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/T0309/ # command:# Making conformation for sequence T0309 numbered 1 through 76 Created new target T0309 from T0309.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0309/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0309//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0309/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0309//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0309/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0309/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0309/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iz5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1iz5A expands to /projects/compbio/data/pdb/1iz5.pdb.gz 1iz5A:# T0309 read from 1iz5A/merged-good-all-a2m # 1iz5A read from 1iz5A/merged-good-all-a2m # adding 1iz5A to template set # found chain 1iz5A in template set T0309 13 :GFFDM 1iz5A 185 :GLLDI # choosing archetypes in rotamer library T0309 21 :EVTEQTK 1iz5A 190 :EVQEETK T0309 31 :YTYDFKEILSEFNG 1iz5A 197 :SAYGVSYLSDMVKG T0309 45 :KNVSITVKEENELPV 1iz5A 213 :KADEVTIKFGNEMPM Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 Number of alignments=1 # 1iz5A read from 1iz5A/merged-good-all-a2m # found chain 1iz5A in template set T0309 13 :GFFDM 1iz5A 185 :GLLDI T0309 21 :EVTEQTK 1iz5A 190 :EVQEETK T0309 31 :YTYDFKEILSEFNG 1iz5A 197 :SAYGVSYLSDMVKG T0309 45 :KNVSITVKEENELPV 1iz5A 213 :KADEVTIKFGNEMPM Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 Number of alignments=2 # 1iz5A read from 1iz5A/merged-good-all-a2m # found chain 1iz5A in template set T0309 13 :GFFDM 1iz5A 185 :GLLDI T0309 21 :EVTEQTK 1iz5A 190 :EVQEETK T0309 31 :YTYDFKEILSEFNG 1iz5A 197 :SAYGVSYLSDMVKG T0309 45 :KNVSITVKEENELPV 1iz5A 213 :KADEVTIKFGNEMPM Number of specific fragments extracted= 4 number of extra gaps= 0 total=12 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wmhB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0309 read from 1wmhB/merged-good-all-a2m # 1wmhB read from 1wmhB/merged-good-all-a2m # found chain 1wmhB in training set T0309 8 :QINVKGFFDMDVMEVTEQTKEAEYTYDFKEILSEF 1wmhB 15 :IVEVKSKFDAEFRRFALPRASVSGFQEFSRLLRAV T0309 43 :NGKNVSITVKEE 1wmhB 53 :PGLDVLLGYTDA T0309 55 :NELPV 1wmhB 67 :DLLPL Number of specific fragments extracted= 3 number of extra gaps= 0 total=15 Number of alignments=4 # 1wmhB read from 1wmhB/merged-good-all-a2m # found chain 1wmhB in training set T0309 8 :QINVKGFFDMDVMEVTEQTKEAEYTYDFKEILSEF 1wmhB 15 :IVEVKSKFDAEFRRFALPRASVSGFQEFSRLLRAV T0309 43 :NGKNVSITVKEE 1wmhB 53 :PGLDVLLGYTDA T0309 55 :NELPV 1wmhB 67 :DLLPL Number of specific fragments extracted= 3 number of extra gaps= 0 total=18 Number of alignments=5 # 1wmhB read from 1wmhB/merged-good-all-a2m # found chain 1wmhB in training set T0309 8 :QINVKGFFDMDVMEVTEQTKEAEYTYDFKEILSEF 1wmhB 15 :IVEVKSKFDAEFRRFALPRASVSGFQEFSRLLRAV T0309 43 :NGKNVSITVKEE 1wmhB 53 :PGLDVLLGYTDA T0309 55 :NELPV 1wmhB 67 :DLLPL Number of specific fragments extracted= 3 number of extra gaps= 0 total=21 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fvtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fvtA expands to /projects/compbio/data/pdb/2fvt.pdb.gz 2fvtA:# T0309 read from 2fvtA/merged-good-all-a2m # 2fvtA read from 2fvtA/merged-good-all-a2m # adding 2fvtA to template set # found chain 2fvtA in template set T0309 34 :DFKEILSE 2fvtA 108 :TYNIMIGE T0309 44 :GKNVSITVKE 2fvtA 116 :RRRVAAALIA T0309 67 :DPLEHHHHHH 2fvtA 126 :VPLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=24 Number of alignments=7 # 2fvtA read from 2fvtA/merged-good-all-a2m # found chain 2fvtA in template set T0309 34 :DFKEILSE 2fvtA 108 :TYNIMIGE T0309 44 :GKNVSITVKE 2fvtA 116 :RRRVAAALIA T0309 67 :DPLEHHHHHH 2fvtA 126 :VPLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=27 Number of alignments=8 # 2fvtA read from 2fvtA/merged-good-all-a2m # found chain 2fvtA in template set T0309 34 :DFKEILSE 2fvtA 108 :TYNIMIGE T0309 44 :GKNVSITVKE 2fvtA 116 :RRRVAAALIA T0309 67 :DPLEHHHHHH 2fvtA 126 :VPLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=30 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m93A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0309 read from 1m93A/merged-good-all-a2m # 1m93A read from 1m93A/merged-good-all-a2m # found chain 1m93A in training set T0309 35 :FKEILSEFNGKNVSI 1m93A 4 :FREIASSMKGENVFI Number of specific fragments extracted= 1 number of extra gaps= 0 total=31 # 1m93A read from 1m93A/merged-good-all-a2m # found chain 1m93A in training set T0309 35 :FKEILSEFNGKNVSI 1m93A 4 :FREIASSMKGENVFI Number of specific fragments extracted= 1 number of extra gaps= 0 total=32 # 1m93A read from 1m93A/merged-good-all-a2m # found chain 1m93A in training set T0309 35 :FKEILSEFNGKNVSI 1m93A 4 :FREIASSMKGENVFI Number of specific fragments extracted= 1 number of extra gaps= 0 total=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dyqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0309 read from 1dyqA/merged-good-all-a2m # 1dyqA read from 1dyqA/merged-good-all-a2m # found chain 1dyqA in training set T0309 5 :KVHQINVKGFFDMD 1dyqA 48 :RQHTILFKGFFTDH T0309 24 :EQTKEAEYTYDFKEILSEFNGKNVSITVKE 1dyqA 62 :SWYNDLLVRFDSKDIVDKYKGKKVDLYGAY Number of specific fragments extracted= 2 number of extra gaps= 0 total=35 Number of alignments=10 # 1dyqA read from 1dyqA/merged-good-all-a2m # found chain 1dyqA in training set T0309 5 :KVHQINVKGFFDMD 1dyqA 48 :RQHTILFKGFFTDH T0309 24 :EQTKEAEYTYDFKEILSEFNGKNVSITVKE 1dyqA 62 :SWYNDLLVRFDSKDIVDKYKGKKVDLYGAY Number of specific fragments extracted= 2 number of extra gaps= 0 total=37 Number of alignments=11 # 1dyqA read from 1dyqA/merged-good-all-a2m # found chain 1dyqA in training set T0309 5 :KVHQINVKGFFDMD 1dyqA 48 :RQHTILFKGFFTDH T0309 24 :EQTKEAEYTYDFKEILSEFNGKNVSITVKE 1dyqA 62 :SWYNDLLVRFDSKDIVDKYKGKKVDLYGAY Number of specific fragments extracted= 2 number of extra gaps= 0 total=39 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2snv/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2snv expands to /projects/compbio/data/pdb/2snv.pdb.gz 2snv:Warning: there is no chain 2snv will retry with 2snvA # T0309 read from 2snv/merged-good-all-a2m # 2snv read from 2snv/merged-good-all-a2m # adding 2snv to template set # found chain 2snv in template set Warning: unaligning (T0309)V6 because of BadResidue code BAD_PEPTIDE in next template residue (2snv)V227 Warning: unaligning (T0309)H7 because of BadResidue code BAD_PEPTIDE at template residue (2snv)V227 Warning: unaligning (T0309)T23 because of BadResidue code BAD_PEPTIDE in next template residue (2snv)S249 Warning: unaligning (T0309)E24 because of BadResidue code BAD_PEPTIDE at template residue (2snv)S249 Warning: unaligning (T0309)E28 because of BadResidue code BAD_PEPTIDE in next template residue (2snv)I254 Warning: unaligning (T0309)A29 because of BadResidue code BAD_PEPTIDE at template residue (2snv)I254 T0309 2 :ASKK 2snv 222 :NSGR T0309 8 :QINVKG 2snv 228 :AIVLGG T0309 14 :FFDMDVMEV 2snv 239 :RTALSVVTW T0309 25 :QTK 2snv 250 :KGK T0309 30 :EYT 2snv 255 :KTT Number of specific fragments extracted= 5 number of extra gaps= 3 total=44 Number of alignments=13 # 2snv read from 2snv/merged-good-all-a2m # found chain 2snv in template set Warning: unaligning (T0309)V6 because of BadResidue code BAD_PEPTIDE in next template residue (2snv)V227 Warning: unaligning (T0309)H7 because of BadResidue code BAD_PEPTIDE at template residue (2snv)V227 Warning: unaligning (T0309)T23 because of BadResidue code BAD_PEPTIDE in next template residue (2snv)S249 Warning: unaligning (T0309)E24 because of BadResidue code BAD_PEPTIDE at template residue (2snv)S249 Warning: unaligning (T0309)E28 because of BadResidue code BAD_PEPTIDE in next template residue (2snv)I254 Warning: unaligning (T0309)A29 because of BadResidue code BAD_PEPTIDE at template residue (2snv)I254 T0309 2 :ASKK 2snv 222 :NSGR T0309 8 :QINVKG 2snv 228 :AIVLGG T0309 14 :FFDMDVMEV 2snv 239 :RTALSVVTW T0309 25 :QTK 2snv 250 :KGK T0309 30 :EYT 2snv 255 :KTT Number of specific fragments extracted= 5 number of extra gaps= 3 total=49 Number of alignments=14 # 2snv read from 2snv/merged-good-all-a2m # found chain 2snv in template set Warning: unaligning (T0309)V6 because of BadResidue code BAD_PEPTIDE in next template residue (2snv)V227 Warning: unaligning (T0309)H7 because of BadResidue code BAD_PEPTIDE at template residue (2snv)V227 Warning: unaligning (T0309)T23 because of BadResidue code BAD_PEPTIDE in next template residue (2snv)S249 Warning: unaligning (T0309)E24 because of BadResidue code BAD_PEPTIDE at template residue (2snv)S249 Warning: unaligning (T0309)E28 because of BadResidue code BAD_PEPTIDE in next template residue (2snv)I254 Warning: unaligning (T0309)A29 because of BadResidue code BAD_PEPTIDE at template residue (2snv)I254 T0309 2 :ASKK 2snv 222 :NSGR T0309 8 :QINVKG 2snv 228 :AIVLGG T0309 14 :FFDMDVMEV 2snv 239 :RTALSVVTW T0309 25 :QTK 2snv 250 :KGK T0309 30 :EYT 2snv 255 :KTT Number of specific fragments extracted= 5 number of extra gaps= 3 total=54 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rslA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2rslA expands to /projects/compbio/data/pdb/2rsl.pdb.gz 2rslA:Skipped atom 455, because occupancy 0.27 <= existing 0.730 in 2rslA Skipped atom 457, because occupancy 0.270 <= existing 0.730 in 2rslA Skipped atom 459, because occupancy 0.270 <= existing 0.730 in 2rslA Skipped atom 461, because occupancy 0.270 <= existing 0.730 in 2rslA # T0309 read from 2rslA/merged-good-all-a2m # 2rslA read from 2rslA/merged-good-all-a2m # adding 2rslA to template set # found chain 2rslA in template set T0309 31 :YTYDFKEILSEFNGKNVSITV 2rslA 72 :DTADMIQLIKEFDAQGVSIRF Number of specific fragments extracted= 1 number of extra gaps= 0 total=55 Number of alignments=16 # 2rslA read from 2rslA/merged-good-all-a2m # found chain 2rslA in template set T0309 31 :YTYDFKEILSEFNGKNVSITV 2rslA 72 :DTADMIQLIKEFDAQGVSIRF Number of specific fragments extracted= 1 number of extra gaps= 0 total=56 Number of alignments=17 # 2rslA read from 2rslA/merged-good-all-a2m # found chain 2rslA in template set T0309 31 :YTYDFKEILSEFNGKNVSITV 2rslA 72 :DTADMIQLIKEFDAQGVSIRF Number of specific fragments extracted= 1 number of extra gaps= 0 total=57 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdqA/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/T0309/2bdqA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0309/2bdqA/merged-good-all-a2m.gz for input Trying 2bdqA/merged-good-all-a2m Error: Couldn't open file 2bdqA/merged-good-all-a2m or 2bdqA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a2pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a2pA expands to /projects/compbio/data/pdb/2a2p.pdb.gz 2a2pA:# T0309 read from 2a2pA/merged-good-all-a2m # 2a2pA read from 2a2pA/merged-good-all-a2m # adding 2a2pA to template set # found chain 2a2pA in template set T0309 15 :FDMDVMEVTEQTKEAEYT 2a2pA 78 :ADPELVLLSRNYQELERI T0309 34 :DFKEILSEFNGKNVS 2a2pA 104 :EINALVQELGFYRKS T0309 52 :KEENELPVKGVEMAG 2a2pA 119 :APEAQVPPEYLWAPA T0309 67 :DPLEHHHHHH 2a2pA 143 :DDLEHHHHHH Number of specific fragments extracted= 4 number of extra gaps= 0 total=61 Number of alignments=19 # 2a2pA read from 2a2pA/merged-good-all-a2m # found chain 2a2pA in template set T0309 15 :FDMDVMEVTEQTKEAEYT 2a2pA 78 :ADPELVLLSRNYQELERI T0309 34 :DFKEILSEFNGKNVS 2a2pA 104 :EINALVQELGFYRKS T0309 52 :KEENELPVKGVEMAG 2a2pA 119 :APEAQVPPEYLWAPA T0309 67 :DPLEHHHHHH 2a2pA 143 :DDLEHHHHHH Number of specific fragments extracted= 4 number of extra gaps= 0 total=65 Number of alignments=20 # 2a2pA read from 2a2pA/merged-good-all-a2m # found chain 2a2pA in template set T0309 15 :FDMDVMEVTEQTKEAEYT 2a2pA 78 :ADPELVLLSRNYQELERI T0309 34 :DFKEILSEFNGKNVS 2a2pA 104 :EINALVQELGFYRKS T0309 52 :KEENELPVKGVEMAG 2a2pA 119 :APEAQVPPEYLWAPA T0309 67 :DPLEHHHHHH 2a2pA 143 :DDLEHHHHHH Number of specific fragments extracted= 4 number of extra gaps= 0 total=69 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tzaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tzaA expands to /projects/compbio/data/pdb/1tza.pdb.gz 1tzaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0309 read from 1tzaA/merged-good-all-a2m # 1tzaA read from 1tzaA/merged-good-all-a2m # adding 1tzaA to template set # found chain 1tzaA in template set T0309 3 :SKKVHQINVKGFFDMDVMEVT 1tzaA 77 :PNTAYQYTSGTVLDTPFGIMY T0309 29 :AEYT 1tzaA 98 :GTYG T0309 43 :NGKNVSITVKE 1tzaA 106 :SGEHFNAIIKP T0309 55 :NELPVKGV 1tzaA 117 :FRLATPGL T0309 67 :DPLEHHHHHH 1tzaA 125 :LHLEHHHHHH Number of specific fragments extracted= 5 number of extra gaps= 0 total=74 Number of alignments=22 # 1tzaA read from 1tzaA/merged-good-all-a2m # found chain 1tzaA in template set T0309 3 :SKKVHQINVKGFFDMDVMEVT 1tzaA 77 :PNTAYQYTSGTVLDTPFGIMY T0309 29 :AEYT 1tzaA 98 :GTYG T0309 43 :NGKNVSITVKE 1tzaA 106 :SGEHFNAIIKP T0309 55 :NELPVKGV 1tzaA 117 :FRLATPGL T0309 67 :DPLEHHHHHH 1tzaA 125 :LHLEHHHHHH Number of specific fragments extracted= 5 number of extra gaps= 0 total=79 Number of alignments=23 # 1tzaA read from 1tzaA/merged-good-all-a2m # found chain 1tzaA in template set T0309 3 :SKKVHQINVKGFFDMDVMEVT 1tzaA 77 :PNTAYQYTSGTVLDTPFGIMY T0309 29 :AEYT 1tzaA 98 :GTYG T0309 43 :NGKNVSITVKE 1tzaA 106 :SGEHFNAIIKP T0309 55 :NELPVKGV 1tzaA 117 :FRLATPGL T0309 67 :DPLEHHHHHH 1tzaA 125 :LHLEHHHHHH Number of specific fragments extracted= 5 number of extra gaps= 0 total=84 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ma3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ma3A expands to /projects/compbio/data/pdb/1ma3.pdb.gz 1ma3A:# T0309 read from 1ma3A/merged-good-all-a2m # 1ma3A read from 1ma3A/merged-good-all-a2m # adding 1ma3A to template set # found chain 1ma3A in template set T0309 15 :FDMDVMEVTEQT 1ma3A 119 :GSMDKLDCLDCH T0309 31 :YTYDFKEILSEFNGKNV 1ma3A 131 :ETYDWSEFVEDFNKGEI T0309 52 :KEENELPVKGVEMAGDPL 1ma3A 152 :KCGSYYVKPRVVLFGEPL Number of specific fragments extracted= 3 number of extra gaps= 0 total=87 Number of alignments=25 # 1ma3A read from 1ma3A/merged-good-all-a2m # found chain 1ma3A in template set T0309 15 :FDMDVMEVTEQT 1ma3A 119 :GSMDKLDCLDCH T0309 31 :YTYDFKEILSEFNGKNV 1ma3A 131 :ETYDWSEFVEDFNKGEI T0309 52 :KEENELPVKGVEMAGDPL 1ma3A 152 :KCGSYYVKPRVVLFGEPL Number of specific fragments extracted= 3 number of extra gaps= 0 total=90 Number of alignments=26 # 1ma3A read from 1ma3A/merged-good-all-a2m # found chain 1ma3A in template set T0309 15 :FDMDVMEVTEQT 1ma3A 119 :GSMDKLDCLDCH T0309 31 :YTYDFKEILSEFNGKNV 1ma3A 131 :ETYDWSEFVEDFNKGEI T0309 52 :KEENELPVKGVEMAGDPL 1ma3A 152 :KCGSYYVKPRVVLFGEPL Number of specific fragments extracted= 3 number of extra gaps= 0 total=93 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a53/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a53 expands to /projects/compbio/data/pdb/1a53.pdb.gz 1a53:Warning: there is no chain 1a53 will retry with 1a53A # T0309 read from 1a53/merged-good-all-a2m # 1a53 read from 1a53/merged-good-all-a2m # adding 1a53 to template set # found chain 1a53 in template set T0309 33 :YDFKEILSEFNGKNVSITV 1a53 192 :ENQRKLISMIPSNVVKVAE Number of specific fragments extracted= 1 number of extra gaps= 0 total=94 # 1a53 read from 1a53/merged-good-all-a2m # found chain 1a53 in template set T0309 33 :YDFKEILSEFNGKNVSITV 1a53 192 :ENQRKLISMIPSNVVKVAE Number of specific fragments extracted= 1 number of extra gaps= 0 total=95 # 1a53 read from 1a53/merged-good-all-a2m # found chain 1a53 in template set T0309 33 :YDFKEILSEFNGKNVSITV 1a53 192 :ENQRKLISMIPSNVVKVAE Number of specific fragments extracted= 1 number of extra gaps= 0 total=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ghtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ghtA expands to /projects/compbio/data/pdb/1ght.pdb.gz 1ghtA:# T0309 read from 1ghtA/merged-good-all-a2m # 1ghtA read from 1ghtA/merged-good-all-a2m # adding 1ghtA to template set # found chain 1ghtA in template set T0309 22 :VTEQTKEAEYTYDFKEILSEFN 1ghtA 63 :VKKLDRLGRDTADMIQLIKEFD Number of specific fragments extracted= 1 number of extra gaps= 0 total=97 Number of alignments=28 # 1ghtA read from 1ghtA/merged-good-all-a2m # found chain 1ghtA in template set T0309 22 :VTEQTKEAEYTYDFKEILSEFN 1ghtA 63 :VKKLDRLGRDTADMIQLIKEFD Number of specific fragments extracted= 1 number of extra gaps= 0 total=98 Number of alignments=29 # 1ghtA read from 1ghtA/merged-good-all-a2m # found chain 1ghtA in template set T0309 22 :VTEQTKEAEYTYDFKEILSEFN 1ghtA 63 :VKKLDRLGRDTADMIQLIKEFD Number of specific fragments extracted= 1 number of extra gaps= 0 total=99 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aioA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aioA expands to /projects/compbio/data/pdb/2aio.pdb.gz 2aioA:# T0309 read from 2aioA/merged-good-all-a2m # 2aioA read from 2aioA/merged-good-all-a2m # adding 2aioA to template set # found chain 2aioA in template set T0309 43 :NGKNVSITVK 2aioA 210 :NGKPVRIAYA T0309 55 :NELPVKGVEMAGDPL 2aioA 220 :DSLSAPGYQLQGNPR Number of specific fragments extracted= 2 number of extra gaps= 0 total=101 Number of alignments=31 # 2aioA read from 2aioA/merged-good-all-a2m # found chain 2aioA in template set T0309 43 :NGKNVSITVK 2aioA 210 :NGKPVRIAYA T0309 55 :NELPVKGVEMAGDPL 2aioA 220 :DSLSAPGYQLQGNPR Number of specific fragments extracted= 2 number of extra gaps= 0 total=103 Number of alignments=32 # 2aioA read from 2aioA/merged-good-all-a2m # found chain 2aioA in template set T0309 43 :NGKNVSITVK 2aioA 210 :NGKPVRIAYA T0309 55 :NELPVKGVEMAGDPL 2aioA 220 :DSLSAPGYQLQGNPR Number of specific fragments extracted= 2 number of extra gaps= 0 total=105 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y96B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y96B expands to /projects/compbio/data/pdb/1y96.pdb.gz 1y96B:# T0309 read from 1y96B/merged-good-all-a2m # 1y96B read from 1y96B/merged-good-all-a2m # adding 1y96B to template set # found chain 1y96B in template set T0309 24 :EQTKEAEYTYDFKEILSEFNGKNVSITVKEENELPV 1y96B 55 :EQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAA Number of specific fragments extracted= 1 number of extra gaps= 0 total=106 Number of alignments=34 # 1y96B read from 1y96B/merged-good-all-a2m # found chain 1y96B in template set T0309 24 :EQTKEAEYTYDFKEILSEFNGKNVSITVKEENELPV 1y96B 55 :EQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAA Number of specific fragments extracted= 1 number of extra gaps= 0 total=107 Number of alignments=35 # 1y96B read from 1y96B/merged-good-all-a2m # found chain 1y96B in template set T0309 24 :EQTKEAEYTYDFKEILSEFNGKNVSITVKEENELPV 1y96B 55 :EQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAA Number of specific fragments extracted= 1 number of extra gaps= 0 total=108 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdtA/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/T0309/2bdtA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0309/2bdtA/merged-good-all-a2m.gz for input Trying 2bdtA/merged-good-all-a2m Error: Couldn't open file 2bdtA/merged-good-all-a2m or 2bdtA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tf7A/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/T0309/1tf7A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0309/1tf7A/merged-good-all-a2m.gz for input Trying 1tf7A/merged-good-all-a2m Error: Couldn't open file 1tf7A/merged-good-all-a2m or 1tf7A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pe0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pe0A expands to /projects/compbio/data/pdb/1pe0.pdb.gz 1pe0A:# T0309 read from 1pe0A/merged-good-all-a2m # 1pe0A read from 1pe0A/merged-good-all-a2m # adding 1pe0A to template set # found chain 1pe0A in template set Warning: unaligning (T0309)A2 because first residue in template chain is (1pe0A)A2 T0309 3 :SKKVHQINVKGFFDMDVM 1pe0A 3 :SKRALVILAKGAEEMETV T0309 34 :DFKEILSEFNGKNVSITVKEENELP 1pe0A 21 :IPVDVMRRAGIKVTVAGLAGKDPVQ T0309 64 :MAGD 1pe0A 46 :CSRD Number of specific fragments extracted= 3 number of extra gaps= 0 total=111 Number of alignments=37 # 1pe0A read from 1pe0A/merged-good-all-a2m # found chain 1pe0A in template set Warning: unaligning (T0309)A2 because first residue in template chain is (1pe0A)A2 T0309 3 :SKKVHQINVKGFFDMDVM 1pe0A 3 :SKRALVILAKGAEEMETV T0309 34 :DFKEILSEFNGKNVSITVKEENELP 1pe0A 21 :IPVDVMRRAGIKVTVAGLAGKDPVQ T0309 64 :MAGD 1pe0A 46 :CSRD Number of specific fragments extracted= 3 number of extra gaps= 0 total=114 Number of alignments=38 # 1pe0A read from 1pe0A/merged-good-all-a2m # found chain 1pe0A in template set Warning: unaligning (T0309)A2 because first residue in template chain is (1pe0A)A2 T0309 3 :SKKVHQINVKGFFDMDVM 1pe0A 3 :SKRALVILAKGAEEMETV T0309 34 :DFKEILSEFNGKNVSITVKEENEL 1pe0A 21 :IPVDVMRRAGIKVTVAGLAGKDPV T0309 63 :EMAGD 1pe0A 45 :QCSRD Number of specific fragments extracted= 3 number of extra gaps= 0 total=117 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d2oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d2oA expands to /projects/compbio/data/pdb/1d2o.pdb.gz 1d2oA:# T0309 read from 1d2oA/merged-good-all-a2m # 1d2oA read from 1d2oA/merged-good-all-a2m # adding 1d2oA to template set # found chain 1d2oA in template set T0309 3 :SKKVHQINVKGFFDMDVMEVTEQTKEAEYTYDFKE 1d2oA 553 :GKRPEKVSVNLLANGEKVKTLDVTSETNWKYEFKD T0309 43 :NGKNVSITVKEE 1d2oA 593 :EGKKIEYTVTED T0309 58 :PVKGVE 1d2oA 605 :HVKDYT Number of specific fragments extracted= 3 number of extra gaps= 0 total=120 Number of alignments=40 # 1d2oA read from 1d2oA/merged-good-all-a2m # found chain 1d2oA in template set T0309 3 :SKKVHQINVKGFFDMDVMEVTEQTKEAEYTYDFKE 1d2oA 553 :GKRPEKVSVNLLANGEKVKTLDVTSETNWKYEFKD T0309 43 :NGKNVSITVKEE 1d2oA 593 :EGKKIEYTVTED T0309 58 :PVKGVE 1d2oA 605 :HVKDYT Number of specific fragments extracted= 3 number of extra gaps= 0 total=123 Number of alignments=41 # 1d2oA read from 1d2oA/merged-good-all-a2m # found chain 1d2oA in template set T0309 4 :KKVHQINVKGFFDMDVMEVTEQTKEAEYTYDFKE 1d2oA 554 :KRPEKVSVNLLANGEKVKTLDVTSETNWKYEFKD T0309 43 :NGKNVSITVKEE 1d2oA 593 :EGKKIEYTVTED T0309 58 :PVKGVE 1d2oA 605 :HVKDYT Number of specific fragments extracted= 3 number of extra gaps= 0 total=126 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zynA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zynA expands to /projects/compbio/data/pdb/1zyn.pdb.gz 1zynA:# T0309 read from 1zynA/merged-good-all-a2m # 1zynA read from 1zynA/merged-good-all-a2m # adding 1zynA to template set # found chain 1zynA in template set T0309 9 :INVKGFFDM 1zynA 21 :VELIATLDD T0309 25 :QTK 1zynA 30 :SAK T0309 32 :TYDFKEILSEFNGKNVSITVKEENELPV 1zynA 33 :SAEIKELLAEIAELSDKVTFKEDNTLPV T0309 60 :KGVEMAGDPLEH 1zynA 74 :QGPRFAGSPLGH Number of specific fragments extracted= 4 number of extra gaps= 0 total=130 Number of alignments=43 # 1zynA read from 1zynA/merged-good-all-a2m # found chain 1zynA in template set T0309 9 :INVKGFFDM 1zynA 21 :VELIATLDD T0309 25 :QTK 1zynA 30 :SAK T0309 32 :TYDFKEILSEFNGKNVSITVKEENELPV 1zynA 33 :SAEIKELLAEIAELSDKVTFKEDNTLPV T0309 60 :KGVEMAGDPLEH 1zynA 74 :QGPRFAGSPLGH Number of specific fragments extracted= 4 number of extra gaps= 0 total=134 Number of alignments=44 # 1zynA read from 1zynA/merged-good-all-a2m # found chain 1zynA in template set T0309 9 :INVKGFFDM 1zynA 21 :VELIATLDD T0309 25 :QTK 1zynA 30 :SAK T0309 32 :TYDFKEILSEFNGKNVSITVKEENELPV 1zynA 33 :SAEIKELLAEIAELSDKVTFKEDNTLPV T0309 60 :KGVEMAGDPLEH 1zynA 74 :QGPRFAGSPLGH Number of specific fragments extracted= 4 number of extra gaps= 0 total=138 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q59A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1q59A expands to /projects/compbio/data/pdb/1q59.pdb.gz 1q59A:# T0309 read from 1q59A/merged-good-all-a2m # 1q59A read from 1q59A/merged-good-all-a2m # adding 1q59A to template set # found chain 1q59A in template set T0309 35 :FKEILSEFNG 1q59A 140 :LDGWIHQQGG T0309 54 :ENELP 1q59A 155 :EDNIP T0309 64 :MAGDPLEHHHHHH 1q59A 160 :GDDDDLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=141 Number of alignments=46 # 1q59A read from 1q59A/merged-good-all-a2m # found chain 1q59A in template set T0309 35 :FKEILSEFNG 1q59A 140 :LDGWIHQQGG T0309 54 :ENELP 1q59A 155 :EDNIP T0309 64 :MAGDPLEHHHHHH 1q59A 160 :GDDDDLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=144 Number of alignments=47 # 1q59A read from 1q59A/merged-good-all-a2m # found chain 1q59A in template set T0309 35 :FKEILSEFNG 1q59A 140 :LDGWIHQQGG T0309 54 :EN 1q59A 155 :ED T0309 61 :GVEMAGDPLEHHHHHH 1q59A 157 :NIPGDDDDLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=147 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kkdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kkdA expands to /projects/compbio/data/pdb/1kkd.pdb.gz 1kkdA:# T0309 read from 1kkdA/merged-good-all-a2m # 1kkdA read from 1kkdA/merged-good-all-a2m # adding 1kkdA to template set # found chain 1kkdA in template set Warning: unaligning (T0309)P68 because last residue in template chain is (1kkdA)Q92 T0309 54 :ENELPVKGVEMAGD 1kkdA 78 :LNDQANTLVDLAKT Number of specific fragments extracted= 1 number of extra gaps= 0 total=148 # 1kkdA read from 1kkdA/merged-good-all-a2m # found chain 1kkdA in template set Warning: unaligning (T0309)P68 because last residue in template chain is (1kkdA)Q92 T0309 54 :ENELPVKGVEMAGD 1kkdA 78 :LNDQANTLVDLAKT Number of specific fragments extracted= 1 number of extra gaps= 0 total=149 # 1kkdA read from 1kkdA/merged-good-all-a2m # found chain 1kkdA in template set Warning: unaligning (T0309)P68 because last residue in template chain is (1kkdA)Q92 T0309 53 :EENELPVKGVEMAGD 1kkdA 77 :KLNDQANTLVDLAKT Number of specific fragments extracted= 1 number of extra gaps= 0 total=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d2pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d2pA expands to /projects/compbio/data/pdb/1d2p.pdb.gz 1d2pA:# T0309 read from 1d2pA/merged-good-all-a2m # 1d2pA read from 1d2pA/merged-good-all-a2m # adding 1d2pA to template set # found chain 1d2pA in template set T0309 3 :SKKVHQINVKGFFDMDVMEVTEQTKEAEYTYDFKEI 1d2pA 740 :GKRPEKVSVNLLANGEKVKTLDVTSETNWKYEFKDL T0309 43 :NGKNVSITVKEE 1d2pA 780 :EGKKIEYTVTED T0309 58 :PVKGVE 1d2pA 792 :HVKDYT Number of specific fragments extracted= 3 number of extra gaps= 0 total=153 Number of alignments=49 # 1d2pA read from 1d2pA/merged-good-all-a2m # found chain 1d2pA in template set T0309 3 :SKKVHQINVKGFFDMDVMEVTEQTKEAEYTYDFKEI 1d2pA 740 :GKRPEKVSVNLLANGEKVKTLDVTSETNWKYEFKDL T0309 43 :NGKNVSITVKEE 1d2pA 780 :EGKKIEYTVTED T0309 58 :PVKGVE 1d2pA 792 :HVKDYT Number of specific fragments extracted= 3 number of extra gaps= 0 total=156 Number of alignments=50 # 1d2pA read from 1d2pA/merged-good-all-a2m # found chain 1d2pA in template set T0309 3 :SKKVHQINVKGFFDMDVMEVTEQTKEAEYTYDFKEI 1d2pA 740 :GKRPEKVSVNLLANGEKVKTLDVTSETNWKYEFKDL T0309 43 :NGKNVSITVKEEN 1d2pA 780 :EGKKIEYTVTEDH T0309 59 :VKGVE 1d2pA 793 :VKDYT Number of specific fragments extracted= 3 number of extra gaps= 0 total=159 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kxrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kxrA expands to /projects/compbio/data/pdb/1kxr.pdb.gz 1kxrA:# T0309 read from 1kxrA/merged-good-all-a2m # 1kxrA read from 1kxrA/merged-good-all-a2m # adding 1kxrA to template set # found chain 1kxrA in template set Warning: unaligning (T0309)E53 because last residue in template chain is (1kxrA)N352 T0309 23 :TEQTKEAEYTYDFKEILSEFN 1kxrA 326 :RVKMEDGEFWMSFRDFIREFT T0309 48 :SITVK 1kxrA 347 :KLEIC Number of specific fragments extracted= 2 number of extra gaps= 0 total=161 Number of alignments=52 # 1kxrA read from 1kxrA/merged-good-all-a2m # found chain 1kxrA in template set Warning: unaligning (T0309)E53 because last residue in template chain is (1kxrA)N352 T0309 23 :TEQTKEAEYTYDFKEILSEFN 1kxrA 326 :RVKMEDGEFWMSFRDFIREFT T0309 48 :SITVK 1kxrA 347 :KLEIC Number of specific fragments extracted= 2 number of extra gaps= 0 total=163 Number of alignments=53 # 1kxrA read from 1kxrA/merged-good-all-a2m # found chain 1kxrA in template set Warning: unaligning (T0309)E53 because last residue in template chain is (1kxrA)N352 T0309 23 :TEQTKEAEYTYDFKEILSEFN 1kxrA 326 :RVKMEDGEFWMSFRDFIREFT T0309 48 :SITVK 1kxrA 347 :KLEIC Number of specific fragments extracted= 2 number of extra gaps= 0 total=165 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d1rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d1rA expands to /projects/compbio/data/pdb/1d1r.pdb.gz 1d1rA:# T0309 read from 1d1rA/merged-good-all-a2m # 1d1rA read from 1d1rA/merged-good-all-a2m # adding 1d1rA to template set # found chain 1d1rA in template set Warning: unaligning (T0309)E70 because last residue in template chain is (1d1rA)E111 T0309 14 :FFDMDVMEVTEQTKE 1d1rA 77 :AVKDGVIEIQGDKRD T0309 34 :DFKEILSEFNGK 1d1rA 92 :LLKSLLEAKGMK T0309 62 :VEMAGD 1d1rA 104 :VKLAGG T0309 69 :L 1d1rA 110 :L Number of specific fragments extracted= 4 number of extra gaps= 0 total=169 Number of alignments=55 # 1d1rA read from 1d1rA/merged-good-all-a2m # found chain 1d1rA in template set Warning: unaligning (T0309)E70 because last residue in template chain is (1d1rA)E111 T0309 14 :FFDMDVMEVTEQTKE 1d1rA 77 :AVKDGVIEIQGDKRD T0309 34 :DFKEILSEFNGK 1d1rA 92 :LLKSLLEAKGMK T0309 62 :VEMAGD 1d1rA 104 :VKLAGG T0309 69 :L 1d1rA 110 :L Number of specific fragments extracted= 4 number of extra gaps= 0 total=173 Number of alignments=56 # 1d1rA read from 1d1rA/merged-good-all-a2m # found chain 1d1rA in template set Warning: unaligning (T0309)E70 because last residue in template chain is (1d1rA)E111 T0309 14 :FFDMDVMEVTEQTKE 1d1rA 77 :AVKDGVIEIQGDKRD T0309 34 :DFKEILSEFNGK 1d1rA 92 :LLKSLLEAKGMK T0309 62 :VEMAGD 1d1rA 104 :VKLAGG T0309 69 :L 1d1rA 110 :L Number of specific fragments extracted= 4 number of extra gaps= 0 total=177 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d1uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2d1uA expands to /projects/compbio/data/pdb/2d1u.pdb.gz 2d1uA:# T0309 read from 2d1uA/merged-good-all-a2m # 2d1uA read from 2d1uA/merged-good-all-a2m # adding 2d1uA to template set # found chain 2d1uA in template set T0309 24 :EQTKEAEYTYDFKEILSE 2d1uA 35 :KQSNGLHGDYDVESGLQQ T0309 42 :FNGKNV 2d1uA 54 :LDGSGL T0309 48 :SITVKEENELPVKGVEMAGD 2d1uA 68 :SWTLEPAPAPKEDALTVVGD T0309 68 :PLEHHHHHH 2d1uA 96 :DLEHHHHHH Number of specific fragments extracted= 4 number of extra gaps= 0 total=181 Number of alignments=58 # 2d1uA read from 2d1uA/merged-good-all-a2m # found chain 2d1uA in template set T0309 24 :EQTKEAEYTYDFKEILSE 2d1uA 35 :KQSNGLHGDYDVESGLQQ T0309 42 :FNGKNV 2d1uA 54 :LDGSGL T0309 48 :SITVKEENELPVKGVEMAGD 2d1uA 68 :SWTLEPAPAPKEDALTVVGD T0309 68 :PLEHHHHHH 2d1uA 96 :DLEHHHHHH Number of specific fragments extracted= 4 number of extra gaps= 0 total=185 Number of alignments=59 # 2d1uA read from 2d1uA/merged-good-all-a2m # found chain 2d1uA in template set T0309 24 :EQTKEAEYTYDFKEILSE 2d1uA 35 :KQSNGLHGDYDVESGLQQ T0309 42 :FNGKNV 2d1uA 54 :LDGSGL T0309 48 :SITVKEENELPVKGVEMAGD 2d1uA 68 :SWTLEPAPAPKEDALTVVGD T0309 68 :PLEHHHHHH 2d1uA 96 :DLEHHHHHH Number of specific fragments extracted= 4 number of extra gaps= 0 total=189 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1repC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1repC expands to /projects/compbio/data/pdb/1rep.pdb.gz 1repC:# T0309 read from 1repC/merged-good-all-a2m # 1repC read from 1repC/merged-good-all-a2m # adding 1repC to template set # found chain 1repC in template set Warning: unaligning (T0309)T50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1repC)E110 T0309 27 :KEAEYTYDFKEILSEFNGKNVSI 1repC 74 :TSAEASKDIRQALKSFAGKEVVF Number of specific fragments extracted= 1 number of extra gaps= 0 total=190 Number of alignments=61 # 1repC read from 1repC/merged-good-all-a2m # found chain 1repC in template set Warning: unaligning (T0309)T50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1repC)E110 T0309 27 :KEAEYTYDFKEILSEFNGKNVSI 1repC 74 :TSAEASKDIRQALKSFAGKEVVF Number of specific fragments extracted= 1 number of extra gaps= 0 total=191 Number of alignments=62 # 1repC read from 1repC/merged-good-all-a2m # found chain 1repC in template set Warning: unaligning (T0309)T50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1repC)E110 Warning: unaligning (T0309)E63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1repC)E110 T0309 27 :KEAEYTYDFKEILSEFNGKNVSI 1repC 74 :TSAEASKDIRQALKSFAGKEVVF Number of specific fragments extracted= 1 number of extra gaps= 0 total=192 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mejA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mejA expands to /projects/compbio/data/pdb/1mej.pdb.gz 1mejA:# T0309 read from 1mejA/merged-good-all-a2m # 1mejA read from 1mejA/merged-good-all-a2m # adding 1mejA to template set # found chain 1mejA in template set T0309 32 :TYDFKEILSEFNGKNVSITV 1mejA 117 :GSNAHEQALETGVTVTGCTV Number of specific fragments extracted= 1 number of extra gaps= 0 total=193 Number of alignments=64 # 1mejA read from 1mejA/merged-good-all-a2m # found chain 1mejA in template set T0309 32 :TYDFKEILSEFNGKNVSITV 1mejA 117 :GSNAHEQALETGVTVTGCTV Number of specific fragments extracted= 1 number of extra gaps= 0 total=194 Number of alignments=65 # 1mejA read from 1mejA/merged-good-all-a2m # found chain 1mejA in template set T0309 32 :TYDFKEILSEFNGKNVSITV 1mejA 117 :GSNAHEQALETGVTVTGCTV Number of specific fragments extracted= 1 number of extra gaps= 0 total=195 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hyuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hyuA expands to /projects/compbio/data/pdb/1hyu.pdb.gz 1hyuA:# T0309 read from 1hyuA/merged-good-all-a2m # 1hyuA read from 1hyuA/merged-good-all-a2m # adding 1hyuA to template set # found chain 1hyuA in template set T0309 5 :KVHQI 1hyuA 20 :PVELI T0309 20 :MEVTEQTKEA 1hyuA 25 :ATLDDSAKSA T0309 34 :DFKEILSEFNGKNVSITVKEENELPV 1hyuA 35 :EIKELLAEIAELSDKVTFKEDNTLPV T0309 60 :KGVEMAGDPLEHH 1hyuA 74 :QGPRFAGSPLGHE Number of specific fragments extracted= 4 number of extra gaps= 0 total=199 Number of alignments=67 # 1hyuA read from 1hyuA/merged-good-all-a2m # found chain 1hyuA in template set T0309 5 :KVHQI 1hyuA 20 :PVELI T0309 20 :MEVTEQTKEA 1hyuA 25 :ATLDDSAKSA T0309 34 :DFKEILSEFNGKNVSITVKEENELPV 1hyuA 35 :EIKELLAEIAELSDKVTFKEDNTLPV T0309 60 :KGVEMAGDPLEHH 1hyuA 74 :QGPRFAGSPLGHE Number of specific fragments extracted= 4 number of extra gaps= 0 total=203 Number of alignments=68 # 1hyuA read from 1hyuA/merged-good-all-a2m # found chain 1hyuA in template set T0309 5 :KVHQI 1hyuA 20 :PVELI T0309 20 :MEVTEQTKEA 1hyuA 25 :ATLDDSAKSA T0309 34 :DFKEILSEFNGKNVSITVKEENELPV 1hyuA 35 :EIKELLAEIAELSDKVTFKEDNTLPV T0309 60 :KGVEMAGDPLEHH 1hyuA 74 :QGPRFAGSPLGHE Number of specific fragments extracted= 4 number of extra gaps= 0 total=207 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bg5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bg5A expands to /projects/compbio/data/pdb/2bg5.pdb.gz 2bg5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0309 read from 2bg5A/merged-good-all-a2m # 2bg5A read from 2bg5A/merged-good-all-a2m # adding 2bg5A to template set # found chain 2bg5A in template set T0309 20 :MEVTEQTKEAEYTYDFKEILSEFNGKNVSITV 2bg5A 302 :MDRNSLPSEEEQFEAYKEVVEKMGGRPVTIRT T0309 52 :KEENELPVKGVEMAGDPLEHHHH 2bg5A 335 :DIGGDKELPYLDMPKEMNPFLGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=209 Number of alignments=70 # 2bg5A read from 2bg5A/merged-good-all-a2m # found chain 2bg5A in template set T0309 20 :MEVTEQTKEAEYTYDFKEILSEFNGKNVSITV 2bg5A 302 :MDRNSLPSEEEQFEAYKEVVEKMGGRPVTIRT T0309 52 :KEENELPVKGVEMAGDPLEHHHH 2bg5A 335 :DIGGDKELPYLDMPKEMNPFLGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=211 Number of alignments=71 # 2bg5A read from 2bg5A/merged-good-all-a2m # found chain 2bg5A in template set T0309 20 :MEVTEQTKEAEYTYDFKEILSEFNGKNVSITV 2bg5A 302 :MDRNSLPSEEEQFEAYKEVVEKMGGRPVTIRT T0309 52 :KEENELPVKGVEMAGDPLEHHHH 2bg5A 335 :DIGGDKELPYLDMPKEMNPFLGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=213 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1souA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1souA expands to /projects/compbio/data/pdb/1sou.pdb.gz 1souA:# T0309 read from 1souA/merged-good-all-a2m # 1souA read from 1souA/merged-good-all-a2m # adding 1souA to template set # found chain 1souA in template set T0309 33 :YDFKEILSEFNG 1souA 134 :GYYDRLLKRVKG T0309 45 :KNVSITVKEENELPVK 1souA 167 :IPVDVLVTEKNVRRLR T0309 65 :AGDPLEHHHHHH 1souA 183 :DGRSLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=216 Number of alignments=73 # 1souA read from 1souA/merged-good-all-a2m # found chain 1souA in template set T0309 33 :YDFKEILSEFNG 1souA 134 :GYYDRLLKRVKG T0309 45 :KNVSITVKEENELPVK 1souA 167 :IPVDVLVTEKNVRRLR T0309 65 :AGDPLEHHHHHH 1souA 183 :DGRSLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=219 Number of alignments=74 # 1souA read from 1souA/merged-good-all-a2m # found chain 1souA in template set T0309 34 :DFKEILSEFNG 1souA 135 :YYDRLLKRVKG T0309 45 :KNVSITVKEENELPVK 1souA 167 :IPVDVLVTEKNVRRLR T0309 65 :AGDPLEHHHHHH 1souA 183 :DGRSLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=222 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1esfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1esfA expands to /projects/compbio/data/pdb/1esf.pdb.gz 1esfA:# T0309 read from 1esfA/merged-good-all-a2m # 1esfA read from 1esfA/merged-good-all-a2m # adding 1esfA to template set # found chain 1esfA in template set Warning: unaligning (T0309)D16 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1esfA)Y64 Warning: unaligning (T0309)T26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1esfA)Y64 T0309 7 :HQINVKGFF 1esfA 50 :HTILFKGFF T0309 27 :KEAEYTYDFKEILSEFNGKNVSITV 1esfA 65 :NDLLVDFDSKDIVDKYKGKKVDLYG Number of specific fragments extracted= 2 number of extra gaps= 0 total=224 Number of alignments=76 # 1esfA read from 1esfA/merged-good-all-a2m # found chain 1esfA in template set Warning: unaligning (T0309)D16 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1esfA)Y64 Warning: unaligning (T0309)T26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1esfA)Y64 T0309 7 :HQINVKGFF 1esfA 50 :HTILFKGFF T0309 27 :KEAEYTYDFKEILSEFNGKNVSITV 1esfA 65 :NDLLVDFDSKDIVDKYKGKKVDLYG Number of specific fragments extracted= 2 number of extra gaps= 0 total=226 Number of alignments=77 # 1esfA read from 1esfA/merged-good-all-a2m # found chain 1esfA in template set Warning: unaligning (T0309)D16 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1esfA)Y64 Warning: unaligning (T0309)T26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1esfA)Y64 T0309 7 :HQINVKGFF 1esfA 50 :HTILFKGFF T0309 27 :KEAEYTYDFKEILSEFNGKNVSITV 1esfA 65 :NDLLVDFDSKDIVDKYKGKKVDLYG Number of specific fragments extracted= 2 number of extra gaps= 0 total=228 Number of alignments=78 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 78 Done printing distance constraints # command: