.000 apart, marking (T0374)D58.C as missing WARNING: atoms too close: (T0374)L26.C and (T0374)D58.C only 0.000 apart, marking (T0374)D58.C as missing WARNING: atoms too close: (T0374)D58.N and (T0374)G59.N only 0.000 apart, marking (T0374)D58.N as missing WARNING: atoms too close: (T0374)H57.N and (T0374)G59.N only 0.000 apart, marking (T0374)H57.N as missing WARNING: atoms too close: (T0374)V56.N and (T0374)G59.N only 0.000 apart, marking (T0374)V56.N as missing WARNING: atoms too close: (T0374)A55.N and (T0374)G59.N only 0.000 apart, marking (T0374)A55.N as missing WARNING: atoms too close: (T0374)V54.N and (T0374)G59.N only 0.000 apart, marking (T0374)V54.N as missing WARNING: atoms too close: (T0374)T53.N and (T0374)G59.N only 0.000 apart, marking (T0374)T53.N as missing WARNING: atoms too close: (T0374)S52.N and (T0374)G59.N only 0.000 apart, marking (T0374)S52.N as missing WARNING: atoms too close: (T0374)F27.N and (T0374)G59.N only 0.000 apart, marking (T0374)F27.N as missing WARNING: atoms too close: (T0374)L26.N and (T0374)G59.N only 0.000 apart, marking (T0374)G59.N as missing WARNING: atoms too close: (T0374)D58.CA and (T0374)G59.CA only 0.000 apart, marking (T0374)G59.CA as missing WARNING: atoms too close: (T0374)H57.CA and (T0374)G59.CA only 0.000 apart, marking (T0374)G59.CA as missing WARNING: atoms too close: (T0374)V56.CA and (T0374)G59.CA only 0.000 apart, marking (T0374)G59.CA as missing WARNING: atoms too close: (T0374)A55.CA and (T0374)G59.CA only 0.000 apart, marking (T0374)G59.CA as missing WARNING: atoms too close: (T0374)V54.CA and (T0374)G59.CA only 0.000 apart, marking (T0374)G59.CA as missing WARNING: atoms too close: (T0374)T53.CA and (T0374)G59.CA only 0.000 apart, marking (T0374)G59.CA as missing WARNING: atoms too close: (T0374)S52.CA and (T0374)G59.CA only 0.000 apart, marking (T0374)G59.CA as missing WARNING: atoms too close: (T0374)F27.CA and (T0374)G59.CA only 0.000 apart, marking (T0374)G59.CA as missing WARNING: atoms too close: (T0374)L26.CA and (T0374)G59.CA only 0.000 apart, marking (T0374)G59.CA as missing WARNING: atoms too close: (T0374)D58.O and (T0374)G59.O only 0.000 apart, marking (T0374)G59.O as missing WARNING: atoms too close: (T0374)H57.O and (T0374)G59.O only 0.000 apart, marking (T0374)G59.O as missing WARNING: atoms too close: (T0374)V56.O and (T0374)G59.O only 0.000 apart, marking (T0374)G59.O as missing WARNING: atoms too close: (T0374)A55.O and (T0374)G59.O only 0.000 apart, marking (T0374)G59.O as missing WARNING: atoms too close: (T0374)V54.O and (T0374)G59.O only 0.000 apart, marking (T0374)G59.O as missing WARNING: atoms too close: (T0374)T53.O and (T0374)G59.O only 0.000 apart, marking (T0374)G59.O as missing WARNING: atoms too close: (T0374)S52.O and (T0374)G59.O only 0.000 apart, marking (T0374)G59.O as missing WARNING: atoms too close: (T0374)F27.O and (T0374)G59.O only 0.000 apart, marking (T0374)G59.O as missing WARNING: atoms too close: (T0374)L26.O and (T0374)G59.O only 0.000 apart, marking (T0374)G59.O as missing WARNING: atoms too close: (T0374)D58.C and (T0374)G59.C only 0.000 apart, marking (T0374)G59.C as missing WARNING: atoms too close: (T0374)H57.C and (T0374)G59.C only 0.000 apart, marking (T0374)G59.C as missing WARNING: atoms too close: (T0374)V56.C and (T0374)G59.C only 0.000 apart, marking (T0374)G59.C as missing WARNING: atoms too close: (T0374)A55.C and (T0374)G59.C only 0.000 apart, marking (T0374)G59.C as missing WARNING: atoms too close: (T0374)V54.C and (T0374)G59.C only 0.000 apart, marking (T0374)G59.C as missing WARNING: atoms too close: (T0374)T53.C and (T0374)G59.C only 0.000 apart, marking (T0374)G59.C as missing WARNING: atoms too close: (T0374)S52.C and (T0374)G59.C only 0.000 apart, marking (T0374)G59.C as missing WARNING: atoms too close: (T0374)F27.C and (T0374)G59.C only 0.000 apart, marking (T0374)G59.C as missing WARNING: atoms too close: (T0374)L26.C and (T0374)G59.C only 0.000 apart, marking (T0374)G59.C as missing WARNING: atoms too close: (T0374)G59.N and (T0374)R105.N only 0.000 apart, marking (T0374)G59.N as missing WARNING: atoms too close: (T0374)D58.N and (T0374)R105.N only 0.000 apart, marking (T0374)D58.N as missing WARNING: atoms too close: (T0374)H57.N and (T0374)R105.N only 0.000 apart, marking (T0374)H57.N as missing WARNING: atoms too close: (T0374)V56.N and (T0374)R105.N only 0.000 apart, marking (T0374)V56.N as missing WARNING: atoms too close: (T0374)A55.N and (T0374)R105.N only 0.000 apart, marking (T0374)A55.N as missing WARNING: atoms too close: (T0374)V54.N and (T0374)R105.N only 0.000 apart, marking (T0374)V54.N as missing WARNING: atoms too close: (T0374)T53.N and (T0374)R105.N only 0.000 apart, marking (T0374)T53.N as missing WARNING: atoms too close: (T0374)S52.N and (T0374)R105.N only 0.000 apart, marking (T0374)S52.N as missing WARNING: atoms too close: (T0374)F27.N and (T0374)R105.N only 0.000 apart, marking (T0374)F27.N as missing WARNING: atoms too close: (T0374)L26.N and (T0374)R105.N only 0.000 apart, marking (T0374)R105.N as missing WARNING: atoms too close: (T0374)G59.CA and (T0374)R105.CA only 0.000 apart, marking (T0374)R105.CA as missing WARNING: atoms too close: (T0374)D58.CA and (T0374)R105.CA only 0.000 apart, marking (T0374)R105.CA as missing WARNING: atoms too close: (T0374)H57.CA and (T0374)R105.CA only 0.000 apart, marking (T0374)R105.CA as missing WARNING: atoms too close: (T0374)V56.CA and (T0374)R105.CA only 0.000 apart, marking (T0374)R105.CA as missing WARNING: atoms too close: (T0374)A55.CA and (T0374)R105.CA only 0.000 apart, marking (T0374)R105.CA as missing WARNING: atoms too close: (T0374)V54.CA and (T0374)R105.CA only 0.000 apart, marking (T0374)R105.CA as missing WARNING: atoms too close: (T0374)T53.CA and (T0374)R105.CA only 0.000 apart, marking (T0374)R105.CA as missing WARNING: atoms too close: (T0374)S52.CA and (T0374)R105.CA only 0.000 apart, marking (T0374)R105.CA as missing WARNING: atoms too close: (T0374)F27.CA and (T0374)R105.CA only 0.000 apart, marking (T0374)R105.CA as missing WARNING: atoms too close: (T0374)L26.CA and (T0374)R105.CA only 0.000 apart, marking (T0374)R105.CA as missing WARNING: atoms too close: (T0374)D58.CB and (T0374)R105.CB only 0.000 apart, marking (T0374)R105.CB as missing WARNING: atoms too close: (T0374)H57.CB and (T0374)R105.CB only 0.000 apart, marking (T0374)R105.CB as missing WARNING: atoms too close: (T0374)V56.CB and (T0374)R105.CB only 0.000 apart, marking (T0374)R105.CB as missing WARNING: atoms too close: (T0374)A55.CB and (T0374)R105.CB only 0.000 apart, marking (T0374)R105.CB as missing WARNING: atoms too close: (T0374)V54.CB and (T0374)R105.CB only 0.000 apart, marking (T0374)R105.CB as missing WARNING: atoms too close: (T0374)T53.CB and (T0374)R105.CB only 0.000 apart, marking (T0374)R105.CB as missing WARNING: atoms too close: (T0374)S52.CB and (T0374)R105.CB only 0.000 apart, marking (T0374)R105.CB as missing WARNING: atoms too close: (T0374)F27.CB and (T0374)R105.CB only 0.000 apart, marking (T0374)R105.CB as missing WARNING: atoms too close: (T0374)L26.CB and (T0374)R105.CB only 0.000 apart, marking (T0374)R105.CB as missing WARNING: atoms too close: (T0374)G59.O and (T0374)R105.O only 0.000 apart, marking (T0374)R105.O as missing WARNING: atoms too close: (T0374)D58.O and (T0374)R105.O only 0.000 apart, marking (T0374)R105.O as missing WARNING: atoms too close: (T0374)H57.O and (T0374)R105.O only 0.000 apart, marking (T0374)R105.O as missing WARNING: atoms too close: (T0374)V56.O and (T0374)R105.O only 0.000 apart, marking (T0374)R105.O as missing WARNING: atoms too close: (T0374)A55.O and (T0374)R105.O only 0.000 apart, marking (T0374)R105.O as missing WARNING: atoms too close: (T0374)V54.O and (T0374)R105.O only 0.000 apart, marking (T0374)R105.O as missing WARNING: atoms too close: (T0374)T53.O and (T0374)R105.O only 0.000 apart, marking (T0374)R105.O as missing WARNING: atoms too close: (T0374)S52.O and (T0374)R105.O only 0.000 apart, marking (T0374)R105.O as missing WARNING: atoms too close: (T0374)F27.O and (T0374)R105.O only 0.000 apart, marking (T0374)R105.O as missing WARNING: atoms too close: (T0374)L26.O and (T0374)R105.O only 0.000 apart, marking (T0374)R105.O as missing WARNING: atoms too close: (T0374)G59.C and (T0374)R105.C only 0.000 apart, marking (T0374)R105.C as missing WARNING: atoms too close: (T0374)D58.C and (T0374)R105.C only 0.000 apart, marking (T0374)R105.C as missing WARNING: atoms too close: (T0374)H57.C and (T0374)R105.C only 0.000 apart, marking (T0374)R105.C as missing WARNING: atoms too close: (T0374)V56.C and (T0374)R105.C only 0.000 apart, marking (T0374)R105.C as missing WARNING: atoms too close: (T0374)A55.C and (T0374)R105.C only 0.000 apart, marking (T0374)R105.C as missing WARNING: atoms too close: (T0374)V54.C and (T0374)R105.C only 0.000 apart, marking (T0374)R105.C as missing WARNING: atoms too close: (T0374)T53.C and (T0374)R105.C only 0.000 apart, marking (T0374)R105.C as missing WARNING: atoms too close: (T0374)S52.C and (T0374)R105.C only 0.000 apart, marking (T0374)R105.C as missing WARNING: atoms too close: (T0374)F27.C and (T0374)R105.C only 0.000 apart, marking (T0374)R105.C as missing WARNING: atoms too close: (T0374)L26.C and (T0374)R105.C only 0.000 apart, marking (T0374)R105.C as missing # WARNING: incomplete conformation T0374 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: incomplete conformation T0374 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 159 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 0.2822 model score 0.2860 model score 0.3589 model score 0.4331 model score 0.6081 model score 0.4312 model score 0.4311 model score 0.4280 model score 0.4282 model score 0.4868 model score 0.4397 model score 0.4282 model score 0.3367 model score 0.2478 model score 0.2750 model score -0.4115 model score -0.5214 model score -0.3724 model score 0.0673 model score 0.0948 model score 1.1667 model score 0.8673 model score 1.1182 model score 1.1212 model score 0.9056 model score -0.6524 model score -0.3766 model score -0.4044 model score -0.4050 model score -0.2118 model score -0.3889 model score -0.4690 model score -0.3935 model score -0.4290 model score -0.4426 model score -0.5546 model score 0.4734 model score -0.4301 model score -0.0068 model score -0.3080 model score -0.3583 model score -0.2665 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.4173 model score -0.4223 model score -0.3102 model score -0.3206 model score -0.3492 model score -0.4086 model score -0.4690 model score -0.4223 model score -0.4458 model score -0.4371 model score -0.0314 model score -0.4115 model score 0.3176 model score 0.2322 model score 0.0948 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.3651 model score 2.1000 model score 2.4098 model score 2.0169 model score 2.1394 model score -0.4020 model score -0.3830 model score -0.1869 model score -0.0744 model score -0.2108 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.4458 model score -0.2008 model score -0.3404 model score -0.4371 model score -0.5445 model score 0.1278 model score 0.1407 model score -0.0281 model score 0.4610 model score -0.0186 model score -0.2999 model score -0.4032 model score -0.2061 model score -0.4441 model score -0.1816 model score -0.5691 model score -0.5394 model score -0.5646 model score -0.0527 model score 0.1406 model score -0.3818 model score 0.5962 model score 0.0617 model score -0.2348 model score -0.0214 model score -0.1688 model score -0.0194 model score -0.0757 model score 1.2771 model score -0.3737 model score -0.3718 model score -0.2841 model score -0.2192 model score 0.0156 model score -0.3718 model score -0.4268 model score -0.4341 model score -0.2536 model score -0.2779 model score -0.6651 model score -0.3883 model score -0.2348 model score 1.3684 model score 1.3739 model score 1.3527 model score 1.3750 model score 1.3174 model score -0.4482 model score -0.4540 model score -0.4527 model score -0.4453 model score -0.4492 model score -0.4448 model score 0.1118 model score 0.1343 model score 1.3096 model score 0.1071 model score -0.3956 model score -0.4016 model score -0.0953 model score -0.2382 model score -0.1262 model score -0.5140 model score -0.4213 model score -0.3469 model score -0.3819 model score -0.3819 model score -0.3819 model score -0.4472 model score -0.4343 model score -0.1028 model score -0.4502 model score -0.0659 model score -0.3001 model score -0.5255 model score -0.3415 model score -0.3184 model score -0.3560 model score -0.4543 model score -0.5188 model score -0.2192 model score -0.4229 model score -0.4377 model score -0.4637 model score -0.5415 model score -0.2444 model score -0.4523 model score -0.4570 model score -0.4502 model score -0.4313 model score -0.4343 model score -0.4472 model score -0.4606 model score -0.4703 model score -0.4003 model score -0.3987 model score -0.3970 model score -0.1421 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.5798 model score -0.4334 model score -0.0737 model score -0.2113 model score -0.3629 model score -0.4731 model score -0.3560 model score -0.1602 model score -0.3427 model score -0.4588 model score -0.3716 model score -0.4543 model score -0.3612 model score -0.2353 model score -0.4669 model score -0.4291 model score -0.3379 model score -0.1399 model score -0.4476 model score -0.1406 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.4030 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.5630 model score -0.6080 model score -0.5708 model score -0.5333 model score -0.4946 model score -0.4791 model score -0.4627 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.3553 model score 0.6507 model score 0.6596 model score 0.5734 model score 0.6313 model score 1.8538 model score 1.6519 model score 1.6162 model score 1.6056 model score 1.5469 model score -0.4348 model score -0.4090 model score -0.0874 model score -0.2597 model score 0.0409 model score -0.4011 model score -0.4067 model score -0.3630 model score -0.3911 model score -0.1723 model score -0.2981 model score -0.0530 model score -0.0438 model score -0.1237 model score -0.0578 model score 0.0125 model score 0.5413 model score 1.5652 model score -0.4792 USE_META, weight: 0.7227 cost: 0.2822 min: -0.6651 max: 2.4098 USE_META, weight: 0.7216 cost: 0.2860 min: -0.6651 max: 2.4098 USE_META, weight: 0.7003 cost: 0.3589 min: -0.6651 max: 2.4098 USE_META, weight: 0.6786 cost: 0.4331 min: -0.6651 max: 2.4098 USE_META, weight: 0.6274 cost: 0.6081 min: -0.6651 max: 2.4098 USE_META, weight: 0.6791 cost: 0.4312 min: -0.6651 max: 2.4098 USE_META, weight: 0.6792 cost: 0.4311 min: -0.6651 max: 2.4098 USE_META, weight: 0.6801 cost: 0.4280 min: -0.6651 max: 2.4098 USE_META, weight: 0.6800 cost: 0.4282 min: -0.6651 max: 2.4098 USE_META, weight: 0.6629 cost: 0.4868 min: -0.6651 max: 2.4098 USE_META, weight: 0.6766 cost: 0.4397 min: -0.6651 max: 2.4098 USE_META, weight: 0.6800 cost: 0.4282 min: -0.6651 max: 2.4098 USE_META, weight: 0.7068 cost: 0.3367 min: -0.6651 max: 2.4098 USE_META, weight: 0.7328 cost: 0.2478 min: -0.6651 max: 2.4098 USE_META, weight: 0.7248 cost: 0.2750 min: -0.6651 max: 2.4098 USE_META, weight: 0.9258 cost: -0.4115 min: -0.6651 max: 2.4098 USE_META, weight: 0.9579 cost: -0.5214 min: -0.6651 max: 2.4098 USE_META, weight: 0.9143 cost: -0.3724 min: -0.6651 max: 2.4098 USE_META, weight: 0.7856 cost: 0.0673 min: -0.6651 max: 2.4098 USE_META, weight: 0.7776 cost: 0.0948 min: -0.6651 max: 2.4098 USE_META, weight: 0.4638 cost: 1.1667 min: -0.6651 max: 2.4098 USE_META, weight: 0.5515 cost: 0.8673 min: -0.6651 max: 2.4098 USE_META, weight: 0.4781 cost: 1.1182 min: -0.6651 max: 2.4098 USE_META, weight: 0.4772 cost: 1.1212 min: -0.6651 max: 2.4098 USE_META, weight: 0.5403 cost: 0.9056 min: -0.6651 max: 2.4098 USE_META, weight: 0.9963 cost: -0.6524 min: -0.6651 max: 2.4098 USE_META, weight: 0.9156 cost: -0.3766 min: -0.6651 max: 2.4098 USE_META, weight: 0.9237 cost: 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max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.1127 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.1127 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.1127 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9988 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9988 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9988 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9994 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9994 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9994 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.7621 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.7621 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.7621 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9987 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9987 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9987 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 Number of contacts in models: 267 Number of contacts in alignments: 147 NUMB_ALIGNS: 147 Adding 4583 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -275.4819, CN propb: -275.4819 weights: 0.3929 constraints: 430 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 430 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 430 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 4153 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 4153 # 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 4583 # command: