parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0300/ # command:# Making conformation for sequence T0300 numbered 1 through 102 Created new target T0300 from T0300.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0300/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0300//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0300/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0300//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0300/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0300/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0300/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0300 read from 1y8aA/merged-good-all-a2m # 1y8aA read from 1y8aA/merged-good-all-a2m # found chain 1y8aA in training set T0300 26 :TLKQKVKS 1y8aA 108 :QYLRRTAS # choosing archetypes in rotamer library T0300 39 :SDDSILTAAKRESIIVSSSRALGAVAMRKIEAKVRSRAA 1y8aA 129 :DFDSIAVPEGLREELLSIIDVIASLSGEELFRKLDELFS T0300 82 :EQELTSLLQSLT 1y8aA 168 :RSEVRKIVESVK Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Number of alignments=1 # 1y8aA read from 1y8aA/merged-good-all-a2m # found chain 1y8aA in training set T0300 24 :NKTLKQKVKSSGAV 1y8aA 86 :AEKAMATLQERWTP T0300 39 :SDDSILTAAKRESIIVSSSRALGAVAMRKIEAKVRSRAA 1y8aA 129 :DFDSIAVPEGLREELLSIIDVIASLSGEELFRKLDELFS T0300 82 :EQELTSLLQSLT 1y8aA 168 :RSEVRKIVESVK Number of specific fragments extracted= 3 number of extra gaps= 0 total=6 Number of alignments=2 # 1y8aA read from 1y8aA/merged-good-all-a2m # found chain 1y8aA in training set T0300 25 :KTLKQKVKS 1y8aA 87 :EKAMATLQE T0300 34 :SGAVS 1y8aA 116 :MIGVR T0300 39 :SDDSILTAAKRESIIVSSSRALGAVAMRKIEAKVRSRAA 1y8aA 129 :DFDSIAVPEGLREELLSIIDVIASLSGEELFRKLDELFS T0300 82 :EQELTSLLQSLT 1y8aA 168 :RSEVRKIVESVK Number of specific fragments extracted= 4 number of extra gaps= 0 total=10 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fmhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fmhA expands to /projects/compbio/data/pdb/1fmh.pdb.gz 1fmhA:# T0300 read from 1fmhA/merged-good-all-a2m # 1fmhA read from 1fmhA/merged-good-all-a2m # adding 1fmhA to template set # found chain 1fmhA in template set Warning: unaligning (T0300)T9 because first residue in template chain is (1fmhA)E1 T0300 10 :YEEMVKEVERLKLENKTLKQKVKS 1fmhA 2 :VAQLEKEVAQAEAENYQLEQEVAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=11 Number of alignments=4 # 1fmhA read from 1fmhA/merged-good-all-a2m # found chain 1fmhA in template set Warning: unaligning (T0300)T9 because first residue in template chain is (1fmhA)E1 T0300 10 :YEEMVKEVERLKLENKTLKQKVKS 1fmhA 2 :VAQLEKEVAQAEAENYQLEQEVAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=12 Number of alignments=5 # 1fmhA read from 1fmhA/merged-good-all-a2m # found chain 1fmhA in template set Warning: unaligning (T0300)T9 because first residue in template chain is (1fmhA)E1 T0300 10 :YEEMVKEVERLKLENKTLKQKVKS 1fmhA 2 :VAQLEKEVAQAEAENYQLEQEVAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=13 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cs4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0300/1cs4A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0300/1cs4A/merged-good-all-a2m.gz for input Trying 1cs4A/merged-good-all-a2m Error: Couldn't open file 1cs4A/merged-good-all-a2m or 1cs4A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fmhB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fmhB expands to /projects/compbio/data/pdb/1fmh.pdb.gz 1fmhB:# T0300 read from 1fmhB/merged-good-all-a2m # 1fmhB read from 1fmhB/merged-good-all-a2m # adding 1fmhB to template set # found chain 1fmhB in template set T0300 12 :EMVKEVERLKLENKTLKQKVK 1fmhB 4 :ALKKRVQALKARNYAAKQKVQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=14 Number of alignments=7 # 1fmhB read from 1fmhB/merged-good-all-a2m # found chain 1fmhB in template set T0300 12 :EMVKEVERLKLENKTLKQKVK 1fmhB 4 :ALKKRVQALKARNYAAKQKVQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=15 Number of alignments=8 # 1fmhB read from 1fmhB/merged-good-all-a2m # found chain 1fmhB in template set Warning: unaligning (T0300)T9 because first residue in template chain is (1fmhB)E1 T0300 10 :YEEMVKEVERLKLENKTLKQKVK 1fmhB 2 :VQALKKRVQALKARNYAAKQKVQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=16 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1culA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1culA expands to /projects/compbio/data/pdb/1cul.pdb.gz 1culA:# T0300 read from 1culA/merged-good-all-a2m # 1culA read from 1culA/merged-good-all-a2m # adding 1culA to template set # found chain 1culA in template set T0300 10 :YEEMVKEVERLKLENK 1culA 416 :LNELFARFDKLAAENH T0300 39 :SDDS 1culA 449 :PEAR T0300 47 :AKRESIIVSSSRALGAVAMRKIEAK 1culA 453 :ADHAHCCVEMGMDMIEAISLVREMT T0300 91 :SLTLRVDV 1culA 480 :NVNMRVGI Number of specific fragments extracted= 4 number of extra gaps= 0 total=20 Number of alignments=10 # 1culA read from 1culA/merged-good-all-a2m # found chain 1culA in template set T0300 10 :YEEMVKEVERLKLENK 1culA 416 :LNELFARFDKLAAENH T0300 39 :SDDS 1culA 449 :PEAR T0300 47 :AKRESIIVSSSRALGAVAMRKIEAK 1culA 453 :ADHAHCCVEMGMDMIEAISLVREMT T0300 91 :SLTLRVDV 1culA 480 :NVNMRVGI Number of specific fragments extracted= 4 number of extra gaps= 0 total=24 Number of alignments=11 # 1culA read from 1culA/merged-good-all-a2m # found chain 1culA in template set T0300 10 :YEEMVKEVERLKLENK 1culA 416 :LNELFARFDKLAAENH T0300 37 :VSSDD 1culA 448 :LPEAR T0300 47 :AKRESIIVSSSRALGAVAMRKIEAK 1culA 453 :ADHAHCCVEMGMDMIEAISLVREMT T0300 91 :SLTLRVDV 1culA 480 :NVNMRVGI Number of specific fragments extracted= 4 number of extra gaps= 0 total=28 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aucA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aucA expands to /projects/compbio/data/pdb/2auc.pdb.gz 2aucA:Skipped atom 32, because occupancy 0.5 <= existing 0.500 in 2aucA Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2aucA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2aucA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 2aucA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2aucA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2aucA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 2aucA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 2aucA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0300 read from 2aucA/merged-good-all-a2m # 2aucA read from 2aucA/merged-good-all-a2m # adding 2aucA to template set # found chain 2aucA in template set Warning: unaligning (T0300)K5 because first residue in template chain is (2aucA)N88 T0300 6 :PDKTYEEMVKEVER 2aucA 89 :GKLRIEDASHNARK T0300 25 :KTLKQKVKS 2aucA 109 :STDEKKIRD T0300 34 :SGA 2aucA 120 :GDS T0300 44 :LTAA 2aucA 123 :LTYE T0300 49 :RESIIVSSSRALGAV 2aucA 127 :QYLEYLTMCVHDRDN T0300 65 :MRKIEAKVRSRA 2aucA 142 :MEELIKMFSHFD T0300 77 :AKAVTEQELTSLLQS 2aucA 157 :SGFLTKNQMKNILTT Number of specific fragments extracted= 7 number of extra gaps= 0 total=35 Number of alignments=13 # 2aucA read from 2aucA/merged-good-all-a2m # found chain 2aucA in template set Warning: unaligning (T0300)K5 because first residue in template chain is (2aucA)N88 T0300 6 :PDKTYEEMVKEVER 2aucA 89 :GKLRIEDASHNARK T0300 25 :KTLKQKVKS 2aucA 109 :STDEKKIRD T0300 34 :SGA 2aucA 120 :GDS T0300 44 :LTAA 2aucA 123 :LTYE T0300 49 :RESIIVSSSRALGAV 2aucA 127 :QYLEYLTMCVHDRDN T0300 65 :MRKIEAKVRSRA 2aucA 142 :MEELIKMFSHFD T0300 77 :AKAVTEQELTSLLQS 2aucA 157 :SGFLTKNQMKNILTT Number of specific fragments extracted= 7 number of extra gaps= 0 total=42 Number of alignments=14 # 2aucA read from 2aucA/merged-good-all-a2m # found chain 2aucA in template set Warning: unaligning (T0300)K5 because first residue in template chain is (2aucA)N88 T0300 6 :PDKTYEEMVKEVER 2aucA 89 :GKLRIEDASHNARK T0300 25 :KTLKQKVKS 2aucA 109 :STDEKKIRD T0300 34 :S 2aucA 120 :G T0300 42 :SILTA 2aucA 121 :DSLTY T0300 48 :KRESIIVSSSRALGAV 2aucA 126 :EQYLEYLTMCVHDRDN T0300 65 :MRKIEAKVRSRA 2aucA 142 :MEELIKMFSHFD T0300 77 :AKAVTEQELTSLLQS 2aucA 157 :SGFLTKNQMKNILTT Number of specific fragments extracted= 7 number of extra gaps= 0 total=49 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w4xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w4xA expands to /projects/compbio/data/pdb/1w4x.pdb.gz 1w4xA:Skipped atom 2639, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2641, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2643, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2645, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2647, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2649, because occupancy 0.500 <= existing 0.500 in 1w4xA # T0300 read from 1w4xA/merged-good-all-a2m # 1w4xA read from 1w4xA/merged-good-all-a2m # adding 1w4xA to template set # found chain 1w4xA in template set T0300 4 :KKPDKTYEE 1w4xA 226 :RNAPLDPEF T0300 17 :VERLKLENKTLKQKVKS 1w4xA 235 :LADLKKRYAEFREESRN T0300 34 :S 1w4xA 255 :G T0300 35 :GAVSSDDSILTAAKRESIIVSSSRA 1w4xA 259 :YQGPKSALEVSDEELVETLERYWQE T0300 62 :AVAMRKIEAKVRSRAAKAVTEQELTSLL 1w4xA 299 :RDANERVAEFIRNKIRNTVRDPEVAERL Number of specific fragments extracted= 5 number of extra gaps= 0 total=54 Number of alignments=16 # 1w4xA read from 1w4xA/merged-good-all-a2m # found chain 1w4xA in template set T0300 4 :KKPDKTYEE 1w4xA 226 :RNAPLDPEF T0300 17 :VERLKLENKTLKQKVKS 1w4xA 235 :LADLKKRYAEFREESRN T0300 34 :S 1w4xA 255 :G T0300 35 :GAVSSDDSILTAAKRESIIVSSSRA 1w4xA 259 :YQGPKSALEVSDEELVETLERYWQE T0300 62 :AVAMRKIEAKVRSRAAKAVTEQELTSLL 1w4xA 299 :RDANERVAEFIRNKIRNTVRDPEVAERL Number of specific fragments extracted= 5 number of extra gaps= 0 total=59 Number of alignments=17 # 1w4xA read from 1w4xA/merged-good-all-a2m # found chain 1w4xA in template set T0300 4 :KKPDKTYEE 1w4xA 226 :RNAPLDPEF T0300 17 :VERLKLENKTLKQKVKS 1w4xA 235 :LADLKKRYAEFREESRN T0300 34 :SGAVSSDDSILTAAKRESIIVSSSRA 1w4xA 258 :RYQGPKSALEVSDEELVETLERYWQE T0300 62 :AVAMRKIEAKVRSRAAKAVTEQELTSLL 1w4xA 299 :RDANERVAEFIRNKIRNTVRDPEVAERL Number of specific fragments extracted= 4 number of extra gaps= 0 total=63 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j8bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0300 read from 1j8bA/merged-good-all-a2m # 1j8bA read from 1j8bA/merged-good-all-a2m # found chain 1j8bA in training set Warning: unaligning (T0300)K78 because last residue in template chain is (1j8bA)G98 T0300 18 :ERLKLENKTLKQKVKS 1j8bA 15 :QQMQEKMQKMQEEIAQ T0300 34 :SGA 1j8bA 48 :GAH T0300 38 :SSDDSILTAAKRESIIVSSSRALGAVAMRKIEAKVRSRAA 1j8bA 58 :DPSLMEDDKEMLEDLIAAAFNDAVRRAEELQKEKMASVTA Number of specific fragments extracted= 3 number of extra gaps= 0 total=66 Number of alignments=19 # 1j8bA read from 1j8bA/merged-good-all-a2m # found chain 1j8bA in training set Warning: unaligning (T0300)K78 because last residue in template chain is (1j8bA)G98 T0300 18 :ERLKLENKTLKQKVKS 1j8bA 15 :QQMQEKMQKMQEEIAQ T0300 34 :SGA 1j8bA 48 :GAH T0300 38 :SSDDSILTAAKRESIIVSSSRALGAVAMRKIEAKVRSRAA 1j8bA 58 :DPSLMEDDKEMLEDLIAAAFNDAVRRAEELQKEKMASVTA Number of specific fragments extracted= 3 number of extra gaps= 0 total=69 Number of alignments=20 # 1j8bA read from 1j8bA/merged-good-all-a2m # found chain 1j8bA in training set Warning: unaligning (T0300)K78 because last residue in template chain is (1j8bA)G98 T0300 18 :ERLKLENKTLKQKVKS 1j8bA 15 :QQMQEKMQKMQEEIAQ T0300 37 :VSSDDSILTAAKRESIIVSSSRALGAVAMRKIEAKVRSRAA 1j8bA 57 :IDPSLMEDDKEMLEDLIAAAFNDAVRRAEELQKEKMASVTA Number of specific fragments extracted= 2 number of extra gaps= 0 total=71 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f45B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f45B expands to /projects/compbio/data/pdb/1f45.pdb.gz 1f45B:# T0300 read from 1f45B/merged-good-all-a2m # 1f45B read from 1f45B/merged-good-all-a2m # adding 1f45B to template set # found chain 1f45B in template set Warning: unaligning (T0300)D40 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)R129 Warning: unaligning (T0300)D41 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)R129 Warning: unaligning (T0300)I43 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)F132 Warning: unaligning (T0300)L44 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)F132 T0300 12 :EMVKEVERLKLENKTLKQKVKS 1f45B 104 :SIYEDLKMYQVEFKTMNAKLLM T0300 38 :SS 1f45B 126 :DP T0300 42 :S 1f45B 130 :Q T0300 49 :RESIIVSSSRALGAV 1f45B 133 :LDQNMLAVIDELMQA T0300 64 :AMRKIEAKVRSRAAKAV 1f45B 169 :TKIKLCILLHAFRIRAV T0300 84 :ELTSLL 1f45B 186 :TIDRVM Number of specific fragments extracted= 6 number of extra gaps= 2 total=77 Number of alignments=22 # 1f45B read from 1f45B/merged-good-all-a2m # found chain 1f45B in template set Warning: unaligning (T0300)D40 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)R129 Warning: unaligning (T0300)D41 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)R129 Warning: unaligning (T0300)I43 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)F132 Warning: unaligning (T0300)L44 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)F132 T0300 13 :MVKEVERLKLENKTLKQKVKSS 1f45B 105 :IYEDLKMYQVEFKTMNAKLLMD T0300 39 :S 1f45B 127 :P T0300 42 :S 1f45B 130 :Q T0300 49 :RESIIVSSSRALGAV 1f45B 133 :LDQNMLAVIDELMQA T0300 64 :AMRKIEAKVRSRAAKAV 1f45B 169 :TKIKLCILLHAFRIRAV T0300 84 :ELTSLL 1f45B 186 :TIDRVM Number of specific fragments extracted= 6 number of extra gaps= 2 total=83 Number of alignments=23 # 1f45B read from 1f45B/merged-good-all-a2m # found chain 1f45B in template set Warning: unaligning (T0300)A36 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)R129 Warning: unaligning (T0300)V37 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)R129 T0300 11 :EEMVKEVERLKLENKTLKQKVKSSG 1f45B 103 :SSIYEDLKMYQVEFKTMNAKLLMDP T0300 38 :S 1f45B 130 :Q T0300 49 :RESIIVSSSRALGAV 1f45B 133 :LDQNMLAVIDELMQA T0300 64 :AMRKIEAKVRSRAAKAV 1f45B 169 :TKIKLCILLHAFRIRAV T0300 84 :ELTSLLQ 1f45B 186 :TIDRVMS Number of specific fragments extracted= 5 number of extra gaps= 1 total=88 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1guvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0300/1guvA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0300/1guvA/merged-good-all-a2m.gz for input Trying 1guvA/merged-good-all-a2m Error: Couldn't open file 1guvA/merged-good-all-a2m or 1guvA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hkmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0300/1hkmA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0300/1hkmA/merged-good-all-a2m.gz for input Trying 1hkmA/merged-good-all-a2m Error: Couldn't open file 1hkmA/merged-good-all-a2m or 1hkmA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1og6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1og6A expands to /projects/compbio/data/pdb/1og6.pdb.gz 1og6A:# T0300 read from 1og6A/merged-good-all-a2m # 1og6A read from 1og6A/merged-good-all-a2m # adding 1og6A to template set # found chain 1og6A in template set T0300 5 :KPDK 1og6A 93 :ENVI T0300 9 :TYEEMVKEVERLKLEN 1og6A 102 :DRDHIIKSAEQSLINL T0300 33 :SSGAV 1og6A 118 :ATDHL T0300 38 :SSDDSILTAAK 1og6A 128 :HRPDPLMDADE T0300 53 :IVSSSRALGA 1og6A 139 :VADAFKHLHQ T0300 81 :TEQELTSLLQSLT 1og6A 161 :TPAQFALLQSRLP T0300 94 :LRVDVSM 1og6A 179 :NQVEISP Number of specific fragments extracted= 7 number of extra gaps= 0 total=95 Number of alignments=25 # 1og6A read from 1og6A/merged-good-all-a2m # found chain 1og6A in template set T0300 9 :TYEEMVKEVERLKLEN 1og6A 102 :DRDHIIKSAEQSLINL T0300 33 :SSGAV 1og6A 118 :ATDHL T0300 38 :SSDDSILTAAK 1og6A 128 :HRPDPLMDADE T0300 53 :IVSSSRALGA 1og6A 139 :VADAFKHLHQ T0300 81 :TEQELTSLLQSLT 1og6A 161 :TPAQFALLQSRLP T0300 94 :LRVDVSM 1og6A 179 :NQVEISP Number of specific fragments extracted= 6 number of extra gaps= 0 total=101 Number of alignments=26 # 1og6A read from 1og6A/merged-good-all-a2m # found chain 1og6A in template set T0300 9 :TYEEMVKEVERLKLENK 1og6A 102 :DRDHIIKSAEQSLINLA T0300 37 :VS 1og6A 119 :TD T0300 39 :SDDSILTAAK 1og6A 129 :RPDPLMDADE T0300 53 :IVSSSRALGA 1og6A 139 :VADAFKHLHQ T0300 81 :TEQELTSLLQSLT 1og6A 161 :TPAQFALLQSRLP T0300 94 :LRVDVSM 1og6A 179 :NQVEISP Number of specific fragments extracted= 6 number of extra gaps= 0 total=107 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sauA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0300 read from 1sauA/merged-good-all-a2m # 1sauA read from 1sauA/merged-good-all-a2m # found chain 1sauA in training set Warning: unaligning (T0300)S42 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1sauA)E45 Warning: unaligning (T0300)I43 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1sauA)E45 T0300 25 :KTLKQKVKSSGAVSSDD 1sauA 27 :EEVAEALAKDTRFSPQP T0300 44 :LTA 1sauA 46 :LTE T0300 48 :KRESIIVSSSRALGAV 1sauA 49 :EHWKIIRYLRDYFIKY T0300 65 :MRKIEAKVRSRAAKAVTEQELTSLLQS 1sauA 70 :VRMLVKHCKKEVRPDCNLQYIYKLFPQ Number of specific fragments extracted= 4 number of extra gaps= 1 total=111 Number of alignments=28 # 1sauA read from 1sauA/merged-good-all-a2m # found chain 1sauA in training set Warning: unaligning (T0300)S42 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1sauA)E45 Warning: unaligning (T0300)I43 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1sauA)E45 T0300 25 :KTLKQKVKSSGAVSSDD 1sauA 27 :EEVAEALAKDTRFSPQP T0300 44 :LTA 1sauA 46 :LTE T0300 48 :KRESIIVSSSRALGAV 1sauA 49 :EHWKIIRYLRDYFIKY T0300 65 :MRKIEAKVRSRAAKAVTEQELTSLLQS 1sauA 70 :VRMLVKHCKKEVRPDCNLQYIYKLFPQ Number of specific fragments extracted= 4 number of extra gaps= 1 total=115 Number of alignments=29 # 1sauA read from 1sauA/merged-good-all-a2m # found chain 1sauA in training set Warning: unaligning (T0300)S42 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1sauA)E45 Warning: unaligning (T0300)I43 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1sauA)E45 T0300 25 :KTLKQKVKSSGAVSSDD 1sauA 27 :EEVAEALAKDTRFSPQP T0300 44 :LTAA 1sauA 46 :LTEE T0300 49 :RESIIVSSSRALGAV 1sauA 50 :HWKIIRYLRDYFIKY T0300 65 :MRKIEAKVRSRAAKAVTEQELTSLLQS 1sauA 70 :VRMLVKHCKKEVRPDCNLQYIYKLFPQ Number of specific fragments extracted= 4 number of extra gaps= 1 total=119 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a6cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a6cA expands to /projects/compbio/data/pdb/2a6c.pdb.gz 2a6cA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 94, because occupancy 0.500 <= existing 0.500 in 2a6cA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 2a6cA Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 2a6cA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 2a6cA Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 2a6cA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 2a6cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0300 read from 2a6cA/merged-good-all-a2m # 2a6cA read from 2a6cA/merged-good-all-a2m # adding 2a6cA to template set # found chain 2a6cA in template set Warning: unaligning (T0300)S3 because first residue in template chain is (2a6cA)I-6 T0300 4 :KKPDKTYEEM 2a6cA -5 :HHHHHHMKMR T0300 18 :ERLKL 2a6cA 5 :SQLLI T0300 26 :TLKQKVKSSG 2a6cA 10 :VLQEHLRNSG T0300 44 :LTAAKRESII 2a6cA 20 :LTQFKAAELL T0300 54 :VSSS 2a6cA 33 :QPRV T0300 70 :AKVRSRAAKAVTEQELTSLLQSLTLRV 2a6cA 37 :SDLMRGKIDLFSLESLIDMITSIGLKV Number of specific fragments extracted= 6 number of extra gaps= 0 total=125 Number of alignments=31 # 2a6cA read from 2a6cA/merged-good-all-a2m # found chain 2a6cA in template set Warning: unaligning (T0300)S3 because first residue in template chain is (2a6cA)I-6 T0300 4 :KKPDKTYEEM 2a6cA -5 :HHHHHHMKMR T0300 18 :ERLK 2a6cA 5 :SQLL T0300 25 :KTLKQKVKSSG 2a6cA 9 :IVLQEHLRNSG T0300 44 :LTAAKRESII 2a6cA 20 :LTQFKAAELL T0300 54 :VSSS 2a6cA 33 :QPRV T0300 70 :AKVRSRAAKAVTEQELTSLLQSLTLRVD 2a6cA 37 :SDLMRGKIDLFSLESLIDMITSIGLKVE Number of specific fragments extracted= 6 number of extra gaps= 0 total=131 Number of alignments=32 # 2a6cA read from 2a6cA/merged-good-all-a2m # found chain 2a6cA in template set Warning: unaligning (T0300)S3 because first residue in template chain is (2a6cA)I-6 T0300 4 :KKPDKTYEEMVKE 2a6cA -5 :HHHHHHMKMRSQL T0300 24 :NKTLKQKVKSSG 2a6cA 8 :LIVLQEHLRNSG T0300 44 :LTAAKRESII 2a6cA 20 :LTQFKAAELL T0300 54 :VSSS 2a6cA 33 :QPRV T0300 70 :AKVRSRAAKAVTEQELTSLLQSLTLRVDVSMEE 2a6cA 37 :SDLMRGKIDLFSLESLIDMITSIGLKVEINIKD Number of specific fragments extracted= 5 number of extra gaps= 0 total=136 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jkw/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jkw expands to /projects/compbio/data/pdb/1jkw.pdb.gz 1jkw:Warning: there is no chain 1jkw will retry with 1jkwA # T0300 read from 1jkw/merged-good-all-a2m # 1jkw read from 1jkw/merged-good-all-a2m # adding 1jkw to template set # found chain 1jkw in template set Warning: unaligning (T0300)K5 because first residue in template chain is (1jkw)W11 T0300 6 :PDKTYEEMVKEVER 1jkw 12 :TFSSEEQLARLRAD T0300 23 :ENKTLKQKVKSSGAVSSDDSI 1jkw 26 :ANRKFRCKAVANGKVLPNDPV T0300 44 :LTAAKRESIIVSSSRALGAVAMR 1jkw 48 :LEPHEEMTLCKYYEKRLLEFCSV Number of specific fragments extracted= 3 number of extra gaps= 0 total=139 Number of alignments=34 # 1jkw read from 1jkw/merged-good-all-a2m # found chain 1jkw in template set Warning: unaligning (T0300)K5 because first residue in template chain is (1jkw)W11 T0300 6 :PDKTYEEMVKEVER 1jkw 12 :TFSSEEQLARLRAD T0300 23 :ENKTLKQKVKSSGAVSSDDSI 1jkw 26 :ANRKFRCKAVANGKVLPNDPV T0300 44 :LTAAKRESIIVSSSRALGAVAMR 1jkw 48 :LEPHEEMTLCKYYEKRLLEFCSV Number of specific fragments extracted= 3 number of extra gaps= 0 total=142 Number of alignments=35 # 1jkw read from 1jkw/merged-good-all-a2m # found chain 1jkw in template set Warning: unaligning (T0300)K5 because first residue in template chain is (1jkw)W11 T0300 6 :PDKTYEEMVKEVER 1jkw 12 :TFSSEEQLARLRAD T0300 23 :ENKTLKQKVKSSGAVSSDDSILTAAKRESII 1jkw 26 :ANRKFRCKAVANGKVLPNDPVFLEPHEEMTL T0300 54 :VSSSRALGAVAMR 1jkw 58 :KYYEKRLLEFCSV Number of specific fragments extracted= 3 number of extra gaps= 0 total=145 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q8kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0300/1q8kA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0300/1q8kA/merged-good-all-a2m.gz for input Trying 1q8kA/merged-good-all-a2m Error: Couldn't open file 1q8kA/merged-good-all-a2m or 1q8kA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u2uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0300/1u2uA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0300/1u2uA/merged-good-all-a2m.gz for input Trying 1u2uA/merged-good-all-a2m Error: Couldn't open file 1u2uA/merged-good-all-a2m or 1u2uA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p9iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0300 read from 1p9iA/merged-good-all-a2m # 1p9iA read from 1p9iA/merged-good-all-a2m # found chain 1p9iA in training set T0300 59 :ALGAVAMRKIEAKVRSRAAKA 1p9iA 9 :ASLEAENKQLKAKVEELLAKV Number of specific fragments extracted= 1 number of extra gaps= 0 total=146 Number of alignments=37 # 1p9iA read from 1p9iA/merged-good-all-a2m # found chain 1p9iA in training set T0300 59 :ALGAVAMRKIEAKVRSRAAKA 1p9iA 9 :ASLEAENKQLKAKVEELLAKV Number of specific fragments extracted= 1 number of extra gaps= 0 total=147 Number of alignments=38 # 1p9iA read from 1p9iA/merged-good-all-a2m # found chain 1p9iA in training set T0300 18 :ERLKLENKTLKQKVKS 1p9iA 9 :ASLEAENKQLKAKVEE Number of specific fragments extracted= 1 number of extra gaps= 0 total=148 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1debA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1debA expands to /projects/compbio/data/pdb/1deb.pdb.gz 1debA:# T0300 read from 1debA/merged-good-all-a2m # 1debA read from 1debA/merged-good-all-a2m # adding 1debA to template set # found chain 1debA in template set Warning: unaligning (T0300)P6 because first residue in template chain is (1debA)A2 T0300 7 :DKTYEEMVKEVERLKLENKTLKQKVKS 1debA 3 :AASYDQLLKQVEALKMENSNLRQELED T0300 56 :SSRALGAVAMRKIEAKVRSRA 1debA 30 :NSNHLTKLETEASNMKEVLKQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=150 Number of alignments=39 # 1debA read from 1debA/merged-good-all-a2m # found chain 1debA in template set Warning: unaligning (T0300)P6 because first residue in template chain is (1debA)A2 T0300 7 :DKTYEEMVKEVERLKLENKTLKQKVKS 1debA 3 :AASYDQLLKQVEALKMENSNLRQELED T0300 56 :SSRALGAVAMRKIEAK 1debA 30 :NSNHLTKLETEASNMK T0300 72 :VRSRA 1debA 47 :VLKQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=153 Number of alignments=40 # 1debA read from 1debA/merged-good-all-a2m # found chain 1debA in template set Warning: unaligning (T0300)P6 because first residue in template chain is (1debA)A2 T0300 7 :DKTYEEMVKEVERLKLENKTLKQKVKSS 1debA 3 :AASYDQLLKQVEALKMENSNLRQELEDN T0300 57 :SRALGAVAMRKIEAKV 1debA 31 :SNHLTKLETEASNMKE Number of specific fragments extracted= 2 number of extra gaps= 0 total=155 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oqcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0300 read from 1oqcA/merged-good-all-a2m # 1oqcA read from 1oqcA/merged-good-all-a2m # found chain 1oqcA in training set Warning: unaligning (T0300)K4 because first residue in template chain is (1oqcA)E13 T0300 5 :KPDKTYEEMVKE 1oqcA 14 :DCPQDREELGRN T0300 23 :ENKTLKQKVKSS 1oqcA 26 :TWAFLHTLAAYY T0300 41 :DSILTAAKRE 1oqcA 38 :PDMPTPEQQQ T0300 52 :IIVSSSRALGA 1oqcA 48 :DMAQFIHIFSK T0300 63 :VAMRKIEAKVRSRAAKAVTEQELTSLL 1oqcA 64 :ECAEDIRKRIDRSQPDTSTRVSFSQWL Number of specific fragments extracted= 5 number of extra gaps= 0 total=160 Number of alignments=42 # 1oqcA read from 1oqcA/merged-good-all-a2m # found chain 1oqcA in training set Warning: unaligning (T0300)K4 because first residue in template chain is (1oqcA)E13 T0300 5 :KPDKTYEEMVKE 1oqcA 14 :DCPQDREELGRN T0300 23 :ENKTLKQKVKSS 1oqcA 26 :TWAFLHTLAAYY T0300 41 :DSILTAAKRE 1oqcA 38 :PDMPTPEQQQ T0300 52 :IIVSSSRALGA 1oqcA 48 :DMAQFIHIFSK T0300 63 :VAMRKIEAKVRSRAAKAVTEQELTSLL 1oqcA 64 :ECAEDIRKRIDRSQPDTSTRVSFSQWL Number of specific fragments extracted= 5 number of extra gaps= 0 total=165 Number of alignments=43 # 1oqcA read from 1oqcA/merged-good-all-a2m # found chain 1oqcA in training set Warning: unaligning (T0300)K4 because first residue in template chain is (1oqcA)E13 T0300 5 :KPDKTYEEMVKE 1oqcA 14 :DCPQDREELGRN T0300 23 :ENKTLKQKVKS 1oqcA 26 :TWAFLHTLAAY T0300 37 :VSSDD 1oqcA 37 :YPDMP T0300 46 :AAKRESIIVSSSRALGA 1oqcA 42 :TPEQQQDMAQFIHIFSK T0300 63 :VAMRKIEAKVRSRAAKAVTEQELTSLLQS 1oqcA 64 :ECAEDIRKRIDRSQPDTSTRVSFSQWLCR Number of specific fragments extracted= 5 number of extra gaps= 0 total=170 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kxu/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kxu expands to /projects/compbio/data/pdb/1kxu.pdb.gz 1kxu:Warning: there is no chain 1kxu will retry with 1kxuA # T0300 read from 1kxu/merged-good-all-a2m # 1kxu read from 1kxu/merged-good-all-a2m # adding 1kxu to template set # found chain 1kxu in template set Warning: unaligning (T0300)K5 because first residue in template chain is (1kxu)W11 T0300 6 :PDKTYEEMVKEVER 1kxu 12 :TFSSEEQLARLRAD T0300 23 :ENKTLKQKVKSSGAVSSDDSI 1kxu 26 :ANRKFRCKAVANGKVLPNDPV T0300 44 :LTAAKRESIIVSSSRALGAVAM 1kxu 48 :LEPHEEMTLCKYYEKRLLEFCS Number of specific fragments extracted= 3 number of extra gaps= 0 total=173 Number of alignments=45 # 1kxu read from 1kxu/merged-good-all-a2m # found chain 1kxu in template set Warning: unaligning (T0300)K5 because first residue in template chain is (1kxu)W11 T0300 6 :PDKTYEEMVKEVER 1kxu 12 :TFSSEEQLARLRAD T0300 23 :ENKTLKQKVKSSGAVSSDDSI 1kxu 26 :ANRKFRCKAVANGKVLPNDPV T0300 44 :LTAAKRESIIVSSSRALGAVAM 1kxu 48 :LEPHEEMTLCKYYEKRLLEFCS Number of specific fragments extracted= 3 number of extra gaps= 0 total=176 Number of alignments=46 # 1kxu read from 1kxu/merged-good-all-a2m # found chain 1kxu in template set Warning: unaligning (T0300)K5 because first residue in template chain is (1kxu)W11 T0300 6 :PDKTYEEMVKEVER 1kxu 12 :TFSSEEQLARLRAD T0300 23 :ENKTLKQKVKSSGAVSSDDSILTAAKRESII 1kxu 26 :ANRKFRCKAVANGKVLPNDPVFLEPHEEMTL T0300 54 :VSSSRALGAVAM 1kxu 58 :KYYEKRLLEFCS Number of specific fragments extracted= 3 number of extra gaps= 0 total=179 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lg2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lg2A expands to /projects/compbio/data/pdb/1lg2.pdb.gz 1lg2A:# T0300 read from 1lg2A/merged-good-all-a2m # 1lg2A read from 1lg2A/merged-good-all-a2m # adding 1lg2A to template set # found chain 1lg2A in template set Warning: unaligning (T0300)V37 because of BadResidue code BAD_PEPTIDE in next template residue (1lg2A)Y141 Warning: unaligning (T0300)S38 because of BadResidue code BAD_PEPTIDE at template residue (1lg2A)Y141 T0300 10 :YEEMVKEV 1lg2A 116 :RQTFVNSA T0300 28 :KQKVKSSGA 1lg2A 124 :IRFLRKYSF T0300 39 :SDDSILTAAKRE 1lg2A 142 :PGSQGSPAVDKE T0300 52 :IIVSSSRALGAVAMRKIEAK 1lg2A 154 :RFTTLVQDLANAFQQEAQTS T0300 91 :SLTLRVDVSM 1lg2A 177 :RLLLSAAVPA Number of specific fragments extracted= 5 number of extra gaps= 1 total=184 Number of alignments=48 # 1lg2A read from 1lg2A/merged-good-all-a2m # found chain 1lg2A in template set T0300 10 :YEEMVKEV 1lg2A 116 :RQTFVNSA T0300 28 :KQKVKSSGA 1lg2A 124 :IRFLRKYSF T0300 39 :SDDSILTAAKRE 1lg2A 142 :PGSQGSPAVDKE T0300 52 :IIVSSSRALGAVAMRKIEAK 1lg2A 154 :RFTTLVQDLANAFQQEAQTS T0300 91 :SLTLRVDVSM 1lg2A 177 :RLLLSAAVPA Number of specific fragments extracted= 5 number of extra gaps= 0 total=189 Number of alignments=49 # 1lg2A read from 1lg2A/merged-good-all-a2m # found chain 1lg2A in template set T0300 17 :VERLKLENKTL 1lg2A 116 :RQTFVNSAIRF T0300 31 :VKS 1lg2A 127 :LRK T0300 41 :DSILTAAKRESIIVSSSRALGAVAMRKIEAK 1lg2A 143 :GSQGSPAVDKERFTTLVQDLANAFQQEAQTS T0300 81 :TEQE 1lg2A 187 :GQTY T0300 85 :LTSLLQSLTLRVDV 1lg2A 197 :VDKIAQNLDFVNLM Number of specific fragments extracted= 5 number of extra gaps= 0 total=194 Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2adoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2adoA expands to /projects/compbio/data/pdb/2ado.pdb.gz 2adoA:# T0300 read from 2adoA/merged-good-all-a2m # 2adoA read from 2adoA/merged-good-all-a2m # adding 2adoA to template set # found chain 2adoA in template set T0300 26 :TLKQKVKSSGAV 2adoA 1951 :DWLHQSRKAGFF T0300 38 :SSDDSILTAAKRESIIVSSSRALGAVAMR 2adoA 1964 :PPDEYVVTDPEQEKNFGFSLQDALSRARE T0300 88 :LLQSLTLRV 2adoA 1995 :LLEGYEIYV T0300 99 :S 2adoA 2004 :T Number of specific fragments extracted= 4 number of extra gaps= 0 total=198 Number of alignments=51 # 2adoA read from 2adoA/merged-good-all-a2m # found chain 2adoA in template set T0300 26 :TLKQKVKSSGAV 2adoA 1951 :DWLHQSRKAGFF T0300 38 :SSDDSILTAAKRESIIVSSSRALGAVAMR 2adoA 1964 :PPDEYVVTDPEQEKNFGFSLQDALSRARE T0300 88 :LLQSLTLRV 2adoA 1995 :LLEGYEIYV T0300 99 :S 2adoA 2004 :T Number of specific fragments extracted= 4 number of extra gaps= 0 total=202 Number of alignments=52 # 2adoA read from 2adoA/merged-good-all-a2m # found chain 2adoA in template set T0300 26 :TLKQKVKSSGAV 2adoA 1951 :DWLHQSRKAGFF T0300 38 :SSDDSILTAAKRESIIVSSSRALGAVAMR 2adoA 1964 :PPDEYVVTDPEQEKNFGFSLQDALSRARE T0300 88 :LLQSL 2adoA 1995 :LLEGY T0300 95 :RVDVSM 2adoA 2000 :EIYVTP Number of specific fragments extracted= 4 number of extra gaps= 0 total=206 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cq3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cq3A expands to /projects/compbio/data/pdb/1cq3.pdb.gz 1cq3A:# T0300 read from 1cq3A/merged-good-all-a2m # 1cq3A read from 1cq3A/merged-good-all-a2m # adding 1cq3A to template set # found chain 1cq3A in template set T0300 78 :KAVTEQELTSLLQSLTLRVDVSM 1cq3A 110 :PAITREEALSMIKDCEMSINIKC Number of specific fragments extracted= 1 number of extra gaps= 0 total=207 Number of alignments=54 # 1cq3A read from 1cq3A/merged-good-all-a2m # found chain 1cq3A in template set T0300 78 :KAVTEQELTSLLQSLTLRVDVSM 1cq3A 110 :PAITREEALSMIKDCEMSINIKC Number of specific fragments extracted= 1 number of extra gaps= 0 total=208 Number of alignments=55 # 1cq3A read from 1cq3A/merged-good-all-a2m # found chain 1cq3A in template set T0300 78 :KAVTEQELTSLLQSLTLRVDVSM 1cq3A 110 :PAITREEALSMIKDCEMSINIKC Number of specific fragments extracted= 1 number of extra gaps= 0 total=209 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sesA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sesA expands to /projects/compbio/data/pdb/1ses.pdb.gz 1sesA:# T0300 read from 1sesA/merged-good-all-a2m # 1sesA read from 1sesA/merged-good-all-a2m # adding 1sesA to template set # found chain 1sesA in template set Warning: unaligning (T0300)S34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1sesA)P59 Warning: unaligning (T0300)S42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1sesA)P59 Warning: unaligning (T0300)T45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1sesA)P63 Warning: unaligning (T0300)A46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1sesA)P63 T0300 7 :DKTYEEMVKEVERLKLENKTL 1sesA 24 :ALDLEALLALDREVQELKKRL T0300 28 :KQKVKS 1sesA 51 :RNQVAK T0300 43 :IL 1sesA 60 :KA T0300 47 :AKRESIIVSS 1sesA 64 :EEKEALIARG T0300 58 :RAL 1sesA 74 :KAL T0300 62 :AVAMRKIEAKVRSR 1sesA 77 :GEEAKRLEEALREK T0300 82 :EQELTSLLQSL 1sesA 91 :EARLEALLLQV Number of specific fragments extracted= 7 number of extra gaps= 2 total=216 Number of alignments=57 # 1sesA read from 1sesA/merged-good-all-a2m # found chain 1sesA in template set Warning: unaligning (T0300)S34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1sesA)P59 Warning: unaligning (T0300)S42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1sesA)P59 Warning: unaligning (T0300)T45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1sesA)P63 Warning: unaligning (T0300)A46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1sesA)P63 T0300 8 :KTYEEMVKEVERLKLENKTL 1sesA 25 :LDLEALLALDREVQELKKRL T0300 28 :KQKVKS 1sesA 51 :RNQVAK T0300 43 :IL 1sesA 60 :KA T0300 47 :AKRESIIVSS 1sesA 64 :EEKEALIARG T0300 58 :RAL 1sesA 74 :KAL T0300 62 :AVAMRKIEAKVRSR 1sesA 77 :GEEAKRLEEALREK T0300 82 :EQELTSLLQSL 1sesA 91 :EARLEALLLQV Number of specific fragments extracted= 7 number of extra gaps= 2 total=223 Number of alignments=58 # 1sesA read from 1sesA/merged-good-all-a2m # found chain 1sesA in template set Warning: unaligning (T0300)V37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1sesA)P59 Warning: unaligning (T0300)S38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1sesA)P59 Warning: unaligning (T0300)T45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1sesA)P63 Warning: unaligning (T0300)A46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1sesA)P63 T0300 7 :DKTYEEMVKEVERLKLENKTLKQKVKS 1sesA 24 :ALDLEALLALDREVQELKKRLQEVQTE T0300 34 :S 1sesA 57 :R T0300 39 :S 1sesA 60 :K T0300 44 :L 1sesA 61 :A T0300 47 :AKRESIIVS 1sesA 64 :EEKEALIAR T0300 57 :SRALGAV 1sesA 73 :GKALGEE T0300 65 :MRKIEAKVRSR 1sesA 80 :AKRLEEALREK T0300 82 :EQELTSLLQSLT 1sesA 91 :EARLEALLLQVP Number of specific fragments extracted= 8 number of extra gaps= 2 total=231 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l8dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1l8dA expands to /projects/compbio/data/pdb/1l8d.pdb.gz 1l8dA:# T0300 read from 1l8dA/merged-good-all-a2m # 1l8dA read from 1l8dA/merged-good-all-a2m # adding 1l8dA to template set # found chain 1l8dA in template set Warning: unaligning (T0300)L92 because last residue in template chain is (1l8dA)L498 T0300 10 :YEEMVKEVERLKLENKTLKQKVKS 1l8dA 413 :RNEITQRIGELKNKIGDLKTAIEE T0300 34 :S 1l8dA 440 :A T0300 35 :GAVSSDDSILTAAKRESIIVSSSRALGAV 1l8dA 442 :GKCPVCGRELTDEHREELLSKYHLDLNNS T0300 65 :MRKIEAKVRSRAAKAVTEQELTSLLQS 1l8dA 471 :KNTLAKLIDRKSELERELRRIDMEIKR Number of specific fragments extracted= 4 number of extra gaps= 0 total=235 Number of alignments=60 # 1l8dA read from 1l8dA/merged-good-all-a2m # found chain 1l8dA in template set Warning: unaligning (T0300)L92 because last residue in template chain is (1l8dA)L498 T0300 10 :YEEMVKEVERLKLENKTLKQKVKS 1l8dA 413 :RNEITQRIGELKNKIGDLKTAIEE T0300 34 :S 1l8dA 440 :A T0300 35 :GAVSSDDSILTAAKRESIIVSSSRALGAV 1l8dA 442 :GKCPVCGRELTDEHREELLSKYHLDLNNS T0300 65 :MRKIEAKVRSRAAKAVTEQELTSLLQS 1l8dA 471 :KNTLAKLIDRKSELERELRRIDMEIKR Number of specific fragments extracted= 4 number of extra gaps= 0 total=239 Number of alignments=61 # 1l8dA read from 1l8dA/merged-good-all-a2m # found chain 1l8dA in template set T0300 10 :YEEMVKEVERLKLENKTLKQKVKSSGAVS 1l8dA 413 :RNEITQRIGELKNKIGDLKTAIEELKKAK T0300 39 :SDDSILTAAKRESIIVSSSRALGAV 1l8dA 446 :VCGRELTDEHREELLSKYHLDLNNS T0300 65 :MRKIEAKVRS 1l8dA 471 :KNTLAKLIDR T0300 76 :AAKA 1l8dA 481 :KSEL T0300 82 :EQELTSL 1l8dA 485 :ERELRRI Number of specific fragments extracted= 5 number of extra gaps= 0 total=244 Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ad1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ad1A expands to /projects/compbio/data/pdb/1ad1.pdb.gz 1ad1A:# T0300 read from 1ad1A/merged-good-all-a2m # 1ad1A read from 1ad1A/merged-good-all-a2m # adding 1ad1A to template set # found chain 1ad1A in template set T0300 2 :ASKKPDKTYEEMVKEVERLKLE 1ad1A 18 :SDGGKFNNVESAVTRVKAMMDE T0300 34 :SGAVSSDDSILTAAKRESIIVSSSRAL 1ad1A 48 :GVSTRPGHEMITVEEELNRVLPVVEAI T0300 79 :AVTEQELTSLLQ 1ad1A 85 :TFRSEVAEACLK T0300 91 :SLTLRVD 1ad1A 98 :GVDIIND Number of specific fragments extracted= 4 number of extra gaps= 0 total=248 Number of alignments=63 # 1ad1A read from 1ad1A/merged-good-all-a2m # found chain 1ad1A in template set T0300 2 :ASKKPDKTYEEMVKEVERLKLE 1ad1A 18 :SDGGKFNNVESAVTRVKAMMDE T0300 34 :SGAVSSDDSILTAAKRESIIVSSSRAL 1ad1A 48 :GVSTRPGHEMITVEEELNRVLPVVEAI T0300 79 :AVTEQELTSLLQ 1ad1A 85 :TFRSEVAEACLK T0300 91 :SLTLRVD 1ad1A 98 :GVDIIND Number of specific fragments extracted= 4 number of extra gaps= 0 total=252 Number of alignments=64 # 1ad1A read from 1ad1A/merged-good-all-a2m # found chain 1ad1A in template set T0300 1 :MASKKPDKTYEEMVKEVERLKLE 1ad1A 17 :FSDGGKFNNVESAVTRVKAMMDE T0300 34 :SGAVSSDDSILTAAKRESIIVSSSRAL 1ad1A 48 :GVSTRPGHEMITVEEELNRVLPVVEAI T0300 79 :AVTEQELTSLLQ 1ad1A 85 :TFRSEVAEACLK T0300 91 :SLTLRV 1ad1A 98 :GVDIIN Number of specific fragments extracted= 4 number of extra gaps= 0 total=256 Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pb6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pb6A expands to /projects/compbio/data/pdb/1pb6.pdb.gz 1pb6A:# T0300 read from 1pb6A/merged-good-all-a2m # 1pb6A read from 1pb6A/merged-good-all-a2m # adding 1pb6A to template set # found chain 1pb6A in template set T0300 17 :VERLKLENKTLKQKVKSSGAVSS 1pb6A 133 :LKALIDEKSALIAGWVKSGKLAP T0300 44 :LTAAKRESIIVSSSRALG 1pb6A 156 :IDPQHLIFMIWASTQHYA T0300 62 :AVAMRKIEAKVRSRA 1pb6A 190 :EVFFNQTVENVQRII Number of specific fragments extracted= 3 number of extra gaps= 0 total=259 Number of alignments=66 # 1pb6A read from 1pb6A/merged-good-all-a2m # found chain 1pb6A in template set T0300 17 :VERLKLENKTLKQKVKSSGAVSS 1pb6A 133 :LKALIDEKSALIAGWVKSGKLAP T0300 44 :LTAAKRESIIVSSSRALG 1pb6A 156 :IDPQHLIFMIWASTQHYA T0300 62 :AVAMRKIEAKVRSRA 1pb6A 190 :EVFFNQTVENVQRII Number of specific fragments extracted= 3 number of extra gaps= 0 total=262 Number of alignments=67 # 1pb6A read from 1pb6A/merged-good-all-a2m # found chain 1pb6A in template set T0300 17 :VERLKLENKTLKQKVKSSGAVSS 1pb6A 133 :LKALIDEKSALIAGWVKSGKLAP T0300 44 :LTAAKRESIIVSSSRALG 1pb6A 156 :IDPQHLIFMIWASTQHYA T0300 62 :AVAMRKIEAKVRS 1pb6A 194 :NQTVENVQRIIIE Number of specific fragments extracted= 3 number of extra gaps= 0 total=265 Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nh1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nh1A expands to /projects/compbio/data/pdb/1nh1.pdb.gz 1nh1A:# T0300 read from 1nh1A/merged-good-all-a2m # 1nh1A read from 1nh1A/merged-good-all-a2m # adding 1nh1A to template set # found chain 1nh1A in template set T0300 9 :TYEEMVKEVERLKLEN 1nh1A 183 :DTEYLRDRVAHLRTEL T0300 25 :KTLKQKVKSSGAV 1nh1A 201 :KALKQHLQRYNPD T0300 38 :SSDDSIL 1nh1A 217 :HTNASYL T0300 51 :SIIVSSSRALGAVA 1nh1A 224 :PIIKDHLNDLYRQA T0300 76 :AAKAVTEQELTSLL 1nh1A 238 :ISSDLSQAELISLI Number of specific fragments extracted= 5 number of extra gaps= 0 total=270 Number of alignments=69 # 1nh1A read from 1nh1A/merged-good-all-a2m # found chain 1nh1A in template set T0300 9 :TYEEMVKEVERLKLEN 1nh1A 183 :DTEYLRDRVAHLRTEL T0300 25 :KTLKQKVKSSGAV 1nh1A 201 :KALKQHLQRYNPD T0300 38 :SSDDSIL 1nh1A 217 :HTNASYL T0300 51 :SIIVSSSRALGAVA 1nh1A 224 :PIIKDHLNDLYRQA T0300 76 :AAKAVTEQELTSLL 1nh1A 238 :ISSDLSQAELISLI Number of specific fragments extracted= 5 number of extra gaps= 0 total=275 Number of alignments=70 # 1nh1A read from 1nh1A/merged-good-all-a2m # found chain 1nh1A in template set T0300 9 :TYEEMVKEVERLKLEN 1nh1A 183 :DTEYLRDRVAHLRTEL T0300 25 :KTLKQKVKSSGAV 1nh1A 201 :KALKQHLQRYNPD T0300 39 :SDDSIL 1nh1A 218 :TNASYL T0300 51 :SIIVSSSRALGAVA 1nh1A 224 :PIIKDHLNDLYRQA T0300 76 :AAKAVTEQELTSLLQ 1nh1A 238 :ISSDLSQAELISLIA Number of specific fragments extracted= 5 number of extra gaps= 0 total=280 Number of alignments=71 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 71 Done printing distance constraints # command: